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

Example 56 with Issue

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

the class IssueManagerContainer method hasErrorIssues.

public boolean hasErrorIssues(Displayable owner, MolecularComponent mc) {
    if (issueManager == null) {
        return false;
    }
    if (owner == null) {
        return false;
    }
    List<Issue> allIssueList = issueManager.getIssueList();
    for (Issue issue : allIssueList) {
        if (issue.getSeverity() != Issue.Severity.ERROR) {
            continue;
        }
        Object source = issue.getSource();
        Object detailedSource = issue.getDetailedSource();
        if (mc != null && source == owner && mc.getComponentStateDefinitions().size() > 0) {
            for (ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
                if (detailedSource == csd) {
                    return true;
                }
            }
        }
    }
    return false;
}

Example 57 with Issue

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

the class MolecularComponentLargeShape method setComponentColor.

private Color setComponentColor() {
    boolean highlight = isHighlighted();
    if (owner == null) {
        return highlight == true ? componentBad.brighter() : componentBad;
    }
    Color componentColor = highlight == true ? componentBad.brighter() : componentBad;
    if (owner instanceof MolecularType) {
        componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
    } else if (owner instanceof SpeciesContext) {
        if (shapePanel != null && !shapePanel.isShowNonTrivialOnly()) {
            componentColor = componentHidden;
        } else {
            componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
        }
    } else if (mcp != null && owner instanceof RbmObservable) {
        if (shapePanel != null && !shapePanel.isEditable()) {
            componentColor = componentHidden;
        } else {
            componentColor = highlight == true ? componentHidden.brighter() : componentHidden;
        }
        if (mcp.getBondType() != BondType.Possible) {
            componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
        }
    } else if (owner instanceof ReactionRule) {
        ReactionRule reactionRule = (ReactionRule) owner;
        if (shapePanel.getDisplayMode() == DisplayMode.participantSignatures) {
            componentColor = componentHidden;
            if (shapePanel.isShowNonTrivialOnly() == true) {
                if (mcp.getBondType() != BondType.Possible) {
                    componentColor = componentPaleYellow;
                } else {
                    componentColor = componentHidden;
                }
            }
            if (shapePanel.isShowDifferencesOnly()) {
                switch(shapePanel.hasBondChanged(reactionRule.getName(), mcp)) {
                    case CHANGED:
                        componentColor = Color.orange;
                        break;
                    case ANALYSISFAILED:
                        ArrayList<Issue> issueList = new ArrayList<Issue>();
                        reactionRule.gatherIssues(new IssueContext(), issueList);
                        boolean bRuleHasErrorIssues = false;
                        for (Issue issue : issueList) {
                            if (issue.getSeverity() == Severity.ERROR) {
                                bRuleHasErrorIssues = true;
                                break;
                            }
                        }
                        if (bRuleHasErrorIssues) {
                            componentColor = componentHidden;
                        } else {
                            System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                            componentColor = Color.red.darker();
                        }
                        break;
                    default:
                        break;
                }
            }
        } else if (shapePanel.getDisplayMode() == DisplayMode.rules) {
            componentColor = componentHidden;
            if (shapePanel.isShowNonTrivialOnly() == true) {
                if (mcp.getBondType() != BondType.Possible) {
                    componentColor = componentPaleYellow;
                } else {
                    componentColor = componentHidden;
                }
            }
            if (shapePanel.isShowDifferencesOnly()) {
                switch(shapePanel.hasBondChanged(mcp)) {
                    case CHANGED:
                        componentColor = Color.orange;
                        break;
                    case ANALYSISFAILED:
                        ArrayList<Issue> issueList = new ArrayList<Issue>();
                        reactionRule.gatherIssues(new IssueContext(), issueList);
                        boolean bRuleHasErrorIssues = false;
                        for (Issue issue : issueList) {
                            if (issue.getSeverity() == Severity.ERROR) {
                                bRuleHasErrorIssues = true;
                                break;
                            }
                        }
                        if (bRuleHasErrorIssues) {
                            componentColor = componentHidden;
                        } else {
                            System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                            componentColor = Color.red.darker();
                        }
                        break;
                    default:
                        break;
                }
            }
        } else {
            componentColor = highlight == true ? componentHidden.brighter() : componentHidden;
            if (mcp.getBondType() != BondType.Possible) {
                componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
            }
        }
    }
    if (hasErrorIssues(owner, mcp, mc)) {
        componentColor = highlight == true ? componentBad.brighter() : componentBad;
    }
    return componentColor;
}

Example 58 with Issue

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

the class MolecularTypeLargeShape method paintSpecies.

