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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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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);
}
}
}