/**
*
- * BH j2s SwingJS Added PropertyChangeListener for returns from VueUI.
+ * BH (early) j2s SwingJS Added PropertyChangeListener for returns from VueUI.
+ *
+ * BH 2019.05.15 flashes white background solution: replaced during-paint
+ * setBackground() with g.setColor();g.fill();
+ *
+ * BH 2019.05.15 initialization shows popup menu raw creation objects solution:
+ * moved menu creation out of paintComponent()
*
- *
- *
*
* The RNA 2D Panel is a lightweight component that allows for an automatic
* basic drawing of an RNA secondary structures. The drawing algorithms do not
*
*/
-public class VARNAPanel extends JPanel implements PropertyChangeListener {
-
- /**
- * SwingJS uses a PropertyChangeEvent to signal that a pseudo-modal dialog has been closed.
- *
- * @param event
- */
- @Override
- public void propertyChange(PropertyChangeEvent event) {
- Object val = event.getNewValue();
- switch (event.getPropertyName()) {
- case "value":
- _UI.onDialogReturn(val == null ? JOptionPane.CLOSED_OPTION : ((Integer) val).intValue());
- return;
- case "SelectedFile":
- case "SelectedColor":
- case "inputValue":
- _UI.onDialogReturn(val);
- break;
- }
- }
-
-
-
- private static final long serialVersionUID = 8194421570308956001L;
-
- private RNA _RNA = new RNA();
-
- private boolean _debug = false;
-
- private VARNAConfig _conf = new VARNAConfig();
-
- private ArrayList<InterfaceVARNAListener> _VARNAListeners = new ArrayList<InterfaceVARNAListener>();
- private ArrayList<InterfaceVARNASelectionListener> _selectionListeners = new ArrayList<InterfaceVARNASelectionListener>();
- private ArrayList<InterfaceVARNARNAListener> _RNAListeners = new ArrayList<InterfaceVARNARNAListener>();
- private ArrayList<InterfaceVARNABasesListener> _basesListeners = new ArrayList<InterfaceVARNABasesListener>();
-
- UndoManager _manager;
-
- // private boolean _foldMode = true;
-
- private Point2D.Double[] _realCoords = new Point2D.Double[0];
- private Point2D.Double[] _realCenters = new Point2D.Double[0];
- private double _scaleFactor = 1.0;
- private Point2D.Double _offsetPanel = new Point2D.Double();
- private Point2D.Double _offsetRNA = new Point2D.Double();
-
- private double _offX;
- private double _offY;
-
- private ControleurBlinkingThread _blink;
- private BaseList _selectedBases = new BaseList("selection");
- private ArrayList<ModeleBase> _backupSelection = new ArrayList<ModeleBase>();
- private Integer _nearestBase = null;
- private Point2D.Double _lastSelectedCoord = new Point2D.Double(0.0, 0.0);
-
- private Point2D.Double _linkOrigin = null;
- private Point2D.Double _linkDestination = null;
-
- private Rectangle _selectionRectangle = null;
-
- private boolean _highlightAnnotation = false;
-
- private int _titleHeight;
- private Dimension _border = new Dimension(0, 0);
-
- private boolean _drawBBox = false;
- private boolean _drawBorder = false;
-
- // private Point _positionRelativeSouris;
- private Point _translation;
- private boolean _horsCadre;
- private boolean _premierAffichage;
-
- private ControleurInterpolator _interpolator;
- /**
- * If comparison mode is TRUE (ON), then the application will be used to
- * display a super-structure resulting on an RNA secondary structure
- * comparison. Else, the application is used by default.
- */
-
- private VueMenu _popup = new VueMenu(this);
-
- private VueUI _UI = new VueUI(this);
-
- private TextAnnotation _selectedAnnotation;
-
- /**
- * Creates an RNA 2D panel with initially displays the empty structure.
- *
- * @throws ExceptionNonEqualLength
- *
- */
- public VARNAPanel() {
- init();
- drawRNA();
- }
-
- /**
- * Creates an RNA 2D panel, and creates and displays an RNA coupled with its
- * secondary structure formatted as a well-balanced parenthesis with dots
- * word (DBN format).
- *
- * @param seq
- * The raw nucleotide sequence
- * @param str
- * The secondary structure in DBN format
- * @throws ExceptionNonEqualLength
- */
-
- public VARNAPanel(String seq, String str) throws ExceptionNonEqualLength {
- this(seq, str, RNA.DRAW_MODE_RADIATE);
- }
-
- /**
- * Creates a VARNAPanel instance, and creates and displays an RNA coupled
- * with its secondary structure formatted as a well-balanced parenthesis
- * with dots word (DBN format). Allows the user to choose the drawing
- * algorithm to be used.
- *
- * @param seq
- * The raw nucleotide sequence
- * @param str
- * The secondary structure in DBN format
- * @param drawMode
- * The drawing mode
- * @throws ExceptionNonEqualLength
- * @see RNA#DRAW_MODE_RADIATE
- * @see RNA#DRAW_MODE_CIRCULAR
- * @see RNA#DRAW_MODE_NAVIEW
- */
- public VARNAPanel(String seq, String str, int drawMode)
- throws ExceptionNonEqualLength {
- this(seq, str, drawMode, "");
- }
-
- public VARNAPanel(Reader r) throws ExceptionNonEqualLength,
- ExceptionFileFormatOrSyntax {
- this(r, RNA.DRAW_MODE_RADIATE);
- }
-
- public VARNAPanel(Reader r, int drawMode) throws ExceptionNonEqualLength,
- ExceptionFileFormatOrSyntax {
- this(r, drawMode, "");
- }
-
- public VARNAPanel(Reader r, int drawMode, String title)
- throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax {
- init();
- drawRNA(r, drawMode);
- setTitle(title);
- }
-
- public void setOriginLink(Point2D.Double p) {
- _linkOrigin = (p);
- }
-
- public void setDestinationLink(Point2D.Double p) {
- _linkDestination = (p);
- }
-
- public void removeLink() {
- _linkOrigin = null;
- _linkDestination = null;
- }
-
- /**
- * Creates a VARNAPanel instance, and displays an RNA.
- *
- * @param r
- * The RNA to be displayed within this panel
- */
-
- public VARNAPanel(RNA r) {
- showRNA(r);
- init();
- }
-
- /**
- * Creates a VARNAPanel instance, and creates and displays an RNA coupled
- * with its secondary structure formatted as a well-balanced parenthesis
- * with dots word (DBN format). Allows the user to choose the drawing
- * algorithm to be used. Additionally, sets the panel's title.
- *
- * @param seq
- * The raw nucleotide sequence
- * @param str
- * The secondary structure in DBN format
- * @param drawMode
- * The drawing mode
- * @param title
- * The panel title
- * @throws ExceptionNonEqualLength
- * @see RNA#DRAW_MODE_CIRCULAR
- * @see RNA#DRAW_MODE_RADIATE
- * @see RNA#DRAW_MODE_NAVIEW
- */
-
- public VARNAPanel(String seq, String str, int drawMode, String title)
- throws ExceptionNonEqualLength {
- drawRNA(seq, str, drawMode);
- init();
- setTitle(title);
- // VARNASecDraw._vp = this;
- }
-
- public VARNAPanel(String seq1, String struct1, String seq2, String struct2,
- int drawMode, String title) {
- _conf._comparisonMode = true;
- drawRNA(seq1, struct1, seq2, struct2, drawMode);
- init();
- setTitle(title);
- }
-
- private void init() {
- setBackground(VARNAConfig.DEFAULT_BACKGROUND_COLOR);
- _manager = new UndoManager();
- _manager.setLimit(10000);
- _UI.addUndoableEditListener(_manager);
-
- _blink = new ControleurBlinkingThread(this,
- ControleurBlinkingThread.DEFAULT_FREQUENCY, 0, 1.0, 0.0, 0.2);
- _blink.start();
-
- _premierAffichage = true;
- _translation = new Point(0, 0);
-
- _horsCadre = false;
- this.setFont(_conf._fontBasesGeneral);
-
- // ajout des controleurs au VARNAPanel
- ControleurClicMovement controleurClicMovement = new ControleurClicMovement(
- this);
- this.addMouseListener(controleurClicMovement);
- this.addMouseMotionListener(controleurClicMovement);
- this.addMouseWheelListener(new ControleurMolette(this));
-
- ControleurDraggedMolette ctrlDraggedMolette = new ControleurDraggedMolette(
- this);
- this.addMouseMotionListener(ctrlDraggedMolette);
- this.addMouseListener(ctrlDraggedMolette);
-
- ControleurVARNAPanelKeys ctrlKey = new ControleurVARNAPanelKeys(this);
- this.addKeyListener(ctrlKey);
- this.addFocusListener(ctrlKey);
-
- _interpolator = new ControleurInterpolator(this);
- /**
- *
- * BH SwingJS do not start this thread
- *
- * @j2sNative
- */
- {
- _interpolator.start();
- }
-
- }
-
- public void undo() {
- if (_manager.canUndo())
- _manager.undo();
- }
-
- public void redo() {
- if (_manager.canRedo())
- _manager.redo();
- }
-
- /**
- * Sets the new style of the title font.