// --------------------------------------------------------------------------------------
private void paintSpecies(Graphics g) {
    Graphics2D g2 = (Graphics2D) g;
    Font fontOld = g2.getFont();
    Color colorOld = g2.getColor();
    Stroke strokeOld = g2.getStroke();
    Color primaryColor = null;
    g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    if (mt == null && mtp == null) {
        // plain species context
        Color exterior;
        if (owner == null) {
            // for plain species, we just draw a circle based on height!!! we ignore width!!!
            // error
            exterior = Color.red.darker();
        } else {
            if (!shapePanel.isShowMoleculeColor()) {
                exterior = Color.GRAY;
            } else {
                // plain species
                exterior = Color.green.darker().darker();
            }
        }
        Point2D center = new Point2D.Float(xPos + baseHeight / 3, yPos + baseHeight / 3);
        float radius = baseHeight * 0.5f;
        Point2D focus = new Point2D.Float(xPos + baseHeight / 3 - 1, yPos + baseHeight / 3 - 1);
        float[] dist = { 0.1f, 1.0f };
        Color[] colors = { Color.white, exterior };
        RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
        g2.setPaint(p);
        Ellipse2D circle = new Ellipse2D.Double(xPos, yPos, baseHeight, baseHeight);
        g2.fill(circle);
        Ellipse2D circle2 = new Ellipse2D.Double(xPos - 1, yPos - 1, baseHeight + 0.7, baseHeight + 0.7);
        g2.setPaint(getDefaultColor(Color.DARK_GRAY));
        int z = shapePanel.getZoomFactor();
        g2.setStroke(new BasicStroke(2.0f + 0.14f * z));
        g2.draw(circle2);
        if (owner == null) {
            Font font = fontOld.deriveFont(Font.BOLD);
            g.setFont(font);
            g.setColor(Color.red.darker().darker());
            g2.drawString("Error parsing generated species!", xPos + baseHeight + 10, yPos + baseHeight - 9);
        }
        g2.setFont(fontOld);
        g2.setColor(colorOld);
        g2.setStroke(strokeOld);
        return;
    } else {
        // molecular type, species pattern, observable
        if (mt == null || mt.getModel() == null) {
            primaryColor = Color.blue.darker().darker();
        } else {
            if (shapePanel.getDisplayMode() == DisplayMode.participantSignatures) {
                if (!shapePanel.isShowMoleculeColor()) {
                    primaryColor = AbstractComponentShape.componentVeryLightGray;
                } else {
                    RbmModelContainer rbmmc = mt.getModel().getRbmModelContainer();
                    List<MolecularType> mtList = rbmmc.getMolecularTypeList();
                    int index = mtList.indexOf(mt);
                    index = index % 7;
                    primaryColor = colorTable[index].darker().darker();
                }
                if (shapePanel.isShowDifferencesOnly()) {
                    ReactionRule reactionRule = (ReactionRule) owner;
                    switch(shapePanel.hasNoMatch(reactionRule.getName(), mtp)) {
                        case CHANGED:
                            primaryColor = AbstractComponentShape.deepOrange;
                            break;
                        case // keep whatever color we set above
                        UNCHANGED:
                            break;
                        case ANALYSISFAILED:
                            ArrayList<Issue> issueList = new ArrayList<Issue>();
                            reactionRule.gatherIssues(new IssueContext(), issueList);
                            boolean bRuleHasErrorIssues = false;
                            for (Issue issue : issueList) {
                                if (issue.getSeverity() == Severity.ERROR) {
                                    bRuleHasErrorIssues = true;
                                    break;
                                }
                            }
                            if (bRuleHasErrorIssues) {
                                primaryColor = AbstractComponentShape.componentHidden;
                            } else {
                                System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                                primaryColor = Color.red.darker();
                            }
                            break;
                        default:
                            break;
                    }
                }
            } else if (shapePanel.getDisplayMode() == DisplayMode.rules) {
                if (!shapePanel.isShowMoleculeColor()) {
                    primaryColor = AbstractComponentShape.componentVeryLightGray;
                } else {
                    RbmModelContainer rbmmc = mt.getModel().getRbmModelContainer();
                    List<MolecularType> mtList = rbmmc.getMolecularTypeList();
                    int index = mtList.indexOf(mt);
                    index = index % 7;
                    primaryColor = colorTable[index].darker().darker();
                }
                // if we show difference, we apply that now and override the color
                if (shapePanel.isShowDifferencesOnly()) {
                    ReactionRule reactionRule = (ReactionRule) owner;
                    switch(shapePanel.hasNoMatch(mtp)) {
                        case CHANGED:
                            primaryColor = AbstractComponentShape.deepOrange;
                            break;
                        case // keep whatever color we set above
                        UNCHANGED:
                            break;
                        case ANALYSISFAILED:
                            ArrayList<Issue> issueList = new ArrayList<Issue>();
                            reactionRule.gatherIssues(new IssueContext(), issueList);
