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Merge branch 'master' into sbml-to-prism

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cjmyers 2023-03-28 08:57:59 -06:00 • committed by GitHub
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11 changed files with 128 additions and 230 deletions
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65
analysis/log4j2.xml
View file

@ -1,65 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<Configuration status="WARN" name="XMLConfigTest" packages="org.sbml.*">
<Properties>
<Property name="filename">jsbml.log</Property>
</Properties>
<ThresholdFilter level="trace"/>
<Appenders>
<Console name="console">
<PatternLayout pattern="%5p (%F:%L) - %m%n"/>
</Console>
<File name="file" fileName="${filename}">
<PatternLayout>
<pattern>%d %p %C{1.} [%t] %m%n</pattern>
</PatternLayout>
</File>
</Appenders>
<Loggers>
<Logger name="org.sbml" level="info" additivity="false">
<AppenderRef ref="console"/>
<AppenderRef ref="file"/>
</Logger>
<!--
<Logger name="org.sbml.jsbml.xml.stax.SBMLWriter" level="debug" additivity="false">
<AppenderRef ref="console"/>
<AppenderRef ref="file"/>
</Logger>
<Logger name="org.sbml.jsbml.xml.stax.SBMLReader" level="debug" additivity="false">
<AppenderRef ref="console"/>
<AppenderRef ref="file"/>
</Logger>
-->
<!--
# org.sbml.jsbml.test.SimpleSBaseChangeListener - DEBUG : it will display all add, remove or change event (lot of output when reading an SBML file)
# org.sbml.jsbml.xml.parsers.SBMLCoreParser - ERROR to DEBUG : anything related to problems when parsing the SBML core elements.
# org.sbml.jsbml.xml.parsers.StringParser - ERROR to DEBUG : (lot of output) display all the event when reading XHTML
# org.sbml.jsbml.xml.parsers.AnnotationParser - DEBUG : output when reading non RDF annotations.
# org.sbml.jsbml.xml.parsers.XMLNodeWriter - DEBUG : output events when writing XMLNode, so HTML block
# org.sbml.jsbml.xml.stax.SBMLReader - ERROR to DEBUG : (lot of output) display all the event when reading an SBML file
# org.sbml.jsbml.xml.stax.SBMLWriter - ERROR to DEBUG : (lot of output) display all the event when writing an SBML file
# org.sbml.jsbml.util.StringTools - WARN : warning when there is a problem with the conversion of a String into a number or boolean.
# org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler - WARN to DEBUG : (lot of output) display all the event when writing mathML
# org.sbml.jsbml.xml.parsers.MathMLStaxParser - ERROR to DEBUG : (lot of output) display all the event when reading a MathML block
# org.sbml.jsbml.SBMLDocument - ERROR to DEBUG : will display problems related to the checkConsistency call
# org.sbml.jsbml.validator.SBMLValidator - DEBUG : will print the xml result file from http://sbml.org/validator/ with few others checks when the parsing is done
# org.sbml.jsbml.util.SubModel - DEBUG : will print the details of the submodel building
# org.sbml.jsbml.ASTNode - ERROR to DEBUG
# org.sbml.jsbml.xml.parsers.AbstractReaderWriter - DEBUG : events when reading or writing L3 packages block (if the parser extends this abstract class)
# org.sbml.jsbml.xml.parsers.QualParser - DEBUG : events when reading/writing the qual package/extension.
# org.sbml.jsbml.ext.comp.CompModelPlugin - DEBUG: register and unregister debug output for the comp package id namespace
# org.sbml.jsbml.ext.comp.ArraysSBasePlugin - DEBUG: register and unregister debug output for the arrays package id namespace
# org.sbml.jsbml.Model - DEBUG: register and unregister debug output for the core package id namespace
# org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser - DEBUG: debug output when reading and writing RDF annotations
-->
<Root level="info">
<AppenderRef ref="file"/>
</Root>
</Loggers>
</Configuration>

