Changeset 2400

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Timestamp:
08/12/08 14:01:33 (3 months ago)
Author:
kelleyt
Message:

Corrected the Name of the algorithm.

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  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/OSGI-INF/algorithm.properties

    r2377 r2400  
    44in_data=prefuse.data.Table 
    55out_data=prefuse.data.Graph,file:text/nwb 
    6 service.pid=edu.iu.nwb.modeling.discretenetworkdynamics.DVDAlgorithm 
     6service.pid=edu.iu.nwb.modeling.discretenetworkdynamics.DNDAlgorithm 
    77remotable=true 
    88authors=Reinhard Laubenbacher, Abdul Jarrah, Hussein Vastani, Brandily Stigler, Timothy Kelley 

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/OSGI-INF/component.xml

    r2153 r2400  
    11<?xml version="1.0" encoding="UTF-8"?> 
    2 <component name="edu.iu.nwb.modeling.discretenetworkdynamics.DVDAlgorithm.component" immediate="false"> 
    3         <implementation class="edu.iu.nwb.modeling.discretenetworkdynamics.DVDAlgorithmFactory"/> 
     2<component name="edu.iu.nwb.modeling.discretenetworkdynamics.DNDAlgorithm.component" immediate="false"> 
     3        <implementation class="edu.iu.nwb.modeling.discretenetworkdynamics.DNDAlgorithmFactory"/> 
    44        <properties entry="OSGI-INF/algorithm.properties"/> 
    55        <reference name="LOG" interface="org.osgi.service.log.LogService"/> 

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/OSGI-INF/metatype/METADATA.XML

    r2377 r2400  
    22<metatype:MetaData xmlns:metatype="http://www.osgi.org/xmlns/metatype/v1.0.0"> 
    33        <OCD name="Discrete Network Dynamics (DND)" 
    4                 id="edu.iu.nwb.modeling.discretenetworkdynamics.DVDAlgorithm.network.OCD" 
     4                id="edu.iu.nwb.modeling.discretenetworkdynamics.DNDAlgorithm.network.OCD" 
    55                description="A tool for enumerating the state space of discrete network models."> 
    66                <AD default="function" 
    …… 
    4747 
    4848        </OCD> 
    49         <Designate pid="edu.iu.nwb.modeling.discretenetworkdynamics.DVDAlgorithm"> 
    50                 <Object ocdref="edu.iu.nwb.modeling.discretenetworkdynamics.DVDAlgorithm.network.OCD" /> 
     49        <Designate pid="edu.iu.nwb.modeling.discretenetworkdynamics.DNDAlgorithm"> 
     50                <Object ocdref="edu.iu.nwb.modeling.discretenetworkdynamics.DNDAlgorithm.network.OCD" /> 
    5151        </Designate> 
    5252</metatype:MetaData> 

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/src/edu/iu/nwb/modeling/discretenetworkdynamics/DNDAlgorithm.java

    • Property svn:mergeinfo set
    r2165 r2400  
    2929 
    3030 
    31 public class DVDAlgorithm implements Algorithm, ProgressTrackable { 
     31public class DNDAlgorithm implements Algorithm, ProgressTrackable { 
    3232        Data[] data; 
    3333        Dictionary parameters; 
    …… 
    4545        } 
    4646 
    47         public DVDAlgorithm(Data[] data, Dictionary parameters, CIShellContext context) { 
     47        public DNDAlgorithm(Data[] data, Dictionary parameters, CIShellContext context) { 
    4848                this.data = data; 
    4949                this.parameters = parameters; 
    …… 
    9898                         
    9999                         
    100                         if(!DVDAlgorithm.verifyInitialConditions(initCondition, dependencyGraph.getNodeCount(), numberOfStates)){ 
     100                        if(!DNDAlgorithm.verifyInitialConditions(initCondition, dependencyGraph.getNodeCount(), numberOfStates)){ 
    101101                                this.logger.log(LogService.LOG_WARNING, "The provided initial condition is invalid. Please provide a series of numbers or *'s separated" + 
    102102                                                " by spaces. There should be as many numbers or *'s as functions in your function file. Each number provided must be at least 0 and no greater" + 
    …… 
    106106                        } 
    107107                         
    108                         if(!DVDAlgorithm.verifyUpdateSchedule(schedule, dependencyGraph.getNodeCount())){ 
     108                        if(!DNDAlgorithm.verifyUpdateSchedule(schedule, dependencyGraph.getNodeCount())){ 
    109109                                this.logger.log(LogService.LOG_WARNING, "The provided update schedule is invalid. Please provide a series of unique numbers, separated by spaces, " + 
    110110                                                "corresponding to the function rows in your file.\n"); 
    …… 
    120120                                        final Data outputData3 = constructData(this.data[0],generateStateSpaceFile(stateSpace,cssg),"file:text/nwb",DataProperty.NETWORK_TYPE, "Generated State Space Graph"); 
    121121                                        monitor.done(); 
     122                                        System.gc(); 
    122123                                        return new Data[] {outputData1, outputData2, outputData3}; 
    123124                                 

