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

Example 41 with Issue

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

the class BioCartoonTool method getMoleculesFromStrict.

// returns a list with the "from" molecules we need to add to the modelTo
// it's a "strict" list, where we have eliminated any conflicting molecules and the ones already present
private static Set<MolecularType> getMoleculesFromStrict(ReactionSpeciesCopy rsCopy, Model modelTo, Vector<Issue> issueVector, IssueContext issueContext) {
    // molecular types
    Set<MolecularType> mtFromListStrict = new HashSet<>();
    Set<MolecularType> mtConflictList = new HashSet<>();
    Set<MolecularType> mtAlreadyList = new HashSet<>();
    RbmModelContainer rbmmcTo = modelTo.getRbmModelContainer();
    if (rsCopy.getMolecularTypeArr() != null) {
        for (MolecularType mtFrom : rsCopy.getMolecularTypeArr()) {
            // the molecules we try to paste here
            MolecularType mtTo = rbmmcTo.getMolecularType(mtFrom.getName());
            if (mtTo == null) {
                // mtTo = new MolecularType(mtFrom, modelTo);
                mtFromListStrict.add(mtFrom);
            } else {
                if (!mtTo.compareEqual(mtFrom)) {
                    // conflict: a different mt with the same name already exists
                    String msg = "Molecule " + RbmUtils.toBnglString(mtFrom, null, CompartmentMode.hide);
                    msg += " to be pasted conflicts with an existing molecule " + RbmUtils.toBnglString(mtTo, null, CompartmentMode.hide) + ".";
                    Issue issue = new Issue(mtFrom, issueContext, IssueCategory.CopyPaste, msg, Issue.Severity.ERROR);
                    issueVector.add(issue);
                    mtConflictList.add(mtFrom);
                } else {
                    mtAlreadyList.add(mtFrom);
                }
            }
        }
        if (!mtConflictList.isEmpty()) {
            System.out.println("Found " + mtConflictList.size() + " conflicting molecule(s).");
        }
        if (!mtAlreadyList.isEmpty()) {
            System.out.println("Found " + mtAlreadyList.size() + " molecule(s) already there.");
        }
    }
    return mtFromListStrict;
}

Example 42 with Issue

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

the class BioCartoonTool method checkStructuresCompatibility.

// --------------------------------------------------------------------------------------------------------------------------------------
private static void checkStructuresCompatibility(ReactionSpeciesCopy rsCopy, Model modelTo, Structure structTo, Vector<Issue> issueVector, IssueContext issueContext) {
    Structure fromStruct = rsCopy.getFromStructure();
    if (rsCopy.getFromStructure().getDimension() != structTo.getDimension()) {
        // the source and destination structures need to have the same dimension, can't paste from compartment to membrane or vice-versa
        String msg = "Unable to paste from a " + fromStruct.getTypeName() + " to a " + structTo.getTypeName();
        msg += ". Both source and destination Structures need to have the same dimension.";
        Issue issue = new Issue(fromStruct, issueContext, IssueCategory.CopyPaste, msg, Issue.Severity.ERROR);
        issueVector.add(issue);
    }
    for (Structure from : rsCopy.getStructuresArr()) {
        Structure to = modelTo.getStructure(from.getName());
        if (to != null && from.getDimension() != to.getDimension()) {
            String msg = "Unable to paste " + from.getTypeName() + " " + from.getName();
            msg += " because a " + to.getTypeName() + " with the same name already exists.";
            Issue issue = new Issue(from, issueContext, IssueCategory.CopyPaste, msg, Issue.Severity.ERROR);
            issueVector.add(issue);
        }
    }
}

Example 43 with Issue

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

the class BioCartoonTool method mapStructures.