- *
- * @param newStyle
- * An int that describes the new font style ("PLAIN","BOLD",
- * "BOLDITALIC", or "ITALIC")
- */
- public void setTitleFontStyle(int newStyle) {
- _conf._titleFont = _conf._titleFont.deriveFont(newStyle);
- updateTitleHeight();
- }
-
- /**
- * Sets the new size of the title font.
- *
- * @param newSize
- * The new size of the title font
- */
- public void setTitleFontSize(float newSize) {
- //System.err.println("Applying title size "+newSize);
- _conf._titleFont = _conf._titleFont.deriveFont(newSize);
- updateTitleHeight();
- }
-
- /**
- * Sets the new font family to be used for the title. Available fonts are
- * system-specific, yet it seems that "Arial", "Dialog", and "MonoSpaced"
- * are almost always available.
- *
- * @param newFamily
- * New font family used for the title
- */
- public void setTitleFontFamily(String newFamily) {
- _conf._titleFont = new Font(newFamily, _conf._titleFont.getStyle(),
- _conf._titleFont.getSize());
- updateTitleHeight();
- }
-
- /**
- * Sets the color to be used for the title.
- *
- * @param newColor
- * A color used to draw the title
- */
- public void setTitleFontColor(Color newColor) {
- _conf._titleColor = newColor;
- updateTitleHeight();
- }
-
- /**
- * Sets the font size for displaying bases
- *
- * @param size
- * Font size for base caption
- */
-
- public void setBaseFontSize(Float size) {
- _conf._fontBasesGeneral = _conf._fontBasesGeneral.deriveFont(size);
- }
-
- /**
- * Sets the font size for displaying base numbers
- *
- * @param size
- * Font size for base numbers
- */
-
- public void setNumbersFontSize(Float size) {
- _conf._numbersFont = _conf._numbersFont.deriveFont(size);
- }
-
- /**
- * Sets the font style for displaying bases
- *
- * @param style
- * An int that describes the new font style ("PLAIN","BOLD",
- * "BOLDITALIC", or "ITALIC")
- */
-
- public void setBaseFontStyle(int style) {
- _conf._fontBasesGeneral = _conf._fontBasesGeneral.deriveFont(style);
- }
-
- private void updateTitleHeight() {
- if (!getTitle().equals("")) {
- _titleHeight = (int) (_conf._titleFont.getSize() * 1.5);
- } else {
- _titleHeight = 0;
- }
- if (Math.abs(this.getZoom() - 1) < .02) {
- _translation.y = (int) (-getTitleHeight() / 2.0);
- }
- }
-
- /**
- * Sets the panel's title, giving a short description of the RNA secondary
- * structure.
- *
- * @param title
- * The new title
- */
- public void setTitle(String title) {
- _RNA.setName(title);
- updateTitleHeight();
- }
-
- /**
- * Sets the distance between consecutive base numbers. Please notice that :
- * <ul>
- * <li>The first and last base are always numbered</li>
- * <li>The numbering is based on the base numbers, not on the indices. So
- * base numbers may appear more frequently than expected if bases are
- * skipped</li>
- * <li>The periodicity is measured starting from 0. This means that for a
- * period of 10 and bases numbered from 1 to 52, the base numbers
- * [1,10,20,30,40,50,52] will be drawn.</li>
- * </ul>
- *
- * @param n
- * New numbering period
- */
- public void setNumPeriod(int n) {
- _conf._numPeriod = n;
- }
-
- /**
- * Returns the current numbering period. Please notice that :
- * <ul>
- * <li>The first and last base are always numbered</li>
- * <li>The numbering is based on the base numbers, not on the indices. So
- * base numbers may appear more frequently than expected if bases are
- * skipped</li>
- * <li>The periodicity is measured starting from 0. This means that for a
- * period of 10 and bases numbered from 1 to 52, the base numbers
- * [1,10,20,30,40,50,52] will be drawn.</li>
- * </ul>
- *
- * @return Current numbering period
- */
- public int getNumPeriod() {
- return _conf._numPeriod;
- }
-
- private void setScaleFactor(double d) {
- _scaleFactor = d;
- }
-
- private double getScaleFactor() {
- return _scaleFactor;
- }
-
- private void setAutoFit(boolean fit) {
- _conf._autoFit = fit;
- repaint();
- }
-
- public void lockScrolling() {
- setAutoFit(false);
- setAutoCenter(false);
- }
-
- public void unlockScrolling() {
- setAutoFit(true);
- setAutoCenter(true);
- }
-
- private void drawStringOutline(VueVARNAGraphics g2D, String res, double x,
- double y, double margin) {
- Dimension d = g2D.getStringDimension(res);
- x -= (double) d.width / 2.0;
- y += (double) d.height / 2.0;
- g2D.setColor(Color.GRAY);
- g2D.setSelectionStroke();
- g2D.drawRect((x - margin), (y - d.height - margin),
- (d.width + 2.0 * margin), (d.height + 2.0 * margin));
- }
-
- private void drawSymbol(VueVARNAGraphics g2D, double posx, double posy,
- double normx, double normy, double radius, boolean isCIS,
- ModeleBP.Edge e) {
- Color bck = g2D.getColor();
- switch (e) {
- case WC:
- if (isCIS) {
- g2D.setColor(bck);
- g2D.fillCircle((posx - (radius) / 2.0),
- (posy - (radius) / 2.0), radius);
- g2D.drawCircle((posx - (radius) / 2.0),
- (posy - (radius) / 2.0), radius);
- } else {
- g2D.setColor(Color.white);
- g2D.fillCircle(posx - (radius) / 2.0, (posy - (radius) / 2.0),
- (radius));
- g2D.setColor(bck);
- g2D.drawCircle((posx - (radius) / 2.0),
- (posy - (radius) / 2.0), (radius));
- }
- break;
- case HOOGSTEEN: {
- GeneralPath p2 = new GeneralPath();
- radius /= 1.05;
- p2.moveTo((float) (posx - radius * normx / 2.0 - radius * normy
- / 2.0), (float) (posy - radius * normy / 2.0 + radius
- * normx / 2.0));
- p2.lineTo((float) (posx + radius * normx / 2.0 - radius * normy
- / 2.0), (float) (posy + radius * normy / 2.0 + radius
- * normx / 2.0));
- p2.lineTo((float) (posx + radius * normx / 2.0 + radius * normy
- / 2.0), (float) (posy + radius * normy / 2.0 - radius
- * normx / 2.0));
- p2.lineTo((float) (posx - radius * normx / 2.0 + radius * normy
- / 2.0), (float) (posy - radius * normy / 2.0 - radius
- * normx / 2.0));
- p2.closePath();
-
- if (isCIS) {
- g2D.setColor(bck);
- g2D.fill(p2);
- g2D.draw(p2);
- } else {
- g2D.setColor(Color.white);
- g2D.fill(p2);
- g2D.setColor(bck);
- g2D.draw(p2);
- }
- }
- break;
- case SUGAR: {
- double ix = radius * normx / 2.0;
- double iy = radius * normy / 2.0;
- double jx = radius * normy / 2.0;
- double jy = -radius * normx / 2.0;
-
- GeneralPath p2 = new GeneralPath();
- p2.moveTo((float) (posx - ix + jx), (float) (posy - iy + jy));
- p2.lineTo((float) (posx + ix + jx), (float) (posy + iy + jy));
- p2.lineTo((float) (posx - jx), (float) (posy - jy));
- p2.closePath();
-
- if (isCIS) {
- g2D.setColor(bck);
- g2D.fill(p2);
- g2D.draw(p2);
- } else {
- g2D.setColor(Color.white);
- g2D.fill(p2);
- g2D.setColor(bck);
- g2D.draw(p2);
- }
- }
- break;
- }
- g2D.setColor(bck);
- }
-
- private void drawBasePairArc(VueVARNAGraphics g2D, int i, int j,
- Point2D.Double orig, Point2D.Double dest, double scaleFactor,