1
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Analysis.java
View file

@ -412,6 +412,7 @@ public class Analysis implements BioObserver
if (modelSource.indexOf("/")!=-1) {
modelSource = modelSource.substring(modelSource.lastIndexOf("/")+1);
}
System.out.println("Reading: " + root + File.separator + modelSource);
SBMLDocument sbmlDoc = SBMLReader.read(new File(root + File.separator + modelSource));
if (model.getListOfChanges().size() != 0) {
try {

6
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java
View file

@ -77,7 +77,6 @@ public class Converter {
+ "and can convert to/from SBOL 1.1, to/from SBML, GenBank, and FASTA formats.");
System.err.println();
System.err.println("Usage:");
//TODO PEDRO shouldnt this be conersion 3.0.0-SNAPSHOT?
System.err.println("\tjava -jar iBioSim-conversion-0.0.1-SNAPSHOT-jar-with-dependencies.jar [options] inputFile ");
System.err.println();
System.err.println("Convert SBOL to SBML Example:");
@ -554,6 +553,7 @@ public class Converter {
SBOLDocument sbolDoc = SBOLUtility.loadSBOLFile(fullInputFileName, URIPrefix);
String circuit_name = file.getName();
circuit_name = circuit_name.replace(".xml", "");
circuit_name = circuit_name.replace(".sbol", "");
String vpr_output = circuit_name + "_topModule";
if(!topLevelURIStr.isEmpty())
@ -610,9 +610,8 @@ public class Converter {
SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
}
}
if (topModelId != null) {
SBMLDocument topModel = SBMLutilities.readSBML(vpr_output+".xml", null, null);
SBMLDocument topModel = SBMLutilities.readSBML(outputDir + File.separator + vpr_output+ ".xml", null, null);
topModel.getModel().setId(topModelId);
SBMLWriter writer = new SBMLWriter();
try {
@ -629,7 +628,6 @@ public class Converter {
e.printStackTrace();
}
}
if (doVPR) {
if (topEnvir) {
SBMLDocument topEnvironment = SBMLutilities.readSBML(environment, null, null);

2
dataModels/pom.xml
View file

@ -71,7 +71,7 @@
<dependency>
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml</artifactId>
<version>1.6-SNAPSHOT</version>
<version>1.7-SNAPSHOT</version>
</dependency>
<dependency>

108
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -195,125 +195,125 @@ public class BioModel extends CoreObservable{
private void loadDefaultParameters() {
Preferences biosimrc = Preferences.userRoot();
createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_KREP_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_KACT_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING,
biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
}
private void loadDefaultParameterMap() {
Preferences biosimrc = Preferences.userRoot();
defaultParameters = new HashMap<String,String>();
defaultParameters.put(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
defaultParameters.put(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
defaultParameters.put(GlobalConstants.REVERSE_KREP_STRING, "1");
defaultParameters.put(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
defaultParameters.put(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
defaultParameters.put(GlobalConstants.REVERSE_KACT_STRING, "1");
defaultParameters.put(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
defaultParameters.put(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
defaultParameters.put(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
defaultParameters.put(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING,
biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
defaultParameters.put(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
defaultParameters.put(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
defaultParameters.put(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
defaultParameters.put(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
defaultParameters.put(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
defaultParameters.put(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
defaultParameters.put(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
defaultParameters.put(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
defaultParameters.put(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
defaultParameters.put(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
defaultParameters.put(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
defaultParameters.put(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
defaultParameters.put(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
defaultParameters.put(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
defaultParameters.put(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
defaultParameters.put(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
defaultParameters.put(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
defaultParameters.put(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
defaultParameters.put(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
defaultParameters.put(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
defaultParameters.put(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
defaultParameters.put(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
defaultParameters.put(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
defaultParameters.put(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
defaultParameters.put(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
defaultParameters.put(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
defaultParameters.put(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
defaultParameters.put(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
}
private void createDegradationDefaultParameters() {
Preferences biosimrc = Preferences.userRoot();
createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
}
private void createDiffusionDefaultParameters() {
Preferences biosimrc = Preferences.userRoot();
createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
}
private void createComplexDefaultParameters() {
Preferences biosimrc = Preferences.userRoot();
createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
}
private void createConstitutiveDefaultParameters() {
Preferences biosimrc = Preferences.userRoot();
createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
}
private void createProductionDefaultParameters() {
Preferences biosimrc = Preferences.userRoot();
createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_KREP_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_KACT_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
createGlobalParameter(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING,
biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
createGlobalParameter(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
}
public static boolean IsDefaultParameter(String paramId) {