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/src/edu/iu/nwb/modeling/discretenetworkdynamics/DNDAlgorithmFactory.java

    • Property svn:mergeinfo set
    r2165 r2400  
    2121 
    2222 
    23 public class DVDAlgorithmFactory implements AlgorithmFactory,ParameterMutator { 
     23public class DNDAlgorithmFactory implements AlgorithmFactory,ParameterMutator { 
    2424 
    2525        private MetaTypeInformation originalProvider; 
    …… 
    7575 
    7676    public Algorithm createAlgorithm(Data[] data, Dictionary parameters, CIShellContext context) { 
    77         return new DVDAlgorithm(data, parameters, context); 
     77        return new DNDAlgorithm(data, parameters, context); 
    7878    } 
    7979     

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/src/edu/iu/nwb/modeling/discretenetworkdynamics/components/CreateStateSpaceGraph.java

    r2222 r2400  
    3434                BigInteger start; 
    3535                BigInteger end; 
    36                 final int numProcessors = Math.min(totalSpace.intValue(),Math.max(Runtime.getRuntime().availableProcessors(),10)); 
     36                final int numProcessors = Math.min(totalSpace.intValue(),Runtime.getRuntime().availableProcessors()); 
    3737                Thread[] pool = new Thread[numProcessors]; 
    3838 
    …… 
    5555                        pool[i].join(); 
    5656                } 
    57 /* 
     57 
     58                /* 
    5859                NodeCleaningThread nct = new NodeCleaningThread(stateSpaceGraph); 
    5960                EdgeCleaningThread ect = new EdgeCleaningThread(stateSpaceGraph); 
    …… 
    6162                ect.run(); 
    6263                nct.join(); 
    63                 ect.join();*/ 
     64                ect.join(); 
     65                */ 
    6466                 
    6567                return stateSpaceGraph;  

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/src/edu/iu/nwb/modeling/discretenetworkdynamics/components/GraphFillerThread.java

    r2165 r2400  
    2929                this.updateScheme = updateSchedule; 
    3030                this.initialCondition = ic; 
     31                 
    3132        } 
    3233 

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/src/edu/iu/nwb/modeling/discretenetworkdynamics/components/ParseDependencyGraphs.java

    r2165 r2400  
    137137        private static String parseFunctionString(String func)throws FunctionFormatException{ 
    138138                String s = func; 
    139  
     139         
    140140                s = s.replaceAll("\\s",""); 
    141                 s = s.replace("^f\\d*=", ""); 
     141                //s = s.replace("^f\\d*=", ""); 
    142142                String[] functionArray = s.split("="); 
    143  
     143                 
    144144                if(functionArray.length != 2){ 
    145145                        throw new FunctionFormatException("Your expression must begin with \"f\" followed by a row number followed by \"=\". " + 

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/src/edu/iu/nwb/modeling/discretenetworkdynamics/functions/NegationFunction.java

    r2165 r2400  
    3434                         
    3535                                value = value.negate(); 
     36                                value = value.add(numberOfStates); 
    3637                                value = value.mod(numberOfStates); 
    3738                                 

  • trunk/plugins/modeling/edu.iu.nwb.modeling.discretenetworkdynamics/src/edu/iu/nwb/modeling/discretenetworkdynamics/parser/FunctionContainer.java

    r2179 r2400  
    3131                                if(!isSequential){ 
    3232                                        value = new Integer(stateSpace[index]); 
     33                                         
    3334                                }else{ 
    3435                                        value = new Integer(nextState[index]); 
    …… 
    6263                int returnValue = ((BigInteger)executionStack.pop()).intValue(); 
    6364         
    64                  
    65                  
    6665                return returnValue; 
    6766        }