Examples with Displayable org.vcell.util.Displayable used on opensource projects

Example 6 with Displayable

use of org.vcell.util.Displayable in project vcell by virtualcell.

the class BioModelEditorModelPanel method deleteButtonPressed.

private void deleteButtonPressed() {
    try {
        ArrayList<Object> deleteList = new ArrayList<Object>();
        int selectedIndex = tabbedPane.getSelectedIndex();
        if (selectedIndex == ModelPanelTabID.reaction_diagram.ordinal()) {
            deleteList.addAll(Arrays.asList(reactionCartoonEditorPanel.getReactionCartoon().getSelectedObjects()));
        // } else if (selectedIndex == ModelPanelTabID.structure_diagram.ordinal()) {
        // deleteList.addAll(Arrays.asList(cartoonEditorPanel.getStructureCartoon().getSelectedObjects()));
        } else {
            computeCurrentSelectedTable();
            int[] rows = currentSelectedTable.getSelectedRows();
            if (rows == null || rows.length == 0) {
                return;
            }
            if (currentSelectedTable == speciesTable) {
                for (int r : rows) {
                    if (r < speciesTableModel.getRowCount()) {
                        SpeciesContext speciesContext = speciesTableModel.getValueAt(r);
                        if (speciesContext != null) {
                            deleteList.add(speciesContext);
                        }
                    }
                }
            } else if (currentSelectedTable == molecularTypeTable) {
                // TODO: delete stuff
                for (int r : rows) {
                    if (r < molecularTypeTableModel.getRowCount()) {
                        MolecularType mt = molecularTypeTableModel.getValueAt(r);
                        if (mt != null) {
                            deleteList.add(mt);
                        }
                    }
                }
            } else if (currentSelectedTable == observablesTable) {
                for (int r : rows) {
                    if (r < observableTableModel.getRowCount()) {
                        RbmObservable o = observableTableModel.getValueAt(r);
                        if (o != null) {
                            deleteList.add(o);
                        }
                    }
                }
            } else if (currentSelectedTable == structuresTable) {
                for (int r : rows) {
                    if (r < structureTableModel.getRowCount()) {
                        Structure rowValue = structureTableModel.getValueAt(r);
                        if (rowValue instanceof Feature || rowValue instanceof Membrane) {
                            deleteList.add(rowValue);
                        }
                    }
                }
            } else if (currentSelectedTable == reactionsTable) {
                for (int r : rows) {
                    if (r < reactionTableModel.getRowCount()) {
                        ModelProcess reaction = reactionTableModel.getValueAt(r);
                        if (reaction != null) {
                            deleteList.add(reaction);
                        }
                    }
                }
            }
        }
        if (deleteList.size() == 0) {
            return;
        }
        StringBuilder deleteListText = new StringBuilder();
        for (Object object : deleteList) {
            if (object instanceof SpeciesContext) {
                deleteListText.append("Species\t'" + ((SpeciesContext) object).getName() + "'\n");
            } else if (object instanceof MolecularType) {
                deleteListText.append(((MolecularType) object).getDisplayType() + "\t'" + ((MolecularType) object).getDisplayName() + "'\n");
            } else if (object instanceof RbmObservable) {
                deleteListText.append("Observable\t'" + ((RbmObservable) object).getName() + "'\n");
            } else if (object instanceof ReactionStep) {
                deleteListText.append("Reaction\t'" + ((ReactionStep) object).getName() + "'\n");
            } else if (object instanceof ReactionRule) {