1
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java
View file

@ -461,6 +461,7 @@ public class SBMLutilities extends CoreObservable
}
public static void copyDimensionsToEdgeIndex(SBase source,SBase target,SBase edge,String attribute) {
if (source==null || target==null) return;
if (SBMLutilities.dimensionsMatch(source,target)) {
ArraysSBasePlugin sBasePlugin = SBMLutilities.getArraysSBasePlugin(source);
ArraysSBasePlugin sBasePluginEdge = SBMLutilities.getArraysSBasePlugin(edge);

43
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/GlobalConstants.java
View file

@ -72,19 +72,25 @@ public class GlobalConstants {
public static final String TRANSCRIPTION_FACTOR = "transcription factor";
// public static final String KREP_VALUE = ".5";
// public static final String KACT_VALUE = ".0033";
// public static final String KBIO_VALUE = ".05";
// public static final String PROMOTER_COUNT_VALUE = "2";
// public static final String KASSOCIATION_VALUE = ".05";
// public static final String KBASAL_VALUE = ".0001";
// public static final String OCR_VALUE = ".05";
// public static final String KDECAY_VALUE = ".0075";
// public static final String RNAP_VALUE = "30";
// public static final String RNAP_BINDING_VALUE = ".033";
// public static final String STOICHIOMETRY_VALUE = "10";
// public static final String COOPERATIVITY_VALUE = "2";
// public static final String ACTIVED_VALUE = ".25";
public static final String KREP_VALUE = ".5";
public static final String KACT_VALUE = ".0033";
public static final String KBIO_VALUE = ".05";
public static final String PROMOTER_COUNT_VALUE = "2";
public static final String KASSOCIATION_VALUE = ".05";
public static final String KBASAL_VALUE = ".0001";
public static final String OCR_VALUE = ".05";
public static final String KDECAY_VALUE = ".0075";
public static final String KECDECAY_VALUE = ".005";
public static final String KCOMPLEX_VALUE = ".05";
public static final String RNAP_VALUE = "30";
public static final String RNAP_BINDING_VALUE = ".033";
public static final String STOICHIOMETRY_VALUE = "10";
public static final String COOPERATIVITY_VALUE = "2";
public static final String ACTIVED_VALUE = ".25";
public static final String ACTIVATED_RNAP_BINDING_VALUE = "1";
public static final String FORWARD_MEMDIFF_VALUE = "1";
public static final String REVERSE_MEMDIFF_VALUE = ".01";
public static final String KECDIFF_VALUE = "1.0";
public static final String ID = "ID";
public static final String COMPONENT = "Component";
@ -290,22 +296,27 @@ public class GlobalConstants {
public static final String KISAO_GILLESPIE = "KISAO:0000241";
public static final String KISAO_GILLESPIE_DIRECT = "KISAO:0000029";
public static final String KISAO_SSA_CR = "KISAO:0000329";
public static final String KISAO_BUNKER = "KISAO:0000618";
public static final String KISAO_EMC = "KISAO:0000619";
public static final String KISAO_EULER = "KISAO:0000030";
public static final String KISAO_GEAR = "KISAO:0000288";
public static final String KISAO_RUNGE_KUTTA_FEHLBERG = "KISAO:0000086";
public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000087";
public static final String KISAO_RUNGE_KUTTA_IMPLICIT = "KISAO:0000612";
public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000609";
public static final String KISAO_LSODA = "KISAO:0000088";
public static final String KISAO_FBA = "KISAO:0000437";
public static final String KISAO_MINIMUM_STEP_SIZE = "KISAO:0000485";
public static final String KISAO_MAXIMUM_STEP_SIZE = "KISAO:0000467";
public static final String KISAO_ABSOLUTE_TOLERANCE = "KISAO:0000211";
public static final String KISAO_RELATIVE_TOLERANCE = "KISAO:0000209";
public static final String KISAO_ORDER = "KISAO:0000594";
public static final String KISAO_SEED = "KISAO:0000488";
public static final String KISAO_SAMPLES = "KISAO:0000326";
public static final String KISAO_NUMBER_OF_RUNS = "KISAO:0000498";
public static final String KISAO_DFBA = "KISAO_0000499";
public static final String KISAO_DFBA_SOA = "KISAO:0000500";
public static final String KISAO_DFBA_DOA = "KISAO:0000501 ";
public static final String KISAO_DFBA_DA = "KISAO:0000501 ";
public static final String KISAO_DFBA_DOA = "KISAO:0000501";
public static final String KISAO_DFBA_DA = "KISAO:0000501";
public static final String TRUE = "true";
public static final String FALSE = "false";