                            boolean bRuleHasErrorIssues = false;
                            for (Issue issue : issueList) {
                                if (issue.getSeverity() == Severity.ERROR) {
                                    bRuleHasErrorIssues = true;
                                    break;
                                }
                            }
                            if (bRuleHasErrorIssues) {
                                primaryColor = AbstractComponentShape.componentHidden;
                            } else {
                                System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                                primaryColor = Color.red.darker();
                            }
                            break;
                        default:
                            break;
                    }
                }
            } else {
                // TODO: do we ever get here legitimately? if not throw an exception!
                RbmModelContainer rbmmc = mt.getModel().getRbmModelContainer();
                List<MolecularType> mtList = rbmmc.getMolecularTypeList();
                int index = mtList.indexOf(mt);
                index = index % 7;
                if (!shapePanel.isShowMoleculeColor()) {
                    primaryColor = AbstractComponentShape.componentVeryLightGray;
                } else {
                    primaryColor = isHighlighted() == true ? Color.white : colorTable[index].darker().darker();
                }
                if (hasErrorIssues(owner, mt)) {
                    primaryColor = isHighlighted() ? Color.white : Color.red;
                }
            }
        }
    }
    // paint the structure contour if applicable (only for anchored molecules!)
    if (structure != null && mt != null && !mt.isAnchorAll() && mt.getAnchors().size() > 0) {
        paintNarrowCompartmentRight(g);
    } else if (owner instanceof MolecularType && !mt.isAnchorAll()) {
        paintNarrowCompartmentRight(g);
    }
    // paint the shape of the molecule and fill it with color
    GradientPaint p = new GradientPaint(xPos, yPos, primaryColor, xPos, yPos + baseHeight / 2, Color.WHITE, true);
    g2.setPaint(p);
    RoundRectangle2D rect = new RoundRectangle2D.Float(xPos, yPos, width, baseHeight, cornerArc, cornerArc);
    g2.fill(rect);
    RoundRectangle2D inner = new RoundRectangle2D.Float(xPos + 1, yPos + 1, width - 2, baseHeight - 2, cornerArc - 3, cornerArc - 3);
    if (isHighlighted()) {
        if (hasErrorIssues(owner, mt)) {
            g2.setPaint(Color.red);
        } else {
            g2.setPaint(getDefaultColor(Color.BLACK));
        }
        g2.draw(inner);
        if (hasErrorIssues(owner, mt)) {
            g2.setPaint(Color.red);
        } else {
            g2.setPaint(getDefaultColor(Color.BLACK));
        }
        g2.draw(rect);
    } else {
        if (hasErrorIssues(owner, mt)) {
            g2.setPaint(Color.red.darker());
        } else {
            g2.setPaint(getDefaultColor(Color.GRAY));
        }
        g2.draw(inner);
        if (hasErrorIssues(owner, mt)) {
            g2.setPaint(Color.red.darker());
        } else {
            g2.setPaint(getDefaultColor(Color.DARK_GRAY));
        }
        g2.draw(rect);
    }
    // paint the anchor glyph
    Rectangle r = getAnchorHotspot();
    if (r != null) {
        // g2.drawRect(r.x, r.y, r.width, r.height);	// anchor tooltip hotspot area
        int z = shapePanel.getZoomFactor();
        int w = r.width;
        int x = r.x + w / 2;
        int y = r.y;
        int h = 12 + z / 2;
        h = z < -2 ? h - 1 : h;
        h = z < -4 ? h - 1 : h;
        Line2D line = new Line2D.Float(x, y, x, y + h);
        g2.setPaint(getDefaultColor(Color.RED.darker().darker()));
        g2.setStroke(new BasicStroke(2.6f + 0.13f * z));
        g2.draw(line);
        // TODO: adjust the arc at deep zoom!
        double a1 = z < -3 ? 245 : 240;
        // 60
        double a2 = z < -3 ? 52 : 59;
        Arc2D arc = new Arc2D.Double(x - h, y - h, 2 * h, 2 * h, a1, a2, Arc2D.OPEN);
        g2.setStroke(new BasicStroke(2.6f + 0.20f * z));
        g2.draw(arc);
        g2.setPaint(colorOld);
        g2.setStroke(strokeOld);
    }
    // the text inside the molecule shape
    if (mt == null && mtp == null) {
    // plain species context
    // don't write any text inside
    } else {
        // molecular type, species pattern
        Graphics gc = shapePanel.getGraphics();
        Font font = deriveMoleculeFontBold(g, shapePanel);
        g.setFont(font);
        // font color
        g.setColor(getDefaultColor(Color.BLACK));
        int fontSize = font.getSize();
        int textX = xPos + 11;
        int textY = yPos + baseHeight - (baseHeight - fontSize) / 2;
        g2.drawString(name, textX, textY);
        if (owner instanceof ReactionRule && mtp != null && mtp.hasExplicitParticipantMatch()) {
            int z = shapePanel.getZoomFactor();
            if (z >= LargeShapeCanvas.SmallestZoomFactorWithText) {
                // hide the matching too when we don't display the name
                FontMetrics fm = gc.getFontMetrics(font);
                int stringWidth = fm.stringWidth(name);
                Font smallerFont = font.deriveFont(font.getSize() * 0.8F);
                g.setFont(smallerFont);
                g2.drawString(mtp.getParticipantMatchLabel(), textX + stringWidth + 2, textY + 2);
            }
        }
    }
    g.setFont(fontOld);
    g.setColor(colorOld);
    g2.setStroke(strokeOld);
    for (MolecularComponentLargeShape mcls : componentShapes) {
        // paint the components
        mcls.paintSelf(g);
    }
    g2.setFont(fontOld);
    g2.setColor(colorOld);
    g2.setStroke(strokeOld);
}