- ModeleBP style, double newRadius) {
- double distance, coef;
- if (j - i == 1)
- coef = getBPHeightIncrement() * 1.75;
- else
- coef = getBPHeightIncrement();
- distance = dest.x - orig.x;
- switch (_conf._mainBPStyle) {
- case LW: {
- double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0)
- * scaleFactor;
- if (style.isCanonical()) {
- if (style.isCanonicalGC()) {
- if ((orig.x != dest.x) || (orig.y != dest.y)) {
- g2D.drawArc((dest.x + orig.x) / 2., dest.y
- - scaleFactor * _RNA.BASE_RADIUS / 2.0,
- (distance - scaleFactor * _RNA.BASE_RADIUS
- / 3.0), (distance * coef - scaleFactor
- * _RNA.BASE_RADIUS / 3.0), 0, 180);
- g2D.drawArc((dest.x + orig.x) / 2., dest.y
- - scaleFactor * _RNA.BASE_RADIUS / 2.0,
- (distance + scaleFactor * _RNA.BASE_RADIUS
- / 3.0), (distance * coef + scaleFactor
- * _RNA.BASE_RADIUS / 3.0), 0, 180);
- }
- } else if (style.isCanonicalAU()) {
- g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor
- * _RNA.BASE_RADIUS / 2.0, (distance),
- (distance * coef), 0, 180);
- } else if (style.isWobbleUG()) {
- Point2D.Double midtop = new Point2D.Double(
- (dest.x + orig.x) / 2., dest.y - distance * coef
- / 2. - scaleFactor * _RNA.BASE_RADIUS / 2.0);
- g2D.drawArc(midtop.x, dest.y - scaleFactor
- * _RNA.BASE_RADIUS / 2.0, (distance),
- (distance * coef), 0, 180);
- drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle,
- false, ModeleBP.Edge.WC);
- } else {
- Point2D.Double midtop = new Point2D.Double(
- (dest.x + orig.x) / 2., dest.y - distance * coef
- / 2. - scaleFactor * _RNA.BASE_RADIUS / 2.0);
- g2D.drawArc(midtop.x, dest.y - scaleFactor
- * _RNA.BASE_RADIUS / 2.0, (distance),
- (distance * coef), 0, 180);
- drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle,
- style.isCIS(), style.getEdgePartner5());
- }
- } else {
- ModeleBP.Edge p1 = style.getEdgePartner5();
- ModeleBP.Edge p2 = style.getEdgePartner3();
- Point2D.Double midtop = new Point2D.Double(
- (dest.x + orig.x) / 2., dest.y - distance * coef / 2.
- - scaleFactor * _RNA.BASE_RADIUS / 2.0);
- g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS
- / 2.0, (distance), (distance * coef), 0, 180);
- if (p1 == p2) {
- drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle,
- false, style.getEdgePartner5());
- } else {
- drawSymbol(g2D, midtop.x - scaleFactor * _RNA.BASE_RADIUS,
- midtop.y, 1., 0., radiusCircle, style.isCIS(), p1);
- drawSymbol(g2D, midtop.x + scaleFactor * _RNA.BASE_RADIUS,
- midtop.y, -1., 0., radiusCircle, style.isCIS(), p2);
- }
- }
- }
- break;
- case LW_ALT: {
- double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0)
- * scaleFactor;
- double distFromBaseCenter = DISTANCE_FACT*scaleFactor;
- orig = new Point2D.Double(orig.x,orig.y-(distFromBaseCenter+newRadius));
- dest = new Point2D.Double(dest.x,dest.y-(distFromBaseCenter+newRadius));
- if (style.isCanonical()) {
- if (style.isCanonicalGC()) {
- if ((orig.x != dest.x) || (orig.y != dest.y)) {
- g2D.drawArc((dest.x + orig.x) / 2., dest.y
- - scaleFactor * _RNA.BASE_RADIUS / 2.0,
- (distance - scaleFactor * _RNA.BASE_RADIUS
- / 3.0), (distance * coef - scaleFactor
- * _RNA.BASE_RADIUS / 3.0), 0, 180);
- g2D.drawArc((dest.x + orig.x) / 2., dest.y
- - scaleFactor * _RNA.BASE_RADIUS / 2.0,
- (distance + scaleFactor * _RNA.BASE_RADIUS
- / 3.0), (distance * coef + scaleFactor
- * _RNA.BASE_RADIUS / 3.0), 0, 180);
- }
- } else if (style.isCanonicalAU()) {
- g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor
- * _RNA.BASE_RADIUS / 2.0, (distance),
- (distance * coef), 0, 180);
- }
- } else {
- ModeleBP.Edge p1 = style.getEdgePartner5();
- ModeleBP.Edge p2 = style.getEdgePartner3();
- Point2D.Double midtop = new Point2D.Double(
- (dest.x + orig.x) / 2., dest.y - distance * coef / 2.
- - scaleFactor * _RNA.BASE_RADIUS / 2.0);
- g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS
- / 2.0, (distance), (distance * coef), 0, 180);
- drawSymbol(g2D, orig.x,
- orig.y-radiusCircle*.95, 1., 0., radiusCircle, style.isCIS(), p1);
- drawSymbol(g2D, dest.x,
- dest.y-radiusCircle*.95, -1., 0., radiusCircle, style.isCIS(), p2);
- }
- }
- break;
- default:
- g2D.drawArc((dest.x + orig.x) / 2., dest.y - scaleFactor
- * _RNA.BASE_RADIUS / 2.0, (distance), (distance * coef), 0,
- 180);
- break;
- }
-
- }
-
- public static double DISTANCE_FACT = 2.;
-
-
- private void drawBasePair(VueVARNAGraphics g2D, Point2D.Double orig,
- Point2D.Double dest, ModeleBP style, double newRadius,
- double scaleFactor) {
-
- double dx = dest.x - orig.x;
- double dy = dest.y - orig.y;
- double dist = Math.sqrt((dest.x - orig.x) * (dest.x - orig.x)
- + (dest.y - orig.y) * (dest.y - orig.y));
- dx /= dist;
- dy /= dist;
- double nx = -dy;
- double ny = dx;
- orig = new Point2D.Double(orig.x + newRadius * dx, orig.y + newRadius
- * dy);
- dest = new Point2D.Double(dest.x - newRadius * dx, dest.y - newRadius
- * dy);
- switch (_conf._mainBPStyle) {
- case LW: {
- double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0)
- * scaleFactor;
- if (style.isCanonical()) {
- if (style.isCanonicalGC()) {
- if ((orig.x != dest.x) || (orig.y != dest.y)) {
- nx *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
- ny *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
- g2D.drawLine((orig.x + nx), (orig.y + ny),
- (dest.x + nx), (dest.y + ny));
- g2D.drawLine((orig.x - nx), (orig.y - ny),
- (dest.x - nx), (dest.y - ny));
- }
- } else if (style.isCanonicalAU()) {
- g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
- } else if (style.isWobbleUG()) {
- double cx = (dest.x + orig.x) / 2.0;
- double cy = (dest.y + orig.y) / 2.0;
- g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
- drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, false,
- ModeleBP.Edge.WC);
- } else {
- double cx = (dest.x + orig.x) / 2.0;
- double cy = (dest.y + orig.y) / 2.0;
- g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
- drawSymbol(g2D, cx, cy, nx, ny, radiusCircle,
- style.isCIS(), style.getEdgePartner5());
- }
- } else {
- ModeleBP.Edge p1 = style.getEdgePartner5();
- ModeleBP.Edge p2 = style.getEdgePartner3();
- double cx = (dest.x + orig.x) / 2.0;
- double cy = (dest.y + orig.y) / 2.0;
- g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
- if (p1 == p2) {
- drawSymbol(g2D, cx, cy, nx, ny, radiusCircle,
- style.isCIS(), p1);
-
- } else {
- double vdx = (dest.x - orig.x);
- double vdy = (dest.y - orig.y);
- vdx /= 6.0;
- vdy /= 6.0;
- drawSymbol(g2D, cx + vdx, cy + vdy, -nx, -ny, radiusCircle,
- style.isCIS(), p2);
- drawSymbol(g2D, cx - vdx, cy - vdy, nx, ny, radiusCircle,
- style.isCIS(), p1);
- }
- }
- }
- break;
- case LW_ALT: {
- double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0)