34
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/IBioSimPreferences.java
View file

@ -282,55 +282,55 @@ public enum IBioSimPreferences {
modelPreferences.put(modelPreference, Preferences.userRoot().get(modelPreference, ""));
if (modelPreferences.get(modelPreference).equals("")) {
if (modelPreference.equals("biosim.gcm.KREP_VALUE")) {
modelPreferences.put("biosim.gcm.KREP_VALUE", ".5");
modelPreferences.put("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE);
}
if (modelPreference.equals("biosim.gcm.KACT_VALUE")) {
modelPreferences.put("biosim.gcm.KACT_VALUE", ".0033");
modelPreferences.put("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE);
}
if (modelPreference.equals("biosim.gcm.PROMOTER_COUNT_VALUE")) {
modelPreferences.put("biosim.gcm.PROMOTER_COUNT_VALUE", "2");
modelPreferences.put("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE);
}
if (modelPreference.equals("biosim.gcm.KBASAL_VALUE")) {
modelPreferences.put("biosim.gcm.KBASAL_VALUE", ".0001");
modelPreferences.put("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE);
}
if (modelPreference.equals("biosim.gcm.OCR_VALUE")) {
modelPreferences.put("biosim.gcm.OCR_VALUE", ".05");
modelPreferences.put("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE);
}
if (modelPreference.equals("biosim.gcm.KDECAY_VALUE")) {
modelPreferences.put("biosim.gcm.KDECAY_VALUE", ".0075");
modelPreferences.put("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE);
}
if (modelPreference.equals("biosim.gcm.KECDECAY_VALUE")) {
modelPreferences.put("biosim.gcm.KECDECAY_VALUE", ".005");
modelPreferences.put("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE);
}
if (modelPreference.equals("biosim.gcm.RNAP_VALUE")) {
modelPreferences.put("biosim.gcm.RNAP_VALUE", "30");
modelPreferences.put("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE);
}
if (modelPreference.equals("biosim.gcm.RNAP_BINDING_VALUE")) {
modelPreferences.put("biosim.gcm.RNAP_BINDING_VALUE", ".033");
modelPreferences.put("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE);
}
if (modelPreference.equals("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE")) {
modelPreferences.put("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", "1");
modelPreferences.put("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE);
}
if (modelPreference.equals("biosim.gcm.STOICHIOMETRY_VALUE")) {
modelPreferences.put("biosim.gcm.STOICHIOMETRY_VALUE", "10");
modelPreferences.put("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE);
}
if (modelPreference.equals("biosim.gcm.KCOMPLEX_VALUE")) {
modelPreferences.put("biosim.gcm.KCOMPLEX_VALUE", "0.05");
modelPreferences.put("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE);
}
if (modelPreference.equals("biosim.gcm.COOPERATIVITY_VALUE")) {
modelPreferences.put("biosim.gcm.COOPERATIVITY_VALUE", "2");
modelPreferences.put("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE);
}
if (modelPreference.equals("biosim.gcm.ACTIVED_VALUE")) {
modelPreferences.put("biosim.gcm.ACTIVED_VALUE", ".25");
modelPreferences.put("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE);
}
if (modelPreference.equals("biosim.gcm.FORWARD_MEMDIFF_VALUE")) {
modelPreferences.put("biosim.gcm.FORWARD_MEMDIFF_VALUE", "1.0");
modelPreferences.put("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE);
}
if (modelPreference.equals("biosim.gcm.REVERSE_MEMDIFF_VALUE")) {
modelPreferences.put("biosim.gcm.REVERSE_MEMDIFF_VALUE", "0.01");
modelPreferences.put("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE);
}
if (modelPreference.equals("biosim.gcm.KECDIFF_VALUE")) {
modelPreferences.put("biosim.gcm.KECDIFF_VALUE", "1.0");
modelPreferences.put("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE);
}
}
}

