Fix default model conversion parameters
This commit is contained in:
Chris Myers
parent
518bbc1383
commit
88d02ca2d4
3 changed files with 98 additions and 87 deletions
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@ -195,125 +195,125 @@ public class BioModel extends CoreObservable{
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private void loadDefaultParameters() {
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Preferences biosimrc = Preferences.userRoot();
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createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_KREP_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_KACT_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING,
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biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
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biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
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createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
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createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
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createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
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createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
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createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
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createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
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createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
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createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
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createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
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createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
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createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
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createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
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createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
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createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
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createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
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createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
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createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
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createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
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createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
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createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
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createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
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}
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private void loadDefaultParameterMap() {
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Preferences biosimrc = Preferences.userRoot();
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defaultParameters = new HashMap<String,String>();
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defaultParameters.put(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
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defaultParameters.put(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
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defaultParameters.put(GlobalConstants.REVERSE_KREP_STRING, "1");
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defaultParameters.put(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
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defaultParameters.put(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
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defaultParameters.put(GlobalConstants.REVERSE_KACT_STRING, "1");
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defaultParameters.put(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
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defaultParameters.put(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
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defaultParameters.put(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
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defaultParameters.put(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING,
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biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
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biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
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defaultParameters.put(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
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defaultParameters.put(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
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defaultParameters.put(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
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defaultParameters.put(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
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defaultParameters.put(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
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defaultParameters.put(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
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defaultParameters.put(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
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defaultParameters.put(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
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defaultParameters.put(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
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defaultParameters.put(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
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defaultParameters.put(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
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defaultParameters.put(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
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defaultParameters.put(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
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defaultParameters.put(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
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defaultParameters.put(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
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defaultParameters.put(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
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defaultParameters.put(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
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defaultParameters.put(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
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defaultParameters.put(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
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defaultParameters.put(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
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defaultParameters.put(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
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defaultParameters.put(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
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defaultParameters.put(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
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defaultParameters.put(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
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defaultParameters.put(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
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defaultParameters.put(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
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defaultParameters.put(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
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defaultParameters.put(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
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}
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private void createDegradationDefaultParameters() {
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Preferences biosimrc = Preferences.userRoot();
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createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
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createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
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}
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private void createDiffusionDefaultParameters() {
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Preferences biosimrc = Preferences.userRoot();
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createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
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createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
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createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
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createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
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createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
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createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
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}
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private void createComplexDefaultParameters() {
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Preferences biosimrc = Preferences.userRoot();
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createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
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createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
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createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
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}
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private void createConstitutiveDefaultParameters() {
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Preferences biosimrc = Preferences.userRoot();
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createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
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createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
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createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
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createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
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}
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private void createProductionDefaultParameters() {
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Preferences biosimrc = Preferences.userRoot();
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createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_KREP_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_KACT_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
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createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
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createGlobalParameter(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING,
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biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
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biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
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createGlobalParameter(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
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createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
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createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
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createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
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createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
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createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
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createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
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createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
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createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
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createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
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createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
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createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
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createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
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createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
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createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
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}
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public static boolean IsDefaultParameter(String paramId) {
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@ -72,19 +72,25 @@ public class GlobalConstants {
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public static final String TRANSCRIPTION_FACTOR = "transcription factor";
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// public static final String KREP_VALUE = ".5";
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// public static final String KACT_VALUE = ".0033";
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// public static final String KBIO_VALUE = ".05";
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// public static final String PROMOTER_COUNT_VALUE = "2";
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// public static final String KASSOCIATION_VALUE = ".05";
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// public static final String KBASAL_VALUE = ".0001";
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// public static final String OCR_VALUE = ".05";
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// public static final String KDECAY_VALUE = ".0075";
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// public static final String RNAP_VALUE = "30";
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// public static final String RNAP_BINDING_VALUE = ".033";
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// public static final String STOICHIOMETRY_VALUE = "10";
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// public static final String COOPERATIVITY_VALUE = "2";
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// public static final String ACTIVED_VALUE = ".25";
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public static final String KREP_VALUE = ".5";
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public static final String KACT_VALUE = ".0033";
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public static final String KBIO_VALUE = ".05";
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public static final String PROMOTER_COUNT_VALUE = "2";
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public static final String KASSOCIATION_VALUE = ".05";
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public static final String KBASAL_VALUE = ".0001";
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public static final String OCR_VALUE = ".05";
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public static final String KDECAY_VALUE = ".0075";
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public static final String KECDECAY_VALUE = ".005";
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public static final String KCOMPLEX_VALUE = ".05";
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public static final String RNAP_VALUE = "30";
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public static final String RNAP_BINDING_VALUE = ".033";
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public static final String STOICHIOMETRY_VALUE = "10";
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public static final String COOPERATIVITY_VALUE = "2";
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public static final String ACTIVED_VALUE = ".25";
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public static final String ACTIVATED_RNAP_BINDING_VALUE = "1";
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public static final String FORWARD_MEMDIFF_VALUE = "1";
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public static final String REVERSE_MEMDIFF_VALUE = ".01";
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public static final String KECDIFF_VALUE = "1.0";
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public static final String ID = "ID";
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public static final String COMPONENT = "Component";
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@ -290,22 +296,27 @@ public class GlobalConstants {
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public static final String KISAO_GILLESPIE = "KISAO:0000241";
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public static final String KISAO_GILLESPIE_DIRECT = "KISAO:0000029";
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public static final String KISAO_SSA_CR = "KISAO:0000329";
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public static final String KISAO_BUNKER = "KISAO:0000618";
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public static final String KISAO_EMC = "KISAO:0000619";
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public static final String KISAO_EULER = "KISAO:0000030";
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public static final String KISAO_GEAR = "KISAO:0000288";
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public static final String KISAO_RUNGE_KUTTA_FEHLBERG = "KISAO:0000086";
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public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000087";
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public static final String KISAO_RUNGE_KUTTA_IMPLICIT = "KISAO:0000612";
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public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000609";
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public static final String KISAO_LSODA = "KISAO:0000088";
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public static final String KISAO_FBA = "KISAO:0000437";
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public static final String KISAO_MINIMUM_STEP_SIZE = "KISAO:0000485";
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public static final String KISAO_MAXIMUM_STEP_SIZE = "KISAO:0000467";
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public static final String KISAO_ABSOLUTE_TOLERANCE = "KISAO:0000211";
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public static final String KISAO_RELATIVE_TOLERANCE = "KISAO:0000209";
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public static final String KISAO_ORDER = "KISAO:0000594";
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public static final String KISAO_SEED = "KISAO:0000488";
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||||
public static final String KISAO_SAMPLES = "KISAO:0000326";
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||||
public static final String KISAO_NUMBER_OF_RUNS = "KISAO:0000498";
|
||||
public static final String KISAO_DFBA = "KISAO_0000499";
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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";
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue