Examples with BondType org.vcell.model.rbm.MolecularComponentPattern.BondType used on opensource projects

Example 6 with BondType

use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.

the class SpeciesPropertiesTreeModel method valueForPathChanged.

@Override
public void valueForPathChanged(TreePath path, Object newValue) {
    Object obj = path.getLastPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    BioModelNode parentNode = (BioModelNode) selectedNode.getParent();
    Object userObject = selectedNode.getUserObject();
    try {
        if (newValue instanceof String) {
            String inputString = (String) newValue;
            if (inputString == null || inputString.length() == 0) {
                return;
            }
        // if (userObject instanceof SeedSpecies) {
        // ((SeedSpecies) userObject).setSpeciesPattern(inputString);
        // }
        } else if (newValue instanceof MolecularComponentPattern) {
            MolecularComponentPattern newMcp = (MolecularComponentPattern) newValue;
            Object parentObject = parentNode == null ? null : parentNode.getUserObject();
            if (parentObject instanceof MolecularTypePattern) {
                MolecularTypePattern mtp = (MolecularTypePattern) parentObject;
                MolecularComponent mc = newMcp.getMolecularComponent();
                MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
                // TODO: what's correct here ?
                mcp.setComponentStatePattern(newMcp.getComponentStatePattern());
                BondType bp = mcp.getBondType();
                BondType newbp = newMcp.getBondType();
                mcp.setBondType(newbp);
                // specified -> specified
                if (bp == BondType.Specified && newbp == BondType.Specified) {
                // bond didn't change
                } else if (bp == BondType.Specified && newbp != BondType.Specified) {
                    // specified -> non specified
                    // change the partner to possible
                    mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                    mcp.setBond(null);
                } else if (bp != BondType.Specified && newbp == BondType.Specified) {
                    // non specified -> specified
                    int newBondId = newMcp.getBondId();
                    mcp.setBondId(newBondId);
                    mcp.setBond(newMcp.getBond());
                    mcp.getBond().molecularComponentPattern.setBondId(newBondId);
                    speciesContext.getSpeciesPattern().resolveBonds();
                } else {
                }
            }
        }
    } catch (Exception ex) {
        DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
    }
}

Example 7 with BondType

use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.

the class SpeciesPattern method removeMolecularTypePattern.

public void removeMolecularTypePattern(MolecularTypePattern molecularTypePattern) {
    List<MolecularTypePattern> newValue = new ArrayList<MolecularTypePattern>(molecularTypePatterns);
    newValue.remove(molecularTypePattern);
    for (MolecularComponentPattern mcp : molecularTypePattern.getComponentPatternList()) {
        BondType btBefore = mcp.getBondType();
        if (btBefore == BondType.Specified) {
            // specified -> not specified
            // change the partner to possible
            mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
            mcp.getBond().molecularComponentPattern.setBond(null);
        }
        mcp.setBondType(BondType.None);
        mcp.setBond(null);
    }
    setMolecularTypePatterns(newValue);
}

Example 8 with BondType

use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.

the class Xmlproducer method getXML.

private Element getXML(MolecularComponentPattern param) {
    Element e = new Element(XMLTags.RbmMolecularComponentPatternTag);
    // e.setAttribute(XMLTags.NameAttrTag, mangle(param.getId()));
    e.setAttribute(XMLTags.RbmMolecularComponentTag, mangle(param.getMolecularComponent().getName()));
    ComponentStatePattern cs = param.getComponentStatePattern();
    if (cs != null) {
        if (cs.isAny()) {
            e.setAttribute(XMLTags.RbmMolecularTypeAnyTag, String.valueOf(cs.isAny()));
        } else {
            if (cs.getComponentStateDefinition() != null) {
                e.setAttribute(XMLTags.RbmMolecularComponentStatePatternTag, mangle(cs.getComponentStateDefinition().getName()));
            } else {
                System.err.println(ComponentStateDefinition.typeName + " is missing!");
            }
        }
    }
    Bond b = param.getBond();
    if (b != null) {
        Element e1 = new Element(XMLTags.RbmBondTag);
        String test = mangle(b.molecularTypePattern.getMolecularType().getName());
        e1.setAttribute(XMLTags.RbmMolecularTypePatternTag, test);
        e1.setAttribute(XMLTags.RbmMolecularComponentPatternTag, mangle(b.molecularComponentPattern.getMolecularComponent().getName()));
        e.addContent(e1);
    }
    BondType bt = param.getBondType();
    if (bt == null) {
        return e;
    }
    if (bt.equals(BondType.Specified)) {
        String s = Integer.toString(param.getBondId());
        e.setAttribute(XMLTags.RbmBondTypeAttrTag, s);
    } else {
        String s = bt.symbol;
        e.setAttribute(XMLTags.RbmBondTypeAttrTag, s);
    }
    return e;
}