- * scaleFactor;
- double distFromBaseCenter = DISTANCE_FACT*scaleFactor;
- Point2D.Double norig = new Point2D.Double(orig.x+(distFromBaseCenter+.5*newRadius)*dx,orig.y+(distFromBaseCenter+.5*newRadius)*dy);
- Point2D.Double ndest = new Point2D.Double(dest.x-(distFromBaseCenter+.5*newRadius)*dx,dest.y-(distFromBaseCenter+.5*newRadius)*dy);
- if (style.isCanonical()) {
- if (style.isCanonicalGC()) {
- if ((norig.x != ndest.x) || (norig.y != ndest.y)) {
- nx *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
- ny *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
- g2D.drawLine((norig.x + nx), (norig.y + ny),
- (ndest.x + nx), (ndest.y + ny));
- g2D.drawLine((norig.x - nx), (norig.y - ny),
- (ndest.x - nx), (ndest.y - ny));
- }
- } else if (style.isCanonicalAU()) {
- g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
- } else if (style.isWobbleUG()) {
- double cx = (ndest.x + norig.x) / 2.0;
- double cy = (ndest.y + norig.y) / 2.0;
- g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
- drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, false,
- ModeleBP.Edge.WC);
- } else {
- double cx = (ndest.x + norig.x) / 2.0;
- double cy = (ndest.y + norig.y) / 2.0;
- g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
- drawSymbol(g2D, cx, cy, nx, ny, radiusCircle,
- style.isCIS(), style.getEdgePartner5());
- }
- } else {
- ModeleBP.Edge p1 = style.getEdgePartner5();
- ModeleBP.Edge p2 = style.getEdgePartner3();
- double cx = (ndest.x + norig.x) / 2.0;
- double cy = (ndest.y + norig.y) / 2.0;
- g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
- if (p1 == p2) {
- drawSymbol(g2D, cx, cy, nx, ny, radiusCircle,
- style.isCIS(), p1);
-
- } else {
- double fac = .4;
- drawSymbol(g2D, ndest.x - fac*radiusCircle*dx, ndest.y - fac*radiusCircle*dy, -nx, -ny, radiusCircle,
- style.isCIS(), p2);
- drawSymbol(g2D, norig.x + fac*radiusCircle*dx, norig.y + fac*radiusCircle*dy, nx, ny, radiusCircle,
- style.isCIS(), p1);
- }
- }
- }
- break;
- case SIMPLE:
- g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
- break;
- case RNAVIZ:
- double xcenter = (orig.x + dest.x) / 2.0;
- double ycenter = (orig.y + dest.y) / 2.0;
- double radius = Math.max(4.0 * scaleFactor, 1.0);
- g2D.fillCircle((xcenter - radius), (ycenter - radius),
- (2.0 * radius));
- break;
- case NONE:
- break;
- }
- }
-
- private Color getHighlightedVersion(Color c1, Color c2) {
- int r1 = c1.getRed();
- int g1 = c1.getGreen();
- int b1 = c1.getBlue();
- int r2 = c2.getRed();
- int g2 = c2.getGreen();
- int b2 = c2.getBlue();
- double val = _blink.getVal();
- int nr = Math.max(0,
- Math.min((int) ((r1 * val + r2 * (1.0 - val))), 255));
- int ng = Math.max(0,
- Math.min((int) ((g1 * val + g2 * (1.0 - val))), 255));
- int nb = Math.max(0,
- Math.min((int) ((b1 * val + b2 * (1.0 - val))), 255));
- return new Color(nr, ng, nb);
- }
-
- private Color highlightFilter(int index, Color initialColor, Color c1,
- Color c2, boolean localView) {
- if (_selectedBases.contains(_RNA.getBaseAt(index)) && localView) {
- return getHighlightedVersion(c1, c2);
- } else
- return initialColor;
- }
-
- public static Point2D.Double computeExcentricUnitVector(int i,
- Point2D.Double[] points, Point2D.Double[] centers) {
- double dist = points[i].distance(centers[i]);
- Point2D.Double byCenter = new Point2D.Double(
- (points[i].x - centers[i].x) / dist,
- (points[i].y - centers[i].y) / dist);
- if ((i > 0) && (i < points.length - 1)) {
- Point2D.Double p0 = points[i - 1];
- Point2D.Double p1 = points[i];
- Point2D.Double p2 = points[i + 1];
- double dist1 = p2.distance(p1);
- Point2D.Double v1 = new Point2D.Double((p2.x - p1.x) / dist1,
- (p2.y - p1.y) / dist1);
- Point2D.Double vn1 = new Point2D.Double(v1.y, -v1.x);
- double dist2 = p1.distance(p0);
- Point2D.Double v2 = new Point2D.Double((p1.x - p0.x) / dist2,
- (p1.y - p0.y) / dist2);
- Point2D.Double vn2 = new Point2D.Double(v2.y, -v2.x);
- Point2D.Double vn = new Point2D.Double((vn1.x + vn2.x) / 2.0,
- (vn1.y + vn2.y) / 2.0);
- double D = vn.distance(new Point2D.Double(0.0, 0.0));
- vn.x /= D;
- vn.y /= D;
- if (byCenter.x * vn.x + byCenter.y * vn.y < 0) {
- vn.x = -vn.x;
- vn.y = -vn.y;
- }
- return vn;
- }
- else if (((i==0) || (i==points.length-1)) && (points.length>1)) {
- int a = (i==0)?0:points.length-1;
- int b = (i==0)?1:points.length-2;
- double D = points[a].distance(points[b]);
- return new Point2D.Double(
- (points[a].x - points[b].x) / D,
- (points[a].y - points[b].y) / D);
- }
- else {
- return byCenter;
- }
- }
-
- private void drawBase(VueVARNAGraphics g2D, int i, Point2D.Double[] points,
- Point2D.Double[] centers, double newRadius, double _scaleFactor,
- boolean localView) {
- Point2D.Double p = points[i];
- ModeleBase mb = _RNA.get_listeBases().get(i);
- g2D.setFont(_conf._fontBasesGeneral);
- Color baseInnerColor = highlightFilter(i,
- _RNA.getBaseInnerColor(i, _conf), Color.white,
- _RNA.getBaseInnerColor(i, _conf), localView);
- Color baseOuterColor = highlightFilter(i,
- _RNA.getBaseOuterColor(i, _conf),
- _RNA.getBaseOuterColor(i, _conf), Color.white, localView);
- Color baseNameColor = highlightFilter(i,
- _RNA.getBaseNameColor(i, _conf),
- _RNA.getBaseNameColor(i, _conf), Color.white, localView);
- if ( RNA.whiteLabelPreferrable(baseInnerColor))
- {
- baseNameColor=Color.white;
- }
-
- if (mb instanceof ModeleBaseNucleotide) {
- ModeleBaseNucleotide mbn = (ModeleBaseNucleotide) mb;
- String res = mbn.getBase();
- if (_hoveredBase == mb && localView && isModifiable()) {
- g2D.setColor(_conf._hoverColor);
- g2D.fillCircle(p.getX() - 1.5 * newRadius, p.getY() - 1.5
- * newRadius, 3.0 * newRadius);
- g2D.setColor(_conf._hoverColor.darker());
- g2D.drawCircle(p.getX() - 1.5 * newRadius, p.getY() - 1.5
- * newRadius, 3.0 * newRadius);
- g2D.setPlainStroke();
- }
- if (_conf._fillBases) {
- // Filling inner circle
- g2D.setColor(baseInnerColor);
- g2D.fillCircle(p.getX() - newRadius, p.getY() - newRadius,
- 2.0 * newRadius);
- }
-
- if (_conf._drawOutlineBases) {
- // Drawing outline
- g2D.setColor(baseOuterColor);
- g2D.setStrokeThickness(_conf._baseThickness * _scaleFactor);
- g2D.drawCircle(p.getX() - newRadius, p.getY() - newRadius,
- 2.0 * newRadius);
- }
- // Drawing label
- g2D.setColor(baseNameColor);
- g2D.drawStringCentered(String.valueOf(res), p.getX(), p.getY());
- } else if (mb instanceof ModeleBasesComparison) {
-
- ModeleBasesComparison mbc = (ModeleBasesComparison) mb;
-
- // On lui donne l'aspect voulue (on a un trait droit)
- g2D.setPlainStroke(); // On doit avoir un trait droit, sans arrondit
- g2D.setStrokeThickness(_conf._baseThickness * _scaleFactor);
-
- // On dessine l'étiquette, rectangle aux bords arrondies.
