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"#9<* * *8*~* * ***8m`**@*%Y&*8m(n()%Y&*8m(n()* *  $/6GVh!!"U?"#94* %&! "#z+*+*M,N66--26yq-2*:@* *"9%Y&(-2();:9%Y&ն(u);l? J( )*+,#-,.4/?1L2Q3e4h5978,=!\ LBsPT,t?U?"#wxVWh?9D*L+=9%Y&(+();*+9%Y&(+(); AB C"D*ECG!D"#?7=LMLY+MYN,-,*6 ,  . LO M N PQ"R'S.T3U;W!> ="#7'".?( r+N,:6X2+:262,:9%Y&ն(u);LO :\]`b'c1d9e<fAgLmOkQlk`qo!\ 1t?QPT]U?r"#rrjWaW'Ksb+;+`A:S6++2:`AYESA:SjY:- :yz {}~#3}9<BHSY_!\ ##U? /lb"#blb?bB lSg+M>,YM,->,,-:PQR:STU`T(dV* 9W; :"(-5BWf!>g"#ge<c(?52CDPKШUGPGPK(3(neosim/util/SmallLists/CVS/Entries.Extra`/.nbattrs/// /LinkedList.java/// /LinkedListDestPort_Out.java/// /LinkedListSrcPort_Out.java/// PKvke`PK(3*neosim/implementation/PopulationImpl.class1f CD E F G HI E J KL M N O P Q R S T UVWXidIsizemembersLjava/util/Vector; memberIdxLjava/util/Hashtable;locals(Ljava/lang/String;I)VCodeLineNumberTableLocalVariableTablethis&Lneosim/implementation/PopulationImpl;nameLjava/lang/String;getID()IsetID(I)Vi getNumEntsgetIndex(I)IeididxLjava/lang/Integer; getEntityIDisMember(I)Z addMembere getMemberList()Ljava/util/Vector;isLeaf()ZaddLocalMember(Lneosim/iface/Entity;)VLneosim/iface/Entity;getLocalMembers SourceFilePopulationImpl.java Yjava/util/Vector Z   java/util/Hashtable  java/lang/Integer , [\ ]* ^_ /0 `a bc * de$neosim/implementation/PopulationImpl(neosim/implementation/PopulationNodeImplneosim/iface/Population(Ljava/lang/String;)V()Vget&(Ljava/lang/Object;)Ljava/lang/Object;intValue elementAt(I)Ljava/lang/Object;valueOf(I)Ljava/lang/Integer; addElement(Ljava/lang/Object;)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;!  !"7*+*Y**Y*Y *Y#Z +6$ 7%&7'(7)*"/* #$ %&+,">* # $%$%&-.*"/*#)$ %&/0"c!* Y M,,# 23$ !%&!1 2340"F* #;$%&-56"A *#C$ %& 17,"h,** Y Y*d W#J K+L$,%&,89:"/*#R$ %&;<",#U$ %&=>"[**Y*+#_`ab$%&8?@:"/*#g$ %&ABPK<PK(3guikit/resources/Save24.gif GIF89a̙fff!,@|X긣!CdѤc-!eaWJ*t=D|èHXS8ЎgH%Ȋ%)xO$@K3ImЫ]S[Q)QzhOV d !OCopyright 2000 by Sun Microsystems, Inc. All Rights Reserved. JLF GR Ver 1.0 ;PK8z/ PK(3$neuroml/util/simpleresource/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(3"neuroml/sim/run/RunnableCell.classq1getState"()Lneuroml/sim/state/ElementState;getModel()Ljava/lang/Object; handleSpike(DI)Vhandle(Ljava/lang/Object;DI)Vadvance(D)Vreset()VsetInputConnectionParametersC(ILneuroml/sim/run/DestMethod;Lneuroml/sim/run/ConnectionRequest;)V setMeasured8(Lneuroml/model/MeasurementTool/MeasurementCollection;)V9(ILneuroml/model/MeasurementTool/MeasurementCollection;)V SourceFileRunnableCell.javaneuroml/sim/run/RunnableCelljava/lang/Objectjava/io/Serializable    PK 'vqPK(3"neosim/kernel/BasicKernel_Stub.rmiPKPK(3/neuroml/model/MeasurementTool/CVS/Entries.Extra/.nbattrs/// /AverageSynapseIntensity.java/// /CellExternalIntensity.java/// /CellIntensity.java/// /CellInternalIntensity.java/// /CellVoltage.java/// /ChannelIntensityMeasurement.java/// /Channel_h_measurement.java/// /Channel_mORn_measurement.java/// /MeasurementCollection.java/// /MeasurementCollectionCellLevel.java/// /MeasurementMethod.java/// /MeasurementSet.java/// /MeasurementTool.java/// /MeasurementToolPkg.java/// /ModuleMeasurement.java/// /SynapseIntensity.java/// PKcPK(3guikit/Net.classc13 "# " $ % & ' ( )*+nodesLjava/util/Vector;links()VCodeLineNumberTableLocalVariableTablethis Lguikit/Net;addNode(Lguikit/Node;)Vn Lguikit/Node;addLink(Lguikit/Link;)Vl Lguikit/Link; removeNode removeLink SourceFileNet.java java/util/Vector  ,- ./ 01 02 guikit/Netjava/lang/Object addElement(Ljava/lang/Object;)Vsize()Iremove(I)Ljava/lang/Object;(Ljava/lang/Object;)Z!   M**Y*Y  A *+ "#  A *+ %&  @**dW )* @**dW -. B *+ W 1 2  B *+ W 5 6   !PK&dFhcPK(3#neuroml/model/channel/HHVGate.class515 () ( * +,- . / 0 1 2 .34 forwardRateLneuroml/model/channel/HHRate; backwardRatetimeUnitLneuroml/core/Ref; voltageUnitvminDvmaxinstantCalculationZuseState()VCodeLineNumberTableLocalVariableTablethisLneuroml/model/channel/HHVGate;(Ljava/lang/String;)VnameLjava/lang/String; SourceFile HHVGate.java neuroml/model/channel/HHRate  neuroml/core/RefUnit #    neuroml/model/channel/HHVGateneuroml/model/channel/HHGate!?**Y*Y*Y *Y * * "-'4&9+>. ?!"#@*+ *Y*Y*Y *Y * * "1(5&:+?2 @!"@$%&'PK8sPK(3neuroml/sim/run/package.htmlo

Interfaces for running simulations.

This package provides interfaces for running simulations.

They are the interfaces which a loadable module can implement.

Examples are:

  • Runnable cells - with an advance method + spike delivery
  • Runnable channels - which can communicate diffusable things
PKitoPK(3neuroml/core/Logged.classm1 getLog()Lneuroml/core/Log; SourceFile Logged.javaneuroml/core/Loggedjava/lang/ObjectPK `ɗPK(3$neosim/kernel/EntityQueryEvent.class U1 I J K L MNO PQ R S TUV W XY Z X[\]^ _` a b cdef g h ijkleqLneosim/iface/EntityQuery;cbLneosim/iface/Callback;I(Lneosim/iface/Time;ISLneosim/iface/EntityQuery;Lneosim/iface/Callback;)VCodeLineNumberTableLocalVariableTablethis Lneosim/kernel/EntityQueryEvent;tLneosim/iface/Time;srceIsrcportS doOnEntity(Lneosim/iface/Entity;)VeLneosim/iface/Entity;ansLjava/lang/Object; registerClass4(Lneosim/iface/NeosimClasses;)Lneosim/iface/ClassID;ncLneosim/iface/NeosimClasses; readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; Exceptionsmn()V writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput;getSize()I SourceFileEntityQueryEvent.java "o  ! pqr stDoing entity query eventu vw xy zF{ |.!neosim/kernel/EntityCallbackEvent }~ F " EntityQueryEvent EntityEvent neosim.kernel 5 9: neosim/iface/EntityQueryneosim/iface/Callback "@ AB neosim/kernel/EntityQueryEventneosim/kernel/EntityEventjava/io/IOException java/lang/ClassNotFoundException(Lneosim/iface/Time;IS)VdebugZjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)Vquery)(Lneosim/iface/Entity;)Ljava/lang/Object;getSrcEntityIDneosim/iface/PortID SYSTEM_PORTgetTime()Lneosim/iface/Time;neosim/iface/EntitygetIDA(Lneosim/iface/Time;ISLneosim/iface/Callback;Ljava/lang/Object;)V sendEvent(ISLneosim/iface/Event;)Vneosim/iface/NeosimClassesN(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Lneosim/iface/ClassID;cidLneosim/iface/ClassID;java/io/ObjectInput readObject()Ljava/lang/Object;java/io/ObjectOutput writeObject(Ljava/lang/Object;)V! !"#$|*+**%  &>'()*+,-. !/0$ > *+M+* Y* +  *,%=& >'(>12'3456$M*+*% &'(789:$` *+*+*+%& '( ;<=>?"@$3*% "#& '(AB$Z*++*+*%&'()&'(CD=>EF$-d%,& '(GHPKGn PK(3&neosim/implementation/EntityImpl.classA@1L g hi g jk@@ l m n o p qrs tu v w x y z {| g } ~     g          *g * * * *               C                          hg  h      o h  h           *        debugZlast_evlLneosim/iface/EventList;pLneosim/iface/Population;indexIhandleecLneosim/iface/EntityClass; localTimeLneosim/iface/Time;skLneosim/kernel/Kernel;NumberConnection LinkedListCon'Lneosim/implementation/InportsTableOut;inPortsLjava/util/Vector;outPorts inPortClassesoutPortClassesoutConnectionsminOutputDelayrightWindowTime provLocalTimezeroed eventList()VCodeLineNumberTableLocalVariableTablethis"Lneosim/implementation/EntityImpl;compress_finalcompress7(Lneosim/iface/EntityClass;Lneosim/iface/Population;I)Vij classInPorts classOutPortsarray[Ljava/lang/Class;init(Lneosim/iface/Population;I)VgetIndex()I handleEvents@(Lneosim/iface/EventList;Lneosim/iface/Time;)Lneosim/iface/Time;TrucLneosim/iface/Input;eLneosim/iface/Event;elendtpassedgoonresetdestroy sendEvent(SLneosim/iface/Event;)VcS(ISLneosim/iface/Event;)Vdestedestp>(Lneosim/iface/Time;Lneosim/iface/Event;Lneosim/iface/Input;)Vtadvance(Lneosim/iface/Time;)VdefaultEventHandler(Lneosim/iface/Event;)V getPopulation()Lneosim/iface/Population;getEntityClass()Lneosim/iface/EntityClass;getIDsetID(I)VhgetName()Ljava/lang/String;getPopulationTree2(Lneosim/iface/Time;)Lneosim/iface/PopulationTree;getNeosimClasses()Lneosim/iface/NeosimClasses;lookupEntityClass.(Ljava/lang/String;)Lneosim/iface/EntityClass;nameLjava/lang/String;lookupEntityID((Lneosim/iface/Time;Ljava/lang/String;)IlookupPopulation@(Lneosim/iface/Time;Ljava/lang/String;)Lneosim/iface/Population; constructM(Lneosim/iface/Time;Lneosim/iface/PopulationBuilder;Lneosim/iface/Callback;)V Lneosim/iface/PopulationBuilder;Lneosim/iface/Callback;F(Lneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/Callback;)VconnectF(Lneosim/iface/Time;Lneosim/iface/Projection;Lneosim/iface/Callback;)VLneosim/iface/Projection; disconnect updateEntityI(Lneosim/iface/Time;ILneosim/iface/EntityUpdate;Lneosim/iface/Callback;)VeuLneosim/iface/EntityUpdate; queryEntityH(Lneosim/iface/Time;ILneosim/iface/EntityQuery;Lneosim/iface/Callback;)VeqLneosim/iface/EntityQuery;updatePopulationa(Lneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/EntityUpdate;Lneosim/iface/Callback;)VqueryPopulation`(Lneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/EntityQuery;Lneosim/iface/Callback;)VqueryOutputConnectionsL(Lneosim/iface/Time;SLneosim/iface/ConnectionQuery;Lneosim/iface/Callback;)VcqLneosim/iface/ConnectionQuery;cb addOutPort(Lneosim/iface/EventClass;)SLneosim/iface/EventClass;vec(Ljava/util/Vector;)S addInPortgetClassesOfInPort(S)Ljava/util/Vector;pidgetClassesOfOutPortgetNumInConnections(S)IinportgetNumOutConnectionsoutportopLneosim/kernel/OutPortTable;getOutConnection(S)Lneosim/kernel/OutPortTable;getNumOutPorts getNumInPortsgetInConnections(S)[[IaddOutConnection(SJIS)VdelayJdest destinportprocoptremoveOutConnectiondeleteOutConnection(SIS)VaddInConnection(Lneosim/iface/Connection;)ILneosim/iface/Connection;(ISS)IsrcIDsrcPortdestPortdeleteInConnection(SSI)V SrcPortID destPortID(Lneosim/iface/Connection;)VsetSrcConnectionParams2(Lneosim/iface/Connection;SLjava/util/Hashtable;)VsrcpidparamsLjava/util/Hashtable;setDstConnectionParams2(Lneosim/iface/Connection;ILjava/util/Hashtable;)Vdestcid deleteInPort(S)V deleteOutPortzeroOutputDelayresetOutputDelaygetMinOutputDelay()Lneosim/iface/Time;setMinOutputDelay getLocalTime setLocalTimesetProvLocalTimegetRightWindowTime getEventList()Lneosim/iface/EventList; postEventtrace(Ljava/lang/String;)Vmsg compareTo(Ljava/lang/Object;)IoLjava/lang/Object;mLneosim/iface/Entity;t1t2 ExceptionsaddSpike(IJ)VtimegetList)()Lneosim/implementation/InportsTableOut; SourceFileEntityImpl.java %neosim/implementation/InportsTableOut neosim/iface/Time   2THIS SHOULDN'T BE CALLED (except for memory tests) S #neosim/implementation/EventListImpl     java/util/Vector      java/lang/StringBuilder" EntityImpl... Making new Entity     pop       neosim/iface/EventClass    Entity  handleEvents to    !I ' "  about to deliver neosim/iface/Input #$ : %& ' (Entity::sendEvent to port Entity::sent event  Entity::sendEvent to input port  deste ) * + Entity::sentEvent to input port Received default event at time  from input  Advancing time to ,system - . / / 0 1 2 3 4 56  neosim/kernel/OutPortTable  7 8# 9  $neosim/neuroml/NeosimEntityClassImpl: ;< => ?9 error - removing out connection from non existent port @A B CD ED /2 $F G 67 HC Causality violation: ET: IJ  K CLOCK: RS ? at KI:neosim/iface/Entity NI (EntityImpl.addSpike should NOT be called neosim/implementation/EntityImpljava/lang/Objectneosim/iface/DefaultHandlerjava/lang/ClassCastException(D)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintlnneosim/kernel/SimSystem getKernel()Lneosim/kernel/SimKernel;getClass()Ljava/lang/Class;java/lang/Class getInterfaces()[Ljava/lang/Class;neosim/iface/EntityID SYSTEM_ENTITYneosim/iface/Population getEntityID(I)Iappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toStringneosim/kernel/Kernel addEntity%(Lneosim/implementation/EntityImpl;)Vneosim/iface/EntityClass getInPorts()Ljava/util/Vector;size elementAt(I)Ljava/lang/Object; getOutPortsneosim/iface/EventListhasMoreElements()Ztop()Lneosim/iface/Event;neosim/iface/EventgetTimepop getConnection()Lneosim/iface/Connection;deliverToEntity?(Lneosim/iface/Time;Lneosim/iface/Entity;Lneosim/iface/Input;)Vsetclearneosim/iface/PortID SYSTEM_PORT(ISISLneosim/iface/Event;)V,(Lneosim/iface/Entity;Lneosim/iface/Event;)VN(ILneosim/iface/Time;Lneosim/iface/PopulationBuilder;Lneosim/iface/Callback;)VG(ILneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/Callback;)VG(ILneosim/iface/Time;Lneosim/iface/Projection;Lneosim/iface/Callback;)VJ(ILneosim/iface/Time;ILneosim/iface/EntityUpdate;Lneosim/iface/Callback;)VI(ILneosim/iface/Time;ILneosim/iface/EntityQuery;Lneosim/iface/Callback;)Vb(ILneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/EntityUpdate;Lneosim/iface/Callback;)Va(ILneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/EntityQuery;Lneosim/iface/Callback;)VN(ILneosim/iface/Time;ISLneosim/iface/ConnectionQuery;Lneosim/iface/Callback;)V addElement(Ljava/lang/Object;)VnumConnectionsgetInConnectiongetEntityProcessorneosim/iface/SpikeEventinstLneosim/iface/SpikeEvent; getEventClass()Lneosim/iface/EventClass;addremoveneosim/iface/ConnectiongetSrcEntityID getSrcPortID()S getDstPortID(SSI)InotifyZEROs()D(D)Ljava/lang/StringBuilder;!GH***Y*Y *Y *Y * &  x"y.z:{?G H6* #$ 6* +, xt***Y*Y *Y *Y * *,*+**Y *Y:62**Y !*Y "*Y #*Y $*Y %, *&'*,(')(*Y+,-*'./-,01**2+W+3:64*567W+8:64*569W!. x"y.z:{?1Z2e4p5{6579:;<=@ACDHI'J4KCJIMQN^OmNsRf s*T'LQ"ttttp?W /*\ ޲)%*Y+:-*0;-,01>6:+Y:+<6(+=:>?,?+@:>ç :TP*>A)&*Y+:-*0B-01CYDE:>*FY*,A,>svv{vZk(l*-69>FKScknp~H 9*-D*G*H + N)*Y+I-.1**',J)*Y+K-.1.M NNN[)%*Y+L-.M-.1**'N-O)*Y+P-.1(;Z*[[[[~.)%*Y+Q-+0R--01*,S(-*....a))%*Y+:-*0T-+01 ())D **+U   /* /* /*' >*' R(*V*Y+*W-*.1 (? *+X 4 *Y  ? *+Z J *+,[!   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"neosim/neuroml/NeuromlElementStatejava/lang/Objectneuroml/sim/state/ElementState()Vneosim/iface/Entity1  > **+     5   4 *   PKW+PK(3'neuroml/model/morphml/CVS/Entries.Extra/Cell.java/// /Child.java/// /Header.java/// /Morphology.java/// /Parent.java/// /Paths.java/// /Point.java/// /PointId.java/// /Polygon.java/// /Segment.java/// /SetOfFeatures.java/// /annotation.java/// /count.java/// /diam.java/// /label.java/// /x.java/// /y.java/// /z.java/// PK0PK(3MiscTests/DistanceWatcher.classs1 update(F)V SourceFilePathFinder.javaMiscTests/DistanceWatcherjava/lang/ObjectPKbPK(3guikit/CVS/Entriesn/AboutPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /BasicClickablePoint.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /BrowseModulesPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /BrowseObjectsPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ClickablePoint.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ClickablePoints.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ColourEditor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Constants.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ControlPoint.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ConverterRangeModel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /DecimalField.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /DisplayApp.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /DisplayHints.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /DisplayListener.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /DisplayPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditArrayPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditBooleanPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditDValuePanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditDoublePanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditEnumPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditIntegerPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditListPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditModuleRefPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditObjectPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditRefInterfaces.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditRefPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditSetPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditShortPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditStringPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditTreeRefPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EditURLPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EmptyApp.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Environment.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ExampleFileFilter.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /FieldPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /FiringEditObjectPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /FramedPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /GraphPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /GridReshaper.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /GuiKit.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /HTMLPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ImageUtils.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /LabelPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Link.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /LinkProjection.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /MenuPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ModuleEditor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /MyApp.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NameNode.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Navigator.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Net.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetApp.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetEditPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetEditPanel_Animation.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetEditPanel_GuiKit.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetworkDesigner.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetworkTransform.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NetworksPanel_General.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Node.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NodePopulation.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NotifyingSet.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ObjectNode.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationNode.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ProjectionLink.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RGBColour.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RunApp.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ScrolledPanel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SpecialEditors.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SubModelEditor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SubNetNode.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SubnetDisplayer.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SubnetsEditor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SubnetsEditor_Animation.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SubnetsEditor_GuiKit.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SubnetsEditor_StandAlone.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SwingWorker.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /TreeNodeEditor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /WindowManager.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D/resources//// /.nbattrs/1.2/Mon Aug 8 15:52:28 2005// /BasicApp.java/1.2/Mon Aug 8 15:52:42 2005// PK?GPK(3neosim/kernel/RmtApp.class1'!"#$%addRmt,(ILjava/lang/String;Lneosim/kernel/RmtApp;)V Exceptions&doneRmt(I)V removeRmt SendArray([Ljava/lang/Object;)VSendSpikesArray([B)Vsignal()V startTestscallsendByte receiveByte(B)[BsendInt([I)V receiveInt(B)[Isum([I)J([B)J SourceFile RmtApp.javaneosim/kernel/RmtAppjava/lang/Objectjava/rmi/Remoteneosim/kernel/Commandableneosim/kernel/Queryablejava/rmi/RemoteException                  PK֠PK(3%neuroml/model/Synapse_nml/CVS/Entries1/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /Synapse.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SynapticCell.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /synapse_nmlPkg.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PKᔋPK(3"neosim/kernel/ProcManager_Stub.rmiPKPK(3"neuroml/model/synapse/package.html Neuroml definitions for synapses

Neuroml definitions for synapses

This package defines neuroml definitions for synapse models.
Fred Howell
Last modified: Fri Apr 27 10:04:58 BST 2001 PKT^lPK(3guikit/NetApp$1.classU1"  ()VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/NetApp$1; windowClosing(Ljava/awt/event/WindowEvent;)VeLjava/awt/event/WindowEvent; SourceFile NetApp.javaEnclosingMethod   !guikit/NetApp$1java/awt/event/WindowAdapter guikit/NetAppmain([Ljava/lang/String;)Vjava/lang/Systemexit(I)V /*M  = OP   PKaZUPK(3resources/CVS/Entries"/BackPlay24.gif/1.1.1.1/Thu Jul 7 14:31:48 2005/-kb/ /NMLPlay.jpg/1.1.1.1/Thu Jul 7 14:31:48 2005/-kb/ /Thumbs.db/1.1.1.1/Thu Jul 7 14:31:48 2005/-kb/ /marb_blue.jpg/1.1.1.1/Thu Jul 7 14:31:48 2005/-kb/ D/.xvpics//// PK` PK(3'neuroml/util/schema/NeuromlString.class-1   valueLjava/lang/String;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis#Lneuroml/util/schema/NeuromlString;v SourceFileNeuromlString.java String  !neuroml/util/schema/NeuromlString!neuroml/util/schema/NeuromlObject()V neuromlClass!  P***+    PKbXzPK(3neosim/renderer/AnimMat.class1h @ A B C D E F G H I J K L MY NO NPQ R ST UV SWXYZmatLjavax/media/j3d/Material;valsLjava/util/Vector;maxDminr1Fg1b1r2g2b2stepiIskipmyColour$Ljavax/media/j3d/ColoringAttributes;\(Ljavax/media/j3d/Material;Ljava/util/Vector;DDFFFFFFILjavax/media/j3d/ColoringAttributes;)VCodeLineNumberTableLocalVariableTablethisLneosim/renderer/AnimMat;step()Vvaltsivalsvalrvalgvalbval SourceFile AnimApp.java .6 )* +*   !  "# $# %# &# '# (# ,-[ \] ^_java/lang/Double `ab cde fd gdneosim/renderer/AnimMatjava/lang/Objectneosim/renderer/AnimThingjava/util/Vectorsize()I elementAt(I)Ljava/lang/Object; doubleValue()Djavax/media/j3d/MaterialsetAmbientColor(FFF)V"javax/media/j3d/ColoringAttributessetColorsetDiffuseColor0  ! "#$#%#&#'#(#)*+*,-./0T****+*,*)*** * * * * ** 1*  #5GMS2 T34TTT! 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Neuroml top level package

This package defines the top level XML tag:
  <neuroml class="NeuromlPkg" author="joe bloggs" ...>
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Fred Howell
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Animation DemoanimStart demo of activity.ExitstopThis button exits.   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Neuroml definitions for cells

This package provides the neuroml definitions for models of cells.
Fred Howell
Last modified: Mon Mar 12 18:56:19 GMT 2001 PKGI;PK(3)neuroml/model/I_Clamp/ArrayFunction.class!1, !" # $ %& '(Array"[Lneuroml/model/I_Clamp/_Function;dtD(ID)VCodeLineNumberTableLocalVariableTablethis%Lneuroml/model/I_Clamp/ArrayFunction;kIgetValue(D)Ddi setFunction%(Lneuroml/model/I_Clamp/_Function;I)Vstuff!Lneuroml/model/I_Clamp/_Function; getFunction$(I)Lneuroml/model/I_Clamp/_Function; SourceFileArrayFunction.java )neuroml/model/I_Clamp/_Function  * + #neuroml/model/I_Clamp/ArrayFunction()Vjava/lang/Mathfloor!  \***(   t*'*oJ)**)2')*kg ' **   J*+S +, ;*2. PKmپPK(3neosim/util/DoOnBean.class1   action?(Lneosim/util/JarInfo;Ljava/beans/BeanInfo;Ljava/lang/String;)Verror(Ljava/lang/String;)V*(Ljava/lang/String;Ljava/lang/Exception;)V SourceFile DoOnBean.javaneosim/util/DoOnBeanjava/lang/Object PKHKz"PK(3neuroml/data/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(3 ReshapeNetwork/CVS/Entries.Extra+/.nbattrs/// /JarInspectorReshaper.java/// PKy0+PK(3!neosim/rmikernel/StrMessage.class}1  strLjava/lang/String;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLneosim/rmikernel/StrMessage; SourceFileStrMessage.java  neosim/rmikernel/StrMessagejava/lang/Object()V! F **+    PK9?\ }PK(3neuroml/overview.htmlk This package defines the neuroml markup language for specifying models of channels, cells and networks. It also includes a set of interfaces for simulators and editors to use to build and run models and some useful Java tools for reading and writing XML files.

PK#aPK(3neosim/thrkernel/CVS/Entriesb/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /ThrKernel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PK`gbPK(3neuroml/sim/run/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(3'neuroml/util/schema/NeuromlVector.class21$     elementsLjava/util/Vector; elementTypeLjava/lang/String;9(Ljava/util/Vector;Ljava/lang/String;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis#Lneuroml/util/schema/NeuromlVector;els fieldname fieldtype getElements()Ljava/util/Vector;getElementType()Ljava/lang/String; SourceFileNeuromlVector.java !  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srcPortIDSArray&[Lneosim/kernel/LinkedListDestPort_In;(S)VCodeLineNumberTableLocalVariableTablethiscompress()ViIcompress_finalcurrentstuff MaxPortIn TotalLengthNewArrayaddInputConnection(SIIJI)VdestPortsrcIDdestIDdelayJcidgetID()SgetSize()I SourceFileInPortsTable.java !   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" # $ %&' buildModeLjava/lang/String;serverusernProcsInThread()VCodeLineNumberTableLocalVariableTablethis1Lneosim/util/loaders/nmllauncher/RmiKernelParams; SourceFileRmiKernelParams.java java/lang/String-c (     /neosim/util/loaders/nmllauncher/RmiKernelParams/neosim/util/loaders/nmllauncher/SeqKernelParams(Ljava/lang/String;)V!  t2**Y*Y*Y* * ' , 1 2PKPK(3.neuroml/model/Synapse_nml/synapse_nmlPkg.class71 ()VCodeLineNumberTableLocalVariableTablethis*Lneuroml/model/Synapse_nml/synapse_nmlPkg; getClassList()[Ljava/lang/String;ret[Ljava/lang/String; SourceFilesynapse_nmlPkg.java java/lang/StringSynapsesynapse_nmlPkgSynapticCurrent SynapticCell(neuroml/model/Synapse_nml/synapse_nmlPkgneuroml/core/Pkg!  /*    IYSYSYSYSK*  PKI<7PK(3neuroml/sim/CVS/Entries/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /Editable.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Editor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ElementChangedListener.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /package.html/1.1.1.1/Thu Jul 7 14:31:48 2005// D/run//// D/state//// PKPK(3neuroml/data/package.html Definitions of datatypes refering to the simulation's environment