Example 9 with BondType

use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.

the class RbmTreeCellRenderer method toHtmlWork.

private static final String toHtmlWork(BondLocal bl, boolean bSelected) {
    MolecularComponentPattern mcp = bl.getMolecularComponentPattern();
    BondType defaultType = BondType.Possible;
    String bondText = " Bond(<b>" + defaultType.symbol + "</b>): " + "<b>" + BondType.Possible.name() + "</b>";
    if (mcp != null) {
        BondType bondType = mcp.getBondType();
        if (bondType == BondType.Specified) {
            Bond bond = mcp.getBond();
            if (bond == null) {
                bondText = "";
            } else {
                int id = mcp.getBondId();
                String colorTextStart = bSelected ? "" : "<font color=" + "\"rgb(" + GraphConstants.bondHtmlColors[id].getRed() + "," + GraphConstants.bondHtmlColors[id].getGreen() + "," + GraphConstants.bondHtmlColors[id].getBlue() + ")\">";
                String colorTextEnd = bSelected ? "" : "</font>";
                // <sub>&nbsp;</sub>
                bondText = colorTextStart + "<b>" + mcp.getBondId() + "</b>" + colorTextEnd;
                bondText = " Bound(" + bondText + ") to: " + colorTextStart + toHtml(bond) + colorTextEnd;
            }
        } else {
            bondText = " Bond(<b>" + bondType.symbol + "</b>): " + "<b>" + bondType.name() + "</b>";
        }
    }
    return bondText;
}

Example 10 with BondType

use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.

the class ReactionRuleEditorPropertiesPanel method manageComponentPatternFromShape.

