Examples with ReactionDescription cbit.vcell.model.ReactionDescription used on opensource projects

Example 1 with ReactionDescription

use of cbit.vcell.model.ReactionDescription in project vcell by virtualcell.

the class ReactionCartoonTool method pasteReactionsAndSpecies.

private void pasteReactionsAndSpecies(Component requester, Structure pasteToStructure) {
    final String RXSPECIES_PASTERX = "Reactions";
    final String RXSPECIES_SPECIES = "Species";
    ReactionSpeciesCopy reactionSpeciesCopy = (ReactionSpeciesCopy) SimpleTransferable.getFromClipboard(VCellTransferable.REACTION_SPECIES_ARRAY_FLAVOR);
    if (reactionSpeciesCopy != null) {
        // TODO: here we may want to warn the user about compartment number / type / name mismatch
        // between the source and the destination
        String response = null;
        if ((reactionSpeciesCopy.getReactStepArr() != null || reactionSpeciesCopy.getReactionRuleArr() != null) && reactionSpeciesCopy.getSpeciesContextArr() != null) {
            String msg = "There are ";
            msg += reactionSpeciesCopy.getSpeciesContextArr().length + " Species and ";
            int rlen = 0;
            if (reactionSpeciesCopy.getReactStepArr() != null)
                rlen += reactionSpeciesCopy.getReactStepArr().length;
            if (reactionSpeciesCopy.getReactionRuleArr() != null)
                rlen += reactionSpeciesCopy.getReactionRuleArr().length;
            msg += rlen + " Reactions / Rules on the clipboard, choose which set to paste.";
            response = DialogUtils.showWarningDialog(getGraphPane(), "Choose Species or Reactions to paste", msg, new String[] { RXSPECIES_SPECIES, RXSPECIES_PASTERX, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
            if (response == null || response.equals(RXSPECIES_CANCEL)) {
                return;
            }
        }
        if (reactionSpeciesCopy.getSpeciesContextArr() != null && (response == null || response.equals(RXSPECIES_SPECIES))) {
            IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
            Vector<BioModelEntityObject> pastedSpeciesContextV = new Vector<BioModelEntityObject>();
            for (int i = 0; i < reactionSpeciesCopy.getSpeciesContextArr().length; i++) {
                String rootSC = speciesContextRootFinder(reactionSpeciesCopy.getSpeciesContextArr()[i]);
                pastedSpeciesContextV.add(pasteSpecies(getGraphPane(), reactionSpeciesCopy.getSpeciesContextArr()[i].getSpecies(), rootSC, getModel(), pasteToStructure, true, speciesHash, null));
                copyRelativePosition(getGraphModel(), reactionSpeciesCopy.getSpeciesContextArr()[i], pastedSpeciesContextV.lastElement());
            }
            ReactionCartoonTool.selectAndSaveDiagram(ReactionCartoonTool.this, pastedSpeciesContextV);
        }
        if (reactionSpeciesCopy.getReactStepArr() != null && reactionSpeciesCopy.getReactionRuleArr() == null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            BioModel bioModel = null;
            try {
                bioModel = findBioModel(requester);
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
                DialogUtils.showErrorDialog(requester, e.getMessage());
                return;
            }
            ReactionDescription reactionDescription = DBReactionWizardPanel.createReactionDescription(reactionSpeciesCopy.getReactStepArr()[0], null, reactionSpeciesCopy.getFromStructure().getKey());
            RXParticipantResolverPanel rxParticipantResolverPanel = new RXParticipantResolverPanel();
            // rxParticipantResolverPanel.setPasteToModel(getModel());
            rxParticipantResolverPanel.setupRX(reactionDescription, getModel(), pasteToStructure);
            // JDialog j = new JDialog();
            // j.setModal(true);
            // j.setAlwaysOnTop(true);
            // j.getContentPane().add(rxParticipantResolverPanel);
            // j.pack();
            // j.setVisible(true);
            // int result = DialogUtils.showComponentOKCancelDialog(getGraphPane(), rxParticipantResolverPanel, "Assign Reaction elements");
            // if(result != JOptionPane.OK_OPTION) {
            // return;
            // }
            BioCartoonTool.AssignmentHelper assignmentHelper = new BioCartoonTool.AssignmentHelper() {

                @Override
                public JComboBox[] getStructureAssignmentJCB() {
                    return rxParticipantResolverPanel.getStructureAssignmentJCB();
                }

                @Override
                public JComboBox[] getSpeciesAssignmentJCB() {
                    return rxParticipantResolverPanel.getSpeciesAssignmentJCB();
                }

                @Override
                public ArrayList<JTextField> getFinalNames() {
                    // TODO Auto-generated method stub
                    return rxParticipantResolverPanel.getFinalNamesJTF();
                }