// map the structures to be pasted to existing structures in the cloned model
// we may need to generate some name iteratively until we solve all naming conflicts
private static Map<Structure, String> mapStructures(Component requester, ReactionSpeciesCopy rsCopy, Model modelTo, Structure structTo, IssueContext issueContext) {
    // use internally only; we exit the dialog when there are no issues left
    Vector<Issue> issueVector = new Vector<>();
    Structure structFrom = rsCopy.getFromStructure();
    Map<Structure, String> fullyMappedStructures = new LinkedHashMap<>();
    fullyMappedStructures.put(structFrom, structTo.getName());
    StructurePasteMappingPanel structureMappingPanel = null;
    do {
        issueVector.clear();
        if (structureMappingPanel == null) {
            structureMappingPanel = new StructurePasteMappingPanel(rsCopy, modelTo, structTo, issueVector, issueContext);
            structureMappingPanel.setPreferredSize(new Dimension(400, 220));
        }
        int result = DialogUtils.showComponentOKCancelDialog(requester, structureMappingPanel, "Assign 'From' structures to 'To' structures");
        if (result != JOptionPane.OK_OPTION) {
            throw UserCancelException.CANCEL_GENERIC;
        }
    } while (structureMappingPanel.hasErrors());
    for (Map.Entry<Structure, JComboBox<String>> entry : structureMappingPanel.getStructureMap().entrySet()) {
        if (entry.getValue().getSelectedItem().equals(StructurePasteMappingPanel.MAKE_NEW)) {
            // we generate a "to" structure name based on the "from" name
            String newNameTo = entry.getKey().getName();
            while (modelTo.getStructure(newNameTo) != null) {
                newNameTo = org.vcell.util.TokenMangler.getNextEnumeratedToken(newNameTo);
                for (Structure sFrom : rsCopy.getStructuresArr()) {
                    if (newNameTo.equals(sFrom.getName())) {
                        // the new name must not match any existing "from" name either
                        newNameTo = org.vcell.util.TokenMangler.getNextEnumeratedToken(newNameTo);
                        break;
                    }
                }
            }
            try {
                // as to avoid risk of duplicates / conflicting names
                if (entry.getKey() instanceof Membrane) {
                    modelTo.addMembrane(newNameTo);
                } else {
                    modelTo.addFeature(newNameTo);
                }
            } catch (ModelException | PropertyVetoException e) {
                throw new RuntimeException("Failed to generate the missing 'from' Structures in the cloned model, " + e.getMessage());
            }
            fullyMappedStructures.put(entry.getKey(), newNameTo);
        } else {
            // name of an existing "to" structure
            fullyMappedStructures.put(entry.getKey(), (String) entry.getValue().getSelectedItem());
        }
    }
    return fullyMappedStructures;
}

Example 44 with Issue

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

the class BioCartoonTool method printIssues.

/**
 * printIssues : using the issue list passed as argument, gethers them in a string buffer and uses PopupGenerator.showWarning dialog to display
 * the issues to user.
 * @param issueVector : vector of 'Issue's to be printed
 * @param guiRequestComponent : the parent component required to be passed to showWarningDialog
 * @return
 */
public static boolean printIssues(Vector<Issue> issueVector, Component guiRequestComponent) {
    // now print out the issue List as a warning popup
    if (issueVector.size() > 0) {
        boolean hasErrors = false;
        StringBuffer messageBuffer = new StringBuffer("Issues encountered during pasting selected reactions:\n\n");
        for (int j = 0; j < issueVector.size(); j++) {
            Issue issue = issueVector.get(j);
            if (issue.getSeverity() == Issue.Severity.ERROR || issue.getSeverity() == Issue.Severity.WARNING) {
                if (issue.getSeverity() == Issue.Severity.ERROR) {
                    hasErrors = true;
                }
                messageBuffer.append(j + 1 + ". " + issue.getCategory() + " " + issue.getSeverity() + " : " + issue.getMessage() + "\n\n");
            }
        }
        if (issueVector.size() > 0) {
            String[] choices;
            if (hasErrors) {
                choices = new String[] { "Cancel" };
            } else {
                choices = new String[] { "Paste Anyway", "Cancel" };
            }
            String resultStr = DialogUtils.showWarningDialog(guiRequestComponent, messageBuffer.toString(), choices, "Cancel");
            if (resultStr != null && resultStr.equals("Paste Anyway")) {
                return true;
            }
        }
    }
    return false;
}

Example 45 with Issue

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

the class DefaultScrollTableCellRenderer method issueRenderer.