Definitions of simulation datatypes

This package defines the datatypes used in a neuroml simulation's environment.
Fred Howell
Last modified: Mon Mar 12 18:54:52 GMT 2001 PKx zPK(3neuroml/core/Nameable.class"1    getName()Ljava/lang/String;setName(Ljava/lang/String;)V SourceFile Nameable.javaneuroml/core/Nameablejava/lang/Objectjava/io/Serializable PKwPK(3 neosim/rmikernel/RmiKernel.class>x1}   #                              '      5 5 #! " G! # 0$% > & ' ( ) *+ , -. 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"z  ijFailed to construct #%$ %| & '() *+, -`!Kernels all done, killing threads ./ 01Unexported RMIKernel OKFailed to unexport RMIKernelUnexport error @A BC FG DEjava/io/IOException[] RmiKernel: addRmt called  2` | |RmiKernel: connecting to serverRmiKernel: calling server add3 45 6 78 9: ;< 9= >neosim/iface/SpikeArray ? T@ TO_SERVER A `Initialise local SimSystem BC]--- waiting for processors... DE F)]--- Got all processors, trying a barrierWaiting on barrier GH /0 ` Done barrier `]--- Done barrierneosim/kernel/RestartCommand it Reset Done {| b` I` REBUILDING `  %************************************* Event testsjava/util/Vector JKneosim/kernel/ResetExceptionReached Test 1: L msTest 2: tests done. bye.AllgatherSpeed Multi M| NOneosim/kernel/RmtApp Serialization testsMiscTests/Serialized_Class PQ RST UMiscTests/ExternalizedClass"MiscTests/ExternalizedOptimalClass TV W` COMPRESSION X`CALL  RMI testsTEST 1: TEST 2: Y TEST 3(1):  TEST 3(2):  TEST 3(3):  TEST 3(4):  TEST 4(1):  TEST 4(2):  TEST 4(3): Z[ TEST 5(1):  TEST 5(2):  TEST 5(3):  TEST 5(4):  TEST 6(1):  TEST 6(2):  TEST 6(3):  TEST 6(4): \]TEST 7: ^_ TEST 8(1):  TEST 8(2):  TEST 8(3):  TEST 9(1):  TEST 9(2):  TEST 9(3):  TEST 9(4): `a TEST 10(1):  TEST 10(2):  TEST 10(3):  TEST 10(4):  TEST 11(1):  TEST 11(2):  TEST 11(3):  TEST 11(4): \b TEST 12: ID: E trying to build Holger_modules.module.destmethod.SpikeDestMethod on 0Holger_modules/module/destmethod/SpikeDestMethod c`  d` eEjava/net/ServerSocket fCould not listen on port: >?java/net/UnknownHostExceptionjava/lang/String <=java/net/Socketjava/io/BufferedOutputStreamjava/io/BufferedInputStream Tg hi Tj kl Tm no JK p qr st u vw    x| xy z` { {|neosim/kernel/BasicKernelidjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)V5neosim/util/loaders/nmllauncher/NeosimNeuroMLLauncherPlayerLnmlplay/PlayerCallBack;nmlplay/PlayerCallBacksetSecurityManager(Ljava/lang/SecurityManager;)V#java/rmi/server/UnicastRemoteObject exportObject/(Ljava/rmi/Remote;)Ljava/rmi/server/RemoteStub;java/rmi/Naminglookup%(Ljava/lang/String;)Ljava/rmi/Remote;pmgrLneosim/kernel/RmtProcMgr; getMessageprintStackTracecompress getSimSystem()Lneosim/kernel/SimSystem; getGroupsize()IgetIDneosim/kernel/SimSystemrunPar(IIILneosim/iface/Time;)Vothercqs elementAt(I)Ljava/lang/Object;add-(Ljava/lang/Object;)Ljava/lang/StringBuilder; PrintObject'(Ljava/lang/Object;Ljava/lang/String;)V(Ljava/io/OutputStream;)V(Ljava/io/PrintWriter;)Vclosejava/lang/Threadsleep(J)V otherprocsqidneosim/kernel/QueryCommandsetQidgetQidwaitForAnswers(I)Ljava/util/Vector;neosim/kernel/DeadlockTrackertracker%Lneosim/kernel/DeadlockTrackerKernel;#neosim/kernel/DeadlockTrackerKernelkillremove(ILneosim/kernel/RmtApp;)VunexportObject(Ljava/rmi/Remote;Z)Z semSignaljava/net/InetAddress getLocalHost()Ljava/net/InetAddress;getHostAddressindexOf(I)I substring(II)Ljava/lang/String;parseInt(Ljava/lang/String;)I(I)Ljava/lang/String;,(Lneosim/kernel/RmtApp;Ljava/lang/String;I)I arraySpikes(Lneosim/kernel/Commandable;)VsetQName initialise(Lneosim/kernel/SimKernel;I)VsemWait(Ljava/lang/Object;)VprintsortIPs(I)[I kernelInitcurrentTimeMillis()J(J)Ljava/lang/StringBuilder;exitgetDest()Lneosim/kernel/Commandable; sendObject(LMiscTests/SerializedClass;)VgetClass()Ljava/lang/Class;java/lang/ClassgetName(Z)V compressioncallsendByte receiveByte(B)[Bsum([B)JsendInt([I)V receiveInt(B)[I([I)Jnotifywait addElementerr(Ljava/lang/String;I)VgetOutputStream()Ljava/io/OutputStream;(Ljava/io/OutputStream;I)VgetInputStream()Ljava/io/InputStream;(Ljava/io/InputStream;I)Vaccept()Ljava/net/Socket;getSizefill([BI)V arraycopy*(Ljava/lang/Object;ILjava/lang/Object;II)V([BI)IaddSpike(IJS)Vwrite([BII)Vflushread([BII)I1#$%&'()*+,+-%.%/01234567%89:9;9<=>?@ABCDEFGHIJK& LMNLY L+O PQ= RSTUN`****Y* * * Y * Y * Y ****O6 ") +`b" .:F}M$R%Z&_'P `VS`W%`-%TXN****Y* * * Y * Y * Y *`Y*,*+** !6!Y"+#$%&*4Y"+#$%'Y()*! !+&*,W*Y-*./01*Y-*./23!!!Y4*&':Y6785O 7) +`b" .:F}M9U:p<u=z>?@ABCDEFHJBKgLmMQNOPSP>"YZVS[+\+-%.%]^N/*1OUP VS_`NI*9*: *:;OZ[ \^P VSa`N3*<O psP VSb`N^*1=L+? 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##P %[\%]V ^V cdNv* @*7*&YY*M,+*+*+MY*,,LMO6 +,-6.;/>0C1F2K3M4N5p6t7P*6eVN(fgvhVvij klNYN*9*:  !N" "N- -+,#-$Y+,%:*&W'O6 @A BCE"F-G3K7L?MAPLQSSP>0mnL opYhVY]VYq\Wrs tuN2**(M, ,+),*Y++M*,&W,,O"_ `abce'f-gP* rv' wx2hV2q\ yzNAL**-.`/M,0N-1L&NY2,3-+O"oprsvtu?wP4{|"fgAhV?}n2~V N W*+*4:+,567Y+,8:*&W96O" )1ELPf rEWhVW]VWVWWVWWWq\ N8**:N- -+,;-O& )13P4r)8hV8]V8q\ N8**?N- -+,@-AY+,BN*-&-CO& )13P4r)8hV8]V8q\ NS*)*D:+,EFGY+,H:*&WIFO" '/AHP\ rAShVS]VSSSsSSq\PKjePK(3&neuroml/model/ions_channel/CVS/Entries/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /Channel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ChannelCell.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Ions_channelPkg.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ModuleChannel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PKi,e PK(3,neuroml/model/ions_channel/CVS/Entries.Extrac/.nbattrs/// /Channel.java/// /ChannelCell.java/// /Ions_channelPkg.java/// /ModuleChannel.java/// PKQhcPK(3?neuroml/model/MeasurementTool/ChannelIntensityMeasurement.class [1 ,W *X *YZ[ \ ]^ _ ` abc W *de \f gh ijkl m nop q rst m uv wx y z{ !W !| !}~ ! 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"# " $ % & '()this$0Lguikit/DisplayPanel;(Lguikit/DisplayPanel;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/DisplayPanel$4;getMinimumSize()Ljava/awt/Dimension;getPreferredSizegetMaximumSize SourceFileDisplayPanel.javaEnclosingMethod* +, - java/awt/Dimension ./ 0  1/guikit/DisplayPanel$4javax/swing/JPanelguikit/DisplayPanelcreateWidePanel()Ljavax/swing/JPanel;()VheightI(II)Vwidth  4 *+*6  /*/ <Y*2 @Y* *9   PK?iPK(3*neuroml/util/.#JDomNeuroMLParser.java.1.17@package neuroml.util; import neuroml.core.*; import neuroml.model.channel.*; import neuroml.model.cell.*; import neuroml.model.network.*; import java.lang.reflect.*; import java.util.Vector; import java.util.Hashtable; import java.util.Enumeration; import java.beans.*; import java.lang.Integer; import java.io.*; import org.jdom.*; /** * Call a JDOM parser on a NeuroML file * use JDOM on the tree document created in order to fulfill the NeuroML specific data structure * generic process, the data structure is not entirely known -> use of reflection methods * * @author Paul Rogister * * @version 1.0, 02 March 2001 * @version 1.1, 09 March 2001 Fred Howell - added extra facilities for extensions * @version 1.2, 25 July 2001 Fred Howell - move references to NeuromlSys * */ public class JDomNeuroMLParser { Document domDocument; org.jdom.Element root; Object desc; // top level of the neuroNL specific tree Namespace ns; String[] packageslist = neuroml.NeuromlPkg.getPackageList(); private boolean debug = false; public JDomNeuroMLParser(Document document, String namespace) { domDocument = document; ns = NeuromlSys.getNamespace( namespace ); if (ns==null) { ns = NeuromlSys.makeNamespace(namespace); // Put refs into new namespace } root = domDocument.getRootElement(); desc = startElement(root,null); // null : no parent } /** Return namespace of this document */ Namespace getNamespace() { return ns; } /** * Converts string to int * * @param s String to be converted * @return int conversion of String */ protected static int atoi(String s) { return (Integer.valueOf(s)).intValue(); } /** * Converts string to double * * @param s String to be converted * @return double conversion of String */ protected static double atod(String s) { return (Double.valueOf(s)).doubleValue(); } /** * Converts string to boolean * * @param s String to be converted * @return double conversion of String */ protected static boolean atob(String s) {return (s.equals("true")); } /** * Gets the simulation description * * @return Simulation description (Simdesc class) */ public Object getDesc(){ return desc; } /** Try to create an object of the given class */ private Object createObject(String className) { Object object = null; try { Class classDefinition = Class.forName(className); object = classDefinition.newInstance(); } catch (InstantiationException e) { System.out.println(e); } catch (IllegalAccessException e) { System.out.println(e); } catch (ClassNotFoundException e) { if (debug)System.out.println(e); } return object; } /** Set the instance name */ public void setInstName(org.jdom.Element element, Object instElement) { Class classDefinition = instElement.getClass(); if (debug) System.out.println("tag "+element.getName()+"class name = "+classDefinition.getName()); try { if (debug) System.out.println("tag "+element.getName()+" name = "+getFieldName(element)); Class[] parameterTypes = new Class[] {String.class}; Method setMethod; Object[] arguments = new Object[] {getFieldName(element)}; setMethod = classDefinition.getMethod("setName", parameterTypes); setMethod.invoke(instElement, arguments); } catch (NoSuchMethodException e) { System.out.println("JDOM Parser : "+e+" for setName applied to an object of class "+classDefinition.getName()); } catch (IllegalAccessException e) { System.out.println(e); } catch (InvocationTargetException e) { System.out.println(e); } } /** Set the attributes of the object */ public void setAttributes(org.jdom.Element element, Object instElement){ // add attributes to element parameters java.util.List attributesList = element.getAttributes(); Class classDefinition = instElement.getClass(); Field classField; // loop on the attributes for (int i = 0; i < attributesList.size (); i++) { Attribute attr = (Attribute)attributesList.get(i); String an = attr.getName(); String av = attr.getValue(); Object[] arguments = new Object[] {av}; try { classField = classDefinition.getField(an); // need to convert the String to what is expected classField.set(instElement,av ); } catch (Exception e) { System.out.println(e); } } } /** Try to get the field "name" */ public String getFieldName(org.jdom.Element element){ return getFieldParameter(element, "name"); } /** Get a given field, or null if not present */ public String getFieldParameter(org.jdom.Element element, String name){ Attribute a = element.getAttribute(name); if (a!=null) { return a.getValue(); } return null; } /** Set a parameter */ public void setParameter( String fieldName, Object subInstElement, Object instElement){ Class classDefinition = instElement.getClass(); Field classField; if (debug) System.out.println("class name = "+classDefinition.getName()); if (debug) System.out.println("field name = "+fieldName); try { classField = classDefinition.getField(fieldName); classField.set(instElement, subInstElement); } catch (NoSuchFieldException e) { // if the tag name of the sublement is not recognize as a field of the element, we try the subelement superclass name as the field name Class subclass = subInstElement.getClass(); Class superclass = subclass.getSuperclass(); boolean found = false; System.out.println("set field name : no such field "+fieldName); while ((superclass != null)&&(!found)) { String className = getShortClassName(superclass.getName()); try { System.out.println("try field name = "+className); classField = classDefinition.getField(className); classField.set(instElement, subInstElement); found = true; System.out.println("set field name = "+className); } catch (NoSuchFieldException e2) { } catch (IllegalAccessException e2) { //System.out.println(e); } subclass = superclass; superclass = subclass.getSuperclass(); } //System.out.println(e); } catch (IllegalAccessException e) { System.out.println(e); } } /** Try to set a basic type parameter */ public void setParameter( String fieldName, String fieldValue, String fieldType, Object instElement){ Class classDefinition = instElement.getClass(); Field classField; if (instElement==null){ System.out.println("JDOMNeuroMLParser Error setParameter : element target is null"); return; } try { classField = classDefinition.getField(fieldName); if (fieldType.equals("int")){ if (debug) System.out.println("setParameter int "+fieldType+ " fieldvalue "+fieldValue+ " atoi :"+atoi(fieldValue)); classField.setInt(instElement, atoi(fieldValue)); } else if (fieldType.equals("bool")){ if (debug) System.out.println("setParameter bool "+fieldType); classField.setBoolean(instElement, atob(fieldValue)); } else if (fieldType.equals("double")){ if (debug) System.out.println("setParameter double "+fieldType); classField.setDouble(instElement, atod(fieldValue)); } else if (fieldType.equals("String")){ if (debug) System.out.println("setParameter String "+fieldType); classField.set(instElement, fieldValue); } else System.out.println("JDOMNeuroMLParser Error setParameter : type mismatch "+ ": field name : "+fieldName+" field type :"+fieldType); } catch (NoSuchFieldException e) { System.out.println(e); } catch (IllegalAccessException e) { System.out.println(e); } if (debug) System.out.println("end set parameter"); 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*D #$E FGAHCO  *')D & 'E  FG IJ KJALC -*')*Y * Y  *D)  '*,+E4-FG-IJ-KJ-MJ-NJAOC 3*')*Y * Y  * *D-  '.-/20E>3FG3IJ3KJ3MJ3NJ3P> QRCZ Y***** D2E FGSJTJUHC \'*g*g9)*g*g9*'*g*)*g6  *!*  ٱD"7 89$:.;=<U;[>E>1*VW \FG\XJ\YJ OZJB[J\]C *M*N+, -!6+,"6+* #$%+&Y*'c*(c*)**+,+* #%+&Y*'*(*)**+,+-%+-*lf*.D2 CD EFGH,IOJZKuL|MNE>FG^_`@ ab}cWtdWefCY//Y012*232*452*46DPE /FGgfCL*78*789:DR STE FGhiCT*78*78+;DW XZEFGjbkl & PKK PK(3!guikit/HTMLPanel$OpenWindow.class/1%      !panelLguikit/HTMLPanel;urlLjava/lang/String;this$09(Lguikit/HTMLPanel;Lguikit/HTMLPanel;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis OpenWindow InnerClassesLguikit/HTMLPanel$OpenWindow;run()V SourceFileHTMLPanel.java   " #$guikit/HTMLPanel$OpenWindowjava/lang/Threadguikit/HTMLPanelopenURL(Ljava/lang/String;)V    p*+****,*-       : **     PKȒPK(3neosim/iface/Connection.classi1getDstEntityID()I getDstPortID()SgetDelay()JgetSrcEntityID getSrcPortIDgetConnectionIDsetConnectionID(I)V sendEvent(Lneosim/iface/Event;)VaddSpike(J)V SourceFileConnection.javaneosim/iface/Connectionjava/lang/Objectjava/io/Serializable      PK՛PK(3-neuroml/model/cell/OrientedSubstructure.classy10 "#$ % &'( ) *+ " , %-. structureRefLneuroml/core/Ref;attachmentPointLneuroml/core/DValue; orientationLneuroml/core/Orientation;()VCodeLineNumberTableLocalVariableTablethis)Lneuroml/model/cell/OrientedSubstructure;(Ljava/lang/String;)VnameLjava/lang/String; SourceFileOrientedSubstructure.java neuroml/core/RefNeuronStructure  neuroml/core/DValueratio / neuroml/core/Orientation 'neuroml/model/cell/OrientedSubstructureneuroml/core/NamedObject(DLjava/lang/String;)V!e+**Y*Y * Y * +p,*+ *Y*Y * Y  + ,, !PK~(5PK(3neuroml/core/package.html Definitions of basic datatypes

Definitions of basic datatypes

This package defines the basic datatypes used in a neuroml model.
Fred Howell
Last modified: Mon Mar 12 18:54:52 GMT 2001 PKk;PK(3#neosim/util/SimpleClassLoader.class&1   [ [ [ [ [ [ [     [       P P      ' ' *  [ .  [ [ [ [ [ [ !"# [$ [% [& [' '( ')*+ C,-./0 F1234 N5678 Q9 T: *; [<=> X? 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WARNING: file name versus class name mismatch ~.class JAR entry "" was expected to contain class ""! but instead contained class "2 This may cause future class-loading problems.  java/io/File java/io/FileInputStream   java/lang/ClassNotFoundExceptionjava/lang/ExceptionLoadFromFile/caught t when loading from file  .ser   A CLASS FILE   java/lang/Integer1 java/net/URLsimpleresource/SIMPLE/+/  Exception  while building a resource URLneosim/util/InputStreamProducer java/lang/Stringjava/lang/SecurityException0No access through getResource() to .class in 1.1java/io/ByteArrayInputStream   java/lang/Errorinternal error!neosim/util/SimpleClassLoaderimage    file w no such resource   ?NOTE: There are classes that cannot be defined in this JAR fileH Some of these classes will cause the failure of defining or linking & other classes that depend on them. 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!"#$%&'()-* + ,-./)h***** +4,-0"!"#$%&12)8+****!M Y  ,,*37+ 348,-856.7)F**** + ,-89)~6*+*+*+*+*+*  !("59+6,-6:;<=>?@){3+*+*+*+*+**< =>?(@2^+3,-3AB<=CD)2**i+ ,-EF)5 *`*l+  ,-GHPK&m PK(3nmlplay/resources/save.gifgGIF89aƄ!,@8i!_ˁ/(hNfXm9v /t+Dbjm*qBy(;PKRSlgPK(3neosim/util/JarInfo.classI'1 |  { { { { { { { y          { y { | {  { !  ! !   5     !" !#$ !% !&'()*+,-./ &01 !2345678 &9:; h< =>?@ hABC D<EFGHI hJKLMN {OPQ yRS classLoaderLneosim/util/SimpleClassLoader; beanNames[Ljava/lang/String; beanInfos[Ljava/beans/BeanInfo; fromPrototype[Z manifestData[Lneosim/util/MessageHeader;jarNameLjava/lang/String; beanToJarLjava/util/Hashtable;debugZe(Ljava/lang/String;Lneosim/util/SimpleClassLoader;[Ljava/lang/String;[Z[Lneosim/util/MessageHeader;)VCodeLineNumberTableLocalVariableTableexLjava/lang/Exception;cLjava/lang/Class;biLjava/beans/BeanInfo;iIthisLneosim/util/JarInfo;cl getJarName&(Ljava/lang/String;)Ljava/lang/String;beanName()Ljava/lang/String;getCount()I getBeanInfo(I)Ljava/beans/BeanInfo;bLjava/lang/Object;getName(I)Ljava/lang/String;isFromPrototype(Ljava/lang/String;)ZnamegetManifestData/(Ljava/lang/String;)Lneosim/util/MessageHeader; getInstance&(Ljava/lang/String;)Ljava/lang/Object;thLjava/lang/Throwable;diagnoseInstantiationExceptionI(Lneosim/util/SimpleClassLoader;Ljava/lang/String;Ljava/lang/Throwable;)VresultLjava/io/ObjectStreamException;Ljava/io/IOException;"Ljava/lang/ClassNotFoundException;oinsLjava/io/ObjectInputStream; classFileNameLjava/lang/SecurityException;args[Ljava/lang/Class;consLjava/lang/reflect/Constructor;!Ljava/lang/NoSuchMethodException;objrealxserNameinsLjava/io/InputStream;pkg classNameclsmods indexForName(Ljava/lang/String;)I(Ljava/lang/String;)Vmsg()V SourceFile JarInfo.java java/lang/Error8beanNames and fromPrototype need to have the same length }~  java/beans/BeanInfo TUV WXjava/lang/ExceptionY Z[ \]java/lang/StringBuilder$JarInfo: couldn't find BeanInfo for ^_ ^` ; caught ab c JarInfo:: @ ^d ; beanName: ; fromPrototype: ^e fgjava/lang/String hi j kljava/lang/Throwable  mnd Note that file names in manifests must use forward slashes "/" rather than back-slashes "\"& WARNING: Could not instantiate bean "" o from the system class-loader from JAR " pq.ser r st) We found a serialized template file "#neosim/util/ObjectInputStreamLoader uv wx< An object could be read from the serialized template OK.8 But an exception was generated in Beans.instantiate: java/io/ObjectStreamExceptionL But caught an ObjectStreamException while reading the serialized object:M This indicates there is a problem with the contents of the template file.java/io/IOExceptionB But caught an IOException while reading the serialized object: java/lang/ClassNotFoundExceptionL But caught a ClassNotFoundException while reading the serialized object:I This indicates that there was a problem finding a .class file for one of the serialized objectsK But caught an unexpected exception while reading the serialized object:y z.class% We couldn't open the class file " " in the JAR We found the class file "java/lang/SecurityExceptionthe default package {n the package " |} |' But were unable to load the class " " because of, Common reasons for this failure include:7 (1) The class is not defined in the correct package it should be in 5 (2) The class has not been given the correct name it should be called "B (3) The class file contains the wrong class or no class at alljava/lang/ClassFormatError ~Duplicate name R This particular error is often caused by having a mismatch between the name of8 the .class file and the name of the contained class.; In this case make sure that class file contains a class called "" in .  We located the class "" OK  H But the class was not declared public, so we could not create a beanjava/lang/Class 6 But the class did not have a zero-arg constructor.8 All beans must provide public zero-arg constructors.@ But the class's zero-arg constructor was not declared publicjava/lang/NoSuchMethodException: Unexpected exception in disgnoseInstantiationException 4 The class provides a public zero-arg constructor xA But were unable to create an instance of the class because we6 got an exception while doing Class.newInstance() : 8 The stack backtrace at the time of this exception is  JarInfo:: java/util/Hashtableneosim/util/JarInfojava/lang/Objectput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;neosim/util/SimpleClassLoader loadClass%(Ljava/lang/String;)Ljava/lang/Class;java/beans/Introspector((Ljava/lang/Class;)Ljava/beans/BeanInfo;java/lang/SystemerrLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintln(I)Ljava/lang/StringBuilder;(Z)Ljava/lang/StringBuilder;get&(Ljava/lang/Object;)Ljava/lang/Object;getClass()Ljava/lang/Class;java/beans/Beans instantiate=(Ljava/lang/ClassLoader;Ljava/lang/String;)Ljava/lang/Object;indexOf(I)Iprintreplace(CC)Ljava/lang/String;concatgetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;/(Ljava/io/InputStream;Ljava/lang/ClassLoader;)Vjava/io/ObjectInputStream readObject()Ljava/lang/Object;java/io/InputStreamclose lastIndexOf substring(II)Ljava/lang/String; getMessageequals(Ljava/lang/Object;)ZprintStackTrace getModifiersjava/lang/reflect/ModifierisPublic(I)ZgetConstructor3([Ljava/lang/Class;)Ljava/lang/reflect/Constructor;java/lang/reflect/Constructor newInstance!{|}~  *- Y*+*,*-** *- 6- -2+ W3,-2::o:,: Y <* SY-23a[ehmtwj%& ')* +%,+-1.:/D0P1X3[8e?h9j>mBtGwCyDFHI/Lp jy' ette=~ 5 * !R  /*] 0*d a* 2 * 2**2"M,C,#N-:*:Y-* S$*-6 k lnop$s*w-t/uRvTx\y_{>/%$;*5Faa;*2? **+$3 ? * *+$2 /*+%M**+,'(+\) * & %-  %// Y+,,-+ .Y/*,,./012:+3:Y4,5Y+6:7:89Y:-:<Y:=:?Y:^:AY:BC':DY:E:,./0F2:+3:#YGHYI,:K:,:,.L5YM,,.LN,:,,.L`O:+,:0: YP,QY: RSYTUYV,W: YP,QY:  XT YZ[G\]^Y_`a bYc,de6  f gh:  i:  jk l6  fmk@: jk: oYp  bqr: =: stYu v b9Y:--b;>@S&w|JJ$+.$+&nn&&%(&q"*+L[ch&@HPSU]w|$+.0Nhpx!) R U Z [y!"#$%0'()*+,-./24%<(5*627:8T9\:a;b?j@AB)*"2U"L0  ? 6  ( % *8 ~[-c%+] p"=**2+[F GHF K "" R wYx*STV  +yYz w  QPKEN'I'PK(3neosim/kernel/CommandObj.class1A - . /0 123 456789:idIblockingZ(I)VCodeLineNumberTableLocalVariableTablethisLneosim/kernel/CommandObj;()VsetIDgetID()IgetType()Ljava/lang/String; isBlocking()Z setBlocking(Z)Vbdoit(Lneosim/kernel/SimKernel;)VhpLneosim/kernel/SimKernel;doquery-(Lneosim/kernel/SimKernel;)Ljava/lang/Object; isDelayedgetSize SourceFileCommandObj.java   Basic; <=Executing a basic command > ?@Executing a query command resultsneosim/kernel/CommandObjjava/lang/Objectjava/io/Serializablejava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)V!    O***   < **   :* /* - /*!  !:*&"#$A  ,-  %&'(C   34  %&),7 *-< +,PKըxPK(3 neuroml/util/NeuroMLParser.classM1=         R R     ,      } }       R R ( ( ( ,  _ 1 1 1   ,  (        E , , I ,    , ! " #$  % & X' ( ) * *+ _ ,v - ./ 01 2 .34 5 .67 8 .9: ; .<= > .?@ .AB RC D EFGHI }JK LM NO PQ R ST UV WXYZ[\]^_ ` ab cd efghijk lmnopqrstuvwxyz{ (| R}~ R        '   '   ' R  R   R  '  .  9 Z           R R R      R domDocumentLorg/jdom/Document;rootLorg/jdom/Element;descLjava/lang/Object;nsLneuroml/util/Namespace;cwdLjava/lang/String;debugZ nmlschema getNmlSchema()Ljava/lang/String;CodeLineNumberTableLocalVariableTablethisLneuroml/util/NeuroMLParser;((Lorg/jdom/Document;Ljava/lang/String;)Vdocument namespacelIjarPathsLjava/util/Vector;LocalVariableTypeTable"Ljava/util/Vector; getNamespace()Lneuroml/util/Namespace;atoi(Ljava/lang/String;)Isatos(Ljava/lang/String;)Satod(Ljava/lang/String;)Datof(Ljava/lang/String;)Fatob(Ljava/lang/String;)ZgetDesc()Ljava/lang/Object; toFullURL&(Ljava/lang/String;)Ljava/lang/String; extractURL&(Lorg/jdom/Element;)Ljava/util/Vector;eLjava/lang/Exception;ntstLjava/util/StringTokenizer;modulesElementnmlpkgLneuroml/NeuromlPkg;modLneuroml/core/Module;ieurl Ljava/net/MalformedURLException;plvaLorg/jdom/Attribute; classNameobjmsLneuroml/core/Set;mv Signature6(Lorg/jdom/Element;)Ljava/util/Vector; createClass%(Ljava/lang/String;)Ljava/lang/Class; packageNamejkplcLjava/lang/Class; createObject&(Ljava/lang/String;)Ljava/lang/Object;o setInstName'(Lorg/jdom/Element;Ljava/lang/Object;)Velement instElement setAttributesstrings[Ljava/lang/String;trucLneuroml/util/JarClassLoader;dvalueLneuroml/core/DValue;Lneuroml/core/Enum;refLneuroml/core/Reference;fieldObjftsftfvattrfnieattributesListLjava/util/List;cdcfLjava/lang/reflect/Field; getFieldName&(Lorg/jdom/Element;)Ljava/lang/String;getFieldParameter8(Lorg/jdom/Element;Ljava/lang/String;)Ljava/lang/String;name getFieldClass9(Lorg/jdom/Element;Ljava/lang/Object;Z)Ljava/lang/String;parentlistedcn getFieldNamed?(Ljava/lang/String;Ljava/lang/Object;)Ljava/lang/reflect/Field;e2 Ljava/lang/NoSuchFieldException; superclass setParameter9(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)V"Ljava/lang/IllegalAccessException;subInstElement isBasicTypeisBasicTypeInListisArray extractValues((Ljava/lang/String;I)[Ljava/lang/String;indexcontentlengthvaluespreindexgetArray7(Lorg/jdom/Element;Ljava/lang/Class;)Ljava/lang/Object;arrayLneuroml/core/DoubleArray;data[DLneuroml/core/IntArray;[ILneuroml/core/StringArray;expClass charIsAlpha(C)ZC charIsNumeric findUnitIndexvfound getDValue;(Ljava/lang/String;Ljava/lang/String;)Lneuroml/core/DValue; nameAsField valueAndUnitvalueAndUnitTrimmed unitIndexunitNamevaluegetSet<(Ljava/lang/String;Ljava/lang/Object;)Ljava/util/Collection;setNameAsField defaultSetLjava/util/Collection;getMap5(Ljava/lang/String;Ljava/lang/Object;)Ljava/util/Map;mapNameAsField defaultMapLjava/util/Map;startRefP(Ljava/lang/String;Ljava/lang/String;Ljava/lang/Object;)Lneuroml/core/Reference;refNameAsFieldtarget defaultRef startElement8(Lorg/jdom/Element;Ljava/lang/Object;)Ljava/lang/Object; instParentJ(Lorg/jdom/Element;Ljava/lang/Object;Ljava/lang/String;)Ljava/lang/Object;txtr defaultObjvalkeytypechildrenAreElementofSetchildrenAreElementofMapelementTagNameisDerivedFromEnumisDerivedFromRefscnlist subElementgetShortClassName SourceFileNeuroMLParser.java     $    / '    56 `neuroml/util/JarClassLoader java/net/URL [Ljava/net/URL;              true http: 0ftp:file:java/lang/StringBuilder  java/util/Vector  java/util/StringTokenizer;,    34  java/lang/Exception   faulty url   neuromlmodules  wx Vneuroml/NeuromlPkgneuroml/core/Set   neuroml/core/Module  java/net/MalformedURLException)NeuroMLParser extractURL : Malformed URL O O  java/lang/String. NO 2Something strange with neuroml/core/Nameable rs   org/jdom/Attributeclass      4int &'  short )* boolean /0 double +, float -. String module '   is null!Integerjava/lang/IntegerShortjava/lang/ShortDoublejava/lang/DoubleFloatjava/lang/FloatBooleanjava/lang/BooleanDValue neuroml/core/Enum neuroml/core/Reference Error in set Attrs =ft  not handledschemaLocationFWarning - error in JDOMNeuroMLParser.setAttributes findingfield named  in class element  () tu  neuroml/core/ContentRestricted !Object |}Neuroml Parser Warning : , not found in schema. 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import neuroml.sim.run.*; import java.util.*; import java.beans.*; /** * Load a java bean from a .jar file * * @author Fred Howell * * @version 1.0, 18 October 2000 * */ public class SimulatorBean implements DoOnBean { String name; String beanName; Simulator o; static boolean debug = true; public SimulatorBean(String name) { this.name = name; } public void action(JarInfo ji, BeanInfo bi, String beanName) { if (debug) { System.out.println("NeuroML Module Loader Loading "+beanName); } Object obj = ji.getInstance(beanName); if (debug) { System.out.println("NeuroML Module Loaded "+obj); } if (obj instanceof Simulator) { o = (Simulator)obj; } else System.out.println("NeuroML Module not a Simulator "+obj); this.beanName = beanName; } public Simulator getSimulator() { return o; } public String getBeanName() { return beanName; } public void error(String msg) { System.out.println("NeuroML Module Loader error "+msg); } public void error(String msg, Exception ex) { System.out.println("NeuroML Module Loader exception "+msg); } } PKqPK(3nmlplay/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(3%neuroml/util/axiope/CVS/Entries.ExtraT/.nbattrs/// /AccessorFinder.java/// /ObjectAccessor.java/// /ValueAccessor.java/// PKGYTPK(3neosim/rmikernel/RmiServer.rmiPKPK(3(neuroml/sim/ElementChangedListener.class1  elementChanged'(Ljava/lang/Object;Ljava/lang/Object;)VconfirmElementChanged SourceFileElementChangedListener.java"neuroml/sim/ElementChangedListenerjava/lang/ObjectPKq\FPK(3"neuroml/model/morphml/Parent.classD1 valueLjava/lang/String;()VCodeLineNumberTableLocalVariableTablethisLneuroml/model/morphml/Parent; SourceFile Parent.java neuroml/model/morphml/Parentjava/lang/Object!/*    PKۉIDPK(3guikit/HTMLPanel$1.class1'     !"this$0Lguikit/HTMLPanel;(Lguikit/HTMLPanel;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/HTMLPanel$1;getMinimumSize()Ljava/awt/Dimension;getPreferredSizegetMaximumSize SourceFileHTMLPanel.javaEnclosingMethod# $%  % java/awt/Dimension &guikit/HTMLPanel$1javax/swing/JPanelguikit/HTMLPanelwaitURL()V(II)V    4 *+*    /*   7 Y,    /*   PK PK(3+neuroml/model/network/Grid1DStructure.classn1   sizeI()VCodeLineNumberTableLocalVariableTablethis'Lneuroml/model/network/Grid1DStructure;(Ljava/lang/String;)VnameLjava/lang/String;(Ljava/lang/String;I)V SourceFileGrid1DStructure.java   %neuroml/model/network/Grid1DStructure)neuroml/model/network/PopulationStructure!  < **     G *+*      Z*+**    PK ePK(3!neosim/implementation/CVS/Entriesw/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /ConnectionImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ConnectionRequestImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ConnectionSpec.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ControlModuleImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /DestMethodImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Entity3D.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EntityClassImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EntityImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EventClassImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /EventListImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /GUI_Maker.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /GUI_Maker_Population.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /GeneralProjectionImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Grid3DPopulation.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /InportsTableOut.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeosimClassImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeosimClassesImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ParamConnectionSpec.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationBuilderImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationNodeImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationTreeImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationViewImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Position3DPopulation.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ProjectionImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ScriptReaderImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Shape.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SourceMethodImpl.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PK5U|wPK(3neuroml/core/Ref.class16 $% & ' () *+,-./typeLjava/lang/String; 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P@Y PQ PR ST@$U dV VF W ( (X VY Z [\ ] ^ P_` a b Pc Pd e f6 g h Pijk 7 Pl Vm Vd fP Vin op q7rs Vtu vi fw [x y z f{| } ~   q P7 f ~7  V7 f 7 (7        [   vd   ?񙙙 ?Et]   P v    %   q                    D  B  %? @@?L>    1 7 7 1 ~/       (    !0  dY  1   ~ 6  6  6_ 6     A  9networkLneuroml/model/network/Network; ToBeAddedLguikit/ClickablePoint;populationTableLjava/util/Hashtable;hasMovedZ VisibleGrid ZoomingBackMenuPopupVisibledragXI realDragXDeopLguikit/EditObjectPanel;pathLjava/lang/String;menuLjavax/swing/JPopupMenu;envLguikit/Environment; resourcesLjava/util/ResourceBundle;TextureDisplayH(Lguikit/Environment;Lneuroml/model/network/Network;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablestuff"Lneuroml/model/network/Projection;i"Lneuroml/model/network/Attachment;thisLguikit/NetEditPanel;nProjLjava/util/Vector;ElemAttaProb addToDisplay"(Lneuroml/model/network/Network;)VndLguikit/PopulationNode;elem"Lneuroml/model/network/ElementRef; Lguikit/Node;Lneuroml/model/network/Probe;srcXsrcYdstXdstYxmidymidp Lguikit/Link;srcpopdestpopdotindexndSourcendTargetjgridszxszyszndpopnsLneuroml/util/Namespace;SetTargetControls*(Lguikit/Link;Lguikit/Node;Lguikit/Node;)Vcpts[Lguikit/ControlPoint; addMenuNode(Lguikit/ClickablePoint;)VnewnlnewlobjLjava/lang/Object;mySetLneuroml/core/Set;removeMenuNodeListObj[Ljava/lang/Object; RemoveElement(Lguikit/ObjectNode;)VNameneLguikit/ObjectNode;varclassLjava/lang/Class;MyPointfound getNetwork!()Lneuroml/model/network/Network;addControlPoint(Lguikit/ControlPoint;)VtrucLguikit/ControlPoint; mousePressed(Ljava/awt/event/MouseEvent;)VoeLjava/awt/event/MouseEvent;modifrxry mouseReleasedInvZoommuche ancestor_dataancestor target_datactrlp oldTargettarget InavigateMoved mouseDraggedpypxrender(IILjava/awt/Graphics2D;)VmyURLLjava/net/URL;myIconLjavax/swing/ImageIcon; elementImageLjava/awt/Image;w_h_biLjava/awt/image/BufferedImage;giLjava/awt/Graphics2D;gradientLjava/awt/TexturePaint;msgwhg2Y0X0Y1X1X0_Y0_X1_Y1_restelementChanged'(Ljava/lang/Object;Ljava/lang/Object;)VOnmn!Lneuroml/model/cell/ModuleNeuron;mrLneuroml/core/ModuleRef;Lneuroml/core/PermanentSet;exceptLjava/lang/Exception;attLjava/util/Enumeration;vStrOldStrNew oldobject newobjectconfirmElementChangedoldn AdjustLink1(Lneuroml/core/Connector;Lneuroml/core/TreeRef;)VctrlPopnodePop"Lneuroml/model/network/Population;Lneuroml/core/Connector;Lneuroml/core/TreeRef;prprlnkLguikit/ProjectionLink;ThatReftemp ThatTargetgetPath()Ljava/lang/String;setPath(Ljava/lang/String;)VPopupClickedPoint clickedPointgetLastClicked()Lguikit/ClickablePoint;setDisplayTexture(Z)VDisplaygetDisplayTexture()Z RightClick()VTextDispmre$Ljava/util/MissingResourceException; SourceFileNetEditPanel.java B *+java/util/Hashtable ,- ./ 1/ 2/ ?@   9: => {  {  {  { ()  yguikit/NetworkTransform  6  6 6 6 6 6   neuroml/model/network/Projection neuroml/core/TreeRef  RealPopulation  SubNetwork  neuroml/model/network/Attachment STjavax/swing/border/MatteBorder B  javax/swing/JPopupMenu ;< !"# $%& '( neuroml/model/network/ElementRefguikit/PopulationNode )* + ,- ./neuroml/model/network/Element 01 2 3 4 567 89java/lang/StringBuilder*NetEditPanel elem.editorInfo not a Node : :; :< => ?guikit/RGBColour-df25e0 B B@ A*neuroml/model/network/Probe guikit/Node guikit/Link elements. 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Neuroml definitions for channels