public void manageComponentPatternFromShape(final Object selectedObject, PointLocationInShapeContext locationContext, final ReactionRulePropertiesTreeModel treeModel, ShowWhat showWhat, boolean bIsReactant) {
    popupFromShapeMenu.removeAll();
    final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
    final MolecularComponent mc = mcp.getMolecularComponent();
    boolean anyStateProhibited = false;
    boolean explicitStateProhibited = false;
    boolean existBondProhibited = false;
    boolean noneBondProhibited = false;
    boolean possibleBondProhibited = false;
    boolean specifiedBondProhibited = false;
    if (!bIsReactant) {
        // product has restrictions for states and bonds, depending on reactant
        BondType reactantComponentBondType = reactionRule.getReactantComponentBondType(mcp);
        if (reactantComponentBondType != null && reactantComponentBondType == BondType.Exists) {
            // has external		+
            // existBondProhibited = true;
            noneBondProhibited = true;
            possibleBondProhibited = true;
            specifiedBondProhibited = true;
        } else if (reactantComponentBondType != null && reactantComponentBondType == BondType.None) {
            // is unbound		-
            existBondProhibited = true;
            // noneBondProhibited = true;
            possibleBondProhibited = true;
        // specifiedBondProhibited = true;
        } else if (reactantComponentBondType != null && reactantComponentBondType == BondType.Possible) {
            // may be bound		?
            existBondProhibited = true;
            noneBondProhibited = true;
            // possibleBondProhibited = true;
            specifiedBondProhibited = true;
        } else if (reactantComponentBondType != null && reactantComponentBondType == BondType.Specified) {
            existBondProhibited = true;
            // noneBondProhibited = true;
            possibleBondProhibited = true;
        // specifiedBondProhibited = true;
        }
        // if it's null nothing is prohibited
        ComponentStatePattern reactantComponentStatePattern = reactionRule.getReactantComponentState(mcp);
        if (reactantComponentStatePattern != null && reactantComponentStatePattern.isAny()) {
            explicitStateProhibited = true;
        } else if (reactantComponentStatePattern != null && !reactantComponentStatePattern.isAny()) {
            anyStateProhibited = true;
        }
    // if reactantComponentStatePattern is null nothing is prohibited, we may not have a matching reactant for this product
    }
    // ------------------------------------------------------------------- State
    if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
        String prefix = "State:  ";
        String csdCurrentName = "";
        final Map<String, String> itemMap = new LinkedHashMap<String, String>();
        if (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny()) {
            csdCurrentName = "<html>" + prefix + "<b>" + ComponentStatePattern.strAny + "</b></html>";
        } else {
            csdCurrentName = "<html>" + prefix + ComponentStatePattern.strAny + "</html>";
        }
        itemMap.put(csdCurrentName, ComponentStatePattern.strAny);
        for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
            csdCurrentName = "";
            if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
                ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
                csdCurrentName = csdCurrent.getName();
            }
            String name = csd.getName();
            if (name.equals(csdCurrentName)) {
                // currently selected menu item is shown in bold
                name = "<html>" + prefix + "<b>" + name + "</b></html>";
            } else {
                name = "<html>" + prefix + name + "</html>";
            }
            itemMap.put(name, csd.getName());
        }
        for (String key : itemMap.keySet()) {
            JMenuItem menuItem = new JMenuItem(key);
            if (!bIsReactant) {
                String name = itemMap.get(key);
                if (name.equals(ComponentStatePattern.strAny) && anyStateProhibited) {
                    menuItem.setEnabled(false);
                } else if (!name.equals(ComponentStatePattern.strAny) && explicitStateProhibited) {
                    menuItem.setEnabled(false);
                }
            }
            popupFromShapeMenu.add(menuItem);
            menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    String key = e.getActionCommand();
                    String name = itemMap.get(key);
                    ComponentStatePattern csp = new ComponentStatePattern();
                    if (!name.equals(ComponentStatePattern.strAny)) {
                        ComponentStateDefinition csd = mcp.getMolecularComponent().getComponentStateDefinition(name);
                        if (csd == null) {
                            throw new RuntimeException("Missing ComponentStateDefinition " + name + " for Component " + mcp.getMolecularComponent().getName());
                        }
                        csp = new ComponentStatePattern(csd);
                    }
                    mcp.setComponentStatePattern(csp);
                    if (bIsReactant) {
                        reflectStateToProduct(mcp, csp);
                        productTreeModel.populateTree();
                    }
                    treeModel.populateTree();
                    shapePanel.repaint();
                }
            });
        }
    }
    if (showWhat == ShowWhat.ShowState) {
        return;
    }
    // ------------------------------------------------------------------------------------------- Bonds
    final MolecularTypePattern mtp = locationContext.getMolecularTypePattern();
    final SpeciesPattern sp = locationContext.getSpeciesPattern();
    JMenu editBondMenu = new JMenu();
    final String specifiedString = mcp.getBondType() == BondType.Specified ? "<html><b>" + "Site bond specified" + "</b></html>" : "<html>" + "Site bond specified" + "</html>";