- g2D.setColor(baseInnerColor);
- g2D.fillRoundRect((p.getX() - 1.5 * newRadius),
- (p.getY() - newRadius), (3.0 * newRadius),
- (2.0 * newRadius), 10 * _scaleFactor, 10 * _scaleFactor);
-
- /* Dessin du rectangle exterieur (bords) */
- g2D.setColor(baseOuterColor);
- g2D.drawRoundRect((p.getX() - 1.5 * newRadius),
- (p.getY() - newRadius), (3 * newRadius), (2 * newRadius),
- 10 * _scaleFactor, 10 * _scaleFactor);
-
- // On le dessine au centre de l'étiquette.
- g2D.drawLine((p.getX()), (p.getY() + newRadius) - 1, (p.getX()),
- (p.getY() - newRadius) + 1);
-
- /* Dessin du nom de la base (A,C,G,U,etc...) */
- // On créer le texte des étiquettes
- String label1 = String.valueOf(mbc.getBase1());
- String label2 = String.valueOf(mbc.getBase2());
-
- // On leur donne une couleur
- g2D.setColor(getRNA().get_listeBases().get(i).getStyleBase()
- .getBaseNameColor());
-
- // Et on les dessine.
- g2D.drawStringCentered(label1, p.getX() - (.75 * newRadius),
- p.getY());
- g2D.drawStringCentered(label2, p.getX() + (.75 * newRadius),
- p.getY());
- }
-
- // Drawing base number
- if (_RNA.isNumberDrawn(mb, getNumPeriod())) {
-
- Point2D.Double vn = computeExcentricUnitVector(i, points, centers);
- g2D.setColor(mb.getStyleBase().getBaseNumberColor());
- g2D.setFont(_conf._numbersFont);
- double factorMin = Math.min(.5, _conf._distNumbers);
- double factorMax = Math.min(_conf._distNumbers - 1.5,
- _conf._distNumbers);
- g2D.drawLine(p.x + vn.x * ((1 + factorMin) * newRadius), p.y + vn.y
- * ((1 + factorMin) * newRadius), p.x + vn.x
- * ((1 + factorMax) * newRadius), p.y + vn.y
- * ((1 + factorMax) * newRadius));
- g2D.drawStringCentered(mb.getLabel(), p.x + vn.x
- * ((1 + _conf._distNumbers) * newRadius), p.y + vn.y
- * ((1 + _conf._distNumbers) * newRadius));
-
- }
- }
-
- void drawChemProbAnnotation(VueVARNAGraphics g2D, ChemProbAnnotation cpa,
- Point2D.Double anchor, double scaleFactor) {
- g2D.setColor(cpa.getColor());
- g2D.setStrokeThickness(RNA.CHEM_PROB_ARROW_THICKNESS * scaleFactor
- * cpa.getIntensity());
- g2D.setPlainStroke();
- Point2D.Double v = cpa.getDirVector();
- Point2D.Double vn = cpa.getNormalVector();
- Point2D.Double base = new Point2D.Double(
- (anchor.x + _RNA.CHEM_PROB_DIST * scaleFactor * v.x),
- (anchor.y + _RNA.CHEM_PROB_DIST * scaleFactor * v.y));
- Point2D.Double edge = new Point2D.Double(
- (base.x + _RNA.CHEM_PROB_BASE_LENGTH * cpa.getIntensity()
- * scaleFactor * v.x),
- (base.y + _RNA.CHEM_PROB_BASE_LENGTH * cpa.getIntensity()
- * scaleFactor * v.y));
- switch (cpa.getType()) {
- case ARROW: {
- Point2D.Double arrowTip1 = new Point2D.Double(
- (base.x + cpa.getIntensity()
- * scaleFactor
- * (_RNA.CHEM_PROB_ARROW_WIDTH * vn.x + _RNA.CHEM_PROB_ARROW_HEIGHT
- * v.x)),
- (base.y + cpa.getIntensity()
- * scaleFactor
- * (_RNA.CHEM_PROB_ARROW_WIDTH * vn.y + _RNA.CHEM_PROB_ARROW_HEIGHT
- * v.y)));
- Point2D.Double arrowTip2 = new Point2D.Double(
- (base.x + cpa.getIntensity()
- * scaleFactor
- * (-_RNA.CHEM_PROB_ARROW_WIDTH * vn.x + _RNA.CHEM_PROB_ARROW_HEIGHT
- * v.x)),
- (base.y + cpa.getIntensity()
- * scaleFactor
- * (-_RNA.CHEM_PROB_ARROW_WIDTH * vn.y + _RNA.CHEM_PROB_ARROW_HEIGHT
- * v.y)));
- g2D.drawLine(base.x, base.y, edge.x, edge.y);
- g2D.drawLine(base.x, base.y, arrowTip1.x, arrowTip1.y);
- g2D.drawLine(base.x, base.y, arrowTip2.x, arrowTip2.y);
- }
- break;
- case PIN: {
- Point2D.Double side1 = new Point2D.Double(
- (edge.x - cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.x)),
- (edge.y - cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.y)));
- Point2D.Double side2 = new Point2D.Double(
- (edge.x - cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.x)),
- (edge.y - cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.y)));
- Point2D.Double side3 = new Point2D.Double(
- (edge.x + cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.x)),
- (edge.y + cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.y)));
- Point2D.Double side4 = new Point2D.Double(
- (edge.x + cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.x)),
- (edge.y + cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.y)));
- GeneralPath p2 = new GeneralPath();
- p2.moveTo((float) side1.x, (float) side1.y);
- p2.lineTo((float) side2.x, (float) side2.y);
- p2.lineTo((float) side3.x, (float) side3.y);
- p2.lineTo((float) side4.x, (float) side4.y);
- p2.closePath();
- g2D.fill(p2);
- g2D.drawLine(base.x, base.y, edge.x, edge.y);
- }
- break;
- case TRIANGLE: {
- Point2D.Double arrowTip1 = new Point2D.Double(
- (edge.x + cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.x)),
- (edge.y + cpa.getIntensity() * scaleFactor
- * (_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.y)));
- Point2D.Double arrowTip2 = new Point2D.Double(
- (edge.x + cpa.getIntensity() * scaleFactor
- * (-_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.x)),
- (edge.y + cpa.getIntensity() * scaleFactor
- * (-_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.y)));
- GeneralPath p2 = new GeneralPath();
- p2.moveTo((float) base.x, (float) base.y);
- p2.lineTo((float) arrowTip1.x, (float) arrowTip1.y);
- p2.lineTo((float) arrowTip2.x, (float) arrowTip2.y);
- p2.closePath();
- g2D.fill(p2);
- }
- break;
- case DOT: {
- Double radius = scaleFactor * _RNA.CHEM_PROB_DOT_RADIUS
- * cpa.getIntensity();
- Point2D.Double center = new Point2D.Double((base.x + radius * v.x),
- (base.y + radius * v.y));
- g2D.fillCircle((center.x - radius), (center.y - radius),
- (2 * radius));
- }
- break;
- }
- }
-
- Point2D.Double buildCaptionPosition(ModeleBase mb, double scaleFactor,
- double heightEstimate) {
- double radius = 2.0;
- if (_RNA.isNumberDrawn(mb, getNumPeriod())) {
