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

Example 6 with FluxReaction

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

the class ReactionCartoonRule method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.rule;
    for (Shape shape : getShapes()) {
        if (shape instanceof FluxReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.FLUX_REACTION_NODE, ((FluxReaction) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SimpleReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SIMPLE_REACTION_NODE, ((ReactionStep) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        // } else if (shape instanceof ReactionRuleDiagramShape) {
        // nodeList.add(new NodeReference(mode,
        // NodeReference.REACTION_RULE_NODE,
        // ((ReactionRule) shape.getModelObject()).getName(),
        // shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof ReactionRuleShortDiagramShape) {
            // can only be short
            ReactionRuleShortSignature signature = (ReactionRuleShortSignature) shape.getModelObject();
            // the display name is the number of rules in the signature's list of rules
            String name = signature.getDisplayName();
            NodeReference nr = new NodeReference(mode, NodeReference.REACTION_RULE_NODE, name, shape.getSpaceManager().getRelPos());
            nodeList.add(nr);
        } else if (shape instanceof SpeciesContextShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SPECIES_CONTEXT_NODE, ((SpeciesContext) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof RuleParticipantSignatureFullDiagramShape) {
            System.out.println("ReactionCartoonRule, Invalid shape type 'RuleParticipantSignatureFullDiagramShape'");
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        } else if (shape instanceof RuleParticipantSignatureShortDiagramShape) {
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        }
    }
    // add all to nodeRuleList
    diagram.setNodeReferences(mode, nodeList);
}

Example 7 with FluxReaction

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

the class DBReactionWizardPanel method bfnActionPerformed.

/**
 * Comment
 */
private void bfnActionPerformed(java.awt.event.ActionEvent actionEvent) {
    try {
        // 
        javax.swing.DefaultListModel pndlm = (javax.swing.DefaultListModel) getParameterNamesJList().getModel();
        // 
        if (actionEvent.getSource().equals(getBackJButton())) {
            if (getResolverJPanel().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())) {
            if (getSearchCriteriaJPanel().isVisible()) {
                if (getSearchDictionaryJRadioButton().isSelected()) {
                    getParameterJPanel().setVisible(false);
                } else {
                    getParameterJPanel().setVisible(true);
                }
                if (!lastSearchIsSameAsCurrent()) {
                    search();
                    lastReactionSelection = null;
                    return;
                }
            } else if (getParameterJPanel().isVisible()) {
                if (lastReactStepSelection == null || !lastReactStepSelection.equals(getReactionStep0())) {
                    lastReactStepSelection = getReactionStep0();
                    ReactionType rxType = null;
                    if (getReactionStep0() instanceof FluxReaction) {
                        if (getReactionStep0().isReversible()) {
                            rxType = ReactionType.REACTTYPE_FLUX_REVERSIBLE;
                        } else {
                            rxType = ReactionType.REACTTYPE_FLUX_IRREVERSIBLE;
                        }
                    } else {
                        if (getReactionStep0().isReversible()) {
                            rxType = ReactionType.REACTTYPE_SIMPLE_REVERSIBLE;
                        } else {
                            rxType = ReactionType.REACTTYPE_SIMPLE_IRREVERSIBLE;
                        }
                    }
                    KeyValue bmid = mapRXIDtoBMIDs.get(lastReactStepSelection.getKey());
                    KeyValue structRef = mapRXIDtoStructRefIDs.get(lastReactStepSelection.getKey());
                    ReactionDescription dbfr = new ReactionDescription(getReactionStep0().getName(), rxType, getReactionStep0().getKey(), bmid, structRef);
                    // 
                    ReactionParticipant[] rpArr = getReactionStep0().getReactionParticipants();
                    for (int i = 0; i < rpArr.length; i += 1) {
                        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(rpArr[i].getSpecies().getCommonName());
                        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].getStoichiometry(), role);
                    }
                    if (dbfr.isFluxReaction()) {
                        // make sure flux is in right direction
                        Structure outsideStruct = getModel().getStructureTopology().getOutsideFeature((Membrane) getReactionStep0().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;
                            }
                        }
                    }
                    setupRX(dbfr);
                }
            }
            // 
            ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).next(getCardLayoutJPanel());
        } else if (actionEvent.getSource().equals(getFinishJButton())) {
            applySelectedReactionElements();
        }
        // 
        configureBFN();
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, "DBReactionWizard failed\n" + e.getMessage(), e);
    }
}