This package defines neuroml definitions for ion channel models.
Fred Howell
Last modified: Mon Mar 12 18:56:48 GMT 2001 PKPK(3"neuroml/environment/io/CVS/Entriese/IOPkg.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /MethodModule.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /MethodRef.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PK|ޢPK(3guikit/EditEnumPanel.classI1B ' ()* +, - ./ 0 1 23456nsLneuroml/util/Namespace;valLneuroml/core/Enum;.(Lneuroml/util/Namespace;Lguikit/ObjectNode;)VCodeLineNumberTableLocalVariableTablethisLguikit/EditEnumPanel;nodeLguikit/ObjectNode;actionPerformed(Ljava/awt/event/ActionEvent;)VeLjava/awt/event/ActionEvent;cbLjavax/swing/JComboBox; selectNameLjava/lang/String;confirm()V SourceFileEditEnumPanel.java 78 9:javax/swing/JComboBox ;:java/lang/String < => #$ ? @Aguikit/EditEnumPanelguikit/EditPaneljava/awt/event/ActionListener(Lguikit/ObjectNode;)Vjava/awt/event/ActionEvent getSource()Ljava/lang/Object;getSelectedItemneuroml/core/EnumsetValue(Ljava/lang/String;)Vguikit/ObjectNode setContent(Ljava/lang/Object;)V!  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" #$PKo,PK(3neosim/kernel/RmtProcMgr.classU1 getProcessor(I)Lneosim/kernel/RmtProc; Exceptions setSleeping(Lneosim/kernel/RmtProc;)V setRunning-(Lneosim/kernel/RmtProc;Lneosim/iface/Time;)V setStopped getMinTime()Lneosim/iface/Time; setMinTime(Lneosim/iface/Time;)V updateMinTime calcMinTime()V SourceFileRmtProcMgr.javaneosim/kernel/RmtProcMgrjava/lang/Objectjava/rmi/Remotejava/rmi/RemoteException    PK;ZUPK(3!neosim/kernel/CallbackQueue.class-1S * + ,- . / 01 02 3 4 5 67 8 9:;()VCodeLineNumberTableLocalVariableTablethisLneosim/kernel/CallbackQueue;pop!()Lneosim/kernel/CallbackHandler;entLneosim/kernel/CallbackHandler;topremoveCallback(I)VcqidIeLjava/util/Enumeration;iadd"(Lneosim/kernel/CallbackHandler;)Vh SourceFileCallbackQueue.java  <= >?neosim/kernel/CallbackHandler @ ABC D= E? FG HI JKL MN OP QRneosim/kernel/CallbackQueuejava/util/VectorisEmpty()Z firstElement()Ljava/lang/Object;removeElementAtelements()Ljava/util/Enumeration;java/util/EnumerationhasMoreElements nextElementgetQid()IindexOf(Ljava/lang/Object;)IgetTime()Lneosim/iface/Time;neosim/iface/TimetJ addElement(Ljava/lang/Object;)VinsertElementAt(Ljava/lang/Object;I)V!3*  1X**L*+% '()2*2 1@6*M,%,N- *- 6 *NOP!Q)R3T?U4!@@ !8"#=$!1%&Q=*N-0+-: + * = *+ *+& abc d3e=hBiJkPl4 QQ'O$!J"#()PKWg2-PK(3-neosim/implementation/ControlModuleImpl.classu1 ()VCodeLineNumberTableLocalVariableTablethis)Lneosim/implementation/ControlModuleImpl;init(Ljava/util/Hashtable;)VparamsLjava/util/Hashtable;run(Lneosim/iface/ScriptReader;)VsrLneosim/iface/ScriptReader; SourceFileControlModuleImpl.java 'neosim/implementation/ControlModuleImpljava/lang/Objectneosim/iface/ControlModule!/*   5  5  PK$zuPK(3guikit/resources/Back24.gifYGIF89a̽׻չӷѵϵϴͳ̮Ǭƨ33f!1,@ppH,DQy^r StdjBXFeAY4TFCYt;<15H o{azmJpx*u{OQKyiue} # !/0l`A!OCopyright 2000 by Sun Microsystems, Inc. All Rights Reserved. JLF GR Ver 1.0 ;PKЙګPK(3)neosim/kernel/PopulationUpdateEvent.class $1z E F G HI HJ KLMN O P QRST UV W X YZ[ \ ]^_`euLneosim/iface/EntityUpdate;c(Lneosim/iface/Time;ISLneosim/iface/Population;Lneosim/iface/EntityUpdate;Lneosim/iface/Callback;)VCodeLineNumberTableLocalVariableTablethis%Lneosim/kernel/PopulationUpdateEvent;tLneosim/iface/Time;srceIsrcportSpLneosim/iface/Population;cbLneosim/iface/Callback; doOnEntity(Lneosim/iface/Entity;)VeLneosim/iface/Entity;idxpcoLneosim/kernel/PopCBObject; registerClass4(Lneosim/iface/NeosimClasses;)Lneosim/iface/ClassID;ncLneosim/iface/NeosimClasses; readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; Exceptionsab writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput;getSize()I SourceFilePopulationUpdateEvent.java c  d,e fg hBi jkneosim/kernel/PopCBObjectjava/lang/Integer l m noPopulationUpdateEvent EntityEvent neosim.kernelp 2q rs 67t uvneosim/iface/EntityUpdate =>w xy#neosim/kernel/PopulationUpdateEvent"neosim/kernel/PopulationQueryEventjava/io/IOException java/lang/ClassNotFoundExceptionb(Lneosim/iface/Time;ISLneosim/iface/Population;Lneosim/iface/EntityQuery;Lneosim/iface/Callback;)Vupdateneosim/iface/Entity getPopulation()Lneosim/iface/Population;getIDneosim/iface/PopulationgetIndex(I)I(I)V(Ljava/lang/Object;I)V sendCallback(Lneosim/kernel/PopCBObject;)Vneosim/iface/NeosimClassesN(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Lneosim/iface/ClassID;cidLneosim/iface/ClassID;java/io/ObjectInput readObject()Ljava/lang/Object;java/io/ObjectOutput writeObject(Ljava/lang/Object;)V!*+*  H !"#$%&'()*+,3*+++=YY  N*-  -2*3 3-./$-0123M*+  *  4567O*+*+ 89:;<=>L*++*!"# ?@:;AB-P&  CDPKÈ PK(3neosim/iface/EntityID.classt1   SYSTEM_ENTITYI()VCodeLineNumberTableLocalVariableTablethisLneosim/iface/EntityID; SourceFile EntityID.java  neosim/iface/EntityIDjava/lang/Objectjava/io/Serializable!   /*       PKp_㽐PK(3(neosim/util/loaders/nmllauncher/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(3guikit/Constants.class 1 NORMALI ConstantValueDRAGGING HIGHLIGHTED SourceFileConstants.javaguikit/Constantsjava/lang/Object    PKWPK(3'neosim/util/SmallLists/LinkedList.classX1G * + , - . /01 *2 3 4 5 67 8 9:;RealIndex_readIListSizeTotalMemoryLinkedListsNextCompressionStep SizePerStep()VCodeLineNumberTableLocalVariableTablethis#Lneosim/util/SmallLists/LinkedList;compresscompress_finalgetSize()IcheckCompression&(Lneosim/util/SmallLists/LinkedList;)Zobjclear SourceFileLinkedList.java     < =>java/lang/StringBuilder Compress at ?@ ?A BCD EF  !neosim/util/SmallLists/LinkedListjava/lang/Objectjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)V!   B***2    !"#)$%t6.Y  *` $(2 4" 6&)'4%& '(()PK {JPK(3guikit/ClickablePoint.classo1,*+ queryClick(DD)Z intersect(DDDD)Z mouseMoved(DD)V mouseDraggedmovetoString()Ljava/lang/String;notifyTargetChanged(Lguikit/ClickablePoint;)V getSource()Lguikit/ClickablePoint; getTargetgetData()Ljava/lang/Object;setData(Ljava/lang/Object;)V initUserData;(Lguikit/Environment;Lneuroml/core/Set;Ljava/lang/String;)V getParentSet setParentSet getBaseClasssetState(I)VsetHighlighted()VclearHighlighted isHighlighted()ZtoggleHighlightnotifyStateChangegetState()IgetDepthsetDepth SourceFileClickablePoint.javaguikit/ClickablePointjava/lang/Object      !"#$%&%'()PKPtoPK(3guikit/MenuPanel.class1* K J J J J J J K@T J J J J J J J  J J J J J J J J J K J J J  1  4 @> J : < J J  C C C CnepLguikit/NetEditPanel;CurrentYIMaxSizeDMinSize()VCodeLineNumberTableLocalVariableTablethisLguikit/MenuPanel; setNetPanel(Lguikit/NetEditPanel;)VsetInitialScale mousePressed(Ljava/awt/event/MouseEvent;)VeLjava/awt/event/MouseEvent;modifrxry mouseDraggedpy mouseReleasedSetNbComponents(II)VnbperlinecomponentHidden"(Ljava/awt/event/ComponentEvent;)VLjava/awt/event/ComponentEvent;componentMovedorganizen Lguikit/Node;l Lguikit/Link;iLinesCurrentXdLjava/awt/Dimension;Width DoingNodeZcomponentResizedcomponentShownContainProjectionType(Lneuroml/core/Connector;)ZstuffLguikit/ProjectionLink;prLneuroml/core/Connector; equivalentsize mouseMoved throwableLjava/lang/Throwable; SourceFileMenuPanel.java TU MN OP QR SR ]U R P R    2Error: MenuiPanel needs to have setNetPanel called  P R | navigating! R | R      U U e_ P  P    guikit/Node   guikit/Link P pUguikit/ProjectionLink  neuroml/core/Connector ! "|java/lang/Throwable# $Out!java/lang/StringBuilderFound %& %'! ()guikit/MenuPanelguikit/NetPanel java/awt/event/ComponentListenerjava/awt/Color lightGrayLjava/awt/Color;darker()Ljava/awt/Color; setBackground(Ljava/awt/Color;)VaddComponentListener%(Ljava/awt/event/ComponentListener;)VyszpyszplatonicYPixelSizejava/awt/event/MouseEvent getModifiers()IgetXrealX(I)DgetYrealYcpLguikit/ClickablePoints;guikit/ClickablePoints queryClick(DD)Lguikit/ClickablePoint; clickedPointLguikit/ClickablePoint;guikit/NetEditPanel ToBeAddedremoveMenuNode(Lguikit/ClickablePoint;)V addMenuNodejava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)VdragY realDragY navigating zoomFactorhasMovedtytLjava/awt/geom/AffineTransform;java/awt/geom/AffineTransform translate(DD)VrerenderrepaintpxszgetSize()Ljava/awt/Dimension;java/awt/Dimensionwidthnet Lguikit/Net; guikit/NetnodesLjava/util/Vector;java/util/Vector elementAt(I)Ljava/lang/Object;setPoslinksheightgetData()Ljava/lang/Object; IsEquivalentdraggingguikit/BasicClickablePointEmphasizedPointappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;!JKLMNOPQRSRTUVj(******** W% !"&"''(X (YZ[\V>*+W +,XYZMN]UVP* * ** *oW/0 24X YZ^_V9+=*+J*+9~[**)*m*4*******5*~$*+**** !WN89:;<-?4A;BSC^DiFlGtIwK}LMNOQX4YZ`abPcRdRe_Vr* h+*d*"oI*+*#*Y$(c$*$* **$*$* **$*%(&*'*(*+)WBSTUW$X.Y:ZB[C^O_W`XbadeeifqgX RfRrYZr`ag_VG * *#Wjk lX YZ `ahiV`* Fdl`h`*}h*WpqrX YZjPkPlmV5WuXYZ`nomV5WxXYZ`npUV' =*22>*+:*,66<X*-./B2`2>*YF`*-.01:*2d<6*-3/B2`2>*YF`*-304:*5d\**+6*7cg*******%*%*$w&*$W%}~  "'5>ALObnqtvy| X\ bqrstYZ"uPvP wP xyzP {|}mVM *9*'*(W X YZ `n~mV5WXYZ`nVR=*-3/66;7*-30::N+-;<<==W/JPX>/!?uPRYZRP|DP_V2*> *+?}+6*+I*+9:**(A**B$CYDEF*GHFI*A*'*((+@WJ (+-.<GNYzX>-tbPkcR(adRYZ`aPKaФPK(3 nmlplay/resources/CVS/Repository"NMLPLAY_CVS/src/nmlplay/resources PKs$'"PK(3guikit/AboutPanel.classg1m 9: ; < => ? @AB 9 AC 9 DEF G H ;IJ KL @D M N OP QRSTUdialogLjavax/swing/JFrame;7(Ljava/lang/String;Ljava/awt/Image;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablepicLjavax/swing/JPanel;thisLguikit/AboutPanel;titleLjava/lang/String;imageLjava/awt/Image;messagefieldsbuttonspopup()VactionPerformed(Ljava/awt/event/ActionEvent;)VeLjava/awt/event/ActionEvent; SourceFileAboutPanel.java !2javax/swing/JFrame !V  WXjavax/swing/BoxLayout !YZ [\javax/swing/JPaneljava/awt/FlowLayout ]^javax/swing/JLabeljavax/swing/ImageIcon !_ !`OKoka bc d2 efg hij klguikit/AboutPaneljava/lang/Objectjava/awt/event/ActionListener(Ljava/lang/String;)VgetContentPane()Ljava/awt/Container;(Ljava/awt/Container;I)Vjava/awt/Container setLayout(Ljava/awt/LayoutManager;)Vadd*(Ljava/awt/Component;)Ljava/awt/Component;(Ljava/awt/Image;)V(Ljavax/swing/Icon;)Vguikit/EditPanel makeButtonZ(Ljava/lang/String;Ljava/lang/String;Ljava/awt/event/ActionListener;)Ljavax/swing/JButton;pack setVisible(Z)Vjava/awt/event/ActionEventgetActionCommand()Ljava/lang/String;java/lang/Stringequals(Ljava/lang/Object;)Z! !"#`**Y+*Y* Y :Y ,5 Y : Y WYY,WY-W Y :*W*W*W*$B)2 A!E"Z#b$w&)+,-./%HN)&'()*+,-.+2/'00'12#7 *$ 23%  ()34#Q+ *$6 79%()5678PKUPK(3-neosim/neuroml/NeuromlConnectionRequest.classt1Z &' ( ) * + , - . / 01 2 +3 4 5 678 9:;<=#(Lneosim/iface/ConnectionRequest;)VCodeLineNumberTableLocalVariableTableorig#Lneuroml/sim/run/ConnectionRequest;-Lneosim/implementation/ConnectionRequestImpl;this)Lneosim/neuroml/NeuromlConnectionRequest;c Lneosim/iface/ConnectionRequest; SourceFileNeuromlConnectionRequest.java >&neosim/neuroml/NeosimConnectionRequest ?@ AB CD EF GH IJ KL MN OP+neosim/implementation/ConnectionRequestImpl QB neosim/neuroml/NeuromlDestMethod IR ST UV"TEMPORARY CODE: NEED TO BE CHECKEDW XY\Fatal error in neosim.neuroml.NeuromlConnectionRequest --- connection request not recognised'neosim/neuroml/NeuromlConnectionRequest!neuroml/sim/run/ConnectionRequest!(ISLneuroml/sim/run/DestMethod;)VgetNeuromlConnectionRequest%()Lneuroml/sim/run/ConnectionRequest;getSrcID()IsrcIDI getSrcPortID()S srcPortIDS getDestMethod()Lneuroml/sim/run/DestMethod; destMethodLneuroml/sim/run/DestMethod; getSrcData()Ljava/lang/Object;srcDataLjava/lang/Object;getSrcEntityID()Lneosim/iface/DestMethod;(Lneosim/iface/DestMethod;)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)V!x*+.+M*,*,*, *, A+ 2+ M*, *,*Y,  F&.69@ E!M"U#d$l%o'w** E'x !x"#$%PK<ytPK(3 neosim/iface/ObjectHandler.class/1 handleD(Lneosim/iface/Time;Lneosim/iface/ObjectEvent;Lneosim/iface/Input;)V SourceFileObjectHandler.javaneosim/iface/ObjectHandlerjava/lang/ObjectPK6ڟrPK(3neuroml/util/schema/CVS/Entries/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlClass.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlField.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlObject.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlPackage.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlSchema.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlString.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlVector.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /package.html/1.1.1.1/Thu Jul 7 14:31:48 2005// D PK} 6QPK(3guikit/resources/marb_green.jpgDJFIFHH4Photoshop 3.08BIMHH8BIM8BIM' 8BIMH/fflff/ff2Z5-8BIMp8BIMAdobed           s!1AQa"q2B#R3b$r%C4Scs5D'6Tdt& EFVU(eufv7GWgw8HXhx)9IYiy*:JZjzm!1AQa"q2#BRbr3$4CS%cs5DT &6E'dtU7()󄔤euFVfvGWgw8HXhx9IYiy*:JZjz ?z22qo1]8XIʿUŰ(\_^KukETwTVVI:o"nU-yXGdMVUW߼v#?t^I%}>֪|稊T#bCG24+!OJoetE&HaSSj%/Md$wo-sNڴwz/c XDRm@2|1:ư|'dőK$!Eex1g ͯzVHW'?,Y*$}(*߽5W\bcu7Kɖ>2Z䈌⣔Ofo̭*Ȱ"e(6H>Ukȿѳ3[2z>OEbki5zߏv|hQkmlFV[ڔ57ɦV׬qK+}iqs_[Kn/"jU1giq6[m-s-͵\[i|Q |[rD3:c&,岦w2oY%%4,5>~/Y,qc1]Um8tm]lYUZfcOS,IDob7WŬJʱ2ŗ #fKL.O+JM2QYOb\?YY9I_y~*k%żQMˊX'bƖ^4 VH[K>FrN QZN\d}?,#FY[|0o]opzOӟXmy &VY?ř)4)5f^lXY H4ɿc>*b,/Ĝ"~?K/X $d6hY/'ɬS|nܳ0gI_72譔ݟ,% y];zKz^vgO+$4Okcgq ˗#hFW_E1kxp0ѯ$b5Jjz_Y+򭴞ܕ'k%B񮸭~}ՊP֖#1ȏ_Xobזmr_S)+/79EŬVRt0~~I36yoRǒ+4c)ԦXxw/؍?؇Cppf_R6U?x6hXN<T`G#|_,Cf+=Rѫ75Uϊ.ǝe85İč?w'~^S\]mEON)n*Vui"qG9?+M@,V,ޱoDxږw 'ŒeŒ}BoݬUUvOUu<>W$Z_+|1%,;1]Qfx3N8><[#IYy|i'gO_'zæ,#%6R[&HQv߃/1d F_ykiiTf _'x :q~|L[ iN'+SY yؙH&vЭ$p|=+_g>xɼZEaI#ߵ#?YIHYZI1g9"F^Lʍ"YnW$NзP5R q4'~+JN8ܕW9'f*fhoYx7͛?[-W;5c?Q%_Ł(%Oγ*ξagWJhĭy,oWƥk=J딍pNƕ x%FiKi, ۴RwZ6<rO&i●4h$Z4E^G$?1]ePV%/` LYw+Ir2şZIey#}v8bV%YVHOyqjlPzMr^Hѿxos?+H:g';vgqeJU/GI|HZ?zRe$^pO8EojZ$ťFƟȟ\_LYKł[5>|>8a?UMdV[N󓔿?f*iz^ݪT>_'b'oo%kxuo[-^p査3FF>,pXn<˯>mWNz//V#[t?/~p?-9#@8,ql:3?O4摡oO=qZB[jh3*׏ByxƊMxE.'oEd<.,ESHG}'_gŬzI$1KƟZЯגUQ1VYk/k<5N  VG_ޢR;琢oiWqvOo0iJ#3H_fPKIDPK(3 neuroml/model/morphml/diam.class>1 valueLjava/lang/String;()VCodeLineNumberTableLocalVariableTablethisLneuroml/model/morphml/diam; SourceFile diam.java neuroml/model/morphml/diamjava/lang/Object!/*    PK)߇C>PK(3,neuroml/model/network/DestMethodModule.class11  (Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis(Lneuroml/model/network/DestMethodModule;nameLjava/lang/String;()V SourceFileDestMethodModule.java  &neuroml/model/network/DestMethodModuleneuroml/core/Module!>*+     3*    PKrYPK(3"neosim/rmikernel/CVS/Entries.Extra,/.nbattrs/// /AllgatherV.java/// /Barrier.java/// /RmiKernel__._java/// /RmiServer.java/// /RmiServer.rmi/// /RmtServer.java/// /SocketClient.java/// /SocketServer.java/// /StrMessage.java/// /RmiKernel.java/// PK\PK(3$neuroml/model/cell/CVS/Entries.Extra,/.nbattrs/// /AbstractNeuron.java/// /CableNeuron.java/// /CellPkg.java/// /ChannelAssignment.java/// /Mask.java/// /ModuleNeuron.java/// /NeuronModule.java/// /NeuronStructure.java/// /OrientedSubstructure.java/// /PointNeuron.java/// /SectionProperties.java/// /SectionSet.java/// /package.html/// PK욨1,PK(3 neosim/thrkernel/ThrKernel.classu1F # $ % &'( #) * + , -. / 01234nthreadsIdebugZ(I)VCodeLineNumberTableLocalVariableTablethisLneosim/thrkernel/ThrKernel;runRmt(ILneosim/iface/Time;)VridtLneosim/iface/Time; SourceFileThrKernel.java 5  6 78java/lang/StringBuilder TheKernel run remote started to 9: 9; <=> ?@ ABC DE!TheKernel run remote finished at neosim/thrkernel/ThrKernelneosim/kernel/BasicKernel()Vjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)VgetID()Ineosim/kernel/SimSystemrunPar(IIILneosim/iface/Time;)V1O*** N*Y, ** , *Y,  -M  NNN !"PK1H YzuPK(3!neuroml/core/Ref_Decompiled.class1'  ! " # $%&nameLjava/lang/String;type targetName()VCodeLineNumberTableLocalVariableTablethisLneuroml/core/Ref_Decompiled;(Ljava/lang/String;)Vstring'(Ljava/lang/String;Ljava/lang/String;)V string_0_getName()Ljava/lang/String;setName getTargetType setTargetType getTargetName setTargetName SourceFileRef_Decompiled.java   neuroml/core/Ref_Decompiledjava/lang/Object!  G***    Z****+   m****+*,    /* >*+  /*" >*+ &' /** >*+ ./ PK]PK(3/neuroml/model/network/PopulationStructure.class+1  ()VCodeLineNumberTableLocalVariableTablethis+Lneuroml/model/network/PopulationStructure;(Ljava/lang/String;)VnameLjava/lang/String; SourceFilePopulationStructure.java   )neuroml/model/network/PopulationStructureneuroml/core/NamedObject!/*   :*+   PKE2\PK(3neosim/util/Filecmds.class*1 STARTI ConstantValueLINEEOF SourceFile Filecmds.javaneosim/util/Filecmdsjava/lang/Object    PKPK(3"neosim/kernel/RemoveCallback.class@1> '( ) * + , -./01()VCodeLineNumberTableLocalVariableTablethisLneosim/kernel/RemoveCallback;callback*(Lneosim/iface/Entity;Ljava/lang/Object;)VeLneosim/iface/Entity;oLjava/lang/Object;cLneosim/iface/Connection; readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; Exceptions23 writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput; SourceFileConnectionRequestEvent.java neosim/iface/Connection 45 67 89 :5; <=neosim/kernel/RemoveCallbackjava/lang/Objectneosim/iface/Callbackjava/io/IOException java/lang/ClassNotFoundException getSrcPortID()SgetDelay()JgetDstEntityID()I getDstPortIDneosim/iface/EntityremoveOutConnection(SJIS)V     3*  !  t$,N+----$(#.*$$$ 50 !" 53#$%&PKe4PK(3.neuroml/model/ions_channel/ModuleChannel.class618   !"  #$ %& '( ) * +,-moduleLneuroml/core/ModuleRef;()VCodeLineNumberTableLocalVariableTablethis*Lneuroml/model/ions_channel/ModuleChannel;(Ljava/lang/String;)VnLjava/lang/String; SourceFileModuleChannel.java neuroml/core/ModuleRef java/lang/StringBuilder. /01 23 45. 63 7 (neuroml/model/ions_channel/ModuleChannelneuroml/core/Modeljava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringsetName!z@**Y*Y*Y*   ? @A*+*Y*Y*Y*   @AAPKPK(3resources/CVS/RepositoryNMLPLAY_CVS/src/resources PKCXCPK(3!neuroml/core/RandomVariable.class19* +, - +. / 012 3 4 567nameLjava/lang/String;pdfLneuroml/core/PDF;unitLneuroml/core/Ref;()VCodeLineNumberTableLocalVariableTablethisLneuroml/core/RandomVariable;'(Lneuroml/core/PDF;Ljava/lang/String;)VunitNamegetName()Ljava/lang/String;setName(Ljava/lang/String;)VngetPDF()Lneuroml/core/PDF;setPDF(Lneuroml/core/PDF;)V SourceFileRandomVariable.javaneuroml/core/PDF null   neuroml/core/RefUnit "  8"neuroml/core/RandomVariablejava/lang/Object setTargetName!<*Y   w%***+* Y * ,  $ %%% /*  !":*+!#$%/*# &':*+$()PK<؅PK(3resources/BackPlay24.gif[GIF89a00a==naannž!,QI8փ|X@YRfR|-~=@(4>a F^IT>N]%.i1y=?g\;PKއjPK(3$neuroml/core/ContentRestricted.class1   getContentClassName()Ljava/lang/String;setContentClassName(Ljava/lang/String;)V SourceFileContentRestricted.javaneuroml/core/ContentRestrictedjava/lang/ObjectPKPhPK(3neosim/rmikernel/CVS/Repository!NMLPLAY_CVS/src/neosim/rmikernel PK$ &!PK(3$guikit/NetEditPanel_GuiKit$4$2.classz1-     !"#this$1$ InnerClassesLguikit/NetEditPanel_GuiKit$4;!(Lguikit/NetEditPanel_GuiKit$4;)VCodeLineNumberTableLocalVariableTablethis Lguikit/NetEditPanel_GuiKit$4$2; windowClosing(Ljava/awt/event/WindowEvent;)VeLjava/awt/event/WindowEvent; SourceFileNetEditPanel_GuiKit.javaEnclosingMethod %&  ' ()* +' ,'guikit/NetEditPanel_GuiKit$4$2java/awt/event/WindowAdapterguikit/NetEditPanel_GuiKit$4actionPerformed(Ljava/awt/event/ActionEvent;)V()Vval$PanelGuikitLguikit/NetEditPanel_GuiKit;guikit/NetEditPanel_GuiKitrerenderrepaint   4 *+*+  Q**, -.   PKfi3zPK(3guikit/NetworkTransform.classx1    XDYZoom()VCodeLineNumberTableLocalVariableTablethisLguikit/NetworkTransform; SourceFileNetworkTransform.java   guikit/NetworkTransformjava/lang/Object!    N****  PK3zPK(3"guikit/NetEditPanel_GuiKit$5.class,1S u u u u u u u u u v ^          ^ ^   #  & ) , / 2 5 7 : = ? B E G E K M K Q T V Z V    c c        o      val$flds[Ljava/lang/reflect/Field;val$kIval$oLjava/lang/Object;val$PanelGuikitLguikit/NetEditPanel_GuiKit;val$nsLneuroml/util/Namespace;val$Xval$ptLjava/awt/Point;val$Ythis$0(Lguikit/NetEditPanel_GuiKit;[Ljava/lang/reflect/Field;ILjava/lang/Object;Lguikit/NetEditPanel_GuiKit;Lneuroml/util/Namespace;ILjava/awt/Point;I)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/NetEditPanel_GuiKit$5;actionPerformed(Ljava/awt/event/ActionEvent;)VtrucLjava/net/URL;choseLjavax/swing/ImageIcon;exceptLjava/lang/Exception;fobmyFrameLjavax/swing/JFrame;on_Lguikit/ObjectNode;on innerPannelLjavax/swing/JPanel;ExcepeventLjava/awt/event/ActionEvent; SourceFileNetEditPanel_GuiKit.javaEnclosingMethod   xy z{ |} ~ { {   javax/swing/JFramejava/lang/Stringjava/lang/StringBuilderneuroml/core/Nameable  .  guikit/ObjectNodeguikit/NetEditPanel_GuiKit$5$1    ! "#$ %&neuroml/core/Set '&neuroml/core/NamedObject ()javax/swing/JPaneljava/lang/Integerguikit/EditIntegerPanel *java/lang/Shortguikit/EditShortPaneljava/lang/Doubleguikit/EditDoublePanelneuroml/core/DValueguikit/EditDValuePanel +java/lang/Booleanguikit/EditBooleanPanelguikit/EditStringPanel java/net/URLguikit/EditURLPanelneuroml/core/NeuromlArrayguikit/EditArrayPanelguikit/EditSetPanelneuroml/core/Listguikit/EditListPanelneuroml/core/TreeRefguikit/EditTreeRefPanelguikit/NetEditPanel_GuiKit$5$2 , -.neuroml/core/Refguikit/EditRefPanelguikit/NetEditPanel_GuiKit$5$3 /neuroml/core/ModuleRefguikit/EditModuleRefPanelneuroml/core/Enumguikit/EditEnumPanelguikit/EditObjectPanel 012 3guikit/NetEditPanel_GuiKit$5$4 45guikit/NetEditPanel_GuiKit6 78 EditingPopup9 :; <=javax/swing/ImageIcon > ?@ ABjava/lang/ExceptionC DENo icon for the editing windowF G HI J{ K{ LMguikit/NetEditPanel_GuiKit$5$5 N OP QRShould have edited  but I got an exception->JAGguikit/NetEditPanel_GuiKit$5java/lang/Objectjava/awt/event/ActionListener RightClick(Ljava/awt/event/MouseEvent;)V()VMenuPopupVisibleZjava/lang/reflect/Fieldget&(Ljava/lang/Object;)Ljava/lang/Object;getName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString(Ljava/lang/String;)V3(Lguikit/NetEditPanel_GuiKit$5;Ljava/lang/Object;)VK(Ljava/lang/Object;Ljava/lang/String;Lneuroml/sim/ElementChangedListener;)VpathLjava/lang/String; clickedPointLguikit/ClickablePoint;guikit/ClickablePoint getParentSet()Ljava/lang/Object;getDatasetPath'(Ljava/lang/String;Ljava/lang/String;)V(Lguikit/ObjectNode;)V.(Lneuroml/util/Namespace;Lguikit/ObjectNode;)VF(Lguikit/NetEditPanel_GuiKit$5;Lguikit/ObjectNode;Ljava/lang/Object;)VaddElementChangedListener'(Lneuroml/sim/ElementChangedListener;)V4(Lguikit/NetEditPanel_GuiKit$5;Lguikit/ObjectNode;)VgetType()Ljava/lang/Class;java/lang/ClassA(Lneuroml/util/Namespace;Lguikit/ObjectNode;Ljava/lang/String;Z)Vadd*(Ljava/awt/Component;)Ljava/awt/Component;guikit/NetworkDesigner resourcesLjava/util/ResourceBundle;java/util/ResourceBundle getString&(Ljava/lang/String;)Ljava/lang/String; getResource"(Ljava/lang/String;)Ljava/net/URL;(Ljava/net/URL;)VgetImage()Ljava/awt/Image; setIconImage(Ljava/awt/Image;)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintlnpackjava/awt/Pointxy setLocation(II)V!(Lguikit/NetEditPanel_GuiKit$5;)VaddWindowListener"(Ljava/awt/event/WindowListener;)V setVisible(Z)V uvw xyz{|}~{{b 8*+*,******* * A 8 * **2* M YYY***2NY***2Y*,:Y** !*"#$**2%:&Y':,()Y*:,+,Y-:z,./Y0:e,12Y*3:L,45Y6:7,7Y8:",9:Y;: ,<=Y*>:, ?Y*@:,ABY*C:,D(EY*F:EGY*,HI,J'KY*L:KMY*NOk,PQY*R:R,STY*U:9,5VY***2WXY:VZY*,[\-]W^_`ab:cYd:-ef :hij-k-**l`* *m`n-oY*pq-r-MhYs**2tjgg7CEHUIwQRSUVWXYZ[#\2]<^G_Q`\afbqc{defghijkuvw,6ELk~p  }Uwp )^2uGMZoPKdoPK(3neosim/renderer/AnimThing.classy1 step()V SourceFile AnimApp.javaneosim/renderer/AnimThingjava/lang/ObjectPK5PK(3neuroml/util/ClassBean.classe1O 1 2 3 456 17 8 9 :; <= >?@ABCnameLjava/lang/String;cLjava/lang/Class;debugZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLneuroml/util/ClassBean;action@(Lneuroml/util/JarInfo;Ljava/beans/BeanInfo;Ljava/lang/String;)VjiLneuroml/util/JarInfo;biLjava/beans/BeanInfo;beanName getBeanClass()Ljava/lang/Class;errormsg*(Ljava/lang/String;Ljava/lang/Exception;)VexLjava/lang/Exception;()V SourceFileClassBean.java .  D EFjava/lang/StringBuilder$NeuroML Module Loader Loading Class GH IJK LM &N NeuroML Module Loader error  NeuroML Module Loader exception neuroml/util/ClassBeanjava/lang/Objectneuroml/util/DoOnBeanjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintlnneuroml/util/JarInfo%(Ljava/lang/String;)Ljava/lang/Class;!F **+    y)Y- *+- (*))!")#$)%&'/*  (RY +  )(*\Y+  !" )+,-./0PK^jePK(3 neuroml/model/morphml/Cell.classh1(   ! " # $%&SphereLneuroml/core/Set;nameLjava/lang/String; SetOfSegments PolyhedronSetOfFreePoints()VCodeLineNumberTableLocalVariableTablethisLneuroml/model/morphml/Cell; SourceFile Cell.java neuroml/core/SetPointId ' Segment    neuroml/model/morphml/Celljava/lang/Object(Ljava/lang/String;)V!     s9**Y*Y*Y*Y    +  9PK(?mhPK(3,neuroml/model/Synapse_nml/SynapticCell.class@1 addSynapse'(Lneuroml/model/Synapse_nml/Synapse;I)V getSynapse&(I)Lneuroml/model/Synapse_nml/Synapse;7(ILjava/lang/Class;)Lneuroml/model/Synapse_nml/Synapse; getSynapses&()[Lneuroml/model/Synapse_nml/Synapse;%(Ljava/lang/Class;)Ljava/util/Vector;getIntensitySynapse(I)D(ILjava/lang/Class;)DgetAverageIntensitySynapse()D(Ljava/lang/Class;)D SourceFileSynapticCell.java&neuroml/model/Synapse_nml/SynapticCelljava/lang/Object     PK!_jE@PK(3'neuroml/util/schema/NeuromlObject.classj15 () * + , -. ( / 0123 neuromlClassLjava/lang/String; neuromlSchemanamepath fieldValuesLjava/util/List;()VCodeLineNumberTableLocalVariableTablethis#Lneuroml/util/schema/NeuromlObject;setNeuromlClass%(Lneuroml/util/schema/NeuromlClass;)Vnc"Lneuroml/util/schema/NeuromlClass;getName()Ljava/lang/String;setName(Ljava/lang/String;)VngetPathsetPath SourceFileNeuromlObject.java     java/util/Vector 4  !neuroml/util/schema/NeuromlObjectjava/lang/Object neuroml/util/schema/NeuromlClass!  f(******Y      (I + *+     /* !":*+#$ /* %":*+#&'PKPK(3neuroml/sim/run/DrawQuery.class41 ()VCodeLineNumberTableLocalVariableTablethisLneuroml/sim/run/DrawQuery;query&(Ljava/lang/Object;)Ljava/lang/Object;oLjava/lang/Object; SourceFileDrawQuery.java neuroml/sim/run/DrawQueryjava/lang/Objectneuroml/sim/run/Query!3*    6  PK QPK(3neosim/renderer/Netvis$2.class}1i A BCD EF GH I JK LM NO P ?QRSTthis$0Lneosim/renderer/Netvis;(Lneosim/renderer/Netvis;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLneosim/renderer/Netvis$2;callback*(Lneosim/iface/Entity;Ljava/lang/Object;)Ve3d Lneosim/implementation/Entity3D;exLjava/lang/ClassCastException;cdLneosim/renderer/ConnData;iIeLneosim/iface/Entity;oLjava/lang/Object;nLjava/util/Vector;srcpLneosim/kernel/Pos; readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; ExceptionsUV writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput; SourceFileNetvisClass.javaEnclosingMethodW XY  Zjava/util/Vectorneosim/kernel/Pos [neosim/implementation/Entity3D \]java/lang/ClassCastException ^_ `aneosim/renderer/ConnData bcnetvis0d ef g_ hYneosim/renderer/Netvis$2java/lang/Objectneosim/iface/Callbackjava/io/IOException java/lang/ClassNotFoundExceptionneosim/renderer/NetvisclickConnections(I)V()V(DDD)VgetPos()Lneosim/kernel/Pos;size()I elementAt(I)Ljava/lang/Object;getName()Ljava/lang/String;java/lang/Stringequals(Ljava/lang/Object;)Z getDestID highlightDest 4 *+*   V,NY:+:::6- )- :   Ա!2 !#/:GOU\ !"##$:%&&/'(VV)*V+,Q-.E/012534567895:;56<=>?@ PK FPK(3nmlplay/resources/logo.gif@GIF89a̶kkkvvv! ,I8ͻ`(dihlo 43pu%pIAH`PIP(lVj Ĉ"8XBt*D $=UvUzT sQm nzcnW0~:[Ug`WUjB}EzqA6Tnw\6ћ:T`nATe]Q(\8 w&0P1iӾay'J_sM )PB'Lhb3LbA!L"ЕH`, Y > .UN QJ3 Ј6VS2 pA+W$P0 9f }r1ui!Q-r`gC 1754l UقB[*UU&…*'.‚ksЬđdb`n^-{μYْkG;PK oE@PK(3neosim/stats/CVS/Entries(/SimAccum.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimNegexpObj.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimNormalObj.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimUniformObj.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PKZPK(3neuroml/sim/run/SimRunPkg.classE1> &'()*+,-./0123456789:;<=()VCodeLineNumberTableLocalVariableTablethisLneuroml/sim/run/SimRunPkg; getClassList()[Ljava/lang/String;strings[Ljava/lang/String; SourceFileSimRunPkg.java java/lang/StringBuildableProjectionConnectionMakerConnectionRequestConnectionRequestSenderConnectionsQueryable DestMethod NamedQueryNamedQueryable PostSynapse PreSynapseQuery Queryable RunnableCellRunnableCellFactoryRunnableControl SimRunPkg Simulator SourceMethod SpikeSenderSynapseWeightSettableneuroml/sim/run/SimRunPkgneuroml/core/Pkg!3*   !zYSYSYSYSYSYSY SY SY SY  SY  SY SY SY SYSYSYSYSYSYSK* x* x"#$%PK2PK(3 neosim/kernel/SimProcessor.class `1 %S $TU V $W $X $Y $Z[ \ $]^ S $_ `a bc d_ e f $g hij kl m n op qr $st quvwxyz{debugZmeIrestartLneosim/kernel/Semaphore; right_timeLneosim/iface/Time;endTimeSLEEPING ConstantValueeRUNNINGfSTOPPEDgstate(I)VCodeLineNumberTableLocalVariableTablethisLneosim/kernel/SimProcessor;idgetID()IsetStatei getState_()VpausemesetGoingsetIDpoisongetRightWindowTime()Lneosim/iface/Time;setRightWindowTime(Lneosim/iface/Time;)Vt setEndTimerun SourceFileSimProcessor.java 8E '(neosim/iface/Time 8| -. /. 7* )*neosim/kernel/Semaphore 89 +,java/lang/StringBuilder }~     ~   Sim Processor state set to  E N Sim processor run() called E FE Sim processor restarted  Sim processor run a tick Sim processor stopping Sim processor exitingneosim/kernel/SimProcessorjava/lang/Threadneosim/kernel/RmtProc(D)VgetName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;java/lang/ObjectgetClass()Ljava/lang/Class;java/lang/Class(I)Ljava/lang/StringBuilder;toStringsetName(Ljava/lang/String;)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintlnvp(Ljava/lang/Object;)VJneosim/kernel/SimSystempaused runTickPar (ILneosim/kernel/SimProcessor;)Z!$%& '()*+,-./.0*123*145*167* 89:i***Y*Y*g** Y * Y ***;& ! !+'",#8$h%<i=>i?*@A:/*;-< =>B9:i-**# Y *;12,3<-=>-C*DA:/*;4< =>+E:2* ;5< =>FE:3 * *;6<  =>GE:2* ;7< =>H9::*;8<=>?*IE:2* ;9< =>JK:/*;:< =>LM:@ *+;;< => N.OM:@ *+;<< => N.PE:* Y *** Y *** )* Y *!* Y *"* Y *#;* ?#@&A*CMEXG~KMOP< =>QRPKި PK(3&neuroml/model/network/ElementRef.class 1"       elementClassLneuroml/core/Ref;()VCodeLineNumberTableLocalVariableTablethis"Lneuroml/model/network/ElementRef;(Ljava/lang/String;)VnameLjava/lang/String;'(Ljava/lang/String;Ljava/lang/String;)V SourceFileElementRef.java neuroml/core/RefElement  ! neuroml/model/network/ElementRefneuroml/core/Model setTargetName!   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OPKWPn ""PK(3*neosim/kernel/ConnectionRequestEvent.class 1 #Q "R "S T UV "W XYZ "[ \]^ _ ` \ab _c _d efgh ij "k #l mno mp #_ #q rs rtuvcr Lneosim/iface/ConnectionRequest;BuildingConnectionZ9(Lneosim/iface/Time;ISLneosim/iface/ConnectionRequest;Z)VCodeLineNumberTableLocalVariableTablethis&Lneosim/kernel/ConnectionRequestEvent;tLneosim/iface/Time;srceIsrcportS doOnEntity(Lneosim/iface/Entity;)VeLneosim/iface/Entity;dmLneosim/iface/DestMethod;cLneosim/iface/Connection; registerClass4(Lneosim/iface/NeosimClasses;)Lneosim/iface/ClassID;ncLneosim/iface/NeosimClasses; readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; Exceptionswx()V writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput;getSize()I SourceFileConnectionRequestEvent.java (y $% &' z{| }~ N 4!neosim/kernel/EntityCallbackEvent  Nneosim/kernel/ConfirmCallback (H ( neosim/kernel/RemoveCallbackneosim/kernel/CancelCallbackjava/lang/Integer (ConnectionRequestEvent EntityEvent neosim.kernel = AB neosim/iface/ConnectionRequest IJ $neosim/kernel/ConnectionRequestEventneosim/kernel/EntityEventjava/io/IOException java/lang/ClassNotFoundException(Lneosim/iface/Time;IS)V getDestMethod()Lneosim/iface/DestMethod;neosim/iface/DestMethodconsiderRequestQ(Lneosim/iface/Entity;Lneosim/iface/ConnectionRequest;Z)Lneosim/iface/Connection;getSrcEntityIDneosim/iface/PortID SYSTEM_PORTgetTime()Lneosim/iface/Time;neosim/iface/EntitygetIDA(Lneosim/iface/Time;ISLneosim/iface/Callback;Ljava/lang/Object;)V sendEvent(ISLneosim/iface/Event;)V(I)Vneosim/iface/NeosimClassesN(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Lneosim/iface/ClassID;cidLneosim/iface/ClassID;java/io/ObjectInput readObject()Ljava/lang/Object; readBoolean()Zjava/io/ObjectOutput writeObject(Ljava/lang/Object;)V writeBoolean(Z)V!"#$%&'()*|*+**+LM NO,>-./01234$%&'56* *M,+**N-b*/+*Y* +  Y - `+*Y* + Y- 4+*Y* + YY* +* Q RTU%XN^Q`zg}ir,*-.78 9:;<=>*M*+*+ tu,-.?@AB*]*+*+*++z|},-.CDEFG(H*3*+ , -.IJ*Z*++* +*!+,-.KLEFMN*-d+, -.OPPKx PK(3,neuroml/model/network/ModuleAttachment.classA1\ 9: 9 ;< 9 => 9 ?@ AB CD E F F G HI J AKL JM destMethod"Lneuroml/model/network/DestMethod; sourceMethod$Lneuroml/model/network/SourceMethod;()VCodeLineNumberTableLocalVariableTablethis(Lneuroml/model/network/ModuleAttachment;(Ljava/lang/String;)VnameLjava/lang/String;'(Ljava/lang/String;Ljava/lang/String;)Vsourcecopy(Lneuroml/core/Connector;)Ve1Ljava/lang/Exception;e2prLneuroml/core/Connector;prt IsEquivalent(Lneuroml/core/Connector;)ZtoreturnZ SourceFileModuleAttachment.java   neuroml/model/network/DestMethod "neuroml/model/network/SourceMethod java/lang/StringBuilderN OPQ RS TU. VS W& & )&neuroml/model/network/ModuleAttachment XY Z[java/lang/Exception neuroml/model/network/Attachmentjava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringsetName parametersLjava/lang/Object; newInstance()Ljava/lang/Object;! !e**Y*Y*Y *   *Y *   "?d# e$%&!f*+*Y*Y*Y *   *Y *   "@e#f$%f'()!g*+,*Y*Y*Y *   *Y *   " $A%f&# g$%g'(g*(+,!6+M*, N*, N14",/141659#4-.5/.6$%60112%34!+ * p=+N*)-* - =*)-* - =* *">< = >O&P=QBTDUXVoWtZv[x]^`#* k56f2%$%0178PK휣PK(3guikit/FieldPanel.classj1  confirm()Vcancel SourceFileFieldPanel.javaguikit/FieldPaneljava/lang/ObjectPK|̛PK(3neuroml/sim/package.html