public static void issueRenderer(JLabel renderer, String defaultToolTipText, JTable table, int row, int column, SortTableModel tableModel) {
    List<Issue> issueListError = tableModel.getIssues(row, column, Issue.Severity.ERROR);
    List<Issue> issueListWarning = tableModel.getIssues(row, column, Issue.Severity.WARNING);
    Icon icon = null;
    Point mousePosition = table.getMousePosition();
    // hue, saturation, brightness
    Color red = Color.getHSBColor(0f, 0.4f, 1.0f);
    if (issueListError.size() > 0) {
        if (column == 0) {
            icon = VCellIcons.issueErrorIcon;
            if (mousePosition != null && mousePosition.getX() > LEFT_ICON_MARGIN && mousePosition.getX() <= (icon.getIconWidth() + LEFT_ICON_MARGIN)) {
                String tt = Issue.getHtmlIssueMessage(issueListError);
                renderer.setToolTipText(tt);
            } else {
                renderer.setToolTipText(defaultToolTipText);
            }
            // Color.red
            renderer.setBorder(new MatteBorder(1, 1, 1, 0, red));
        } else if (column == table.getColumnCount() - 1) {
            renderer.setBorder(new MatteBorder(1, 0, 1, 1, red));
        } else {
            renderer.setBorder(new MatteBorder(1, 0, 1, 0, red));
        }
    } else if (issueListWarning.size() > 0) {
        if (column == 0) {
            icon = VCellIcons.issueWarningIcon;
            if (mousePosition != null && mousePosition.getX() > LEFT_ICON_MARGIN && mousePosition.getX() <= (icon.getIconWidth() + LEFT_ICON_MARGIN)) {
                renderer.setToolTipText(Issue.getHtmlIssueMessage(issueListWarning));
            } else {
                renderer.setToolTipText(defaultToolTipText);
            }
            renderer.setBorder(new MatteBorder(1, 1, 1, 0, Color.orange));
        } else if (column == table.getColumnCount() - 1) {
            renderer.setBorder(new MatteBorder(1, 0, 1, 1, Color.orange));
        } else {
            renderer.setBorder(new MatteBorder(1, 0, 1, 0, Color.orange));
        }
    } else {
        if (column == 0) {
            icon = VCellIcons.issueGoodIcon;
            // no tooltip for column 0 when we have no issues on that line
            renderer.setToolTipText(null);
        }
        if (column != 0 && defaultToolTipText != null && !defaultToolTipText.isEmpty()) {
            renderer.setToolTipText(defaultToolTipText);
        } else {
            renderer.setToolTipText(null);
        }
        renderer.setBorder(DEFAULT_GAP);
    }
    if (column == 0 && icon != null) {
        // for some tables we combine (concatenate) the issue icon with an entity icon
        if (tableModel instanceof SpatialProcessTableModel) {
            Icon icon2 = null;
            SpatialProcess spatialProcess = (SpatialProcess) (((SpatialProcessTableModel) tableModel).getValueAt(row));
            if (spatialProcess instanceof PointLocation) {
                icon2 = VCellIcons.spatialLocationIcon;
            } else if (spatialProcess instanceof PointKinematics) {
                icon2 = VCellIcons.spatialKinematicsIcon;
            } else if (spatialProcess instanceof SurfaceKinematics) {
                icon2 = VCellIcons.spatialKinematicsIcon;
            } else {
                icon2 = VCellIcons.spatialKinematicsIcon;
            }
            icon = VCellIcons.addIcon(icon, icon2);
        } else if (tableModel instanceof SpatialObjectTableModel) {
            Icon icon2 = null;
            SpatialObject spatialObject = (SpatialObject) (((SpatialObjectTableModel) tableModel).getValueAt(row));
            if (spatialObject instanceof PointObject) {
                icon2 = VCellIcons.spatialPointIcon;
            } else if (spatialObject instanceof SurfaceRegionObject) {
                icon2 = VCellIcons.spatialMembraneIcon;
            } else if (spatialObject instanceof VolumeRegionObject) {
                icon2 = VCellIcons.spatialVolumeIcon;
            } else {
                icon2 = VCellIcons.spatialVolumeIcon;
            }
            icon = VCellIcons.addIcon(icon, icon2);
        }
    }
    renderer.setIcon(icon);
}