Example 59 with Issue

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

the class TestingFrameworkWindowManager method hasDuplicateIdentifiers.

private boolean hasDuplicateIdentifiers(BioModel bioModel) {
    ArrayList<Issue> issueList = new ArrayList<Issue>();
    IssueContext issueContext = new IssueContext();
    bioModel.gatherIssues(issueContext, issueList);
    boolean bFoundIdentifierConflictUponLoading = false;
    for (Issue issue : issueList) {
        if (issue.getCategory() == IssueCategory.Identifiers && issue.getSource() == bioModel.getModel() && issue.getSeverity() == Severity.ERROR) {
            bFoundIdentifierConflictUponLoading = true;
            break;
        }
    }
    return bFoundIdentifierConflictUponLoading;
}

Example 60 with Issue

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

the class SpeciesPattern method checkSpeciesPattern.

public void checkSpeciesPattern(IssueContext issueContext, List<Issue> issueList) {
    for (MolecularTypePattern mtp : getMolecularTypePatterns()) {
        for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
            if (mcp.isImplied()) {
                continue;
            }
            if (mcp.getBondType() == BondType.Specified) {
                Bond b = mcp.getBond();
                if (b == null && issueList != null) {
                    String msg = "The Bonds of Species Pattern " + this.toString() + " do not match.\n";
                    IssueSource parent = issueContext.getContextObject();
                    issueList.add(new Issue(parent, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
                    return;
                }
            }
        }
    }
}