13
gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/movie/MovieContainer.java
View file

@ -819,9 +819,18 @@ public class MovieContainer extends PanelObservable implements ActionListener {
public void savePreferences() {
Gson gson = new Gson();
String out = gson.toJson(this.movieScheme.getAllSpeciesSchemes());
String out;
String fullPath;
String fullPath = getPreferencesFullPath();
try {
out = gson.toJson(this.movieScheme.getAllSpeciesSchemes());
fullPath = getPreferencesFullPath();
}
catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(Gui.frame, "An error occured preparing to save movie preferences " + "\nmessage: " + e.getMessage());
return;
}
FileOutputStream fHandle;

20
gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/schematic/BioGraph.java
View file

@ -209,10 +209,14 @@ public class BioGraph extends mxGraph {
// SBMLutilities.copyIndices(getGlyph(layout,GlobalConstants.GLYPH+"__"+product), speciesReferenceGlyph, "layout:speciesGlyph");
// SBMLutilities.copyIndices(reactionGlyph, speciesReferenceGlyph, "layout:id");
LineSegment lineSegment = speciesReferenceGlyph.createCurve().createLineSegment();
lineSegment.setStart(new Point(this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterX(),
this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterY()));
lineSegment.setEnd(new Point(this.getSpeciesOrPromoterCell(product).getGeometry().getCenterX(),
this.getSpeciesOrPromoterCell(product).getGeometry().getCenterY()));
if (this.getSpeciesOrPromoterCell(reactant)!=null) {
lineSegment.setStart(new Point(this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterX(),
this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterY()));
}
if (this.getSpeciesOrPromoterCell(product)!=null) {
lineSegment.setEnd(new Point(this.getSpeciesOrPromoterCell(product).getGeometry().getCenterX(),
this.getSpeciesOrPromoterCell(product).getGeometry().getCenterY()));
}
}
private static void addSpeciesReferenceGlyph(Layout layout,mxCell cell,ReactionGlyph reactionGlyph,String reactionId,String speciesId, String role) {
@ -223,8 +227,12 @@ public class BioGraph extends mxGraph {
// SBMLutilities.copyIndices(getGlyph(layout,GlobalConstants.GLYPH+"__"+speciesId), speciesReferenceGlyph, "layout:speciesGlyph");
// SBMLutilities.copyIndices(reactionGlyph, speciesReferenceGlyph, "layout:id");
LineSegment lineSegment = speciesReferenceGlyph.createCurve().createLineSegment();
lineSegment.setStart(new Point(cell.getSource().getGeometry().getCenterX(),cell.getSource().getGeometry().getCenterY()));
lineSegment.setEnd(new Point(cell.getTarget().getGeometry().getCenterX(),cell.getTarget().getGeometry().getCenterY()));
if (cell.getSource()!=null) {
lineSegment.setStart(new Point(cell.getSource().getGeometry().getCenterX(),cell.getSource().getGeometry().getCenterY()));
}
if (cell.getTarget()!=null) {
lineSegment.setEnd(new Point(cell.getTarget().getGeometry().getCenterX(),cell.getTarget().getGeometry().getCenterY()));
}
}
}