                deleteListText.append("Reaction rule\t'" + ((ReactionRule) object).getName() + "'\n");
            } else if (object instanceof Structure) {
                deleteListText.append("Structure\t'" + ((Structure) object).getName() + "'\n");
            }
        }
        // TODO: once we display reaction rules in the carton editor panel we'll have to change the way we delete reaction rules
        if (deleteList.get(0) instanceof SpeciesContext || deleteList.get(0) instanceof ReactionStep) {
            try {
                ArrayList<SpeciesContext> speciesContextArrList = new ArrayList<SpeciesContext>();
                ArrayList<ReactionStep> reactionStepArrList = new ArrayList<ReactionStep>();
                for (Object obj : deleteList) {
                    if (obj instanceof SpeciesContext) {
                        speciesContextArrList.add((SpeciesContext) obj);
                    } else if (obj instanceof ReactionStep) {
                        reactionStepArrList.add((ReactionStep) obj);
                    } else {
                        throw new Exception("Unexpected delete object " + obj.getClass().getName());
                    }
                }
                ReactionCartoonTool.deleteReactionsAndSpecies(reactionCartoonEditorPanel, reactionStepArrList.toArray(new ReactionStep[0]), speciesContextArrList.toArray(new SpeciesContext[0]));
            } catch (UserCancelException uce) {
                return;
            }
            return;
        } else {
            String confirm = DialogUtils.showOKCancelWarningDialog(this, "Deleting", "You are going to delete the following:\n\n" + deleteListText + "\n Continue?");
            if (confirm.equals(UserMessage.OPTION_CANCEL)) {
                return;
            }
            for (Object object : deleteList) {
                if (object instanceof ReactionRule) {
                    ReactionRule rr = (ReactionRule) object;
                    bioModel.getModel().getRbmModelContainer().removeReactionRule(rr);
                } else if (object instanceof MolecularType) {
                    Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
                    MolecularType mt = (MolecularType) object;
                    if (!bioModel.getModel().getRbmModelContainer().isDeleteAllowed(mt, usedHere)) {
                        String errMsg = mt.getDisplayType() + " <b>'" + mt + "'</b> cannot be deleted because it's already being used by:<br>";
                        final int MaxListSize = 7;
                        int count = 0;
                        for (String key : usedHere.keySet()) {
                            System.out.println(key);
                            if (count >= MaxListSize) {
                                errMsg += "<br> ... and more.";
                                break;
                            }
                            Pair<Displayable, SpeciesPattern> o = usedHere.get(key);
                            Displayable e = o.one;
                            SpeciesPattern sp = o.two;
                            errMsg += "<br> - " + e.getDisplayType().toLowerCase() + " <b>" + e.getDisplayName() + "</b>";
                            errMsg += ", " + sp.getDisplayType().toLowerCase() + " " + " <b>" + sp.getDisplayName() + "</b>";
                            count++;
                        }
                        errMsg = "<html>" + errMsg + "</html>";
                        throw new RuntimeException(errMsg);
                    }
                    bioModel.getModel().getRbmModelContainer().removeMolecularType(mt);
                } else if (object instanceof RbmObservable) {
                    RbmObservable o = (RbmObservable) object;
                    bioModel.getModel().getRbmModelContainer().removeObservable(o);
                } else {
                    bioModel.getModel().removeObject(object);
                }
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        DialogUtils.showErrorDialog(this, ex.getMessage());
    }
}