Interfaces for building and running simulations.

This package provides interfaces for accessing editors, run time systems etc. associated with a neuroml object tree.

Its use is optional.

PK]<lPK(3neuroml/model/cell/CVS/Entries/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /AbstractNeuron.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /CableNeuron.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /CellPkg.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ChannelAssignment.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Mask.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ModuleNeuron.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuronModule.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuronStructure.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /OrientedSubstructure.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PointNeuron.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SectionProperties.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SectionSet.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /package.html/1.1.1.1/Thu Jul 7 14:31:48 2005// D PK]PK(3(neuroml/util/axiope/AccessorFinder.class-1  getAccessor8(Ljava/lang/Object;)Lneuroml/util/axiope/ObjectAccessor; SourceFileAccessorFinder.java"neuroml/util/axiope/AccessorFinderjava/lang/ObjectPKˢPK(3#neuroml/sim/state/CVS/Entries.Extra./CellInstanceStructure.java/// /CellState.java/// /ConnectionState.java/// /ElementState.java/// /NetworkState.java/// /PopulationState.java/// /PositionState.java/// /ProjectionState.java/// /RequestableState.java/// /Segment.java/// /Shape.java/// /SynapseState.java/// /package.html/// /.nbattrs/// PKvBS3.PK(3$neosim/kernel/Deadlock_Message.class41  ()VCodeLineNumberTableLocalVariableTablethis Lneosim/kernel/Deadlock_Message; SourceFileDeadlock_Message.java neosim/kernel/Deadlock_Messagejava/lang/Exception!3*     PK{Y94PK(3#neuroml/core/SpecialModuleSet.classG1  ()VCodeLineNumberTableLocalVariableTablethisLneuroml/core/SpecialModuleSet;(Ljava/lang/String;)VstrLjava/lang/String; SourceFileSpecialModuleSet.java   neuroml/core/SpecialModuleSetneuroml/core/Set!3*    >*+    PKNbPK(3neuroml/core/PDF.class1, ! 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YWղ @ F WHK*I!*JFL +KWܲ @:89:;=:C=K?Q@^AnBxCEFH .Jx+,e'/0 ef |g?-?a?63Yg^B Y^g^ ;:?N/Y0:? /Y0:" Y^,Y-.Y:.YAY64.Y6.:Y64YABYYY$PQRJWPYVZ\abcdehkl mu w#yBzJ}c 2:Y\{\  JK|g|h||]M/&hijvkKl1 mn o4(pbv> YEFKz+ =>q>r.(st8 *    r.)ubw; Y^+ 2:;k;r. vtr$ Y*L+=D +  # &$w. xy z_%;DEF' !$ & {q7   ;D $6 && ||>  ;DEF(7= & };S ¶>YM,., ö<4 Ķ<.N- Ŷ<4 ƶN$(/5CYgny}4$kKJy JKgEt& ~V',h.*-+|:+-}:.*  &H'JK'+,'Q'R'L_XP fC/Y0/Y0:/Y0>/Y0</Y0g  & %'( 0G8HCNGOKPPKӓ<<PK(3"neosim/renderer/NetvisClass.@java@C`/** * Java3D netvis .jar file */ package neosim.renderer; import neosim.iface.*; import neosim.implementation.*; import neosim.util.BasicApp; import neosim.kernel.*; import neosim.util.*; import neosim.util.SmallLists.*; import java.util.Vector; import java.beans.*; import neuroml.sim.state.*; import neuroml.sim.run.*; import neosim.neuroml.*; import java.util.*; import java.lang.Math; /** Network Visualiser class. */ public final class NetvisClass extends EntityClassImpl { private AnimWindow app; transient private ScriptReader sr; private Netvis myNetvis; short in;//PortID public NetvisClass() { // Bean Constructor!!! - // JavaBeans need a zero argument constructor in = addInPort(SpikeEvent.inst.getEventClass(),"in"); } public NetvisClass(ScriptReader sr) { in = addInPort(SpikeEvent.inst.getEventClass(),"in"); this.sr = sr; } void setApp( AnimWindow app ) { this.app = app; } ScriptReader getScriptReader() { return sr; } // *** This is a nasty way to call runSim() public NetvisClass(String className) { super(className); // This not used from bean!!! in = addInPort(SpikeEvent.inst.getEventClass(),"in"); } public Entity makeEntity(Population p, int i) { myNetvis=new Netvis(this, p, i ); return myNetvis; } //18/04/05 necessary ? /* public void clean() { myNetvis.CheckConnection(); }*/ public boolean IsInParent() { return true; } } /** class for shape data extracted from entity */ final class ShapeData { String n; Pos p; neosim.implementation.Shape s; int eid;//EntityID eid; ShapeData( int eid, String n, Pos p, neosim.implementation.Shape s ) { //EntityID eid this.eid = eid; this.n = n; this.p = p; this.s = s; } int getEntityID() { return eid; }//rerurn EntityID String getName() { return n; } Pos getPos() { return p; } neosim.implementation.Shape getShape() { return s; } } /** class for connection queries */ class ConnData { int destID; // ID of dest entity //EntityID String name; // Name of dest entity Pos p; // Pos of dest entity // Space for pos of connection here, weight, anything else ConnData( int dest, String name, Pos p ) { this.destID = dest; this.name = name; this.p = p; }////EntityID int getDestID() { return destID; } //EntityID String getName() { return name; } Pos getPos() { return p; } } /** Callback for entity queries */ final class AddEntityToVis implements Callback { public AddEntityToVis(){ } public void callback( Entity e, Object o ) { try { //System.out.println(e.getName()+" AddEntityToVis Callback called "); Netvis nv= (Netvis)e; ShapeData sd = (ShapeData) o; nv.addEntityToVis( sd.getEntityID(), sd.getName(), sd.getPos(), sd.getShape() ); } catch ( ClassCastException ex) { System.out.println("AddEntityToVis - exception "+ex); } } public void readExternal(java.io.ObjectInput objectInput) throws java.io.IOException, java.lang.ClassNotFoundException { } public void writeExternal(java.io.ObjectOutput objectOutput) throws java.io.IOException { } } /** Get entity position... */ final class GetPos extends EntityQuery { public Object query( Entity e ) { try { //Entity3D e2 = (Entity3D) e; PositionState e2 = (PositionState) e; // System.out.println(e.getName()+" :GetPos: Got an entity3D "+e2.getXPos()+ " "+e2.getYPos()+" "+ e2.getZPos()); if(e2.getShape()==null){ // System.out.println("No shape"); e2.setShape(new neosim.implementation.Shape("red","sphere",0.3)); } return new ShapeData(e.getID(), e.getName(), new Pos( e2.getXPos(), e2.getYPos(), e2.getZPos()), (neosim.implementation.Shape)(e2.getShape())); } catch (ClassCastException ex) { //System.out.println("GetPos: Not an entity3D but a "+e.getClass().getName() + " name: "+e.getName()+" id: "+e.getID() ); } return new ShapeData( e.getID(), e.getName(), new Pos(-e.getID(),0,0), null ); } } /** Netvis - directs incoming events to J3D display */ final class Netvis extends EntityImpl implements Pausable { transient static AnimWindow app; // static as a hack transient Semaphore s = new Semaphore(); transient short in;//PortID transient Hashtable bars = new Hashtable(); // Table of names/erc entity IDs. transient SpikeIndexTable spTable; transient SpikeFlasher rc=new SpikeFlasher(); /* public int addInConnection(int srcID, short srcPort, short destPort) {//ConnectionID return // Add to local vector of incoming connections. //inConnections.addElement(c); this.LinkedListCon.addOutConnection(srcPort, destPort, srcID); //new ConnectionID( NumberConnection++ );//inConnections.size() ConnectionID cid = new ConnectionID //c.setConnectionID(cid); return NumberConnection++; } */ public Netvis(EntityClass ec, Population p, int i) { super(ec,p,i); spTable=new SpikeIndexTable(); /* Make a default input port (for spikes) */ in = 1;//new PortID( //System.out.println("Starting Java3D applet..."); app = new AnimWindow( this,this ); // Init the AnimWindow with this entity's restart() method ((NetvisClass)ec).setApp(app); app.start(); // Wait for restart... pauseme(); } public void addSpike(int index,long time){ spTable.addSpike(index,time); } void addEntityToVis(int eid, String name, Pos p, neosim.implementation.Shape s ) {////EntityID eid app.addEntityToVis(eid, name, p.x,p.y,p.z, s); } static void addEntityToVis(int eid, String name, Pos p, neosim.implementation.Shape s, Vector v ) {//EntityID eid app.addEntityToVis(eid, name, p.x,p.y,p.z, s, v); } static void addConnToVis( Pos sp, Pos dp ) { app.addConnToVis( sp, dp ); } static void highlightDest( int dest ) {//EntityID dest app.highlightDest( dest ); } static void flash( int dest ) {//EntityID dest //app.highlightDest( dest ); app.flash(dest); } /** Called when user clicks on an entity */ void clickConnections(int eid) {//EntityID eid //System.out.println("Netvis clockconnections called = "+eid); SimSystem.getKernel().queryOutputConnections( eid, getLocalTime(), eid, (short)1,//new PortID( new ConnectionQuery() { public Object query( Entity deste, Connection c ) { if (false) System.out.println("Connection query running on "+deste.getName()); String name = deste.getName(); Pos p = new Pos(0,0,0); try { PositionState e3d = (PositionState)deste; p = new Pos(e3d.getXPos(), e3d.getYPos(),e3d.getZPos()); } catch (ClassCastException e ) { // not an e3d } return new ConnData( deste.getID(), name, p ); } }, new Callback() { public void callback( Entity e, Object o ) { Vector n = (Vector) o; Pos srcp = new Pos(0,0,0); try { Entity3D e3d = (Entity3D)e; srcp = e3d.getPos(); } catch (ClassCastException ex) { } for (int i=0; i advance( e2.getTime() ); //<-18/04/05 //18/04/05-> /*if(e2 instanceof SpikeEvent){ int srce = e2.getConnection().getSrcEntityID();//EntityID srce Netvis.flash(srce); }*/ //<-18/04/05 if (e2.getConnection().getDstPortID()==in) { // This is a bug! // if (e2.getConnection().getDstPortID().id == in.id) { Time outTime = e.getTime(); trace("received spike event at "+outTime.s()); // Check positions of source entities if (!doneQuery) { // lookup population - this is nasty & specific :(- // Should query "all things connected to me" //System.out.println("Getting population details..."); /*Vector v = getInConnections(in); if (v==null) { System.out.println("No input connections!!!"); } else for (int i=0; i advance( endt ); } neosim.kernel.DeadlockTracker.UnLockDeadlockTracker(ecp); //<-18/04/05 return endt; } public synchronized int addInConnection(int srcID, short srcPort, short destPort) { int chose=super.addInConnection(srcID, srcPort, destPort); //System.out.println("NETVIS ADD CONN"); //ASSERT return chose; } public synchronized void CheckConnection(int TotalEntityToCall){ while(this.NumberConnection!=TotalEntityToCall){ try{ //ASSERT System.out.println("Wait with "+NumberConnection+" connections out of "+TotalEntityToCall); neosim.kernel.Deadlock_Message ecp=new neosim.kernel.Deadlock_Message(); neosim.kernel.DeadlockTracker.LockDeadlockTracker(this,ecp); wait(); neosim.kernel.DeadlockTracker.UnLockDeadlockTracker(ecp); } catch(Exception e){ e.printStackTrace(); } } app.clean(); //neosim.kernel.CommandQueue.PrintObject(this.LinkedListCon, "NetvisConnections_before.txt"); ((BasicKernel)this.sk).compress(); // neosim.kernel.CommandQueue.PrintObject(this.LinkedListCon, "NetvisConnections_after.txt"); neosim.kernel.Deadlock_Message ecp=new neosim.kernel.Deadlock_Message(); neosim.kernel.DeadlockTracker.LockDeadlockTracker(this,ecp); int[][] v = getInConnections(in); neosim.kernel.DeadlockTracker.UnLockDeadlockTracker(ecp); // System.out.println("DEBUG Netvis: connected to "+v.size()+" entites"); //Time t=new Time(getLocalTime()); //t.add(new Time(0.1)); if (v==null){ System.out.println("No input connections!!!"); } else{ Vector IdVector=new Vector(); /* for(int i=0;i // queryEntity(getLocalTime(), srce, new OutputQuery(IdVector,getID()),new NullCallback());//was not commented before //<-Parallel 01: 18/04/05-> queryEntity(getLocalTime(), srce, new OutputQuery(),new OutputCallback(machin)); } } } //BuildingThread chose=new BuildingThread(machin); } } } final class SpikeFlasher implements neuroml.sim.run.RunnableCell{ public SpikeFlasher(){ } public void advance(double t) { } public Object getModel() { return null; } public ElementState getState() { return null; } public void handle(Object o, double t, int inputConnection) { } public void handleSpike(double t, int inputConnection) { //int srce = e2.getConnection().getSrcEntityID();//EntityID srce Netvis.flash(inputConnection); } public void reset() { } public void setInputConnectionParameters(int cid, neuroml.sim.run.DestMethod dm, neuroml.sim.run.ConnectionRequest cr) { } public void setMeasured(neuroml.model.MeasurementTool.MeasurementCollection MeasurementList) { } public void setMeasured(int SrcId, neuroml.model.MeasurementTool.MeasurementCollection MeasurementList) { } } final class Couple implements java.io.Serializable { public int[][] array; public Pos myPos; public int id; public String Name; public Couple(Pos myPos,int[][] array,int id,String Name){ this.myPos=myPos; this.array=array; this.id=id; this.Name=Name; } } final class OutputQuery extends EntityQuery implements java.io.Externalizable { //transient neosim.kernel.DeadlockTracker tracker=new neosim.kernel.DeadlockTracker(); public OutputQuery(){ } public Object query( Entity deste) { //System.out.println("queryOutputConnections " +deste.getID()); PositionState e2 = (PositionState)deste; Pos obj1=new Pos( e2.getXPos(), e2.getYPos(), e2.getZPos()); // ((EntityImpl)deste).check_compressed();//compress_final(); neosim.kernel.Deadlock_Message ecp=new neosim.kernel.Deadlock_Message(); neosim.kernel.DeadlockTracker.LockDeadlockTracker(deste,ecp); int[][] TempArray=deste.getInConnections((short)1); neosim.kernel.DeadlockTracker.UnLockDeadlockTracker(ecp); //neosim.kernel.CommandQueue.PrintObject(((EntityImpl)deste).LinkedListCon,"LinkedListCon_"+deste.getID()+".txt"); return new Couple(obj1,TempArray,deste.getID(),deste.getName()); ////return null; } public void readExternal(java.io.ObjectInput objectInput) throws java.io.IOException, java.lang.ClassNotFoundException { } public void writeExternal(java.io.ObjectOutput objectOutput) throws java.io.IOException { } } final class TreatPosition implements java.io.Serializable{ static int Total=0; //TreatPosition is somehow multiplied so you need the static (kind of bug) static int CountDown=0; static Vector v; static Hashtable array; static Vector IdVector; public TreatPosition(int Total, Vector IdVector){ TreatPosition.IdVector=IdVector; TreatPosition.Total=Total; CountDown=Total; array=new Hashtable(); } public synchronized void decount(Couple truc){ CountDown--; //ASSERT //System.out.println(CountDown); array.put(new Integer(truc.id),truc);; if(CountDown==0){ for (Enumeration enum_ = array.elements() ; enum_.hasMoreElements() ;) { Couple temp=(Couple)enum_.nextElement(); int[][] v=temp.array; Vector PosConnections=new Vector(); for(int k=0;k(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis%Lneuroml/environment/io/MethodModule;nameLjava/lang/String;()V SourceFileMethodModule.java  #neuroml/environment/io/MethodModuleneuroml/core/Module!>*+     3*    PK*fPK(3)neuroml/model/ions_channel/CVS/Repository+NMLPLAY_CVS/src/neuroml/model/ions_channel PKUT0+PK(35neuroml/model/network/ModuleProjection_Unstable.classz1    moduleLneuroml/core/ModuleRef;()VCodeLineNumberTableLocalVariableTablethis1Lneuroml/model/network/ModuleProjection_Unstable;(Ljava/lang/String;)VnameLjava/lang/String; 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" #$%cLneosim/iface/Connection;(Lneosim/iface/Connection;)VCodeLineNumberTableLocalVariableTablethisLneosim/iface/Input; getConnection()Lneosim/iface/Connection;toString()Ljava/lang/String; SourceFile Input.java & java/lang/StringBuilder '() *+ ', neosim/iface/Inputjava/lang/Object()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;neosim/iface/ConnectiongetConnectionID()I(I)Ljava/lang/StringBuilder;!  > **+  /* FY*   PKGOY-(PK(3"guikit/NetEditPanel_GuiKit$3.classn1 9n 9o 9p 9q 9r 9s 9t 9u 9v 9w :x $y z{ :| }~        x ~      } ) )     5  val$derivedFromLjava/util/Vector;val$onLguikit/ObjectNode; val$expClassLjava/lang/Class;val$nsLneuroml/util/Namespace;val$PanelGuikitLguikit/NetEditPanel_GuiKit;val$oLjava/lang/Object;val$XIval$ptLjava/awt/Point;val$Ythis$0(Lguikit/NetEditPanel_GuiKit;Ljava/util/Vector;Lguikit/ObjectNode;Ljava/lang/Class;Lneuroml/util/Namespace;Lguikit/NetEditPanel_GuiKit;Ljava/lang/Object;ILjava/awt/Point;I)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/NetEditPanel_GuiKit$3;actionPerformed(Ljava/awt/event/ActionEvent;)VjtrucLjava/net/URL;choseLjavax/swing/ImageIcon;exceptLjava/lang/Exception;eventLjava/awt/event/ActionEvent;currIdxszchoices[Ljava/lang/String; classComboBoxLjavax/swing/JComboBox;myFrameLjavax/swing/JFrame; SourceFileNetEditPanel_GuiKit.javaEnclosingMethod ME <= >? @A BC DE FG HI JK LI N    java/lang/String javax/swing/JComboBox N guikit/NetEditPanel_GuiKit$3$1 N javax/swing/JFramejava/lang/StringBuilderneuroml/core/Nameable  : class selection N guikit/NetEditPanel_GuiKit  EditingPopup javax/swing/ImageIcon N java/lang/Exception No icon for the editing window  I I guikit/NetEditPanel_GuiKit$3$2 guikit/NetEditPanel_GuiKit$3java/lang/Objectjava/awt/event/ActionListener RightClick(Ljava/awt/event/MouseEvent;)V()VMenuPopupVisibleZguikit/ObjectNode getContent()Ljava/lang/Object;getClass()Ljava/lang/Class;java/lang/ClassgetName()Ljava/lang/String;java/util/VectorindexOf(Ljava/lang/Object;)Isize()I elementAt(I)Ljava/lang/Object;([Ljava/lang/Object;)VsetSelectedIndex(I)V!(Lguikit/NetEditPanel_GuiKit$3;)VaddActionListener"(Ljava/awt/event/ActionListener;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString(Ljava/lang/String;)Vadd*(Ljava/awt/Component;)Ljava/awt/Component;guikit/NetworkDesigner resourcesLjava/util/ResourceBundle;java/util/ResourceBundle getString&(Ljava/lang/String;)Ljava/lang/String; getResource"(Ljava/lang/String;)Ljava/net/URL;(Ljava/net/URL;)VgetImage()Ljava/awt/Image; setIconImage(Ljava/awt/Image;)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintlnpackjava/awt/Pointxy setLocation(II)VaddWindowListener"(Ljava/awt/event/WindowListener;)V setVisible(Z)V 9:; <=>?@ABCDEFGHIJKLIMENOPh >*+*,*-****** * * QR >SVWXP * ** `=*`>:*S6*dSY:Y*YY* !":#W$%&'(:)Y*:+, :./01** 2`* * 3`45Y*678-QZ)/:_jp} Rp ="YIZ[ \]^_SV`abI)cI/dejfgphijkl$mU95PKevPK(3$neuroml/sim/state/NetworkState.class1    getElementStates()Ljava/util/List;getProjectionStates SourceFileNetworkState.javaneuroml/sim/state/NetworkStatejava/lang/Objectneuroml/sim/state/ElementStatePKjDPK(3)neosim/neuroml/NeosimConnectionImpl.classA1| T U V W XY XZ X[ \] \^ \_ `ab cdefghdata[BdestcidI (ISISIJ)VCodeLineNumberTableLocalVariableTablethis%Lneosim/neuroml/NeosimConnectionImpl;srcesrcpidSdestedestpidciddelayJsetData(ISISJ)Viarray getSrcPortID()SBshifttemp getDstPortIDgetSrcEntityID()IgetDstEntityIDgetDelay()Jtemp2getConnectionIDsetConnectionID(I)Vc sendEvent(Lneosim/iface/Event;)VevLneosim/iface/Event; readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; Exceptionsij writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput;addSpike(J)Vtime()V SourceFileNeosimConnectionImpl.java Q +,  k lm no p6q r= st u=v wxBneosim.neuroml.NeosimConnectionImpl : I should NOT be called ERRORy z{#neosim/neuroml/NeosimConnectionImpljava/lang/Objectneosim/iface/Connectionjava/io/Externalizablejava/io/IOException java/lang/ClassNotFoundExceptionjava/io/ObjectInputreadByte()Bread([B)IreadIntjava/io/ObjectOutput writeBytewrite([B)VwriteIntjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)V1***BCDE H!"#$%&'%()*+, 6:~~T|=T~ ~T|6T~~T|<T~~T|>T !T}7T* 6* * 3T GH KL!M'N*O4Q<RNSVTYUdXkY|Z[\^_`abdefghijkjl R!"#$%&'%)*-  ./0@<* `<3~>=* 3~* `<3~x>`=nrs!t4s=v *@!">-1,21/340{<* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=* y{|!}4|=L\ox *{!"y-1g21j3561<* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=:!4=L\ox *!"-121376|<* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=J!4=L\ox *!"-1213891<* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=* `<3~>=* 3~* `<3~x>`=* `<3~7=* 3~"* `<3~x7`=Z!4=L\ox%. 41!"/-121 32:*;6/* !"<=:* !">?@5 !"ABCDb"*+  +* W*+  ! "!""EFGHIJK` +* +* +*   !" LMGHNOA    !" P*Q3*  !"RSPKh=`PK(3neuroml/core/Log.class1   authorLjava/lang/String;dateliteratureReference logEntriesLneuroml/core/List;()VCodeLineNumberTableLocalVariableTablethisLneuroml/core/Log; SourceFileLog.java neuroml/core/ListLogEntry  neuroml/core/Logneuroml/core/NamedObject(Ljava/lang/String;)V!    @**Y  PKPK(3 neuroml/model/channel/Pore.class&1*  ! " #$ %&  ' "() permeatorsLneuroml/core/Set;ivlawLjava/lang/String;ErevLneuroml/core/DValue;()VCodeLineNumberTableLocalVariableTablethisLneuroml/model/channel/Pore;(Ljava/lang/String;)Vname SourceFile Pore.java neuroml/core/Set PorePermeator  ohmic neuroml/core/DValue neuroml/model/channel/Poreneuroml/core/NamedObject! ]#**Y**Y   " #h$*+ *Y**Y   #$$PKlPK(3MiscTests/SerializedClass.classj1  SourceFileSerializedClass.javaMiscTests/SerializedClassjava/lang/Objectjava/io/SerializablePK]PK(3)neuroml/model/network/RawProjection.classG11 "#$ % & %' ( ) *+ connectionsLneuroml/core/List;()VCodeLineNumberTableLocalVariableTablethis%Lneuroml/model/network/RawProjection;(Ljava/lang/String;)VnameLjava/lang/String;copy(Lneuroml/core/Connector;)ViIprLneuroml/core/Connector;prtsize SourceFileRawProjection.java neuroml/core/List Connection  #neuroml/model/network/RawProjection , -. /0 neuroml/model/network/Projection()I elementAt(I)Ljava/lang/Object;add(Ljava/lang/Object;)Z!  D**Y    O*+*Y .+M,>6*, W '-4..) ! !PK11PK(31nmlplay/NEOSIMSettings$NEOSIMSettingsDialog.class?1} M~ L    L L L L  L L L   f h L L E  L L L L E L  @ @ @  tf1Ljavax/swing/JTextField;tf2tf3tf4tc1Ljavax/swing/JCheckBox;tc2(Ljavax/swing/JFrame;)VCodeLineNumberTableLocalVariableTablethisNEOSIMSettingsDialog InnerClasses-Lnmlplay/NEOSIMSettings$NEOSIMSettingsDialog;frameLjavax/swing/JFrame;rootLjavax/swing/JPanel; inputPanel buttonPanelcancelLjavax/swing/JButton;ok loadContent()Vpopupd1Ljava/awt/Dimension;pLjava/awt/Point;d2actionPerformed(Ljava/awt/event/ActionEvent;)ViInfe!Ljava/lang/NumberFormatException;stLjava/util/StringTokenizer;eLjava/awt/event/ActionEvent; SourceFileNEOSIMSettings.javaNEOSIM Settings W javax/swing/JPanel Wjjavax/swing/BoxLayout W javax/swing/JTextField OP QP RP SPjavax/swing/JCheckBoxVisualiz. On/Off W TU Debug On/Off VU ijKernel Parameters RuntimeSteppingVisualiz. Delayjavax/swing/JButtonCancel j     t t t t      jjava/util/StringTokenizer   W  java/lang/String     java/lang/NumberFormatException+nmlplay/NEOSIMSettings$NEOSIMSettingsDialogjavax/swing/JDialogjava/awt/event/ActionListener&(Ljava/awt/Frame;Ljava/lang/String;Z)VgetContentPane()Ljava/awt/Container;(Ljava/awt/Container;I)V setLayout(Ljava/awt/LayoutManager;)V(Ljava/lang/String;)Vjavax/swing/BorderFactorycreateTitledBorder5(Ljava/lang/String;)Ljavax/swing/border/TitledBorder; setBorder(Ljavax/swing/border/Border;)V setColumns(I)Vadd*(Ljava/awt/Component;)Ljava/awt/Component;addActionListener"(Ljava/awt/event/ActionListener;)VsetActionCommandpack setResizable(Z)Vnmlplay/NEOSIMSettings mySchedule'Lneuroml/environment/schedule/Schedule;%neuroml/environment/schedule/SchedulecommandLjava/lang/String;setTextruntimeDvalueOf(D)Ljava/lang/String;stepping visudelay ViewOnOffZ setSelected DebugOnOffsetLocationRelativeTo(Ljava/awt/Component;)Vjavax/swing/JFramegetSize()Ljava/awt/Dimension; getLocation()Ljava/awt/Point;java/awt/Pointxjava/awt/Dimensionwidthyheight setLocation(II)V setVisiblejava/awt/event/ActionEventgetActionCommand()Ljava/lang/String;equals(Ljava/lang/Object;)ZdisposegetText'(Ljava/lang/String;Ljava/lang/String;)V countTokens()I kernelParms[Ljava/lang/String; nextTokenjava/lang/Double parseDouble(Ljava/lang/String;)D isSelected()Zneosim/renderer/NetvisCtrlsetRefreshVisualization(DZ)V LMNOPQPRPSPTUVUWXYac*+*MYN,Y,-Y-* Y * Y * Y * Y *Y*Y** * -* W* -* W* -* W*-*W-*W-*W-Y:Y Y!":W*#$% Y&":W*#&%,-W,W*'*(Z'QSTV%W2Y=ZH[S\^]k^x_|abcdefghiklmop rst%u,w7x?yEzL|R}Y~]b[Hc\_c`aSbcKdcfecLfg7,hgijYX* )*+* ),-+* ).-+*)/-+*)01*)21Z -=JW[ X\_kXYA*+3+4M+5N*6:*-7,88dl`-9,::dl`;*<Z ;@[4A\_A`a 7lm2no,pmqrYQ+=$>*?+=&>@Y* ABCM,DEF>FF,GS)* AH,)* AH.)* A*)*AH/)*I0)*I2)/)0J*?NPKZ>-7P`p}[49stuv-wx\_yz{|^ L] PKPK(3neosim/seqkernel/CVS/Repository!NMLPLAY_CVS/src/neosim/seqkernel PK6&!PK(3guikit/SwingWorker$1.class01   this$0Lguikit/SwingWorker;(Lguikit/SwingWorker;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/SwingWorker$1;run()V SourceFileSwingWorker.javaEnclosingMethod   guikit/SwingWorker$1java/lang/Objectjava/lang/Runnableguikit/SwingWorkerfinished   4 *+* g   2* g  PKx50PK(3neuroml/core/IntParameter.class1   valueI(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLneuroml/core/IntParameter;nameLjava/lang/String;()V SourceFileIntParameter.java   neuroml/core/IntParameterneuroml/core/Parameter!  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"#  # $#guikit/Navigator$6java/lang/Objectjava/awt/event/ActionListenerguikit/Navigator buildPanel()VhomeURL   4 *+* v   @* xy  PKPK(3,neosim/implementation/ScriptReaderImpl.classY19 Q  P  P P P P     P P    P # (       P P    skLneosim/kernel/Kernel;tLneosim/iface/Time;cbLneosim/iface/Callback;semLneosim/kernel/Semaphore;debugZcons terminatedanswerLjava/lang/Object;()VCodeLineNumberTableLocalVariableTablethis(Lneosim/implementation/ScriptReaderImpl; initKernel bootstrap([Ljava/lang/String;)Vargs[Ljava/lang/String;needToConstruct()Zatoi(Ljava/lang/String;)IsLjava/lang/String;.([Ljava/lang/String;)Lneosim/kernel/SimKernel;argcI destroyKernelinitSimrunSim(Lneosim/iface/Time;)Vrtreset terminate construct#(Lneosim/iface/PopulationBuilder;)Vp Lneosim/iface/PopulationBuilder;destroy(Lneosim/iface/Population;)VLneosim/iface/Population;connect(Lneosim/iface/Projection;)VLneosim/iface/Projection; disconnect updateEntity(ILneosim/iface/EntityUpdate;)VeeuLneosim/iface/EntityUpdate; queryEntity/(ILneosim/iface/EntityQuery;)Ljava/lang/Object;eqLneosim/iface/EntityQuery;updatePopulation7(Lneosim/iface/Population;Lneosim/iface/EntityUpdate;)VqueryPopulationG(Lneosim/iface/Population;Lneosim/iface/EntityQuery;)Ljava/util/Vector;queryOutputConnections4(ISLneosim/iface/ConnectionQuery;)Ljava/util/Vector;ScqLneosim/iface/ConnectionQuery;getPopulationTree()Lneosim/iface/PopulationTree;getNeosimClasses()Lneosim/iface/NeosimClasses;lookupEntityClass.(Ljava/lang/String;)Lneosim/iface/EntityClass;namelookupEntityIDlookupPopulation-(Ljava/lang/String;)Lneosim/iface/Population; sendSysEvent(Lneosim/kernel/SysEntEvent;)VLneosim/kernel/SysEntEvent;pauseme()Ljava/lang/Object;restart(Ljava/lang/Object;)Vo SourceFileScriptReaderImpl.java abneosim/iface/Time a UVneosim/kernel/Semaphore a YZ [\ ]\ ^\  java/lang/StringBuilderScriptReader constructor       neosim/kernel/ScriptCallback WX   STIniting scriptreaderimpl kernel.Error - kernel null in script reader bootstrap  Wusage: java Basic {seq | thr | rmi [-c] }seq neosim/seqkernel/SeqKernelthrneosim/thrkernel/ThrKernel oprmi-cneosim/rmikernel/RmiKernel a !bneosim/kernel/SimKernel b3ScriptReaderImpl:destroy Kernel - error kernel nullScriptReaderImpl:initSim wb,ScriptReaderImpl:initSim error - kernel nullScriptReaderImpl:initSim done xy "y {b " |b1ScriptReaderImpl Error - terminate() called twice# $u }% & ' ' ( ) _` * +java/util/Vector , SK is NULL! - . /0 123 4 56 7 8b&neosim/implementation/ScriptReaderImpljava/lang/Objectneosim/iface/ScriptReader(D)V(I)Vjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)Vneosim/kernel/SimSystemsetScriptReader+(Lneosim/implementation/ScriptReaderImpl;)V getKernel()Lneosim/kernel/SimKernel;java/lang/IntegervalueOf'(Ljava/lang/String;)Ljava/lang/Integer;intValue()Ijava/lang/Stringequals(Ljava/lang/Object;)Z)(Ljava/lang/String;Ljava/lang/String;II)Vneosim/kernel/Kernelinitsetneosim/iface/EntityID SYSTEM_ENTITYN(ILneosim/iface/Time;Lneosim/iface/PopulationBuilder;Lneosim/iface/Callback;)VG(ILneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/Callback;)VG(ILneosim/iface/Time;Lneosim/iface/Projection;Lneosim/iface/Callback;)VJ(ILneosim/iface/Time;ILneosim/iface/EntityUpdate;Lneosim/iface/Callback;)VI(ILneosim/iface/Time;ILneosim/iface/EntityQuery;Lneosim/iface/Callback;)Vb(ILneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/EntityUpdate;Lneosim/iface/Callback;)Va(ILneosim/iface/Time;Lneosim/iface/Population;Lneosim/iface/EntityQuery;Lneosim/iface/Callback;)VN(ILneosim/iface/Time;ISLneosim/iface/ConnectionQuery;Lneosim/iface/Callback;)V2(Lneosim/iface/Time;)Lneosim/iface/PopulationTree;((Lneosim/iface/Time;Ljava/lang/String;)I@(Lneosim/iface/Time;Ljava/lang/String;)Lneosim/iface/Population;neosim/kernel/SysEntEvent setCallback(Lneosim/iface/Callback;)Vneosim/iface/PortID SYSTEM_PORT sendEvent(ISLneosim/iface/Event;)VsemWait semSignal!PQRSTUVWXYZ[\]\^\_`abc[**Y*Y** * * Y **Y*d. !3&+2KVZe [fghbca+** Y *d#$%*'e +fgijcW** d-./1efgklmnc/* d9e fgopc2*d:e qrhscu =* + +2* Y!* +2""*#Y+2$%* W+2&B+2' * *(Y+2+`2+`2$+`2$) *****+dnEFH IJN"O-P2Q5R8SCTFUWV\W_XbYmZp[\]^_`efge fgkltuvbcV**, -dklmnpe fgwbcA* .***/ 0* 1dstuv&w1x@ye AfgxycO*+2*+3d} ~efgzV{bcD*4*5d e fg|bc_!* *6* 7d e !fg}~cW*8*+*9*:WdefgcW*8*+*;*:WdefgcW*8*+*<*:WdefgcW*8*+*=*:Wdefgcb*8*,*>*:Wde fgucf *8*,*?*:W*@de  fg u cb*8*+,*A*:Wde fgci#*8*+,*B*:W*@Cde #fg##ct$*8*-*D*:W*@Cde*$fg$u$$cK* E**Fd e fgc4 *Gde  fgc? *+Hde fg rpcC**+IdefgrcC**+Jdefgrc^+*K*8L+M*:Wdefgc; **N*@d e  fgcI *+@*Od e fg `PK'^YPK(3!neosim/kernel/RemoveCommand.class.1(    !"#$objLneosim/kernel/RmtApp;getType()Ljava/lang/String;CodeLineNumberTableLocalVariableTablethisLneosim/kernel/RemoveCommand;(ILneosim/kernel/RmtApp;)VidIdoit(Lneosim/kernel/SimKernel;)VhpLneosim/kernel/SimKernel;getSize()I SourceFileRemoveCommand.javaRemove Command %  & '%neosim/kernel/RemoveCommandneosim/kernel/CommandObj(I)Vneosim/kernel/SimKernel removeRmt    -   M **,        ? +*     -   PKJ3.PK(3)neosim/neuroml/NeosimPopulationImpl.class>1k? @A BC D E F @G @H @I @J @K @L @M NO NPQ R S T UVWpop#Lneuroml/sim/state/PopulationState;localsLjava/util/Vector;&(Lneuroml/sim/state/PopulationState;)VCodeLineNumberTableLocalVariableTablethis%Lneosim/neuroml/NeosimPopulationImpl;getID()IsetID(I)ViI getNumEntsgetIndex(I)Ieid getEntityIDisMember(I)Z addMember getMemberList()Ljava/util/Vector;reteidsLjava/util/List;isLeaf()ZaddLocalMember(Lneosim/iface/Entity;)VeLneosim/iface/Entity;getLocalMembers SourceFileNeosimPopulationImpl.javaX Y$ Zjava/util/Vector [   #$ %& *+ \+ ./ ]^ _`a b$ cdjava/lang/Integer e$ fg hi ]j#neosim/neuroml/NeosimPopulationImpl$neosim/implementation/PopulationImpl!neuroml/sim/state/PopulationStategetNumElements(Ljava/lang/String;I)V()V getElementID addElement(ILjava/lang/String;)V getElementIDs()Ljava/util/List;java/util/Listsizeget(I)Ljava/lang/Object;intValuevalueOf(I)Ljava/lang/Integer;add(Ljava/lang/Object;)Z(Ljava/lang/Object;)V1 ]*+*Y*+ T !"#$4 *  !"%&C *   !  !" '()$4 *%  !"*+? * -  !" ,(-+? * 5  !" '(./? * =  !" ,(0&E *  D E  !" ,(12;YL*M>,+,W+JKLM3L9O *%'(;!"33)4567,R !"89= *+Y  !" :;<2/*^ !"=>PKT{ PK(3%neuroml/sim/state/PositionState.classK1setPos(DDD)VgetXPos()DgetYPosgetZPossetShape(Lneuroml/sim/state/Shape;)VgetShape()Lneuroml/sim/state/Shape;draw()V SourceFilePositionState.javaneuroml/sim/state/PositionStatejava/lang/Object   PK\B WPKPK(3*neuroml/model/cell/SectionProperties.classe1#    !"channelsLneuroml/core/Set; solutions()VCodeLineNumberTableLocalVariableTablethis&Lneuroml/model/cell/SectionProperties;(Ljava/lang/String;)VnameLjava/lang/String; SourceFileSectionProperties.java neuroml/core/SetChannel  Solution $neuroml/model/cell/SectionPropertiesneuroml/core/NamedObject!   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Interfaces for accessing state of a simulation.

This package provides interfaces for accessing the run time state of a simulation in a simulator-independent way.

For cells, this returns the cell structure instance in a flattened format (with a pointer back to the neuroml.model specification).

For populations, it returns a vector of cell instance IDs, which can be queried using the EntityQuery routines.