- radius += _conf._distNumbers;
- }
- Point2D.Double center = mb.getCenter();
- Point2D.Double p = mb.getCoords();
- double realDistance = _RNA.BASE_RADIUS * radius + heightEstimate;
- return new Point2D.Double(center.getX() + (p.getX() - center.getX())
- * ((p.distance(center) + realDistance) / p.distance(center)),
- center.getY()
- + (p.getY() - center.getY())
- * ((p.distance(center) + realDistance) / p
- .distance(center)));
- }
-
- private void renderAnnotations(VueVARNAGraphics g2D, double offX,
- double offY, double rnaBBoxX, double rnaBBoxY, double scaleFactor) {
- for (TextAnnotation textAnnotation : _RNA.getAnnotations()) {
- g2D.setColor(textAnnotation.getColor());
- g2D.setFont(textAnnotation
- .getFont()
- .deriveFont(
- (float) (2.0 * textAnnotation.getFont().getSize() * scaleFactor)));
- Point2D.Double position = textAnnotation.getCenterPosition();
- if (textAnnotation.getType() == TextAnnotation.AnchorType.BASE) {
- ModeleBase mb = (ModeleBase) textAnnotation.getAncrage();
- double fontHeight = Math.ceil(textAnnotation.getFont()
- .getSize());
- position = buildCaptionPosition(mb, scaleFactor, fontHeight);
- }
- position = transformCoord(position, offX, offY, rnaBBoxX, rnaBBoxY,
- scaleFactor);
- g2D.drawStringCentered(textAnnotation.getTexte(), position.x,
- position.y);
- if ((_selectedAnnotation == textAnnotation)
- && (_highlightAnnotation)) {
- drawStringOutline(g2D, textAnnotation.getTexte(), position.x,
- position.y, 5);
- }
- }
- for (ChemProbAnnotation cpa : _RNA.getChemProbAnnotations()) {
- Point2D.Double anchor = transformCoord(cpa.getAnchorPosition(),
- offX, offY, rnaBBoxX, rnaBBoxY, scaleFactor);
- drawChemProbAnnotation(g2D, cpa, anchor, scaleFactor);
- }
-
- }
-
- public Rectangle2D.Double getExtendedRNABBox() {
- // We get the logical bounding box
- Rectangle2D.Double rnabbox = _RNA.getBBox();
- rnabbox.y -= _conf._distNumbers * _RNA.BASE_RADIUS;
- rnabbox.height += 2.0 * _conf._distNumbers * _RNA.BASE_RADIUS;
- rnabbox.x -= _conf._distNumbers * _RNA.BASE_RADIUS;
- rnabbox.width += 2.0 * _conf._distNumbers * _RNA.BASE_RADIUS;
- if (_RNA.hasVirtualLoops()) {
- rnabbox.y -= RNA.VIRTUAL_LOOP_RADIUS;
- rnabbox.height += 2.0 * RNA.VIRTUAL_LOOP_RADIUS;
- rnabbox.x -= RNA.VIRTUAL_LOOP_RADIUS;
- rnabbox.width += 2.0 * RNA.VIRTUAL_LOOP_RADIUS;
- }
- return rnabbox;
- }
-
- public void drawBackbone(VueVARNAGraphics g2D, Point2D.Double[] newCoords,
- double newRadius, double _scaleFactor) {
- // Drawing backbone
- if (getDrawBackbone()) {
- g2D.setStrokeThickness(1.5 * _scaleFactor);
- g2D.setColor(_conf._backboneColor);
-
- ModeleBackbone bck = _RNA.getBackbone();
-
-
- for (int i = 1; i < _RNA.get_listeBases().size(); i++) {
- Point2D.Double p1 = newCoords[i - 1];
- Point2D.Double p2 = newCoords[i];
- double dist = p1.distance(p2);
- int a = _RNA.getBaseAt(i - 1).getElementStructure();
- int b = _RNA.getBaseAt(i).getElementStructure();
- boolean consecutivePair = (a == i) && (b == i - 1);
-
- if ((dist > 0)) {
- Point2D.Double vbp = new Point2D.Double();
- vbp.x = (p2.x - p1.x) / dist;
- vbp.y = (p2.y - p1.y) / dist;
-
- BackboneType bt = bck.getTypeBefore(i);
- if (bt!=BackboneType.DISCONTINUOUS_TYPE)
- {
- if (bt==BackboneType.MISSING_PART_TYPE) {
- g2D.setSelectionStroke();
- } else {
- g2D.setPlainStroke();
- }
- g2D.setColor(bck.getColorBefore(i, _conf._backboneColor));
-
- if (consecutivePair
- && (_RNA.getDrawMode() != RNA.DRAW_MODE_LINEAR)
- && (_RNA.getDrawMode() != RNA.DRAW_MODE_CIRCULAR)) {
- int dir = 0;
- if (i + 1 < newCoords.length) {
- dir = (_RNA.testDirectionality(i - 1, i, i + 1) ? -1
- : 1);
- } else if (i - 2 >= 0) {
- dir = (_RNA.testDirectionality(i - 2, i - 1, i) ? -1
- : 1);
- }
- Point2D.Double vn = new Point2D.Double(dir * vbp.y,
- -dir * vbp.x);
- Point2D.Double centerSeg = new Point2D.Double(
- (p1.x + p2.x) / 2.0, (p1.y + p2.y) / 2.0);
- double distp1CenterSeq = p1.distance(centerSeg);
- double centerDist = Math
- .sqrt((RNA.VIRTUAL_LOOP_RADIUS * _scaleFactor
- * RNA.VIRTUAL_LOOP_RADIUS * _scaleFactor)
- - distp1CenterSeq * distp1CenterSeq);
- Point2D.Double centerLoop = new Point2D.Double(
- centerSeg.x + centerDist * vn.x, centerSeg.y
- + centerDist * vn.y);
- double radius = centerLoop.distance(p1);
- double a1 = 360.
- * (Math.atan2(-(p1.y - centerLoop.y),
- (p1.x - centerLoop.x)))
- / (2. * Math.PI);
- double a2 = 360.
- * (Math.atan2(-(p2.y - centerLoop.y),
- (p2.x - centerLoop.x)))
- / (2. * Math.PI);
- double angle = (a2 - a1);
- if (-dir * angle < 0) {
- angle += -dir * 360.;
- }
- // if (angle<0.) angle += 360.;
- // angle = -dir*(360-dir*angle);
- g2D.drawArc(centerLoop.x + .8 * newRadius * vn.x,
- centerLoop.y + .8 * newRadius * vn.y,
- 2 * radius, 2 * radius, a1, angle);
- } else {
- g2D.drawLine((newCoords[i - 1].x + newRadius * vbp.x),
- (newCoords[i - 1].y + newRadius * vbp.y),
- (newCoords[i].x - newRadius * vbp.x),
- (newCoords[i].y - newRadius * vbp.y));
- }
- }
- }
- }
- }
- }
-
- public Point2D.Double logicToPanel(Point2D.Double logicPoint) {
- return new Point2D.Double(_offX
- + (getScaleFactor() * (logicPoint.x - _offsetRNA.x)), _offY
- + (getScaleFactor() * (logicPoint.y - _offsetRNA.y)));
-
- }
-
- public Rectangle2D.Double renderRNA(VueVARNAGraphics g2D,
- Rectangle2D.Double bbox) {
- return renderRNA(g2D, bbox, false, true);
- }
-
- private double computeScaleFactor(Rectangle2D.Double bbox,
- boolean localView, boolean autoCenter) {
- Rectangle2D.Double rnabbox = getExtendedRNABBox();
- double scaleFactor = Math.min((double) bbox.width
- / (double) rnabbox.width, (double) bbox.height
- / (double) rnabbox.height);
-
- // Use it to get an estimate of the font size for numbers ...