                @Override
                public Component getParent() {
                    return getGraphPane();
                }

                @Override
                public Component getAssignmentInterface() {
                    return rxParticipantResolverPanel;
                }

                @Override
                public void close() {
                // Do Nothing
                }
            };
            BioCartoonTool.pasteReactionSteps(requester, ReactionCartoonTool.this, reactionDescription, reactionSpeciesCopy.getReactStepArr()[0].getModel(), reactionSpeciesCopy.getFromStructure(), reactionSpeciesCopy.getReactStepArr()[0], bioModel.getModel(), pasteToStructure, assignmentHelper);
        // pasteReactionSteps(getGraphPane(),reactionSpeciesCopy.getReactStepArr(), getModel(),structure,true, null,ReactionCartoonTool.this);
        } else if (reactionSpeciesCopy.getReactionRuleArr() != null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            pasteReactionsAndRules(getGraphPane(), reactionSpeciesCopy, getModel(), pasteToStructure, ReactionCartoonTool.this);
        }
    // try {
    // for(MolecularType mtOurs : mtNewList) {
    // rbmmcOurs.addMolecularType(mtOurs, false);
    // }
    // } catch (ModelException | PropertyVetoException e) {
    // e.printStackTrace();
    // }
    // 
    // // ReactionRules
    // if(reactionSpeciesCopy.getReactionRuleArr() != null) {
    // for(ReactionRule rrTheirs : reactionSpeciesCopy.getReactionRuleArr()) {
    // 
    // }
    // }
    }
}

Example 2 with ReactionDescription

use of cbit.vcell.model.ReactionDescription in project vcell by virtualcell.

the class BiomodelVCMLModelInfoResource method createReactionDescription.

// Copied from DBReactionWizrdPanel and altered to display speciescontext names in ReactionStep text representation
public static ReactionDescription createReactionDescription(ReactionStep rxStep, KeyValue bmid, KeyValue structRef) {
    ReactionType rxType = null;
    if (rxStep instanceof FluxReaction) {
        if (rxStep.isReversible()) {
            rxType = ReactionType.REACTTYPE_FLUX_REVERSIBLE;
        } else {
            rxType = ReactionType.REACTTYPE_FLUX_IRREVERSIBLE;
        }
    } else {
        if (rxStep.isReversible()) {
            rxType = ReactionType.REACTTYPE_SIMPLE_REVERSIBLE;
        } else {
            rxType = ReactionType.REACTTYPE_SIMPLE_IRREVERSIBLE;
        }
    }
    ReactionDescription dbfr = new ReactionDescription(rxStep.getName(), rxType, rxStep.getKey(), bmid, structRef);
    // 
    ReactionParticipant[] rpArr = rxStep.getReactionParticipants();
    for (int i = 0; i < rpArr.length; i += 1) {
        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(rpArr[i].getSpeciesContext().getName());
        char role;
        if (rpArr[i] instanceof Reactant) {
            role = ReactionDescription.RX_ELEMENT_REACTANT;
        } else if (rpArr[i] instanceof Product) {
            role = ReactionDescription.RX_ELEMENT_PRODUCT;
        } else if (rpArr[i] instanceof Catalyst) {
            role = ReactionDescription.RX_ELEMENT_CATALYST;
        } else {
            throw new RuntimeException("Unsupported ReationParticiapnt=" + rpArr[i].getClass().getName());
        }
        dbfr.addReactionElement(dbnfu, rpArr[i].getSpeciesContext().getName(), rpArr[i].getSpeciesContext().getStructure().getName(), rpArr[i].getStoichiometry(), role);
    }
    if (dbfr.isFluxReaction()) {
        // make sure flux is in right direction
        Structure outsideStruct = rxStep.getModel().getStructureTopology().getOutsideFeature((Membrane) rxStep.getStructure());
        String defaultOutsideSCName = dbfr.getOrigSpeciesContextName(dbfr.getFluxIndexOutside());
        for (int i = 0; i < rpArr.length; i += 1) {
            if (rpArr[i].getSpeciesContext().getName().equals(defaultOutsideSCName)) {
                if (!rpArr[i].getStructure().equals(outsideStruct)) {
                    dbfr.swapFluxSCNames();
                }
                break;
            }
        }
    }
    return dbfr;
}

Example 3 with ReactionDescription

use of cbit.vcell.model.ReactionDescription in project vcell by virtualcell.