    editBondMenu.setText(specifiedString);
    editBondMenu.setToolTipText("Specified");
    editBondMenu.removeAll();
    editBondMenu.setEnabled(!specifiedBondProhibited);
    final Map<String, Bond> itemMap = new LinkedHashMap<String, Bond>();
    String noneString = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
    // Site is bound
    String existsString = mcp.getBondType() == BondType.Exists ? "<html><b>" + "Site has external bond" + "</b></html>" : "<html>" + "Site has external bond" + "</html>";
    String possibleString = mcp.getBondType() == BondType.Possible ? "<html><b>" + "Site may be bound" + "</b></html>" : "<html>" + "Site may be bound" + "</html>";
    itemMap.put(noneString, null);
    itemMap.put(existsString, null);
    itemMap.put(possibleString, null);
    if (mtp != null && sp != null && !specifiedBondProhibited) {
        List<Bond> bondPartnerChoices = sp.getAllBondPartnerChoices(mtp, mc);
        for (Bond b : bondPartnerChoices) {
            // if(b.equals(mcp.getBond())) {
            // continue;	// if the mcp has a bond already we don't offer it
            // }
            int index = 0;
            if (mcp.getBondType() == BondType.Specified) {
                index = mcp.getBondId();
            } else {
                index = sp.nextBondId();
            }
            itemMap.put(b.toHtmlStringLong(sp, mtp, mc, index), b);
        // itemMap.put(b.toHtmlStringLong(sp, index), b);
        }
    }
    int index = 0;
    Graphics gc = shapePanel.getGraphics();
    for (String name : itemMap.keySet()) {
        JMenuItem menuItem = new JMenuItem(name);
        if (!bIsReactant) {
            if (name.equals(noneString) && noneBondProhibited) {
                menuItem.setEnabled(false);
            } else if (name.equals(existsString) && existBondProhibited) {
                menuItem.setEnabled(false);
            } else if (name.equals(possibleString) && possibleBondProhibited) {
                menuItem.setEnabled(false);
            } else if (!name.equals(noneString) && !name.equals(existsString) && !name.equals(possibleString) && specifiedBondProhibited) {
                menuItem.setEnabled(false);
            }
        }
        if (index == 0) {
            menuItem.setIcon(VCellIcons.rbmBondNoneIcon);
            menuItem.setToolTipText("None");
            popupFromShapeMenu.add(menuItem);
        } else if (index == 1) {
            menuItem.setIcon(VCellIcons.rbmBondExistsIcon);
            menuItem.setToolTipText("Exists");
            popupFromShapeMenu.add(menuItem);
        } else if (index == 2) {
            menuItem.setIcon(VCellIcons.rbmBondPossibleIcon);
            menuItem.setToolTipText("Possible");
            popupFromShapeMenu.add(menuItem);
        } else if (index > 2) {
            // we skip None, Exists, Possible
            Bond b = itemMap.get(name);
            // clone of the sp, with only the bond of interest
            SpeciesPattern spBond = new SpeciesPattern(bioModel.getModel(), sp);
            spBond.resetBonds();
            spBond.resetStates();
            MolecularTypePattern mtpFrom = spBond.getMolecularTypePattern(mtp.getMolecularType().getName(), mtp.getIndex());
            MolecularComponentPattern mcpFrom = mtpFrom.getMolecularComponentPattern(mc);
            MolecularTypePattern mtpTo = spBond.getMolecularTypePattern(b.molecularTypePattern.getMolecularType().getName(), b.molecularTypePattern.getIndex());
            MolecularComponentPattern mcpTo = mtpTo.getMolecularComponentPattern(b.molecularComponentPattern.getMolecularComponent());
            spBond.setBond(mtpTo, mcpTo, mtpFrom, mcpFrom);
            Icon icon = new SpeciesPatternSmallShape(3, 4, spBond, gc, reactionRule, false, issueManager);
            ((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
            menuItem.setIcon(icon);
            editBondMenu.add(menuItem);
        }
        menuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                String name = e.getActionCommand();
                BondType btBefore = mcp.getBondType();
                if (name.equals(noneString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> not specified
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.None);
                    mcp.setBond(null);
                } else if (name.equals(existsString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> exists
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Exists);
                    mcp.setBond(null);
                } else if (name.equals(possibleString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> possible
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Possible);
                    mcp.setBond(null);
                } else {
                    if (btBefore != BondType.Specified) {
                        // if we go from a non-specified to a specified we need to find the next available
                        // bond id, so that we can choose the color for displaying the bond
                        // a bad bond id, like -1, will crash badly when trying to choose the color
                        int bondId = sp.nextBondId();
                        mcp.setBondId(bondId);
                    } else {
                        // specified -> specified
                        // change the old partner to possible, continue using the bond id
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Specified);
                    Bond b = itemMap.get(name);
                    mcp.setBond(b);
                    mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
                    sp.resolveBonds();
                }
                // when the tree will be gone
                if (bIsReactant) {
                    reflectBondToProduct(mcp);
                    productTreeModel.populateTree();
                }
                treeModel.populateTree();
                shapePanel.repaint();
            }
        });
        index++;
    }
    popupFromShapeMenu.add(editBondMenu);
}