- float newFontSize = Math.max(1,
- (int) ((1.7 * _RNA.BASE_RADIUS) * scaleFactor));
- // ... and increase bounding box accordingly
- rnabbox.y -= newFontSize;
- rnabbox.height += newFontSize;
- if (_conf._drawColorMap) {
- rnabbox.height += getColorMapHeight();
- }
- rnabbox.x -= newFontSize;
- rnabbox.width += newFontSize;
-
- // Now, compute the final scaling factor and corresponding font size
- scaleFactor = Math.min((double) bbox.width / (double) rnabbox.width,
- (double) bbox.height / (double) rnabbox.height);
- if (localView) {
- if (_conf._autoFit)
- setScaleFactor(scaleFactor);
- scaleFactor = getScaleFactor();
- }
- return scaleFactor;
- }
-
- public synchronized Rectangle2D.Double renderRNA(VueVARNAGraphics g2D,
- Rectangle2D.Double bbox, boolean localView, boolean autoCenter) {
- Rectangle2D.Double rnaMultiBox = new Rectangle2D.Double(0, 0, 1, 1);
- double scaleFactor = computeScaleFactor(bbox, localView, autoCenter);
- float newFontSize = Math.max(1,
- (int) ((1.7 * _RNA.BASE_RADIUS) * scaleFactor));
- double newRadius = Math.max(1.0, (scaleFactor * _RNA.BASE_RADIUS));
- setBaseFontSize(newFontSize);
- setNumbersFontSize(newFontSize);
- double offX = bbox.x;
- double offY = bbox.y;
- Rectangle2D.Double rnabbox = getExtendedRNABBox();
-
- if (_RNA.getSize() != 0) {
-
- Point2D.Double offsetRNA = new Point2D.Double(rnabbox.x, rnabbox.y);
-
- if (autoCenter) {
- offX = (bbox.x + (bbox.width - Math.round(rnabbox.width
- * scaleFactor)) / 2.0);
- offY = (bbox.y + (bbox.height - Math.round(rnabbox.height
- * scaleFactor)) / 2.0);
- if (localView) {
- _offX = offX;
- _offY = offY;
- _offsetPanel = new Point2D.Double(_offX, _offY);
- _offsetRNA = new Point2D.Double(rnabbox.x, rnabbox.y);
- }
- }
-
- if (localView) {
- offX = _offX;
- offY = _offY;
- offsetRNA = _offsetRNA;
- }
-
- // Re-scaling once and for all
- Point2D.Double[] newCoords = new Point2D.Double[_RNA
- .get_listeBases().size()];
- Point2D.Double[] newCenters = new Point2D.Double[_RNA
- .get_listeBases().size()];
- for (int i = 0; i < _RNA.get_listeBases().size(); i++) {
- ModeleBase mb = _RNA.getBaseAt(i);
- newCoords[i] = new Point2D.Double(offX
- + (scaleFactor * (mb.getCoords().x - offsetRNA.x)),
- offY + (scaleFactor * (mb.getCoords().y - offsetRNA.y)));
-
- Point2D.Double centerBck = _RNA.getCenter(i);
- // si la base est dans un angle entre une boucle et une helice
- if (_RNA.get_drawMode() == RNA.DRAW_MODE_NAVIEW
- || _RNA.get_drawMode() == RNA.DRAW_MODE_RADIATE) {
- if ((mb.getElementStructure() != -1)
- && i < _RNA.get_listeBases().size() - 1 && i > 1) {
- ModeleBase b1 = _RNA.get_listeBases().get(i - 1);
- ModeleBase b2 = _RNA.get_listeBases().get(i + 1);
- int j1 = b1.getElementStructure();
- int j2 = b2.getElementStructure();
- if ((j1 == -1) ^ (j2 == -1)) {
- // alors la position du nombre associé doit etre
- Point2D.Double a1 = b1.getCoords();
- Point2D.Double a2 = b2.getCoords();
- Point2D.Double c1 = b1.getCenter();
- Point2D.Double c2 = b2.getCenter();
-
- centerBck.x = mb.getCoords().x + (c1.x - a1.x)
- / c1.distance(a1) + (c2.x - a2.x)
- / c2.distance(a2);
- centerBck.y = mb.getCoords().y + (c1.y - a1.y)
- / c1.distance(a1) + (c2.y - a2.y)
- / c2.distance(a2);
- }
- }
- }
- newCenters[i] = new Point2D.Double(offX
- + (scaleFactor * (centerBck.x - offsetRNA.x)), offY
- + (scaleFactor * (centerBck.y - offsetRNA.y)));
- }
- // Keep track of coordinates for mouse interactions
- if (localView) {
- _realCoords = newCoords;
- _realCenters = newCenters;
- }
-
- g2D.setStrokeThickness(1.5 * scaleFactor);
- g2D.setPlainStroke();
- g2D.setFont(_conf._fontBasesGeneral);
-
- // Drawing region highlights Annotation
- drawRegionHighlightsAnnotation(g2D, _realCoords, _realCenters,
- scaleFactor);
- drawBackbone(g2D, newCoords, newRadius, scaleFactor);
-
- // Drawing base-pairs
- // pour chaque base
- for (int i = 0; i < _RNA.get_listeBases().size(); i++) {
- int j = _RNA.get_listeBases().get(i).getElementStructure();
- // si c'est une parenthese ouvrante (premiere base du
- // couple)
- if (j > i) {
- ModeleBP msbp = _RNA.get_listeBases().get(i).getStyleBP();
- // System.err.println(msbp);
- if (msbp.isCanonical() || _conf._drawnNonCanonicalBP) {
- if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) {
- g2D.setStrokeThickness(_RNA.getBasePairThickness(
- msbp, _conf)
- * 2.0
- * scaleFactor
- * _conf._bpThickness);
- } else {
- g2D.setStrokeThickness(_RNA.getBasePairThickness(
- msbp, _conf) * 1.5 * scaleFactor);
- }
- g2D.setColor(_RNA.getBasePairColor(msbp, _conf));
-
- if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) {
- drawBasePairArc(g2D, i, j, newCoords[i],
- newCoords[j], scaleFactor, msbp, newRadius);
- } else {
- drawBasePair(g2D, newCoords[i], newCoords[j], msbp,
- newRadius, scaleFactor);
- }
- }
- }
- }
-
- // Liaisons additionelles (non planaires)
- if (_conf._drawnNonPlanarBP) {
- ArrayList<ModeleBP> bpaux = _RNA.getStructureAux();
- for (int k = 0; k < bpaux.size(); k++) {
- ModeleBP msbp = bpaux.get(k);
- if (msbp.isCanonical() || _conf._drawnNonCanonicalBP) {
- int i = msbp.getPartner5().getIndex();
- int j = msbp.getPartner3().getIndex();
- if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) {
- g2D.setStrokeThickness(_RNA.getBasePairThickness(
- msbp, _conf)
- * 2.5
- * scaleFactor
- * _conf._bpThickness);
- g2D.setPlainStroke();
- } else {
- g2D.setStrokeThickness(_RNA.getBasePairThickness(
- msbp, _conf) * 1.5 * scaleFactor);
- g2D.setPlainStroke();
- }
-
- g2D.setColor(_RNA.getBasePairColor(msbp, _conf));
- if (j > i) {
- if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) {
- drawBasePairArc(g2D, i, j, newCoords[i],
- newCoords[j], scaleFactor, msbp, newRadius);
- } else {
- drawBasePair(g2D, newCoords[i], newCoords[j],
- msbp, newRadius, scaleFactor);
- }
- }
- }
- }
- }
-
- // Drawing bases
- g2D.setPlainStroke();
- for (int i = 0; i < Math.min(_RNA.get_listeBases().size(),
- newCoords.length); i++) {
- drawBase(g2D, i, newCoords, newCenters, newRadius, scaleFactor,
- localView);
- }
-
- rnaMultiBox = new Rectangle2D.Double(offX, offY,
- (scaleFactor * rnabbox.width) - 1,
- (scaleFactor * rnabbox.height) - 1);
-
- if (localView) {
- // Drawing bbox
- if (_debug || _drawBBox) {
- g2D.setColor(Color.RED);
- g2D.setSelectionStroke();
- g2D.drawRect(rnaMultiBox.x, rnaMultiBox.y,
- rnaMultiBox.width, rnaMultiBox.height);
- }
-
- // Draw color map
- if (_conf._drawColorMap) {
- drawColorMap(g2D, scaleFactor, rnabbox);
- }
-
- if (_debug || _drawBBox) {
- g2D.setColor(Color.GRAY);
- g2D.setSelectionStroke();
- g2D.drawRect(0, 0, getWidth() - 1, getHeight()
- - getTitleHeight() - 1);
- }
- }
- // Draw annotations
- renderAnnotations(g2D, offX, offY, offsetRNA.x, offsetRNA.y,
- scaleFactor);
- // Draw additional debug shape
- if (_RNA._debugShape != null) {
- Color c = new Color(255, 0, 0, 50);
- g2D.setColor(c);
- AffineTransform at = new AffineTransform();
- at.translate(offX - scaleFactor * rnabbox.x, offY - scaleFactor
- * rnabbox.y);
- at.scale(scaleFactor, scaleFactor);
- Shape s = at.createTransformedShape(_RNA._debugShape);
- if (s instanceof GeneralPath) {
- g2D.fill((GeneralPath) s);
- }
- }
- } else {
- g2D.setColor(VARNAConfig.DEFAULT_MESSAGE_COLOR);
- g2D.setFont(VARNAConfig.DEFAULT_MESSAGE_FONT);
- rnaMultiBox = new Rectangle2D.Double(0,0,10,10);
- g2D.drawStringCentered("No RNA here", bbox.getCenterX(),bbox.getCenterY());
- }
- return rnaMultiBox;
- }
-
- public void centerViewOn(double x, double y) {
