Examples with RXParticipantResolverPanel cbit.vcell.model.gui.RXParticipantResolverPanel used on opensource projects

Example 1 with RXParticipantResolverPanel

use of cbit.vcell.model.gui.RXParticipantResolverPanel 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()) {
    // 
    // }
    // }
    }
}