Example 8 with FluxReaction

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

the class ReactionCartoonFull method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.full;
    for (Shape shape : getShapes()) {
        if (shape instanceof FluxReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.FLUX_REACTION_NODE, ((FluxReaction) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SimpleReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SIMPLE_REACTION_NODE, ((ReactionStep) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof ReactionRuleDiagramShape) {
            nodeList.add(new NodeReference(mode, NodeReference.REACTION_RULE_NODE, ((ReactionRule) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SpeciesContextShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SPECIES_CONTEXT_NODE, ((SpeciesContext) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof RuleParticipantSignatureFullDiagramShape) {
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        } else if (shape instanceof RuleParticipantSignatureShortDiagramShape) {
            System.out.println("ReactionCartoonFull, Invalid shape type 'RuleParticipantSignatureShortDiagramShape'");
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        }
    }
    diagram.setNodeReferences(mode, nodeList);
}

Example 9 with FluxReaction

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

the class ReactionCartoonFull method applyDefaults.

public void applyDefaults(Diagram diagram) {
    List<NodeReference> nodeList = diagram.getNodeFullList();
    List<NodeReference> orphansList = new ArrayList<NodeReference>();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        Object obj = null;
        Structure struct = diagram.getStructure();
        boolean found = false;
        switch(node.nodeType) {
            case NodeReference.SIMPLE_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof SimpleReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram reaction " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.FLUX_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof FluxReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram flux " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.SPECIES_CONTEXT_NODE:
                obj = getModel().getSpeciesContext(node.name);
                break;
            case NodeReference.REACTION_RULE_NODE:
                obj = getModel().getRbmModelContainer().getReactionRule(node.name);
                break;
            case // obj is a RuleParticipantSignature
            NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE:
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
            case NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE:
                System.out.println("ReactionCartoonFull, RULE_PARTICIPANT_SIGNATURE_SHORT_NODE detected");
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
        }
        // -- switch
        Shape shape = getShapeFromModelObject(obj);
        if (shape != null) {
            Point relPosOld = shape.getRelPos();
            Point relPosNew = node.location;
            // In old models, the same node can appear in multiple diagrams.
            // Now, we have only one diagram, so if a node has multiple positions,
            // some would overwrite others.
            // This attempts to prevent overwriting a position with a worse one.
            // if(relPosOld.x + relPosOld.y < relPosNew.x + relPosNew.y) {
            shape.setRelPos(relPosNew);
        // }
        }
    }
    if (!orphansList.isEmpty()) {
        diagram.removeNodeReferences(NodeReference.Mode.full, orphansList);
    }
}

Example 10 with FluxReaction

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

the class ReactionCartoonMolecule method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.molecule;
    for (Shape shape : getShapes()) {
        if (shape instanceof FluxReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.FLUX_REACTION_NODE, ((FluxReaction) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SimpleReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SIMPLE_REACTION_NODE, ((ReactionStep) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof ReactionRuleDiagramShape) {
            nodeList.add(new NodeReference(mode, NodeReference.REACTION_RULE_NODE, ((ReactionRule) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SpeciesContextShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SPECIES_CONTEXT_NODE, ((SpeciesContext) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof RuleParticipantSignatureFullDiagramShape) {
            System.out.println("ReactionCartoonMolecule, Invalid shape type 'RuleParticipantSignatureFullDiagramShape'");
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        } else if (shape instanceof RuleParticipantSignatureShortDiagramShape) {
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        }
    }
    diagram.setNodeReferences(mode, nodeList);
}