the class DBReactionWizardPanel method searchUserReactions.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2003 2:45:44 PM)
 */
private void searchUserReactions(final ReactionQuerySpec reactionQuerySpec) {
    if (getDocumentManager() != null) {
        final DocumentManager docManager = getDocumentManager();
        final JList jlist = getReactionsJList();
        // 
        final String RXSTRING_VALUE_KEY = "rxString";
        // 
        AsynchClientTask searchReactions = new AsynchClientTask("searching reactions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                try {
                    mapRXStringtoRXIDs.clear();
                    // 
                    ReactionDescription[] dbrd = docManager.getUserReactionDescriptions(reactionQuerySpec);
                    // 
                    if (dbrd != null && !(getStructure() instanceof Membrane)) {
                        Vector<ReactionDescription> noflux = new Vector<ReactionDescription>();
                        for (int i = 0; i < dbrd.length; i += 1) {
                            if (!dbrd[i].isFluxReaction()) {
                                noflux.add(dbrd[i]);
                            }
                        }
                        if (noflux.size() > 0) {
                            dbrd = new ReactionDescription[noflux.size()];
                            noflux.copyInto(dbrd);
                        }
                    }
                    // 
                    String[] dbrdS = null;
                    if (dbrd != null) {
                        // if(mapRXStringtoRXIDs == null){mapRXStringtoRXIDs = new java.util.Hashtable();}
                        for (int i = 0; i < dbrd.length; i += 1) {
                            String rxString = dbrd[i].toString();
                            if (!mapRXStringtoRXIDs.containsKey(rxString)) {
                                mapRXStringtoRXIDs.put(rxString, new Vector<String>());
                            }
                            mapRXStringtoRXIDs.get(rxString).add(dbrd[i].getVCellRXID().toString());
                            mapRXIDtoBMIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellBioModelID());
                            mapRXIDtoStructRefIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellStructRef());
                        }
                        dbrdS = mapRXStringtoRXIDs.keySet().toArray(new String[0]);
                    }
                    // 
                    if (dbrd != null && dbrd.length > 0) {
                        hash.put(RXSTRING_VALUE_KEY, dbrdS);
                    }
                } catch (DataAccessException e) {
                    PopupGenerator.showErrorDialog(DBReactionWizardPanel.this, e.getMessage());
                }
            }
        };
        // 
        AsynchClientTask updateRXList = new AsynchClientTask("updateRXList", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                String[] dbrdS = (String[]) hash.get(RXSTRING_VALUE_KEY);
                if (dbrdS != null) {
                    jlist.setListData(dbrdS);
                } else {
                    jlist.setListData(new String[0]);
                }
            // afterSearchConfigure();
            }
        };
        // 
        Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
        ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXList }, false);
    }
}

Example 4 with ReactionDescription

use of cbit.vcell.model.ReactionDescription in project vcell by virtualcell.

the class DBReactionWizardPanel method bfnActionPerformed.