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G***   R*+**  PKApO*%PK(3!neuroml/model/morphml/count.classA1 valueLjava/lang/String;()VCodeLineNumberTableLocalVariableTablethisLneuroml/model/morphml/count; SourceFile count.java neuroml/model/morphml/countjava/lang/Object!/*    PKGFAPK(3neosim/implementation/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(3"neosim/rmikernel/RmiKernel__._java/** RMI based SimKernel */ package neosim.rmikernel; import neosim.kernel.*; import neosim.iface.*; import neosim.implementation.*; import java.rmi.*; import java.net.*; import java.io.*; import java.util.Vector; import java.rmi.server.*; import java.util.Random; import java.util.Hashtable; import java.util.Enumeration; /** RMI Simulation Kernel */ public final class RmiKernel extends BasicKernel { // transient DeadlockTracker tracker=new DeadlockTracker(); static int NbKernels=0; public static void main(String args[]){ RmiKernel chose=new RmiKernel(0,10); chose.TestCompressionSpikes(); } private RmiKernel(int kernel, int nprocs){ //for test only super(); this.nprocs=nprocs; AllgatherObject=new Object[nprocs]; this.id=kernel; } double runt = 0.0; private boolean debug = false; /** Name of user, server */ String username, servername; int nprocs; int nthreads; int AllgatherArray[]; Object AllgatherObject[]; RmtServer server; public RmiKernel(String sname, String uname, int nprocs, int nthreads) { super(); NbKernels++; System.out.println("Nb Kernels = "+NbKernels); username = uname; servername = sname; this.nprocs = nprocs; this.nthreads = nthreads; if(neosim.util.loaders.nmllauncher.NeosimNeuroMLLauncher.Player!=null) neosim.util.loaders.nmllauncher.NeosimNeuroMLLauncher.Player.println("RMI Kernel: "+sname+" "+nprocs+" procs, "+nthreads+" threads"); if (debug) System.out.println("RMI Kernel: "+sname+" "+nprocs+" procs, "+nthreads+" threads"); System.setSecurityManager(new RMISecurityManager()); System.out.println("RmiKernel: set security manager"); if(neosim.util.loaders.nmllauncher.NeosimNeuroMLLauncher.Player!=null) neosim.util.loaders.nmllauncher.NeosimNeuroMLLauncher.Player.println("Security manager set"); try{ UnicastRemoteObject.exportObject(this); server = (RmtServer)Naming.lookup("//" + servername + "/RmiServer"); pmgr = (RmtProcMgr)Naming.lookup("//" + servername + "/RmiServer"); if(neosim.util.loaders.nmllauncher.NeosimNeuroMLLauncher.Player!=null) neosim.util.loaders.nmllauncher.NeosimNeuroMLLauncher.Player.println("Found Server "+servername); } catch (Exception e) { System.out.println("RmiKernel exception: " + e.getMessage()); e.printStackTrace(); } // SimSystem.setKernel( this ); // needed? } public final RmtServer getServer() { return server; } /** Kill all threads... */ public final void terminate() { super.terminate(); if(cq!=null) cq.terminate(); } Integer BarrierInteger=new Integer(id); /** Barrier - using allgather */ int CounterServer=0; public final void barrier() { //Huge BUG in RMI : it loses the track of the server when the server is not called for a long period... So let's call it sometimes. /* CounterServer++; if(CounterServer==100){ CounterServer=0; try{ server.call(); }catch(Exception e){ e.printStackTrace(); } }*/ //try{ this.barrierSocket(); //allgather(BarrierInteger); //}catch(neosim.kernel.ResetException e){ e.printStackTrace(); } } public final void barrier_server(){ //to be used when we don't know each other try { server.barrier(); } catch (RemoteException e) { e.printStackTrace(); } } /** Run the simulation */ public final void runRmt(int rid, Time t) { //if (debug) System.out.println("Run Rmt starting, "+getGroupsize()+" procs, "+nthreads+" local threads"); compress(); getSimSystem().runPar(getGroupsize(),nthreads,getID(),t); //if (debug) System.out.println("Run Rmt done"); } /** Send command to given dest */ public final void sendCommand(int p, CommandObj co) { CommandQueue cq = ((CommandQueue)othercqs.elementAt(p)); /* if(co instanceof EventToCommand){ Event ev=((EventToCommand)co).getEvent(); if(ev instanceof EntityCallbackEvent){ new Exception().printStackTrace(); System.out.println(getClass().getName()+" "+ev.getClass().getName()+" ... Just saying I am there since the stack is SO big "); } } */ if (cq!=null) { boolean goon=true; while(goon){ try { goon=false ; //neosim.kernel.Deadlock_Message ecp1=new neosim.kernel.Deadlock_Message(); //neosim.kernel.DeadlockTracker.LockDeadlockTracker(this,ecp1); cq.add(co); //neosim.kernel.DeadlockTracker.UnLockDeadlockTracker(ecp1); } catch (Exception e) { try{ System.out.println(" ... sendCommand exception "+e); neosim.kernel.CommandQueue.PrintObject(co,"ErrorsCommanqueueAdd_"+getID()+".txt"); java.io.PrintWriter trcstream = new java.io.PrintWriter(new java.io.FileOutputStream("CommandQueueAdd_1_Error.txt")); e.printStackTrace(trcstream); trcstream.close(); Thread.sleep(15000); } catch(Exception x){ x.printStackTrace(); } } } } } /** Issue orders to system */ public final void sendCommand(CommandObj co) { try { for (int p=0; p /*try { server.done(id,this); } catch (Exception e) { System.out.println("Exception in server.done :"+e); } // Wait for done signal from all others for (int i=0; i0){ while(AllgatherObject[AllgatherArray[i]-1]==null)//if try{ //neosim.kernel.Deadlock_Message ecp2=new neosim.kernel.Deadlock_Message(); //neosim.kernel.DeadlockTracker.LockDeadlockTracker(obj,ecp2); AllgatherObject.wait(); //neosim.kernel.DeadlockTracker.UnLockDeadlockTracker(ecp2); } catch(Exception e){ e.printStackTrace(); } } } //distribute for(int i=length-1;i>=0;i--){ if(AllgatherArray[i]>0){ CommandQueue cq=(CommandQueue)this.othercqs.elementAt(AllgatherArray[i]-1); RmtApp remoteKernel=(RmtApp)cq.getDest(); try{ remoteKernel.SendArray(AllgatherObject); } catch(java.lang.Exception e){ e.printStackTrace(); } //send my guy //notify } else if(AllgatherArray[i]<0){ while(AllgatherObject[-AllgatherArray[i]-1]==null)//if try{ //neosim.kernel.Deadlock_Message ecp3=new neosim.kernel.Deadlock_Message(); //neosim.kernel.DeadlockTracker.LockDeadlockTracker(this,ecp3); AllgatherObject.wait(); //neosim.kernel.DeadlockTracker.UnLockDeadlockTracker(ecp3); } catch(Exception e){ e.printStackTrace(); } } } v=new Vector(); for(int i=0;i0){ // ArraySocket[i] = new Socket(IPs[AllgatherArray[i]-1],4500+AllgatherArray[i]-1); // osArray[i]=ArraySocket[i].getOutputStream(); // isArray[i]=ArraySocket[i].getInputStream(); bArraySocket[i] = new Socket(IPs[AllgatherArray[i]-1],4500+AllgatherArray[i]-1+nprocs); bosArray[i]=new BufferedOutputStream(bArraySocket[i].getOutputStream(),5); bisArray[i]=new BufferedInputStream(bArraySocket[i].getInputStream(),5); } else if(AllgatherArray[i]<0){ // ArraySocket[i] = serverSocket.accept(); // osArray[i]=ArraySocket[i].getOutputStream(); // isArray[i]=ArraySocket[i].getInputStream(); bArraySocket[i] = bserverSocket.accept(); bosArray[i]=new BufferedOutputStream(bArraySocket[i].getOutputStream(),5); bisArray[i]=new BufferedInputStream(bArraySocket[i].getInputStream(),5); } } catch (java.net.UnknownHostException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } //ensure they are build in proper order //the allgather type of barrier is the fastest available at this stage of the kernel construction this.AllGather_obj(this.BarrierInteger); } arrayBarrierSocket=new boolean[nprocs]; for(int i=0;i128 size++; comp_size>>>=7; } ArrayOfSpikes=new byte[size+nprocs]; int inc=id; //fill with 0 before and after the bytes describing "spikes" while ((compsize2 & ~0x7F) != 0) { byte b = (byte)((compsize2 & 0x7f) | 0x80); ArrayOfSpikes[inc++]=b; compsize2 >>>= 7; } ArrayOfSpikes[inc++]=(byte)compsize2; spikes.fill(ArrayOfSpikes,inc); } private final void include(byte byteArray[]){ byte[] TempArray; int inc1=0,inc2=0,former_inc=0; byte b1,b2; int i1,i2; int totaltoAdd=0; //resizing for(int k=0;k0){ b = ArrayOfSpikes[inc++]; finalinc = b & 0x7F; for (int shift = 7; (b & 0x80) != 0; shift += 7){ b = ArrayOfSpikes[inc++]; finalinc |= (b & 0x7F) << shift; } inc+=finalinc; } if(ArrayOfSpikes[inc]==0) return true; else return false; } public final Vector allgatherSpikes(SpikeArray spikes) { /*java.io.File f=new java.io.File("ARRAY_SPIKES_DECODE_"+id+".txt"); if(f!=null) f.delete(); neosim.kernel.CommandQueue.PrintObject(new StrMessage("SpikeArray"), "ARRAY_SPIKES_DECODE_"+id+".txt"); neosim.kernel.CommandQueue.PrintObject(spikes, "ARRAY_SPIKES_DECODE_"+id+".txt");*/ convert(spikes); /*neosim.kernel.CommandQueue.PrintObject(new StrMessage("ArrayOfSpikes"), "ARRAY_SPIKES_DECODE_"+id+".txt"); neosim.kernel.CommandQueue.PrintObject(ArrayOfSpikes, "ARRAY_SPIKES_DECODE_"+id+".txt");*/ byte[] TempArray=new byte[0]; int j,length; byte b; for(int i=0;i>>= 7; } bosArray[i].write((byte)length); bosArray[i].flush(); //send packets. length=ArrayOfSpikes.length-5; for(j=0;j0){ while(CheckSpikesArrayEmpty(AllgatherArray[i]-1)){ try{ //say you are ready // bosArray[i].write(0); // bosArray[i].flush(); //decode on several bytes because sending int does not seem to work (sometimes some weird 255 offsets happen). b=(byte)bisArray[i].read(); length = b & 0x7F; for (int shift = 7; (b & 0x80) != 0; shift += 7) { b = (byte)bisArray[i].read(); length |= (b & 0x7F) << shift; } //read packets. TempArray=new byte[length]; int bytesRead = 0; // in a single iteration int offset = 0; // current offset in buffer int BUFFER_SIZE = 5; while ((bytesRead != -1) && (offset < length)) { int requestSize = ((int) length - offset) < BUFFER_SIZE ? ((int) length - offset) : BUFFER_SIZE; bytesRead = bisArray[i].read(TempArray, offset, requestSize); offset += bytesRead; } }catch(java.io.IOException e){ e.printStackTrace(); } /*neosim.kernel.CommandQueue.PrintObject(new StrMessage("TempArray"), "ARRAY_SPIKES_DECODE_"+id+".txt"); neosim.kernel.CommandQueue.PrintObject(TempArray, "ARRAY_SPIKES_DECODE_"+id+".txt");*/ include(TempArray); //neosim.kernel.CommandQueue.PrintObject(new StrMessage("ArrayOfSpikes"), "ARRAY_SPIKES_DECODE_"+id+".txt"); } } } // neosim.kernel.CommandQueue.PrintObject(new StrMessage("Passed"), "ARRAY_SPIKES_DECODE_"+id+".txt"); //distribute for(int i=AllgatherArray.length-1;i>=0;i--){ if(AllgatherArray[i]>0){ try{ //wait to be ready // bisArray[i].read(); length=ArrayOfSpikes.length; //write on several bytes because sending int does not seem to work (sometimes some weird 255 offsets happen). while ((length & ~0x7F) != 0) { b = (byte)((length & 0x7f) | 0x80); bosArray[i].write(b); length >>>= 7; } bosArray[i].write((byte)length); bosArray[i].flush(); //send packets. length=ArrayOfSpikes.length-5; for(j=0;j>>= 7; } bosArray[i].write((byte)ID_); bosArray[i].flush(); }catch(java.io.IOException e){ e.printStackTrace(); } } else if(AllgatherArray[i]>0){ while(!arrayBarrierSocket[AllgatherArray[i]-1]){ try{ bosArray[i].write(0); bosArray[i].flush(); //decode on several bytes because sending int does not seem to work (sometimes some weird 255 offsets happen). b=(byte)bisArray[i].read(); idread = b & 0x7F; for (int shift = 7; (b & 0x80) != 0; shift += 7) { b = (byte)bisArray[i].read(); idread |= (b & 0x7F) << shift; } //idread=isArray[i].read(); }catch(java.io.IOException e){ e.printStackTrace(); } arrayBarrierSocket[idread-1]=true; } } } /* //no need for distribution for(int i=AllgatherArray.length-1;i>=0;i--){ if(AllgatherArray[i]>0){ try{ osArray[i].write(id+1); }catch(java.io.IOException e){ e.printStackTrace(); } } else if(AllgatherArray[i]<0){ while(!arrayBarrierSocket[-AllgatherArray[i]-1]){//if try{ idread=isArray[i].read(); }catch(java.io.IOException e){ e.printStackTrace(); } arrayBarrierSocket[idread-1]=true; } } }*/ for(int i=0;i0){ while(CheckSpikesArrayEmpty(AllgatherArray[i]-1))//if try{ AllgatherObject.wait(); } catch(Exception e){ e.printStackTrace(); } } } //distribute for(int i=length-1;i>=0;i--){ if(AllgatherArray[i]>0){ CommandQueue cq=(CommandQueue)this.othercqs.elementAt(AllgatherArray[i]-1); RmtApp remoteKernel=(RmtApp)cq.getDest(); try{ remoteKernel.SendSpikesArray(ArrayOfSpikes); } catch(java.lang.Exception e){ e.printStackTrace(); } //send my guy //notify } else if(AllgatherArray[i]<0){ while(CheckSpikesArrayEmpty(-AllgatherArray[i]-1))//if try{ AllgatherObject.wait(); } catch(Exception e){ e.printStackTrace(); */PK}UZPK(3#neuroml/model/ions_channel/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(3$neosim/kernel/ProcManager_Stub.classw- J K L M N O P Q R S S T U V W X Y Z [ \ ] ^ _ST afe,W0bՠr}IEr"P2UEÌh͸ `} a} b} c} d} e} f} g} wl wn wo wr | m | | | m h p q ~$method_calcMinTime_0$method_getMinTime_1$method_getProcessor_2$method_setMinTime_3$method_setRunning_4$method_setSleeping_5$method_setStopped_6$method_updateMinTime_7()Ljava/lang/String;()Lneosim/iface/Time;()V(I)Lneosim/kernel/RmtProc;(I)V%(Ljava/lang/String;)Ljava/lang/Class;(Ljava/lang/String;)V*(Ljava/lang/String;Ljava/lang/Exception;)V@(Ljava/lang/String;[Ljava/lang/Class;)Ljava/lang/reflect/Method;S(Ljava/rmi/Remote;Ljava/lang/reflect/Method;[Ljava/lang/Object;J)Ljava/lang/Object;(Ljava/rmi/server/RemoteRef;)V(Lneosim/iface/Time;)V(Lneosim/kernel/RmtProc;)V-(Lneosim/kernel/RmtProc;Lneosim/iface/Time;)VCode ConstantValue ExceptionsJLjava/lang/Class;Ljava/lang/reflect/Method;Ljava/rmi/server/RemoteRef; 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"#  # $#guikit/Navigator$4java/lang/Objectjava/awt/event/ActionListenerguikit/Navigator buildPanel()V forwardURL   4 *+* b   @* de  PK[RPK(3(neuroml/util/axiope/ObjectAccessor.class91 getValueAccessors&()[Lneuroml/util/axiope/ValueAccessor; SourceFileObjectAccessor.java"neuroml/util/axiope/ObjectAccessorjava/lang/ObjectPKmWPK(3MiscTests/MapViewer$2.classD1"   this$0LMiscTests/MapViewer;(LMiscTests/MapViewer;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLMiscTests/MapViewer$2; mouseMoved(Ljava/awt/event/MouseEvent;)VeLjava/awt/event/MouseEvent; SourceFileMapViewer.javaEnclosingMethod   !MiscTests/MapViewer$2!java/awt/event/MouseMotionAdapterMiscTests/MapViewer()V access$0003(LMiscTests/MapViewer;Ljava/awt/event/MouseEvent;)V   4 *+* 9   A *+ :;    PK*PK(3 neuroml/environment/package.htmlX Definitions of the simulation's environment

Definitions of simulation's environment

This package defines the environment's parameters for a simulation.

The environment is split into an io section and a schedule. The io section includes all details of probes, stimulii, gui activity viewers etc etc. This typically consists of a number of references to modules along with network connections to the model, defined in the same way as projections within the model. The schedule is typically a pointer to a module which controls the simulation run.

Fred Howell
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F **+! 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X zzz woken up...Failed to do sleeping cmd w  allprocs.proc is null   RunningRmt exc: neosim/kernel/StoppedCommand KN     Stopped Rmt arrived from Stopped Rmt dealt withstoppedRmt exc:>>> AddRmt::- neosim/kernel/SimProcessor OCQ _Test othercqs: ID:  othercqs new size :  class of the RmtApp:  <<< Done Add allprocs size is now BasicKernel::Run Rmt called / BasicKernel::Run Rmt done  compress_final   neosim/implementation/EntityImpl d       a @A!neosim/kernel/EntityCallbackEvent  eventRmt to unknown entity event_rmt_error.txt $neosim/implementation/ConnectionImpl  .   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" # $%  &'debugZtracker%Lneosim/kernel/DeadlockTrackerKernel;()VCodeLineNumberTableLocalVariableTablethisLneosim/kernel/DeadlockTracker;LockDeadlockTracker5(Ljava/lang/Object;Lneosim/kernel/Deadlock_Message;)VcallerLjava/lang/Object;e Lneosim/kernel/Deadlock_Message;UnLockDeadlockTracker#(Lneosim/kernel/Deadlock_Message;)V SourceFileDeadlockTracker.java  () *#neosim/kernel/DeadlockTrackerKernelneosim/kernel/DeadlockTrackerjava/lang/Objectadd5(Lneosim/kernel/Deadlock_Message;Ljava/lang/Object;)Vremove!  3*  9K +*!9H* *#$ %) +Y PKpnPK(3neuroml/util/JarInfo.class](1 }  | | | | | | | z          | z | } |  | !   !  !  6  !"#$%&'( !)* !+ !,-./012345 &67 !89:;<=> &?@A iB CDEF iGHI JBKLMNO iPQRST |UVW zXY classLoader Lneuroml/util/SimpleClassLoader; beanNames[Ljava/lang/String; beanInfos[Ljava/beans/BeanInfo; fromPrototype[Z manifestData[Lneuroml/util/MessageHeader;jarNameLjava/lang/String; beanToJarLjava/util/Hashtable; Signature;Ljava/util/Hashtable;debugZg(Ljava/lang/String;Lneuroml/util/SimpleClassLoader;[Ljava/lang/String;[Z[Lneuroml/util/MessageHeader;)VCodeLineNumberTableLocalVariableTableexLjava/lang/Exception;cLjava/lang/Class;biLjava/beans/BeanInfo;iIthisLneuroml/util/JarInfo;cl getJarName&(Ljava/lang/String;)Ljava/lang/String;beanName()Ljava/lang/String;getCount()I getBeanInfo(I)Ljava/beans/BeanInfo;bLjava/lang/Object;getName(I)Ljava/lang/String;isFromPrototype(Ljava/lang/String;)ZnamegetManifestData0(Ljava/lang/String;)Lneuroml/util/MessageHeader; getInstance&(Ljava/lang/String;)Ljava/lang/Object;thLjava/lang/Throwable; getBeanClass%(Ljava/lang/String;)Ljava/lang/Class;diagnoseInstantiationExceptionJ(Lneuroml/util/SimpleClassLoader;Ljava/lang/String;Ljava/lang/Throwable;)VresultLjava/io/ObjectStreamException;Ljava/io/IOException;"Ljava/lang/ClassNotFoundException;oinsLjava/io/ObjectInputStream; classFileNameLjava/lang/SecurityException;args[Ljava/lang/Class;consLjava/lang/reflect/Constructor;!Ljava/lang/NoSuchMethodException;objrealxserNameinsLjava/io/InputStream;pkg classNameclsmods indexForName(Ljava/lang/String;)I(Ljava/lang/String;)Vmsg()V SourceFile JarInfo.java java/lang/Error8beanNames and fromPrototype need to have the same length ~ java/beans/BeanInfo Z[\ ]java/lang/Exception^ _` abjava/lang/StringBuilder$JarInfo: couldn't find BeanInfo for cd ce ; caught fg h JarInfo:: @ ci ; beanName: ; fromPrototype: cj kljava/lang/String mn o pqjava/lang/Throwable  rsd Note that file names in manifests must use forward slashes "/" rather than back-slashes "\" Jarinfo.getBeanClass error & WARNING: Could not instantiate bean "" t from the system class-loader from JAR " uv.ser w xy) We found a serialized template file "$neuroml/util/ObjectInputStreamLoader z{ |}< An object could be read from the serialized template OK.8 But an exception was generated in Beans.instantiate: java/io/ObjectStreamExceptionL But caught an ObjectStreamException while reading the serialized object:M This indicates there is a problem with the contents of the template file.java/io/IOExceptionB But caught an IOException while reading the serialized object: java/lang/ClassNotFoundExceptionL But caught a ClassNotFoundException while reading the serialized object:I This indicates that there was a problem finding a .class file for one of the serialized objectsK But caught an unexpected exception while reading the serialized object:~ .class% We couldn't open the class file " " in the JAR We found the class file "java/lang/SecurityExceptionthe default package s the package "  ' But were unable to load the class " " because of, Common reasons for this failure include:7 (1) The class is not defined in the correct package it should be in 5 (2) The class has not been given the correct name it should be called "B (3) The class file contains the wrong class or no class at alljava/lang/ClassFormatError Duplicate name R This particular error is often caused by having a mismatch between the name of8 the .class file and the name of the contained class.; In this case make sure that class file contains a class called "" in .  We located the class "" OK  H But the class was not declared public, so we could not create a beanjava/lang/Class 6 But the class did not have a zero-arg constructor.8 All beans must provide public zero-arg constructors.@ But the class's zero-arg constructor was not declared publicjava/lang/NoSuchMethodException: Unexpected exception in disgnoseInstantiationException 4 The class provides a public zero-arg constructor }A But were unable to create an instance of the class because we6 got an exception while doing Class.newInstance() : 8 The stack backtrace at the time of this exception is  JarInfo:: java/util/Hashtableneuroml/util/JarInfojava/lang/Objectput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;neuroml/util/SimpleClassLoader loadClassjava/beans/Introspector((Ljava/lang/Class;)Ljava/beans/BeanInfo;java/lang/SystemerrLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintln(I)Ljava/lang/StringBuilder;(Z)Ljava/lang/StringBuilder;get&(Ljava/lang/Object;)Ljava/lang/Object;getClass()Ljava/lang/Class;java/beans/Beans instantiate=(Ljava/lang/ClassLoader;Ljava/lang/String;)Ljava/lang/Object;indexOf(I)Iprintreplace(CC)Ljava/lang/String;concatgetResourceAsStream)(Ljava/lang/String;)Ljava/io/InputStream;/(Ljava/io/InputStream;Ljava/lang/ClassLoader;)Vjava/io/ObjectInputStream readObject()Ljava/lang/Object;java/io/InputStreamclose lastIndexOf substring(II)Ljava/lang/String; 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D**Y  O*+*Y .+M,>6*, W '-4..) ! !PK?mwPK(3&neuroml/util/.#JarClassLoader.java.1.4package neuroml.util; import java.net.*; import java.util.Hashtable; import java.util.Enumeration; import java.util.zip.*; import java.util.jar.*; import java.io.*; /** * A class loader for loading jar files, both local and remote. */ public class JarClassLoader extends URLClassLoader { Hashtable urlsIn = new Hashtable(); private boolean debug = false; /** * Creates a new JarClassLoader for the specified url. * * @param url the url of the jar file */ public JarClassLoader() { super(new URL[] { }); } public JarClassLoader(URL url) { super(new URL[] { url },ClassLoader.getSystemClassLoader()); } public JarClassLoader(URL[] urls) { super(urls,ClassLoader.getSystemClassLoader()); } /** Check if url already registered */ private boolean alreadyIn(String jarurl){ int slash = jarurl.lastIndexOf('/');// are urls always composed of / ? String key = jarurl.substring(slash+1); return (urlsIn.containsKey(key)); } /** Registers url in hashtable */ private void registerUrl(URL url){ int slash = url.toString().lastIndexOf('/');// are urls always composed of / ? 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  /*  &*Y,:!%"# $%&\  &&&&&&& !&"#$%/*( &'PK(PK(3"neuroml/util/.#NeuromlSys.java.1.3package neuroml.util; import neuroml.core.*; import java.lang.reflect.*; import java.io.*; import java.io.InputStream; import java.io.FileInputStream; import java.io.File; import java.net.URL; import java.util.Hashtable; /** * Static system class for neuroml. * * Contains wrappers for xmlin, xmlout and references. * * @version 1.0, 25 July 2001 * */ public class NeuromlSys { /** * Load an XML file * * @param xmlfilename Name of the xml description file * @return Top level object * */ public static Object loadXML( String xmlfilename ){ return XMLIn.loadXML(xmlfilename); } /** Convert an XML string to an object */ public static Object fromString( String xmltext ){ return XMLIn.fromString(xmltext); } /** Write all fields */ public static String toString(Object top) { return XMLOut.toString(top); } /** Write all fields to a file */ public static void toFile(Object top, String filename) { XMLOut.toFile( top, filename); } /** Write all fields, user specified top level tags */ public static String toString(Object top, String topTag, String bottomTag) { return XMLOut.toString(top, topTag, bottomTag); } /** Write selected fields to XML */ public static String toString(Field[] selectedFields, Object top) { return XMLOut.toString(selectedFields, top); } /** Deal with references / namespaces */ static Hashtable namespaces = new Hashtable(); /** * Make a new namespace (for references - one namespace / file) */ public static Namespace makeNamespace(String name) { Namespace n = new Namespace( name ); namespaces.put( name, n ); return n; } /** * Return namespace */ public static Namespace getNamespace(String name) { return (Namespace)namespaces.get(name); } /** * Delete a namespace */ public static void removeNamespace(String name) { namespaces.remove( name ); } /** Retrieve an Object from a Ref */ public static Object deRef(Ref ref, String namespace ) { Namespace n = getNamespace(namespace); if (n != null) return n.deRef( ref ); else return null; } /** Add a reference in given namespace */ public static void addRef(String key, Object obj, String namespace ) { Namespace n = getNamespace(namespace); if (n==null) n = makeNamespace(namespace); n.addRef( key, obj ); } /** Add all references in the package */ public static void addReferences(Object pkg, String namespace) { Namespace n = getNamespace(namespace); if (n==null) n = makeNamespace(namespace); n.addReferences( pkg ); } /** Return the hashtable of all possible targets */ public static Hashtable getNamespaces(){ return namespaces; } /** Remove a reference in given namespace */ public static void removeRef( String key, Object obj, String namespace) { Namespace n = getNamespace(namespace); if (n != null) n.removeRef( key, obj ); } /** Try to make an object */ private static Object createObject(String className) { Object object = null; try { Class classDefinition = Class.forName(className); object = classDefinition.newInstance(); } catch (Exception e) { } return object; } /** Try to make a class */ private static Class createClass(String className) { Class classDefinition =null; try { classDefinition = Class.forName(className); } catch (Exception e) { } return classDefinition; } /** Get full class given a sort neuroml class name (i.e. without * the package prefix) */ public static Class getClassFromShortName( String cname ) { String[] packageslist = neuroml.NeuromlPkg.getPackageList(); String packageName = new String(); Class c = createClass(cname); for (int j=0;j(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLneuroml/core/DValueParameter;nameLjava/lang/String;()V SourceFileDValueParameter.java neuroml/core/DValue   neuroml/core/DValueParameterneuroml/core/Parameter! 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Ai4 jk q \ \ q!gl ,*5767Y89:*5;<:;=>*?M,ADzB*CDE**FM,6G>ʻHYIN,236,2',2.6-JK -JLW66,&,26,2 ٻMY-N:6,F,296,2,,2.6**!OYPQYRSЄ14@h$EH-K1P4N5O9Q<RBTLXU]Y^a_dalmrn~orsnvwxyzyw~%+i5qu-qpq*qq3pqJqlqM,jk,qU"$PK*APK(3!neuroml/model/cell/CVS/Repository#NMLPLAY_CVS/src/neuroml/model/cell PKR(#PK(39neuroml/model/MeasurementTool/Channel_h_measurement.classc 1 +V )W )XYZ [ \] ^ _`a V )bc [d ef ghij k lmn o pqr k st uv w xy V z{ |}~  )V IndexChannelI NeuronRefLneuroml/core/Ref;()VCodeLineNumberTableLocalVariableTablethis5Lneuroml/model/MeasurementTool/Channel_h_measurement;(Ljava/lang/String;)VstrLjava/lang/String;getValue"(Lneuroml/sim/run/RunnableCell;D)DobjLneuroml/sim/run/RunnableCell;tDbscc&Lneuroml/util/module/BasicChannelCell;toString()Ljava/lang/String;#Lneuroml/model/cell/AbstractNeuron;factory-Lneuroml/util/module/BasicChannelCellFactory;oLjava/lang/Object;obj2ieLjava/lang/Exception;toAddgetXUnitgetYUnitClone()Ljava/lang/Object;truc SourceFileChannel_h_measurement.java 12 -. /0neuroml/core/RefAbstractNeuron 18 8$neuroml/util/module/BasicChannelCell  java/lang/String NOT_  !neuroml/model/cell/AbstractNeuronneuroml/model/cell/ModuleNeuron  I+neuroml/util/module/BasicChannelCellFactory  (neuroml/model/ions_channel/ModuleChannel  D java/lang/StringBuilder h_ CDjava/lang/Exception_ Time(s)3neuroml/model/MeasurementTool/Channel_h_measurement-neuroml/model/MeasurementTool/MeasurementToolneuroml/core/Clonable setTargetName getChannel'(I)Lneuroml/model/ions_channel/Channel;"neuroml/model/ions_channel/Channelget_h()DToBeSentZneuroml/util/NeuromlSysgetNewestNamespace()Lneuroml/util/Namespace;neuroml/util/NamespacedeRef,(Lneuroml/core/Reference;)Ljava/lang/Object;moduleLneuroml/core/ModuleRef;neuroml/core/ModuleRef parametersChannelsLneuroml/core/Set;neuroml/core/Set elementAt(I)Ljava/lang/Object;java/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetName lastIndexOf(I)I substring(I)Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;!)+,-./0123V****Y4 5 67183l$****Y*+4  !#"5$67$9:;<3a+:* 4 %&5*67=>?@ABCD3ӻ Y L*  YL YL*M,N-*:::.6`: Y!+"#""$M*M,.> ,`M Y!+","&"*'$&%4N+,-/&142B3O4\5f6o7t89;=>?@A5p 4d=EBVFGOIHI\<JIf29:o)K.LM67N:29:+K.OD3-(4E5 67PD3-4I5 67QR3Z)Y*L+*+*+4MNOP567S7TUPK[h c PK(3guikit/NameNode.class1A * + ,-. /01 2 3 45 6 789'(Ljava/lang/Object;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLguikit/NameNode;parentLjava/lang/Object;nameLjava/lang/String;getName()Ljava/lang/String; getContent()Ljava/lang/Object; setContent(Ljava/lang/Object;)VeLjava/lang/Exception;ctoStringtitle SourceFile NameNode.java "  :neuroml/core/Nameablejava/lang/String ;<java/lang/Exceptionjava/lang/StringBuilder =  >? : >@ &guikit/NameNodeguikit/ObjectNodecontentsetName(Ljava/lang/String;)V()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;!Q *,*+     -  /* !"r**+M #$%&X Y *  *L+ !" '()PK6PK(3neuroml/util/package.html Utilities to read/write neuroml files

Utilities to read/write neuroml files

This package provides utilities to read/write neuroml files, and to load code modules.
Fred Howell
Last modified: Mon Mar 12 18:55:37 GMT 2001 PK?v PK(3.neosim/implementation/PopulationTreeImpl.class1Z 34 5 6 7 8 9: ; <= > ?@A BCDEFnodesLjava/util/Vector;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis*Lneosim/implementation/PopulationTreeImpl;nameLjava/lang/String;addNode (Lneosim/iface/PopulationNode;)VnLneosim/iface/PopulationNode; deleteNodepniInname getChildren()Ljava/util/Vector; getEntityID(Ljava/lang/String;)I entityNamegetChild1(Ljava/lang/String;)Lneosim/iface/PopulationNode;popNameretisLeaf()Z SourceFilePopulationTreeImpl.java java/util/Vector G  HI JK LMneosim/iface/PopulationNode NOP QR STU VW0Pop Tree Impl :: getEntityID Not yet implementedX Y(neosim/implementation/PopulationTreeImpl(neosim/implementation/PopulationNodeImplneosim/iface/PopulationTree()V addElement(Ljava/lang/Object;)Vsize()I elementAt(I)Ljava/lang/Object;getName()Ljava/lang/String;java/lang/Stringequals(Ljava/lang/Object;)ZremoveElementAt(I)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln!M*+*YA *+    !;=*0*N+-  * ˱ ) 1!4:$*" 8#$;;%&'/*) ()B   01  *+,<M>*.,**:+  M,89:#;1<49:?4#" 6#$<<-:. /0,B 12PKAlPK(3%neosim/util/SourceMethodJarBean.class1_ 6 7 8 9:; 6< = > ?@ ABC DE F GHIJKLMnameLjava/lang/String;paramsLjava/util/Hashtable;smLneosim/iface/SourceMethod;*(Ljava/lang/String;Ljava/util/Hashtable;)VCodeLineNumberTableLocalVariableTablethis!Lneosim/util/SourceMethodJarBean;action?(Lneosim/util/JarInfo;Ljava/beans/BeanInfo;Ljava/lang/String;)VjiLneosim/util/JarInfo;biLjava/beans/BeanInfo;beanNameoLjava/lang/Object;getSourceMethod()Lneosim/iface/SourceMethod;error(Ljava/lang/String;)Vmsg*(Ljava/lang/String;Ljava/lang/Exception;)VexLjava/lang/Exception; SourceFileSourceMethodJarBean.java N  O PQjava/lang/StringBuilderRunning template RS TUV W/X YZneuroml/sim/run/SourceMethod[ \]  ^neosim/iface/SourceMethodStart bean error Start bean exception neosim/util/SourceMethodJarBeanjava/lang/Objectneosim/util/DoOnBean()Vjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintlnneosim/util/JarInfo getInstance&(Ljava/lang/String;)Ljava/lang/Object;neosim/util/NeuromlConverterconvertSourceMethod;(Lneuroml/sim/run/SourceMethod;)Lneosim/iface/SourceMethod;init!Y**+*,  !"#$cY- +- : #* *******&  !(#4%E&H(Q)b+ 4c!"c%&c'(c) C*+,-/*- !"./RY+  /0 !"0.1\Y+  23 !"02345PKMPK(3!neosim/implementation/Shape.classy1, $ % & '()*+colourLjava/lang/String; shapeNamescaleD((Ljava/lang/String;Ljava/lang/String;D)VCodeLineNumberTableLocalVariableTablethisLneosim/implementation/Shape; setColour(Ljava/lang/String;)Vs setShapeNamesetScale(D)V getColour()Ljava/lang/String; getShapeNamegetScale()Ddraw()V SourceFile Shape.java ! neosim/implementation/Shapejava/lang/Objectjava/io/Serializableneuroml/sim/state/Shape! l**+*,*) *   :*+ :*+# :*'( /*) /** /*+  !+. "#PK7EPK(31neosim/implementation/GeneralProjectionImpl.class/1+ " # $ % &'() srcPopNameLjava/lang/String; destPopNamesmLneosim/iface/SourceMethod;dmLneosim/iface/DestMethod;[(Ljava/lang/String;Ljava/lang/String;Lneosim/iface/SourceMethod;Lneosim/iface/DestMethod;)VCodeLineNumberTableLocalVariableTablethis-Lneosim/implementation/GeneralProjectionImpl; getSrcPopName()Ljava/lang/String;getDestPopName getSrcMethod()Lneosim/iface/SourceMethod; getDestMethod()Lneosim/iface/DestMethod;isGeneralProjection()Z SourceFileGeneralProjectionImpl.java * +neosim/implementation/GeneralProjectionImpl$neosim/implementation/ProjectionImplneosim/iface/GeneralProjection()V! **+*,*-* 4   /* /* /* /* ,  !PKCPK(3neuroml/util/axiope/CVS/Entries)/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /AccessorFinder.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ObjectAccessor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ValueAccessor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PKWgPK(3,neosim/implementation/CallBackGUIMaker.class1X 1 234 1 56 78 9 :; <= >?@A BCDEpop,Lneosim/implementation/GUI_Maker_Population;()VCodeLineNumberTableLocalVariableTablethis(Lneosim/implementation/CallBackGUIMaker;callback*(Lneosim/iface/Entity;Ljava/lang/Object;)VexLjava/lang/ClassCastException;eLneosim/iface/Entity;oLjava/lang/Object; readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; ExceptionsFG writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput; SourceFileGUI_Maker_Population.java H IJjava/lang/StringBuilderK LM NO" CallBackGUIMaker Callback called PMQ RS javax/swing/JPanelT UVjava/lang/ClassCastExceptionCallBackGUIMaker - exception NW&neosim/implementation/CallBackGUIMakerjava/lang/Objectneosim/iface/Callbackjava/io/IOException java/lang/ClassNotFoundExceptionjava/lang/SystemoutLjava/io/PrintStream;neosim/iface/EntitygetName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintln(Ljava/lang/String;)V*neosim/implementation/GUI_Maker_Population setPanel_(Ljavax/swing/JPanel;)V-(Ljava/lang/Object;)Ljava/lang/StringBuilder;  3*  FY+ , NY- (+ (+,E*,FF !F"#$%5&'()*+,5-.()/0PK_:PK(3MiscTests/Map.classh1 M  !  ! !          !   ! # % % / / / + + + / 4 4 3 !m !  # ! 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@A ?&E.F7GAHHIKJW4mn$vwAxk.yzLXY {|USY*L VQ R SW y}~] Uf*LY+ LVZ[\]W  y} Ux  !Y"L E F 8#Y$:%Y*&:6':(:  ) *#+Y ,-:  ./: 6      0S  2:  128 1+ 23Y4Y 2564Y 256789 92'  + 2 24Y 256:  ;2; 44Y 256E4Y 256F4Y 2568 <2Y R$=>?$4Y 256j%b8 $v4Y 256jb83Y 7@i A2 +B#Y$:F C2  8=DYEFG GHG IJGIK?#L+V,cdel"o%p,q4t;uQx_zi{t|~{&69JQY\po Wlvw p&i i,];] _ i u] %w Y i iic"PK KPK(3(neosim/kernel/ConnectionQueryEvent.classM1 ,q r s t u v w x %y z {|} ~  ~  ~ ~        ,  , , cqLneosim/iface/ConnectionQuery;cbLneosim/iface/Callback;outeIoutpSqcLneosim/iface/Connection;procqidO(Lneosim/iface/Time;ISLneosim/iface/ConnectionQuery;ISLneosim/iface/Callback;)VCodeLineNumberTableLocalVariableTablethis$Lneosim/kernel/ConnectionQueryEvent;tLneosim/iface/Time;cbecbportsetQid(I)VgetQid()IsetProcgetProc getCallback()Lneosim/iface/Callback;getOutputEntity getOutputPort()SsetQueryConnection(Lneosim/iface/Connection;)V doOnEntity(Lneosim/iface/Entity;)VeLneosim/iface/Entity;ansLjava/lang/Object; sendCallback(Ljava/lang/Object;)VqrLneosim/kernel/QueryResponse;clsLjava/lang/Class;skLneosim/kernel/SimKernel;clone()Ljava/lang/Object;cqe readExternal(Ljava/io/ObjectInput;)V objectInputLjava/io/ObjectInput; Exceptions()V writeExternal(Ljava/io/ObjectOutput;)V objectOutputLjava/io/ObjectOutput;getSize SourceFileConnectionQueryEvent.java 9 12 34 -. /0 56 82 72 WX neosim/kernel/QueryResponseNull 9 neosim/iface/Timeneosim/kernel/QueryResponseTime 2java/lang/Integer"neosim/kernel/QueryResponseIntegerneosim/kernel/QueryResponse "neosim/kernel/ConnectionQueryEvent G N 9: HE DE bc G N `neosim/iface/Callbackneosim/iface/ConnectionQueryneosim/iface/Connection 9i jk E E Xneosim/kernel/EntityEventjava/io/IOException java/lang/ClassNotFoundException(Lneosim/iface/Time;IS)VqueryB(Lneosim/iface/Entity;Lneosim/iface/Connection;)Ljava/lang/Object;neosim/kernel/SimSystem getKernel()Lneosim/kernel/SimKernel;(IILjava/lang/Object;)Vjava/lang/ObjectgetClass()Ljava/lang/Class;indexneosim/kernel/SimKernel sendCommand(ILneosim/kernel/CommandObj;)VgetTime()Lneosim/iface/Time;getSrcEntityIDgetSrcEntityPortIDjava/io/ObjectInputreadInt readShort readObjectjava/io/ObjectOutputwriteInt writeShort writeObject!,-./012345672829:;%*+*****<!" #$%&$'=R%>?%@A%B2%C4%-.%12%34%/0DE;:*<)=>?82FG;/*<*= >?HE;:*<+=>?72IG;/*<,= >?JK;/*<-= >?LG;/*</= >?MN;/*<0= >?OP;:*+<5=>?56QR;Y*+* M*, <: =?= >?ST UVWX;# M+ Y**+ NZ+:Y**+N-0Y**+NY**+N,*-<:HMNOQ"R*S;TCUFVNWbYs[~_=RYZ; YZ_YZ"Q[\>?UV{]^s YZ_`;v 6Y*******L+*+*+<c$e,f4g=6>?$a?bc;U*+ *+!*+"*+!*+!*+#$*+#%*+#&<& klmn#o-p:qGrTs=U>?Udefgh9i;E*'**<vw xy= >?jk;L*+(+*)+**+*)+*)+*++*++*+<& |}~#-7AK=L>?LlmfgnG;.Ȭ<= >?opPK0RMPK(3guikit/SwingWorker$2.class19 !  " # $ %& '()*+val$doFinishedLjava/lang/Runnable;this$0Lguikit/SwingWorker;+(Lguikit/SwingWorker;Ljava/lang/Runnable;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/SwingWorker$2;run()V SourceFileSwingWorker.javaEnclosingMethod,   -. /0 134 56 78guikit/SwingWorker$2java/lang/Objectjava/lang/Runnableguikit/SwingWorker construct()Ljava/lang/Object; access$000)(Lguikit/SwingWorker;Ljava/lang/Object;)V access$100 ThreadVar4(Lguikit/SwingWorker;)Lguikit/SwingWorker$ThreadVar;guikit/SwingWorker$ThreadVarclearjavax/swing/SwingUtilities invokeLater(Ljava/lang/Runnable;)V   9*+*,*k 0***L*+*mpqp&q(s/t 0 %2 PKMPK(3neuroml/sim/run/Simulator.class 1&$% bootstrap([Ljava/lang/String;)V initKernelinitSim()Vrun(D)VrunSim terminate setParameterslaunch buildModel-(Ljava/lang/Object;Lneuroml/util/Namespace;)VgetModel()Ljava/lang/Object;reset queryElement'(ILjava/lang/String;)Ljava/lang/Object;,(ILneuroml/sim/run/Query;)Ljava/lang/Object;queryPopulation8(Ljava/lang/String;Ljava/lang/String;)Ljava/util/Vector;;(Ljava/lang/String;Lneuroml/sim/run/Query;)Ljava/util/List;lookupElementID(Ljava/lang/String;)I lookupElement4(Ljava/lang/String;)Lneuroml/sim/state/ElementState;lookupPopulation7(Ljava/lang/String;)Lneuroml/sim/state/PopulationState;getRootElement%()Lneuroml/sim/state/PopulationState; getReader SourceFileSimulator.javaneuroml/sim/run/Simulatorjava/lang/Object       !"#PKsDdPK(3(neuroml/model/Synapse_nml/CVS/Repository*NMLPLAY_CVS/src/neuroml/model/Synapse_nml PKUGM/*PK(3guikit/EditShortPanel$1.class1B ! " # $ % &' ( )* +,-.this$0Lguikit/EditShortPanel;(Lguikit/EditShortPanel;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/EditShortPanel$1; stateChanged"(Ljavax/swing/event/ChangeEvent;)VeLjavax/swing/event/ChangeEvent; SourceFileEditShortPanel.javaEnclosingMethod/ 01  2 34 56 789 :; <=> ?@ A2guikit/EditShortPanel$1java/lang/Object javax/swing/event/ChangeListenerguikit/EditShortPanel makeSlider,(Ljava/lang/String;SII)Ljavax/swing/JSlider;()VbusyZparamValueFieldLguikit/DecimalField;sliderLjavax/swing/JSlider;javax/swing/JSlidergetValue()I sliderToVal(I)Iguikit/DecimalFieldsetValue(I)Vconfirm   4 *+*o  m-*%**** p q%r,t--   PKx 0 PK(3-neuroml/model/network/ElementPopulation.class(1  ()VCodeLineNumberTableLocalVariableTablethis)Lneuroml/model/network/ElementPopulation;(Ljava/lang/String;)VnameLjava/lang/String; SourceFileElementPopulation.java   'neuroml/model/network/ElementPopulationneuroml/model/network/Element!3*    :*+   PKꖻ4PK(3guikit/resources/Play24.gifGIF89a00a==naannž!,Ox0F=; y`H +pɹpm_8~ 99R^!,#سzH;Yns7&&[e&FO!OCopyright 2000 by Sun Microsystems, Inc. All Rights Reserved. JLF GR Ver 1.0 ;PK@PK(33neosim/util/SmallLists/LinkedListDestPort_Out.class31a J K L M N O P Q R S TUV W X YZnext/Lneosim/util/SmallLists/LinkedListDestPort_Out;Array[B destPortIDS compressedZ(S)VCodeLineNumberTableLocalVariableTablethiscompress()VshiftIkcurrentbBtrucindexstuffitemp[Ijprevious TotalLengthNewArraysort([III)VTalo0hi0lohimidaddOutConnection(I)IsrcIDgetOutConnection()[IdeleteInConnection(I)Vtemp2getID()SgetSize()Icompress_final NumberPerPort SourceFileLinkedListDestPort_Out.java     ["  \" DE ]" 12^ _`-neosim/util/SmallLists/LinkedListDestPort_Out  :;  !neosim/util/SmallLists/LinkedListListSizeTotalMemoryLinkedListsRealIndex_readjava/lang/System arraycopy*(Ljava/lang/Object;ILjava/lang/Object;II)V1  w+******x*` *++! w *L=+ `=+L+ N*L=666+g6+ +36  ~66  ~"+36  ~ x6 `66-O+ x6  i+`3~6  x6  +`3~6  x6  +`3~6  x6  +3~6 - O+`6+L+*--d -x: 66=-I-.d6-.6~#~6   T|6 T* * *- ** ***d`>$%' ()*,./0"4%5,6/788D9K:X;d<q:w>~?@ABEFGHIJKLMNOPRSTV!X)Y,Z/[7\?]D_L`Xabbicldw[}hijklmopO(!" /a#"KE$"DL%& T'" m(" X%& ?>$")*"+,%-"/#".""/")0 12q66+`|.6M+. +. +.6++.O+O666*+ *+ ` buvw xz{ |0}3~6FILSYagjquy}\ Y3"u3"4,5"6"7"8"9"!:;* *"** Y* ** x=*~Tz<*~Tz<*~Tz<*~T*Y ` * : !*1@ETYhm| 1Z$"<"!=> *L=+ `=+L+ N*L=666+g6+ w+36  ~66  ~"+36  ~ x6 `66-O+ -+3O+`6+L+g-  "%,/8DKXdqw~p O(!" /a#"KE$"DL%& )*"+,%-".""/"!?@E *M>, `>,M, :*M>66 6,n6, ,36  ~66  ~",36  ~ x6 `66O, !,36    O ,`6 ,M,U :    :*d x: 66>K.d6.6~#~6   T|6 T* * * ** *** d`:  #&-09ELYerx  + 5 <?JPXelty~P(!" 0h#"LL$"ES%& '" +%& ?$"<")*"t+,&g-"#" m."#j/" A, 0 BC/* DE3 *`"  F 3* (* GEh*L=+ `=+L+-.0 123 )#"HIPKzsPK(3guikit/EditArrayPanel$3.class10 " # $ %&'this$0Lguikit/EditArrayPanel;A(Lguikit/EditArrayPanel;[[Ljava/lang/Object;[Ljava/lang/Object;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/EditArrayPanel$3;x0[[Ljava/lang/Object;x1[Ljava/lang/Object;getColumnClass(I)Ljava/lang/Class; columnIndexIisCellEditable(II)ZrowIndex SourceFileEditArrayPanel.javaEnclosingMethod( )*  + ,- ./guikit/EditArrayPanel$3#javax/swing/table/DefaultTableModelguikit/EditArrayPanel RefreshTable()V*([[Ljava/lang/Object;[Ljava/lang/Object;)V access$500+(Lguikit/EditArrayPanel;)[Ljava/lang/Class; access$600(Lguikit/EditArrayPanel;)[Z   J *+*,-      > *2     H *3      ! PK(|PK(3MiscTests/AutoSnail.classp1                        %   , . ! 1" # $%& 6" '() :" * + > ,- ./0 12 3 14 3 56 789: N" %;< Q" => =? =@ A B =C D 1E FG H FI J K 1L M N %O =P hQ R ST hU hVW kX YZ [ \]It$^ 1_ S ` a bc de df xg `h ai Yj kl mn `o p \q \rstPFThread InnerClassesmapLMiscTests/Map;viewerLMiscTests/MapViewer; pathfinderLMiscTests/PathFinder;fromLMiscTests/Town;toselStageIsearcherLjava/lang/Thread;controlsLjava/awt/Panel;textFontLjava/awt/Font; labelFontfromTextLMiscTests/PassiveTextField;toTextdistText workCheckLjava/awt/Checkbox; heurCheck delayCheck delaySliderLjava/awt/Scrollbar;buttons searchButtonLjava/awt/Button; resetButton quitButtonfmtLjava/text/NumberFormat; makeButtonD(Ljava/lang/String;Ljava/awt/event/ActionListener;)Ljava/awt/Button;CodeLineNumberTableLocalVariableTablethisLMiscTests/AutoSnail;textLjava/lang/String;listenerLjava/awt/event/ActionListener;button makeLabel3(Ljava/lang/String;Ljava/awt/Font;)Ljava/awt/Label;fontlabelLjava/awt/Label;(Z)VisAppletZselect(LMiscTests/Town;)VtsetDelay()Vsearchheurworkupdate(F)VdistFdonesreset resetSearchsetMap(LMiscTests/Map;)V initApplet(LMiscTests/DemoApplet;)VurlLjava/net/URL;e Ljava/net/MalformedURLException;appletLMiscTests/DemoApplet;diemain([Ljava/lang/String;)Vargs[Ljava/lang/String;frame access$000(LMiscTests/AutoSnail;)Vx0 access$100*(LMiscTests/AutoSnail;)Ljava/awt/Checkbox; 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" :#$ R% m& R R@4 8 :' :( )! * + ,-. `/ 01 c2 c3 45 67 8 8 )9 !: ;<=>? referenceLneuroml/core/TreeRef;TreeNetLjavax/swing/JTree;jtfLjavax/swing/JTextField;jspLjavax/swing/JScrollPane;nsLneuroml/util/Namespace; myAttachment"Lneuroml/model/network/Attachment; paramLabelLjavax/swing/JLabel;editorsLjava/util/Hashtable; notifyParent$Lneuroml/sim/ElementChangedListener;addElementChangedListener'(Lneuroml/sim/ElementChangedListener;)VCodeLineNumberTableLocalVariableTablethisLguikit/EditTreeRefPanel;pput'(Ljava/lang/String;Ljava/lang/String;)V classnameLjava/lang/String; eclassnamegetO(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/String;)Lguikit/TreeNodeEditor;cLjava/lang/Class;oLjava/lang/Object;exLjava/lang/Exception;ElementNameeretLguikit/TreeNodeEditor;.(Lneuroml/util/Namespace;Lguikit/ObjectNode;)Va)Ljavax/swing/tree/DefaultMutableTreeNode;kelementenum_Ljava/util/Enumeration;temp arrayNode[Ljavax/swing/tree/TreeNode; thatTreePathLjavax/swing/tree/TreePath;OfClassnodeLguikit/ObjectNode;foundZ NodeToSelect TableNodes TableLeafiIlsizensizejtmptnameleavesLjava/util/Vector;nodesElementsgbLjava/awt/GridBagLayout;Ljava/awt/GridBagConstraints; 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initKernelinitSim()VrunSim(D)VtD Deprecatedrun buildModel-(Ljava/lang/Object;Lneuroml/util/Namespace;)VmodelLjava/lang/Object;nsLneuroml/util/Namespace;launch setParametersreset terminatedestroy(Ljava/lang/String;)VpLjava/lang/String;popLneosim/iface/Population; queryElement'(ILjava/lang/String;)Ljava/lang/Object;eIeqneq%Lneosim/neuroml/NeosimEntityQueryOld;,(ILneuroml/sim/run/Query;)Ljava/lang/Object;qLneuroml/sim/run/Query;"Lneosim/neuroml/NeosimEntityQuery;queryPopulation8(Ljava/lang/String;Ljava/lang/String;)Ljava/util/Vector;;(Ljava/lang/String;Lneuroml/sim/run/Query;)Ljava/util/List;lookupElementID(Ljava/lang/String;)InamelookupPopulation7(Ljava/lang/String;)Lneuroml/sim/state/PopulationState; lookupElement4(Ljava/lang/String;)Lneuroml/sim/state/ElementState;getRootElement%()Lneuroml/sim/state/PopulationState; SourceFileNeuromlSimulator.java 0A ,- ;< ? @A GC ./ java/lang/StringBuilder"NeuromlSimulator.runSim called to  Sneosim/iface/Time 0C B/NeuromlSimulator.buildModel not yet implemented PA QA  neosim/iface/Population R#neosim/neuroml/NeosimEntityQueryOld 0S  neosim/neuroml/NeosimEntityQuery 0!NeuromlSimulator queryPopulation c g i%neosim/neuroml/NeuromlPopulationState 0!lookupElement not yet implemented$neosim/neuroml/NeuromlPopulationTree 0neosim/neuroml/NeuromlSimulatorjava/lang/Objectneuroml/sim/run/Simulatorneosim/iface/ScriptReader.([Ljava/lang/String;)Lneosim/kernel/SimKernel;java/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(D)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Lneosim/iface/Time;)VgetPopulationTree()Lneosim/iface/PopulationTree;neosim/iface/PopulationTreegetChild1(Ljava/lang/String;)Lneosim/iface/PopulationNode;(Lneosim/iface/Population;)V queryEntity/(ILneosim/iface/EntityQuery;)Ljava/lang/Object;(Lneuroml/sim/run/Query;)V-(Ljava/lang/Object;)Ljava/lang/StringBuilder;G(Lneosim/iface/Population;Lneosim/iface/EntityQuery;)Ljava/util/Vector;lookupEntityID-(Ljava/lang/String;)Lneosim/iface/Population; (Lneosim/iface/PopulationTree;)V1)*+,- ./012F **+3 4 56 7-892/*34 56:92,34 56;<2C *+3 % &4 56 =>?<2D *+W3 , -4 56 =>@A28 *3 2 34  56BC2>*'3 :;456DEFGC2m1 Y  ' *Y'3AB0C41561DEHI2Q 3 HI4 56JKLMN<253O456=>O<253V456=>FNA2+3]4 56PA28 *3 b c4  56QA28 *3 h i4  56RS2g!*+M*,3wy z4 !56!TU VWXY2aY,N*-3  4*56Z[\U ]^FX_2aY,N*-3  4*56Z[`a ]bcd2MY,N*+: Y   *-!3 @44M56MTUM\U D]^ -VWFce2MY,N*+: Y   *-!3 @44M56MTUM`a D]b -VWfg2? *+"34 56 hUij2d*+#M, $Y,%3 4 56hU TWkl2B &3 4 56 hUmn2;'Y*(34 56oA23pqPK PK(39neuroml/model/MeasurementTool/MeasurementCollection.class/1+   ! "#$%&MeasurementList0[Lneuroml/model/MeasurementTool/MeasurementTool; DestPortIdS4([Lneuroml/model/MeasurementTool/MeasurementTool;S)VCodeLineNumberTableLocalVariableTablethis5Lneuroml/model/MeasurementTool/MeasurementCollection;Measure#(Lneuroml/sim/run/RunnableCell;D)[DiIoLneuroml/sim/run/RunnableCell;tDArray[D SourceFileMeasurementCollection.java '  ( )*3neuroml/model/MeasurementTool/MeasurementCollectionjava/lang/Objectjava/io/Serializable()V-neuroml/model/MeasurementTool/MeasurementToolgetValue"(Lneuroml/sim/run/RunnableCell;D)D!   Y***+    .*:6*2+(R %+4 ... %PK;3PK(3)neosim/util/loaders/jarload/Jarload.classd1d 89: ; < = >?