65
log4j2.xml
View file

@ -1,65 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<Configuration status="WARN" name="XMLConfigTest" packages="org.sbml.*">
<Properties>
<Property name="filename">jsbml.log</Property>
</Properties>
<ThresholdFilter level="trace"/>
<Appenders>
<Console name="console">
<PatternLayout pattern="%5p (%F:%L) - %m%n"/>
</Console>
<File name="file" fileName="${filename}">
<PatternLayout>
<pattern>%d %p %C{1.} [%t] %m%n</pattern>
</PatternLayout>
</File>
</Appenders>
<Loggers>
<Logger name="org.sbml" level="info" additivity="false">
<AppenderRef ref="console"/>
<AppenderRef ref="file"/>
</Logger>
<!--
<Logger name="org.sbml.jsbml.xml.stax.SBMLWriter" level="debug" additivity="false">
<AppenderRef ref="console"/>
<AppenderRef ref="file"/>
</Logger>
<Logger name="org.sbml.jsbml.xml.stax.SBMLReader" level="debug" additivity="false">
<AppenderRef ref="console"/>
<AppenderRef ref="file"/>
</Logger>
-->
<!--
# org.sbml.jsbml.test.SimpleSBaseChangeListener - DEBUG : it will display all add, remove or change event (lot of output when reading an SBML file)
# org.sbml.jsbml.xml.parsers.SBMLCoreParser - ERROR to DEBUG : anything related to problems when parsing the SBML core elements.
# org.sbml.jsbml.xml.parsers.StringParser - ERROR to DEBUG : (lot of output) display all the event when reading XHTML
# org.sbml.jsbml.xml.parsers.AnnotationParser - DEBUG : output when reading non RDF annotations.
# org.sbml.jsbml.xml.parsers.XMLNodeWriter - DEBUG : output events when writing XMLNode, so HTML block
# org.sbml.jsbml.xml.stax.SBMLReader - ERROR to DEBUG : (lot of output) display all the event when reading an SBML file
# org.sbml.jsbml.xml.stax.SBMLWriter - ERROR to DEBUG : (lot of output) display all the event when writing an SBML file
# org.sbml.jsbml.util.StringTools - WARN : warning when there is a problem with the conversion of a String into a number or boolean.
# org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler - WARN to DEBUG : (lot of output) display all the event when writing mathML
# org.sbml.jsbml.xml.parsers.MathMLStaxParser - ERROR to DEBUG : (lot of output) display all the event when reading a MathML block
# org.sbml.jsbml.SBMLDocument - ERROR to DEBUG : will display problems related to the checkConsistency call
# org.sbml.jsbml.validator.SBMLValidator - DEBUG : will print the xml result file from http://sbml.org/validator/ with few others checks when the parsing is done
# org.sbml.jsbml.util.SubModel - DEBUG : will print the details of the submodel building
# org.sbml.jsbml.ASTNode - ERROR to DEBUG
# org.sbml.jsbml.xml.parsers.AbstractReaderWriter - DEBUG : events when reading or writing L3 packages block (if the parser extends this abstract class)
# org.sbml.jsbml.xml.parsers.QualParser - DEBUG : events when reading/writing the qual package/extension.
# org.sbml.jsbml.ext.comp.CompModelPlugin - DEBUG: register and unregister debug output for the comp package id namespace
# org.sbml.jsbml.ext.comp.ArraysSBasePlugin - DEBUG: register and unregister debug output for the arrays package id namespace
# org.sbml.jsbml.Model - DEBUG: register and unregister debug output for the core package id namespace
# org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser - DEBUG: debug output when reading and writing RDF annotations
-->
<Root level="info">
<AppenderRef ref="file"/>
</Root>
</Loggers>
</Configuration>