/**
 * Invoked when an action occurs.
 */
// public void actionPerformed(java.awt.event.ActionEvent e) {dbfr.get
// 
// ReactionDescription resolvedReaction = getResolverJPanel().getREsolvedReaction();
// JComboBox[] speciesAssignmentJCB = getResolverJPanel().getSpeciesAssignmentJCB();
// if(resolvedReaction.isFluxReaction()){
// if(e.getSource() == speciesAssignmentJCB[0]){
// if(speciesAssignmentJCB[1].getSelectedIndex() != speciesAssignmentJCB[0].getSelectedIndex()){
// speciesAssignmentJCB[1].setSelectedIndex(speciesAssignmentJCB[0].getSelectedIndex());
// }
// }else if(e.getSource() == speciesAssignmentJCB[1]){
// if(speciesAssignmentJCB[0].getSelectedIndex() != speciesAssignmentJCB[1].getSelectedIndex()){
// speciesAssignmentJCB[0].setSelectedIndex(speciesAssignmentJCB[1].getSelectedIndex());
// }
// }
// }
// //for(int i=0;i<speciesAssignmentJCB.length;i+= 1){
// //Species species = speciesOrder[speciesAssignmentJCB[i].getSelectedIndex()];
// //Structure structure = null;
// //if(getStructure() instanceof Feature){
// //structure = getStructure();
// //}else if(resolvedReaction.isFluxReaction() && i == 0){
// //structure = ((Membrane)getStructure()).getOutsideFeature();
// //}else if(resolvedReaction.isFluxReaction() && i == 1){
// //structure = ((Membrane)getStructure()).getInsideFeature();
// //}else if(structureAssignmentJCB[i].getSelectedIndex() == 0){
// //structure = getStructure();
// //}else if(structureAssignmentJCB[i].getSelectedIndex() == 1){
// //structure = ((Membrane)getStructure()).getOutsideFeature();
// //}else if(structureAssignmentJCB[i].getSelectedIndex() == 2){
// //structure = ((Membrane)getStructure()).getInsideFeature();
// //}
// //System.out.println(
// //resolvedReaction.getReactionElement(i).getPreferredName()+
// //" assigned to "+(species != null?species.getCommonName():"New Species")+
// //" in structure "+ structure.getName());
// //}
// 
// }
// /**
// * Insert the method's description here.
// * Creation date: (8/18/2003 2:38:49 PM)
// */
// private void afterSearchConfigure() {
// 
// if(getReactionsJList().getModel().getSize() == 0){
// lastSearchChangeInfo = null;
// PopupGenerator.showInfoDialog(this, "No Reactions found matching search criteria");
// }else{
// lastSearchSaveInfo();
// ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).next(getCardLayoutJPanel());
// }
// configureBFN();
// }
/**
 * Comment
 */
private void bfnActionPerformed(java.awt.event.ActionEvent actionEvent) {
    try {
        // 
        DefaultListModel pndlm = (DefaultListModel) getParameterNamesJList().getModel();
        // 
        if (actionEvent.getSource().equals(getBackJButton())) {
            if (getRXParticipantResolverPanel().isVisible() && pndlm.size() == 0 && getSearchDictionaryJRadioButton().isSelected() == false) {
                // skip Parameters if there are none
                ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).previous(getCardLayoutJPanel());
            }
            ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).previous(getCardLayoutJPanel());
        } else if (actionEvent.getSource().equals(getNextJButton())) {
            // }else
            if (getParameterJPanel().isVisible()) {
                if (lastReactStepSelection == null || !lastReactStepSelection.equals(getReactionStep0())) {
                    lastReactStepSelection = getReactionStep0();
                    KeyValue bmid = mapRXIDtoBMIDs.get(lastReactStepSelection.getKey());
                    KeyValue structRef = mapRXIDtoStructRefIDs.get(lastReactStepSelection.getKey());
                    ReactionDescription dbfr = createReactionDescription(getReactionStep0(), bmid, structRef);
                    getRXParticipantResolverPanel().setupRX(dbfr, getModel(), getStructure());
                }
            }
            // 
            ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).next(getCardLayoutJPanel());
        }
        // else if(actionEvent.getSource().equals(getFinishJButton())){
        // ReactionDescription myResolvedReaction = getRXParticipantResolverPanel().getResolvedReaction();
        // Model fromModel = getDocumentManager().getBioModel(myResolvedReaction.getVCellBioModelID()).getModel();
        // ReactionStep[] rxArr = fromModel.getReactionSteps();
        // ReactionStep fromRXStep = null;
        // for (int i = 0; i < rxArr.length; i++) {
        // if(rxArr[i].getKey().equals(myResolvedReaction.getVCellRXID())){
        // fromRXStep = rxArr[i];
        // break;
        // }
        // }
        // BioCartoonTool.AssignmentHelper assignmentHelper = new BioCartoonTool.AssignmentHelper() {
        // @Override
        // public JComboBox[] getStructureAssignmentJCB() {
        // return getRXParticipantResolverPanel().getStructureAssignmentJCB();
        // }
        // @Override
        // public JComboBox[] getSpeciesAssignmentJCB() {
        // return getRXParticipantResolverPanel().getSpeciesAssignmentJCB();
        // }
        // @Override
        // public ArrayList<JTextField> getFinalNames() {
        // // TODO Auto-generated method stub
        // return getRXParticipantResolverPanel().getFinalNamesJTF();
        // }
        // @Override
        // public Component getParent() {
        // return DBReactionWizardPanel.this;
        // }
        // @Override
        // public Component getAssignmentInterface() {
        // return null;
        // }
        // @Override
        // public boolean shouldCloseParent() {
        // return true;
        // }
        // };
        // BioCartoonTool.pasteReactionSteps(DBReactionWizardPanel.this, rxPasteInterface, myResolvedReaction, fromModel,DBReactionWizardPanel.this.getStructure(),fromRXStep,
        // DBReactionWizardPanel.this.getModel(), DBReactionWizardPanel.this.getStructure(),assignmentHelper);
        // DBReactionWizardPanel.this.getChildWindow().close();
        // }
        // 
        configureBFN();
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, "DBReactionWizard failed\n" + e.getMessage(), e);
    }
}

Example 5 with ReactionDescription

use of cbit.vcell.model.ReactionDescription in project vcell by virtualcell.

the class DBReactionWizardPanel method setReactionDescription.

/**
 * Sets the reactionDescription property (cbit.vcell.dictionary.ReactionDescription) value.
 * @param reactionDescription The new value for the property.
 * @see #getReactionDescription
 */
private void setReactionDescription(ReactionDescription reactionDescription) {
    ReactionDescription oldValue = fieldReactionDescription;
    fieldReactionDescription = reactionDescription;
    firePropertyChange("reactionDescription", oldValue, reactionDescription);
}