Example 7 with Displayable

use of org.vcell.util.Displayable in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method deleteFromTree.

public void deleteFromTree() {
    Object obj = molecularTypeTree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    TreeNode parent = selectedNode.getParent();
    if (!(parent instanceof BioModelNode)) {
        return;
    }
    BioModelNode parentNode = (BioModelNode) parent;
    Object selectedUserObject = selectedNode.getUserObject();
    if (selectedUserObject instanceof MolecularComponent) {
        MolecularComponent mc = (MolecularComponent) selectedUserObject;
        Object userObject = parentNode.getUserObject();
        if (userObject instanceof MolecularType) {
            MolecularType mt = (MolecularType) userObject;
            // detailed verifications will be done there, to see if they are being used in reactions, species, observables
            if (!mc.getComponentStateDefinitions().isEmpty()) {
                String[] options = { "OK" };
                String errMsg = mc.getDisplayType() + " '<b>" + mc.getDisplayName() + "</b>' cannot be deleted because it contains explicit States.";
                errMsg += "<br>Please delete each individual State first.";
                errMsg += "<br><br>Detailed usage information will be provided at that time to help you decide.";
                errMsg = "<html>" + errMsg + "</html>";
                JOptionPane.showOptionDialog(this.getParent().getParent(), errMsg, "Delete " + mc.getDisplayType(), JOptionPane.NO_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
                return;
            }
            // we find and display component usage information to help the user decide
            Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
            bioModel.getModel().getRbmModelContainer().findComponentUsage(mt, mc, usedHere);
            if (!usedHere.isEmpty()) {
                String errMsg = mc.dependenciesToHtml(usedHere);
                errMsg += "<br><br>Delete anyway?";
                errMsg = "<html>" + errMsg + "</html>";
                int dialogButton = JOptionPane.YES_NO_OPTION;
                int returnCode = JOptionPane.showConfirmDialog(this.getParent().getParent(), errMsg, "Delete " + mc.getDisplayType(), dialogButton);
                if (returnCode == JOptionPane.YES_OPTION) {
                    // keep this code in sync with MolecularTypeTableModel.setValueAt
                    if (bioModel.getModel().getRbmModelContainer().delete(mt, mc) == true) {
                        mt.removeMolecularComponent(mc);
                    }
                } else {
                    return;
                }
            } else {
                if (bioModel.getModel().getRbmModelContainer().delete(mt, mc) == true) {
                    mt.removeMolecularComponent(mc);
                }
            }
        }
    } else if (selectedUserObject instanceof ComponentStateDefinition) {
        ComponentStateDefinition csd = (ComponentStateDefinition) selectedUserObject;
        Object userObject = parentNode.getUserObject();
        if (!(userObject instanceof MolecularComponent)) {
            System.out.println("Unexpected parent in tree hierarchy for " + ComponentStateDefinition.typeName + " " + csd.getDisplayName() + "!");
            return;
        }
        MolecularComponent mc = (MolecularComponent) userObject;
        TreeNode grandParent = parentNode.getParent();
        BioModelNode grandParentNode = (BioModelNode) grandParent;
        userObject = grandParentNode.getUserObject();
        if (!(userObject instanceof MolecularType)) {
            System.out.println("Unexpected parent in tree hierarchy for " + mc.getDisplayType() + " " + mc.getDisplayName() + "!");
            return;
        }
        MolecularType mt = (MolecularType) userObject;
        Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
        bioModel.getModel().getRbmModelContainer().findStateUsage(mt, mc, csd, usedHere);
        if (!usedHere.isEmpty()) {
            String errMsg = csd.dependenciesToHtml(usedHere);
            errMsg += "<br><br>Delete anyway?";
            errMsg = "<html>" + errMsg + "</html>";
            int dialogButton = JOptionPane.YES_NO_OPTION;
            int returnCode = JOptionPane.showConfirmDialog(this.getParent().getParent(), errMsg, "Delete " + ComponentStateDefinition.typeName, dialogButton);
            if (returnCode == JOptionPane.YES_OPTION) {
                // keep this code in sync with MolecularTypeTableModel.setValueAt
                if (bioModel.getModel().getRbmModelContainer().delete(mt, mc, csd) == true) {
                    // this stays
                    mc.deleteComponentStateDefinition(csd);
                }
            } else {
                return;
            }
        } else {
            if (bioModel.getModel().getRbmModelContainer().delete(mt, mc, csd) == true) {
                // this stays
                mc.deleteComponentStateDefinition(csd);
            }
        }
    // mc.deleteComponentStateDefinition(csd);
    }
}

Example 8 with Displayable

use of org.vcell.util.Displayable in project vcell by virtualcell.

the class RbmObservable method findComponentUsage.

public void findComponentUsage(MolecularType mt, MolecularComponent mc, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    for (SpeciesPattern sp : getSpeciesPatternList()) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        // we don't care about these
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        // found mc in use
                        String key = sp.getDisplayName();
                        key = getDisplayType() + getDisplayName() + key;
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}

Example 9 with Displayable

use of org.vcell.util.Displayable in project vcell by virtualcell.

the class ReactionRule method findComponentUsage.

// TODO: almost identical to findStateUsage() below - pay attention to keep both in sync
public void findComponentUsage(MolecularType mt, MolecularComponent mc, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    for (ProductPattern pp : getProductPatterns()) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        // we don't care about these
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        // found mc in use
                        String key = getDisplayType() + getDisplayName() + sp.getDisplayName();
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
    for (ReactantPattern rp : getReactantPatterns()) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        String key = getDisplayType() + getDisplayName() + sp.getDisplayName();
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}

Example 10 with Displayable

use of org.vcell.util.Displayable in project vcell by virtualcell.

the class ReactionRule method findStateUsage.

public void findStateUsage(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    for (ProductPattern pp : getProductPatterns()) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        // we don't care about these
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        // found mc in use
                        // now let's look at component state definition
                        ComponentStatePattern csp = mcp.getComponentStatePattern();
                        if (csp == null) {
                            continue;
                        }
                        if (csp.getComponentStateDefinition() == csd) {
                            String key = getDisplayType() + getDisplayName() + sp.getDisplayName();
                            usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                        }
                    }
                }
            }
        }
    }
    for (ReactantPattern rp : getReactantPatterns()) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        ComponentStatePattern csp = mcp.getComponentStatePattern();
                        if (csp == null) {
                            continue;
                        }
                        if (csp.getComponentStateDefinition() == csd) {
                            String key = getDisplayType() + getDisplayName() + sp.getDisplayName();
                            usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                        }
                    }
                }
            }
        }
    }
}