@ 8A B C DE FGHIJ K LMN OP QRSdebugZ()VCodeLineNumberTableLocalVariableTablethis%Lneosim/util/loaders/jarload/Jarload;trunc(([Ljava/lang/String;)[Ljava/lang/String;iIa1[Ljava/lang/String; newlengthanswergetScriptReader([Ljava/lang/String;)Vsb(Lneosim/util/loaders/jarload/ScriptBean;eLjava/lang/Exception;argsmainothers SourceFile Jarload.java java/lang/String&neosim/util/loaders/jarload/ScriptBean $% - T UVjava/lang/StringBuilderGetting script from ... WX YZ[ \]^ _`Script completed OKjava/lang/ExceptionJarloader exception: Wa b$=== NEOSIM - testing jar loader ===  arg Wc: ,-#neosim/util/loaders/jarload/Jarloadneosim/util/BasicAppjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)Vneosim/util/JarLoaderloadJarDoOnBean+(Ljava/lang/String;Lneosim/util/DoOnBean;)V-(Ljava/lang/Object;)Ljava/lang/StringBuilder;printStackTrace(I)Ljava/lang/StringBuilder;1/*  ! "#$%{'*d<M>,*`2S,  %!*&''()"*'+) ,-dY*LY  *2 *2+  !LY  + +BE &  -4B#E F!_"c$!  6./F01d2) 3-WY  *2 *L=+-Y   +2 * '( )(*L)R,V-! "0&'W2) 74)5 67PK:GPK(3'neosim/util/loaders/jarload/CVS/Entriesk/.nbattrs/1.1.1.1/Thu Jul 7 14:31:48 2005// /Jarload.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ScriptBean.java/1.1.1.1/Thu Jul 7 14:31:48 2005// D PKgɰPK(3MiscTests/TipLabel.class1J &'( ) *+ , - . / 012 34 35 6 789tipFontLjava/awt/Font;()VCodeLineNumberTableLocalVariableTablethisLMiscTests/TipLabel;getMinimumSize()Ljava/awt/Dimension;fmLjava/awt/FontMetrics;labelLjava/lang/String;getPreferredSize SourceFileMapViewer.java  java/awt/Font SansSerif : java/awt/Color ; <= >? @A BCjava/awt/DimensionD EF GH I MiscTests/TipLabeljava/awt/Label(Ljava/lang/String;II)V(III)V setBackground(Ljava/awt/Color;)VsetFont(Ljava/awt/Font;)VgetFontMetrics'(Ljava/awt/Font;)Ljava/awt/FontMetrics;getText()Ljava/lang/String;java/awt/FontMetrics stringWidth(Ljava/lang/String;)I getHeight()I(II)V j0**Y *Y**   '/ 0r(** L* M, M Y+,`+  (  !"#/* $%PKcυPK(35neuroml/environment/schedule/ControlledSchedule.class(13      ! "# $ %&'moduleLneuroml/core/ModuleRef;()VCodeLineNumberTableLocalVariableTablethis1Lneuroml/environment/schedule/ControlledSchedule; SourceFileControlledSchedule.java neuroml/core/ModuleRef java/lang/StringBuilder( )*+ ,- ./.module 0- 12/neuroml/environment/schedule/ControlledSchedule%neuroml/environment/schedule/Schedulejava/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetName()Ljava/lang/String;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringsetName(Ljava/lang/String;)V! f0**Y*Y*     / 0PK?-(PK(3,neuroml/model/channel/KSTDepTransition.class}1     alphaLneuroml/core/DValue;beta()VCodeLineNumberTableLocalVariableTablethis(Lneuroml/model/channel/KSTDepTransition;(Ljava/lang/String;)VnameLjava/lang/String; SourceFileKSTDepTransition.java neuroml/core/DValue &neuroml/model/channel/KSTDepTransition"neuroml/model/channel/KSTransition!   Q**Y*Y     \*+*Y*Y PKPK(3$neuroml/sim/run/PlusMinusPanel.class)1   Expand()VOpenReduceCloseRefresh SourceFilePlusMinusPanel.javaneuroml/sim/run/PlusMinusPaneljava/lang/Object  PKFPK(3guikit/ImageUtils.class 41 )XY X (Z ([ (\ (] ^_` (a )b cd efg Xh i j klm n opq X r s tuvw xy (dz ({ | }~imagesLjava/util/Vector;imgNames resourcesLjava/util/ResourceBundle; mainframeLjavax/swing/JFrame;1(Ljavax/swing/JFrame;Ljava/util/ResourceBundle;)VCodeLineNumberTableLocalVariableTablethisLguikit/ImageUtils;mcrbgetResourceString&(Ljava/lang/String;)Ljava/lang/String;mre$Ljava/util/MissingResourceException;nmLjava/lang/String;str getResource"(Ljava/lang/String;)Ljava/net/URL;urlLjava/net/URL;keyname setResourcesgetImage (Ljava/net/URL;)Ljava/awt/Image;e Ljava/lang/InterruptedException;imgUrlimageLjava/awt/Image;icon2Ljavax/swing/ImageIcon;trackLjava/awt/MediaTracker;$(Ljava/lang/String;)Ljava/awt/Image;indexI SourceFileImageUtils.java 1java/util/Vector *+ ,+ -. /0 ;"java/util/MissingResourceException :;  AB java/lang/StringBuilderCouldn't get resource  javax/swing/ImageIcon 1 Hjava/awt/MediaTrackerjavax/swing/JPanel 1 java/lang/InterruptedException Image read OK-Need to call ImageUtils.setResources first!!! Loading image resource:Error - URL null HI java/awt/Imageguikit/ImageUtilsjava/lang/Object()Vjava/util/ResourceBundle getStringgetClass()Ljava/lang/Class;java/lang/Classjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintln(Ljava/lang/String;)V(Ljava/net/URL;)V()Ljava/awt/Image;(Ljava/awt/Component;)VaddImage(Ljava/awt/Image;I)V waitForID(I)VindexOf(Ljava/lang/Object;)I addElement(Ljava/lang/Object;)V elementAt(I)Ljava/lang/Object;!()*+,+-./0123/**Y*Y***+*,4"' "#$()).*5 /67/80/9.:;3q*+MNM, 40 3 1 245* <=67>? @?AB33*+ M,* , N- Y+478 9:<1>5*CD3673E?-F?G23I *+*,4A5  67 80 9. 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*-* \ !"#$%&'()*+,-./ ~Y*L+*=*(*** N+- - ****Y**+**&  1=C#r&}( *1 01-2~!" r3456PK_PK(3!neuroml/model/synapse/CVS/Entriesg/Synapse.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SynapsePkg.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /package.html/1.1.1.1/Thu Jul 7 14:31:48 2005// D PKxPK(3guikit/DisplayApp$1.classa1"  ()VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/DisplayApp$1; windowClosing(Ljava/awt/event/WindowEvent;)VeLjava/awt/event/WindowEvent; SourceFileDisplayApp.javaEnclosingMethod   !guikit/DisplayApp$1java/awt/event/WindowAdapterguikit/DisplayAppmain([Ljava/lang/String;)Vjava/lang/Systemexit(I)V /*j  9j   PK™PfaPK(3neuroml/sim/Editable.class}1 edit()V SourceFile Editable.javaneuroml/sim/Editablejava/lang/ObjectPK4PK(3+neuroml/model/channel/TabulatedHHRate.class)1'   !" # $%&ratesLneuroml/core/DoubleArray;xptsIxminDxmax fillPoints interpolationLjava/lang/String;()VCodeLineNumberTableLocalVariableTablethis'Lneuroml/model/channel/TabulatedHHRate;(Ljava/lang/String;)Vname SourceFileTabulatedHHRate.java neuroml/core/DoubleArray none  %neuroml/model/channel/TabulatedHHRateneuroml/model/channel/HHRate!    L**Y*$ "% W*+*Y*( ")PKPK(3neosim/perf/CVS/Entries.Extra/.nbattrs/// /EntityState.java/// /PerfLogger.java/// /PerfMonitor.java/// /PerfStats.java/// /TypeParam.java/// /Types.java/// PKWd8PK(3!neuroml/sim/state/CellState.class'1   getRunnableCell ()Lneuroml/sim/run/RunnableCell; SourceFileCellState.javaneuroml/sim/state/CellStatejava/lang/Objectneuroml/sim/state/ElementStatePKR$PK(3neuroml/util/ObjectBean.class,1b 9 : ; <=> 9? @ A BC DE FGH I JKL MNOPQRnameLjava/lang/String;beanNameoLjava/lang/Object;debugZ(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLneuroml/util/ObjectBean;action@(Lneuroml/util/JarInfo;Ljava/beans/BeanInfo;Ljava/lang/String;)VjiLneuroml/util/JarInfo;biLjava/beans/BeanInfo; getObject()Ljava/lang/Object; getBeanName()Ljava/lang/String;errormsg*(Ljava/lang/String;Ljava/lang/Exception;)VexLjava/lang/Exception;()V SourceFileObjectBean.java 6  S TUjava/lang/StringBuilderNeuroML Module Loader Loading VW X/Y Z [ \] *neosim/util/loaders/nmllauncher/XML_Readerfound ^_` a/ not found NeuroML Module Loader error  NeuroML Module Loader exception neuroml/util/ObjectBeanjava/lang/Objectneuroml/util/DoOnBeanjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintlnneuroml/util/JarInfo getInstance&(Ljava/lang/String;)Ljava/lang/Object;getClass()Ljava/lang/Class;java/lang/ClassgetName! 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7 14:31:48 2005// /InPortsTable.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /InitCommand.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /InputQueue.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Kernel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /OutPort.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /OutPortTable.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopCBObject.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationCallbackHandler.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationQueryEvent.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /PopulationUpdateEvent.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Pos.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ProcManager.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ProcManager.rmi/1.1.1.1/Thu Jul 7 14:31:48 2005// /ProcManager_Stub.rmi/1.1.1.1/Thu Jul 7 14:31:48 2005// /QueryCommand.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /QueryResponse.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /QueryResponseInteger.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /QueryResponseNull.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /QueryResponseTime.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Queryable.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RemoveCommand.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ResetCommand.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ResetException.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RestartCommand.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RmtApp.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RmtProc.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RmtProcMgr.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RunCommand.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /RunningCommand.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /ScriptCallback.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /Semaphore.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimKernel.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimOutfile.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimOutput.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimProcessor.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimProcessor.rmi/1.1.1.1/Thu Jul 7 14:31:48 2005// /SimProcessor_Stub.rmi/1.1.1.1/Thu Jul 7 14:31:48 2005// 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" # $ %&'genLjava/util/Random;magDmin(Ljava/lang/String;DDI)VCodeLineNumberTableLocalVariableTablethisLneosim/stats/SimUniformObj;nameLjava/lang/String;maxseedIsample()D SourceFileSimUniformObj.java (java/util/Random )  *neosim/stats/SimUniformObjjava/lang/Object()V(J)V nextDouble1     **Y*(g*( !4       <**k*c( PK}PK(3guikit/EditShortPanel.class 1J ^ ] ] ]   ] ] ] ] ] @$ ]      ]?zG{ @Y & ( ( , & < ] 1 ( ( 5 ] 5 5 5 ] < < < < < ] D < < I K ] K K@ K ] I ] 5 ] < 5  valueSsliderLjavax/swing/JSlider;sminIsmax paramLabelLjavax/swing/JLabel;paramValueFieldLguikit/DecimalField;fontLjava/awt/Font;busyZ(Lguikit/ObjectNode;)VCodeLineNumberTableLocalVariableTablethisLguikit/EditShortPanel;nodeLguikit/ObjectNode;valLjava/lang/Short;log10(D)DdDrescale(D)VlgvhLguikit/DisplayHints; valToSlider(D)Ssv sliderToVal(I)IsetMinMaxDisplay(DD)V labelTableLjava/util/Hashtable;l1l2minmax makeSlider,(Ljava/lang/String;SII)Ljavax/swing/JSlider;titleLjava/lang/String;gbLjava/awt/GridBagLayout;cLjava/awt/GridBagConstraints; insertUpdate$(Ljavax/swing/event/DocumentEvent;)Ve!Ljavax/swing/event/DocumentEvent; removeUpdate changedUpdateupdateDisplayValue updateDisplay(Ljava/lang/Object;)VLjava/lang/Exception;newobLjava/lang/Object;confirm()V SourceFileEditShortPanel.java op mn  kl de java/lang/Short  `a ~  fe bc  { vw       java/lang/StringBuilder oError - range out of bounds      z{ {  java/util/Hashtablejavax/swing/JLabel o !"java/lang/Integer o# $% &' ghjava/awt/Dimension o( )* +*guikit/DecimalField o, ij -./ 01javax/swing/JSlider o2 34 guikit/EditShortPanel$1 InnerClasses o5 678 9: ;<java/awt/GridBagLayoutjava/awt/GridBagConstraints => ?e @e A} BC DE F G#java/lang/Exception oH Iguikit/EditShortPanelguikit/EditPanel"javax/swing/event/DocumentListener guikit/GuiKitgetDefaultFont()Ljava/awt/Font;guikit/ObjectNode getContent()Ljava/lang/Object; shortValue()SgetName()Ljava/lang/String;java/lang/MathloggetDisplayHints()Lguikit/DisplayHints;guikit/DisplayHintsgetMin()DgetMax isRangeFixed()Zjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(D)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintln(Ljava/lang/String;)Vfloorpow(DD)DsetFont(Ljava/awt/Font;)V(I)Vput8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object; setLabelTable(Ljava/util/Dictionary;)V(II)VsetPreferredSize(Ljava/awt/Dimension;)VsetMinimumSize(DI)V getDocument()Ljavax/swing/text/Document;javax/swing/text/DocumentaddDocumentListener'(Ljavax/swing/event/DocumentListener;)V(III)VsetPaintLabels(Z)V(Lguikit/EditShortPanel;)VaddChangeListener%(Ljavax/swing/event/ChangeListener;)Vjavax/swing/BorderFactorycreateEmptyBorder!(IIII)Ljavax/swing/border/Border; setBorder(Ljavax/swing/border/Border;)V setLayout(Ljava/awt/LayoutManager;)Vfillgridxweightxadd*(Ljava/awt/Component;)Ljava/awt/Component;setConstraints4(Ljava/awt/Component;Ljava/awt/GridBagConstraints;)VgetValuesetValue(S)V setContent!]^_`abcdefeghijklmn opqH*+***+M*, ** **+ * ** r& ) !"#$&%/&G's HtuHvw*xyz{q@ 'or,s tu |}~q}*N-A*-*- '* #-Y''* +'H*'9* g"c# r. 01 23 415J8T9^:e;|=s*e}}tu}}uqo%$'*gk* o>>dd>r?@A#Bs %tu%}aqL** *dh$ocrEstueq*&Y':(YY)'*:*+(YY))*:*+,Y-.W,Yd-.W*/r"JKL5MZNjO{PRs>t,XhQ3htu}}qOu*(Y+*0*01YP 23*01Y  24*0*+*5Y 67*78*9*71Y( 2:*71Y  2;***?*@*1Yd 2A*1Y  2B*C*DY*EF*GHIYJ:KYL:*MNOPR**0SW*0TRO**SW*TPRO**7SW*7T*rzY Z[0\;]J^W`ia{cehijlnxyz{| }~,4:NV\psHutuuu`aueuewq>*+Ur stuq>*+Ur stuq5rstuqN***7V * * ** *** C*W*** =X*r& &48HMsNtuNq"+M*, *7* Y*UM Zr  !s*xy!"tu"qA*Y* [\r s tu DPK܁#PK(3nmlplay/resources/open.gifvGIF89a!,7H0$,NhlYf ٶ0E8C#^pE;$;PK2*{vPK(3guikit/ColourEditor$1.class,1C ( ) * + , -. /0 12345val$jcLjavax/swing/JColorChooser;val$cLguikit/RGBColour;val$ecl$Lneuroml/sim/ElementChangedListener;this$0Lguikit/ColourEditor;i(Lguikit/ColourEditor;Ljavax/swing/JColorChooser;Lguikit/RGBColour;Lneuroml/sim/ElementChangedListener;)VCodeLineNumberTableLocalVariableTablethis InnerClassesLguikit/ColourEditor$1; stateChanged"(Ljavax/swing/event/ChangeEvent;)VeLjavax/swing/event/ChangeEvent;newColorLjava/awt/Color; SourceFileColourEditor.javaEnclosingMethod6 78    9: ;<= >?@ ABguikit/ColourEditor$1java/lang/Object javax/swing/event/ChangeListenerguikit/ColourEditor editObject9(Ljava/lang/Object;Lneuroml/sim/ElementChangedListener;)V()Vjavax/swing/JColorChoosergetColor()Ljava/awt/Color;guikit/RGBColoursetColor(Ljava/awt/Color;)V"neuroml/sim/ElementChangedListenerelementChanged'(Ljava/lang/Object;Ljava/lang/Object;)V   D*+*,*-** l"*M*,*** !! 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Loading... dljavax/swing/JFramejavax/swing/JProgressBarjavax/swing/JLabelguikit/HTMLPanel$1 d javax/swing/BoxLayout dguikit/HTMLPanel$2      Y  Y  k  e  eguikit/HTMLPaneljavax/swing/JPanelsetContentTypesetPage setEditable(Z)V.(Lguikit/HTMLPanel;Ljavax/swing/JEditorPane;)VaddHyperlinkListener((Ljavax/swing/event/HyperlinkListener;)V(Ljava/awt/Component;)V setLayout(Ljava/awt/LayoutManager;)V removeAlladd*(Ljava/awt/Component;)Ljava/awt/Component; revalidateprintStackTracesize()Iremove(I)Ljava/lang/Object;(ILjava/lang/Object;)V elementAt9(Lguikit/HTMLPanel;Lguikit/HTMLPanel;Ljava/lang/String;)Vjava/lang/Threadstartequals(Ljava/lang/Object;)Zguikit/Navigator enableBack enableForwarddispose(Lguikit/HTMLPanel;)Vjavax/swing/BorderFactorycreateEmptyBorder!(IIII)Ljavax/swing/border/Border; setBorder(Ljavax/swing/border/Border;)V(Ljava/awt/Container;I)VaddWindowListener"(Ljava/awt/event/WindowListener;)VsetContentPane(Ljava/awt/Container;)VgetGraphicsConfiguration"()Ljava/awt/GraphicsConfiguration;java/awt/GraphicsConfiguration getBounds()Ljava/awt/Rectangle;java/awt/Rectanglewidthheight setLocationpack setVisiblerepaint!QRVWXYZY[\]Y^_`abcdefy3****Y*** Y g"  "'!2#h 3ijdkf=****Y*** Y **g* % "'&2'7(<)h =ij=XY=ZYdlf7****Y***+ *+ *+ g* - "'.,/1061h7ij7VWdmfA****Y*****+ *+ *+ g2 5 "'6,71869;:@;h*AijAVWAXYAZYnof>*+g =>hijbcpqf:Y**g@h ijrlf j*YM,,+,*Y*,,*Y,N*Y* *-!W,"*#*$ M,&*$]`%gNIK LMOP)Q1R:SGTKUQVUWYY]]`Za[e\i^h4 Qst:#uvawxjijjVWylf]*' *(W*+)gd efghijVWz{f|4*Yd*Y****d+ ,L+-*go p$q(s0t2vh4ij$w|}{f:*Y`*Y****d+ ,L+-**'g $(68h:ij$w|~{f}5**Y****d+ ,L+-**'g#13h5ijw|lfU*+**d+ .**+)*Y`** */*0g* +5<DLThUijUVWef*1 *12 Y34L*5Y+617Yd8M9Y+:N;Y*<:=>?Y@A-BW,BW*1CY*DE*1F*1G:H:*1IJdlddKLdl2dM*1N*1O*1PgN$/8BN]dkzhHijW/8BE>efA*1 *12gh ijT"*QSQU;CPKnEojPK(3%neosim/neuroml/MeasurementQuery.classA1V ) *+ ,- ./0 )1 2 34 567 869 8: ; < =>?@MeasurementList5Lneuroml/model/MeasurementTool/MeasurementCollection;8(Lneuroml/model/MeasurementTool/MeasurementCollection;)VCodeLineNumberTableLocalVariableTablethis!Lneosim/neuroml/MeasurementQuery;query)(Lneosim/iface/Entity;)Ljava/lang/Object;e2!Lneosim/neuroml/NeosimEntityImpl;exLjava/lang/ClassCastException;eLneosim/iface/Entity; SourceFileMeasurementQuery.java A neosim/neuroml/NeosimEntityImpl Bjava/lang/ClassCastExceptionC DEjava/lang/StringBuilderGetPos: Not an entity3D but a FGH IJK LM name: N id: OP FQ RMS TUneosim/neuroml/MeasurementQueryneosim/iface/EntityQuery()V setMeasuredjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;java/lang/ObjectgetClass()Ljava/lang/Class;java/lang/ClassgetName()Ljava/lang/String;neosim/iface/EntitygetID()I(I)Ljava/lang/StringBuilder;toStringjava/io/PrintStreamprintln(Ljava/lang/String;)V!F **+    P+M,**MY +  +  + N* !";#$PP%&'(PKwPK(3guikit/LabelPanel.classj1!    labelLjava/lang/String;()VCodeLineNumberTableLocalVariableTablethisLguikit/LabelPanel;(Ljava/lang/String;)V paramLabelLjavax/swing/JLabel; SourceFileLabelPanel.java  javax/swing/JLabel   guikit/LabelPanelguikit/EditPaneladd*(Ljava/awt/Component;)Ljava/awt/Component;!   = **     q***+Y+M*,W   PK%)ojPK(3guikit/EditDoublePanel$1.class1? ! 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( ) *+ , - ,./runtimeDstepping visudelay ViewOnOffZ DebugOnOffcommandLjava/lang/String;(Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis'Lneuroml/environment/schedule/Schedule;name()V SourceFile Schedule.java      java/lang/String " %neuroml/environment/schedule/Scheduleneuroml/core/NamedObject!~.*+**** * * Y "  "-. .!"s-***** * * Y "  !, - #$PK%@3.PK(3!neosim/util/FileEventObject.class810 % & ' ( ) *+,-.lineLjava/lang/String;cmdI'(Ljava/lang/Object;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLneosim/util/FileEventObject;oLjava/lang/Object;2(Ljava/lang/Object;Lneosim/util/FileEventObject;)Vt(Ljava/lang/Object;I)Vset(Ljava/lang/String;)V (Lneosim/util/FileEventObject;)V(I)VgetLine()Ljava/lang/String;getCmd()I SourceFileFileEventObject.java /    nullneosim/util/FileEventObjectjava/util/EventObjectneosim/util/Filecmds(Ljava/lang/Object;)V!   Q *+*,     Q *+*,     Q *+*!" #    G *+*'( )  M*+*+-./H **34 5   /*8 !"/*; #$PK =8PK(3!neuroml/util/.#Namespace.java.1.97!package neuroml.util; import neuroml.core.*; import neuroml.*; import neuroml.model.channel.*; import neuroml.model.cell.*; import neuroml.model.network.*; import java.lang.reflect.*; import java.util.Vector; import java.util.Hashtable; import java.util.Enumeration; import java.lang.Integer; import java.net.*; /** * A neuroml namespace. * Used for references / dererefences. *

* * * A separate namespace is used for each xml document. * 

 * "document1"
 *    "Networks"
 *       "nw1"
 *       "nw2"
 * "document2"
 *    "Cells"
 *       "cell1"
 *    "Networks"
 *       "nw1" // distinct from document1.nw1
 *       "nw2"
 * "document3"
 *    "Channels"
 *       "channel1"
 *       "channel2"
 *
* * @author Paul Rogister and Fred Howell * * @version 1.0, 25 July 2001 * @version 1.1, 13 August 2001 -- added "derivedFrom" method * */ public class Namespace { String name; private boolean debug = false; /** The references are stored as a hashtable{type} of hashtables{refname}, * "Network" * "network123" --> Network object * "network456" --> Network object * "network876" --> Network object * "Cell" * "cellpkg.cell2" --> Cell object * "cellpkg.cell6" --> Cell object * "cellpkg.cell9" --> Cell object */ Hashtable references = new Hashtable(); /** The classes available to instantiate * "neuroml.core.Module" * --> "neuroml.core.ProjectionModule" * --> "neuroml.core.PopulationModule" * --> "mycode.MyModule" * "neuroml.model.network.PopulationStructure" * --> "neuroml.model.network.IndexedStructure" * Hashtable{className} of Vector{String} *

* Needs to be updated by the ModuleLoader * And by any applications which add classes which * need to be constructable by the editor. */ Hashtable derivedFrom = new Hashtable(); /** * list of jar file to be used in the classloader classpath */ URL[] jarUrls = new URL[0]; /** Add a parent/child relationship for a class */ public void addClass(String parent, String className) { Vector v = (Vector)( derivedFrom.get(parent) ); if (v==null) { v = new Vector(); derivedFrom.put(parent, v); } if (!v.contains(className)) v.addElement(className); } /** Make a recusrive list of all classes derived from parent */ void addDerivedFrom( Vector ret, String parent ) { Vector v = (Vector) (derivedFrom.get(parent)); if (v!=null) { for (int i=0; i "); if (v!=null) { for (int i=0; ia.b.fred a.b.jim * also rename any sub references. * a.b.fred.jane -> a.b.jim.jane * This is slow! Maybe hashtables aren't the best solution? * Just a tree??? * A treemap??? */ public void rename(String oldkey, String newkey) { if (debug) System.out.println("Namespace: Renaming "+oldkey+" as "+newkey); int okl = oldkey.length(); for (Enumeration t = references.keys(); t.hasMoreElements();) { Hashtable objs = (Hashtable)references.get((String)t.nextElement()); Hashtable movedobjs = new Hashtable(); for (Enumeration o = objs.keys(); o.hasMoreElements();) { String refname = (String)o.nextElement(); if (refname.startsWith(oldkey)) { // We have a replace to do!!! Object theob = objs.remove( refname ); String newstring = newkey+refname.substring(okl); movedobjs.put( newstring, theob ); if (debug) System.out.println("Renaming "+refname+" as "+newstring); } } objs.putAll(movedobjs); } } /** * Add a reference to this object. * (build the key before using this method) */ public void addRef(String key, Object obj) { if (debug) System.out.println(getName()+" adding reference to "+key); if (key==null) return; Class sc = obj.getClass(); boolean doLoop = true; while (doLoop){ if (sc!=null) { Package p = sc.getPackage(); if (p.getName().startsWith("neuroml")) { String className = getShortClassName(sc.getName()); if (references.containsKey(className)){ Hashtable typeReference = (Hashtable)references.get(className); if (typeReference.containsKey(key)) { } else { typeReference.put(key,obj); } } else { Hashtable typeReference = new Hashtable(); typeReference.put(key,obj); references.put(className,typeReference); } sc = sc.getSuperclass(); } else doLoop = false; } else doLoop = false; } } /** * Remove a reference in the hashtable used by deRef * if element without name cannot be added, this has to be checked * by the key building method called before any call to deregisterForRef */ public void removeRef(String key, Object obj) { Class sc = null; sc = obj.getClass(); boolean doLoop = true; //System.out.println("removeRef sc "+sc); while(doLoop){ if (sc!=null) { //System.out.println("removeRef sc "+sc); Package p = sc.getPackage(); //System.out.println("removeRef p "+p); if (p!=null){ //can be null when JarClassLoader is used if (p.getName().startsWith("neuroml")) {// belongs to neuroml package so we carry on String className = getShortClassName(sc.getName()); // use it as a key in the references hashtable if (references.containsKey(className)){ // if the type key exist, try to remove the object from its type hashtable Hashtable typeReference = (Hashtable)references.get(className); // remove typeReference.remove(key); } else { // no such type hashtable, so nothing to remove //System.out.println(" deregisterForRef : no such referenced class : "+className); } sc = sc.getSuperclass(); } else doLoop = false; } else doLoop = false; } else doLoop = false; } } /** * lookupRef : lookup a key in a type hashtable */ private Object lookupRef(String key, Hashtable typeRefs) { Object target = null; if (typeRefs.containsKey(key)){ target = typeRefs.get(key); } else { boolean foundOne = false; for (Enumeration enum = typeRefs.keys() ; enum.hasMoreElements() ;) { String aKey = (String)enum.nextElement(); if (aKey.endsWith(key)){ if (typeRefs.containsKey(aKey)){ target = typeRefs.get(aKey); foundOne = true; } } if (foundOne) break; } } return target; } /** * deRef : return the object targeted by a Ref */ public Object deRef(Ref ref) { Object target = null; String type = ref.getTargetType(); Hashtable typeReference = (Hashtable)references.get(type); if (typeReference==null) { } else { String name = ref.getTargetName(); target = lookupRef(name,typeReference); } return target; } public Hashtable getReferences(){ return references; } } PK 77PK(32neosim/util/loaders/nmllauncher/KernelParams.classI1  ()VCodeLineNumberTableLocalVariableTablethis.Lneosim/util/loaders/nmllauncher/KernelParams; SourceFileKernelParams.java ,neosim/util/loaders/nmllauncher/KernelParamsjava/lang/Object!3*     PK X)NIPK(3neuroml/util/schema/CVS/Root2:pserver:jag@cvs.inf.ed.ac.uk:/disk/cvs/neuroGEMS PKak72PK(32neuroml/util/module/BasicRunnableCellFactory.class1= ] \ \ \  @@ ? 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Save ModelRunningDesign networks or play demo ?  "Exit# $%HelpHelp about Basic ApplicationAboutAbout this programjava/awt/GridBagLayoutjava/awt/GridBagConstraints &javax/swing/JButton ' ( ) * +} ,-javax/swing/JToolBarStop and reset simulation playRun simulationPause simulationstepAdvance single timestep3D Refresh 3DIPGet local IP address .javax/swing/JProgressBar   /0 1t= 2 3settings Settings...javax/swing/JTextArea  4 5 6 70javax/swing/JScrollPane 8 ~ 90 :0$Welcome to NMLPlay v1.00, June 2004. finished. paused at t=; <t=0"Simulation has been reset to t=0.   => ? @0 A BxmlSave NeuroML file CDESaving FGWriten model to H I JK LMSimulation is still running.Oh no!N OP)You have to create or load a model first.Unable to editThere is no data to be saved.Unable to save  Q0@Do you want to save the current model before loading a new one ? RSOpen NeuroML fileOpening NeuroML Player ()Network Designer Tool---------------------University of EdinburghJean-Alain Grunchec, 2004NeuroML/NEOSIM (c) University of Edinburgh, NMLPlay v1.00, June 2004 by Holger Bringmann (hcb@lambdabase.de) Fred Howell (fwh@anc.ad.ac.uk) Jean-Alain Grunchec (jgrunche@informatics.ed.ac.uk)  About NMLPlay OTUnable to build^You must exit the editing mode first in order to display the results in the simulation mode.Unable to launch the simulationUpdating the progress bar U0 VW XY Z [\ ] ^_NSimulation has already been finished. Adjust runtime settings or reset NEOSIM.Simulation finishedRunning simulation to t=...nmlplay/RunSim ` aSimulation is not running. 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JLF GR Ver 1.0 ;PK,z PK(3neosim/util/FileListener.class31    handleFile (Lneosim/util/FileEventObject;)V SourceFileFileListener.javaneosim/util/FileListenerjava/lang/Objectjava/util/EventListenerPK4PK(3neuroml/CVS/EntriesM/.nbintdb/1.1.1.1/Thu Jul 7 14:31:48 2005/-ku/ /NeuromlPkg.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /NeuromlPkg_Unstable.java/1.1.1.1/Thu Jul 7 14:31:48 2005// /overview.html/1.1.1.1/Thu Jul 7 14:31:48 2005// /package.html/1.1.1.1/Thu Jul 7 14:31:48 2005// D/core//// D/data//// D/environment//// D/model//// D/sim//// D/util//// PKh"RMPK(3neosim/iface/CVS/RepositoryNMLPLAY_CVS/src/neosim/iface PK"PK(3guikit/EmptyApp.class 1h         _ _       _ _ ! !  _ _ ` _ _ / _   : : _ @ _  D D H D _  M D Q T ` ` `     envLguikit/Environment; topObjectLjava/lang/Object;nsLneuroml/util/Namespace;filenameLjava/lang/String;menuBarLjavax/swing/JMenuBar;fileMenuLjavax/swing/JMenu;editMenu objBrowserLguikit/BrowseObjectsPanel; modBrowserLguikit/BrowseModulesPanel; aboutPanelLguikit/AboutPanel; resourcesLjava/util/ResourceBundle; imgLoaderLguikit/ImageUtils;addMenuP(Ljavax/swing/JMenuBar;Ljava/lang/String;Ljava/lang/String;I)Ljavax/swing/JMenu;CodeLineNumberTableLocalVariableTablethisLguikit/EmptyApp;parentnamedescmImenuM(Ljavax/swing/JMenu;Ljava/lang/String;Ljava/lang/String;I)Ljavax/swing/JMenu; addMenuItemQ(Ljavax/swing/JMenu;Ljava/lang/String;Ljava/lang/String;I)Ljavax/swing/JMenuItem;miLjavax/swing/JMenuItem; createMenu()V fileChooser()Ljava/lang/String;cwdchooserLjavax/swing/JFileChooser;filterLguikit/ExampleFileFilter; returnVal editObject-(Lneuroml/util/Namespace;Ljava/lang/Object;)VoeopLguikit/EditObjectPanel; importObjectactionPerformed(Ljava/awt/event/ActionEvent;)VeLjava/awt/event/ActionEvent;(Ljava/lang/String;)V frameNamenpLneuroml/NeuromlPkg;tmpLjavax/swing/JPanel;main([Ljava/lang/String;)Vargs[Ljava/lang/String;frameLjavax/swing/JFrame;mre$Ljava/util/MissingResourceException; SourceFile EmptyApp.javajavax/swing/JMenu       javax/swing/JMenuItem! 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Neuroml definitions for networks

This package defines neuroml definitions for describing network models.
Fred Howell
Last modified: Mon Mar 12 18:57:22 GMT 2001 PK;PK(3!neuroml/sim/run/CVS/Entries.Extra</BuildableProjection.java/// /ConnectionMaker.java/// /ConnectionRequest.java/// /ConnectionRequestSender.java/// /ConnectionsQueryable.java/// /DestMethod.java/// /DrawQuery.java/// /MeasurementHandler.java/// /NamedQuery.java/// /NamedQueryable.java/// /PlusMinusPanel.java/// /PostSynapse.java/// /PreSynapse.java/// /Query.java/// /Queryable.java/// /RunnableCell.java/// /RunnableCellFactory.java/// /RunnableControl.java/// /SimRunPkg.java/// /Simulator.java/// /SourceMethod.java/// /SpikeSender.java/// /SynapseWeightSettable.java/// /package.html/// /.nbattrs/// PKF?hA<PK(3neosim/kernel/AddCommand.classz1, ! 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Neuroml Schema Utilities

This package includes basic schema utilities for a schema which is readable using XMLIn/XMLOut.

The schema includes classes for Field, Class and Package corresponding to java class definitions. A NeuromlSchema has a set of packages.

The NeuromlSchema class has a number of methods for generating Java source code and converting a .jar file into a NeuromlSchema representation. This can then be written/read using the standard Neuroml utilities.

See nmlschema test module for example code which uses these classes.

Fred Howell
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