- Rectangle2D.Double r = _RNA.getBBox();
- _target = new Point2D.Double(x, y);
- Point2D.Double q = logicToPanel(_target);
- Point p = new Point((int) (-q.x), (int) (-q.y));
- setTranslation(p);
- repaint();
- }
-
- Point2D.Double _target = new Point2D.Double(0, 0);
- Point2D.Double _target2 = new Point2D.Double(0, 0);
-
- public ModeleBase getBaseAt(Point2D.Double po) {
- ModeleBase mb = null;
- Point2D.Double p = panelToLogicPoint(po);
- double dist = Double.MAX_VALUE;
- for (ModeleBase tmp : _RNA.get_listeBases()) {
- double ndist = tmp.getCoords().distance(p);
- if (dist > ndist) {
- mb = tmp;
- dist = ndist;
- }
- }
- return mb;
- }
-
- public void setColorMapValues(Double[] values) {
- _RNA.setColorMapValues(values, _conf._cm, true);
- _conf._drawColorMap = true;
- repaint();
- }
-
- public void setColorMapMaxValue(double d) {
- _conf._cm.setMaxValue(d);
- }
-
- public void setColorMapMinValue(double d) {
- _conf._cm.setMinValue(d);
- }
-
- public ModeleColorMap getColorMap() {
- return _conf._cm;
- }
-
- public void setColorMap(ModeleColorMap cm) {
- //_RNA.adaptColorMapToValues(cm);
- _conf._cm = cm;
- repaint();
- }
-
- public void setColorMapCaption(String caption) {
- _conf._colorMapCaption = caption;
- repaint();
- }
-
- public String getColorMapCaption() {
- return _conf._colorMapCaption;
- }
-
- public void drawColorMap(boolean draw) {
- _conf._drawColorMap = draw;
- }
-
- private double getColorMapHeight() {
- double result = VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE
- + _conf._colorMapHeight;
- if (!_conf._colorMapCaption.equals(""))
- result += VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE;
- return result;
- }
-
- private void drawColorMap(VueVARNAGraphics g2D, double scaleFactor,
- Rectangle2D.Double rnabbox) {
- double v1 = _conf._cm.getMinValue();
- double v2 = _conf._cm.getMaxValue();
- double x, y;
- g2D.setPlainStroke();
-
- double xSpaceAvail = 0;
- double ySpaceAvail = Math
- .min((getHeight() - rnabbox.height * scaleFactor - getTitleHeight()) / 2.0,
- scaleFactor
- * (_conf._colorMapHeight + VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE));
- if ((int) ySpaceAvail == 0) {
- xSpaceAvail = Math.min(
- (getWidth() - rnabbox.width * scaleFactor) / 2, scaleFactor
- * (_conf._colorMapWidth)
- + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH);
- }
- double xBase = (xSpaceAvail + _offX + scaleFactor
- * (rnabbox.width - _conf._colorMapWidth - _conf._colorMapXOffset));
- double hcaption = VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE;
- double yBase = (ySpaceAvail + _offY + scaleFactor
- * (rnabbox.height - _conf._colorMapHeight
- - _conf._colorMapYOffset - hcaption));
-
- for (int i = 0; i < _conf._colorMapWidth; i++) {
- double ratio = (((double) i) / ((double) _conf._colorMapWidth));
- double val = v1 + (v2 - v1) * ratio;
- g2D.setColor(_conf._cm.getColorForValue(val));
- x = (xBase + scaleFactor * i);
- y = yBase;
- g2D.fillRect(x, y, scaleFactor
- * VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH,
- (scaleFactor * _conf._colorMapHeight));
- }
- g2D.setColor(VARNAConfig.DEFAULT_COLOR_MAP_OUTLINE);
- g2D.drawRect(xBase, yBase,
- (VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH - 1 + scaleFactor
- * _conf._colorMapWidth),
- ((scaleFactor * _conf._colorMapHeight)));
- g2D.setFont(getFont()
- .deriveFont(
- (float) (scaleFactor * VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE)));
- g2D.setColor(VARNAConfig.DEFAULT_COLOR_MAP_FONT_COLOR);
- NumberFormat nf = NumberFormat.getInstance();
- nf.setMaximumFractionDigits(2);
- nf.setMinimumFractionDigits(0);
- g2D.drawStringCentered(nf.format(_conf._cm.getMinValue()), xBase,
- yBase
- + scaleFactor * (_conf._colorMapHeight+(VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7)));
- g2D.drawStringCentered(nf.format(_conf._cm.getMaxValue()), xBase
- + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH + scaleFactor
- * _conf._colorMapWidth,
- yBase
- + scaleFactor * (_conf._colorMapHeight+(VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7)));
- if (!_conf._colorMapCaption.equals(""))
- g2D.drawStringCentered(
- "" + _conf._colorMapCaption,
- xBase + scaleFactor * _conf._colorMapWidth / 2.0,
- yBase
- + scaleFactor
- * (VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7 + _conf._colorMapHeight));
-
- }
-
- public Point2D.Double panelToLogicPoint(Point2D.Double p) {
- return new Point2D.Double(
- ((p.x - getOffsetPanel().x) / getScaleFactor())
- + getRNAOffset().x,
- ((p.y - getOffsetPanel().y) / getScaleFactor())
- + getRNAOffset().y);
- }
-
- public Point2D.Double transformCoord(Point2D.Double coordDebut,
- double offX, double offY, double rnaBBoxX, double rnaBBoxY,
- double scaleFactor) {
- return new Point2D.Double(offX
- + (scaleFactor * (coordDebut.x - rnaBBoxX)), offY
- + (scaleFactor * (coordDebut.y - rnaBBoxY)));
- }
-
- public void eraseSequence() {
- _RNA.eraseSequence();
- }
-
- public Point2D.Double transformCoord(Point2D.Double coordDebut) {
- Rectangle2D.Double rnabbox = getExtendedRNABBox();
- return new Point2D.Double(_offX
- + (getScaleFactor() * (coordDebut.x - rnabbox.x)), _offY
- + (getScaleFactor() * (coordDebut.y - rnabbox.y)));
- }
-
- public void paintComponent(Graphics g) {
- paintComponent(g, false);
- }
-
- public void paintComponent(Graphics g, boolean transparentBackground) {
- if (_premierAffichage) {
- // _border = new Dimension(0, 0);
- _translation.x = 0;
- _translation.y = (int) (-getTitleHeight() / 2.0);
- _popup.buildPopupMenu();
- this.add(_popup);
- _premierAffichage = false;
- }
-
- Graphics2D g2 = (Graphics2D) g;
- Stroke dflt = g2.getStroke();
- VueVARNAGraphics g2D = new SwingGraphics(g2);
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
- this.removeAll();
- super.paintComponent(g2);
- renderComponent(g2D, transparentBackground, getScaleFactor());
- if (isFocusOwner()) {
- g2.setStroke(new BasicStroke(1.5f));
- g2.setColor(Color.decode("#C0C0C0"));
- g2.drawRect(0, 0, getWidth() - 1, getHeight() - 1);
-
- }
- g2.setStroke(dflt);
- /*
- * PSExport e = new PSExport(); SecStrProducerGraphics export = new
- * SecStrProducerGraphics(e); renderRNA(export, getExtendedRNABBox());
- * try { export.saveToDisk("./out.ps"); } catch
- * (ExceptionWritingForbidden e1) { e1.printStackTrace(); }
- */
- }
-
- /**
- * Draws current RNA structure in a given Graphics "device".
- *
- * @param g2D
- * A graphical device
- * @param transparentBackground
- * Whether the background should be transparent, or drawn.
- */
- public synchronized void renderComponent(VueVARNAGraphics g2D,
- boolean transparentBackground, double scaleFactor) {
-
- updateTitleHeight();
-
- if (_debug || _drawBorder) {
- g2D.setColor(Color.BLACK);
- g2D.setPlainStroke();
- g2D.drawRect(getLeftOffset(), getTopOffset(), getInnerWidth(),
- getInnerHeight());
-
- }
-
-
- if (!transparentBackground) {
- super.setBackground(_conf._backgroundColor);
- } else {
- super.setBackground(new Color(0, 0, 0, 120));
- }
-
- // BH 2018 was lt, not lteq here
- // SwingJS sets the minimum panel size -- probably incorrectly -- to the size for VARNAPanel
- if (getMinimumSize().height <= getSize().height
- && getMinimumSize().width <= getSize().width) {
- // Draw Title
- if (!getTitle().equals("")) {
- g2D.setColor(_conf._titleColor);
- g2D.setFont(_conf._titleFont);
- g2D.drawStringCentered(getTitle(), this.getWidth() / 2,
- this.getHeight() - getTitleHeight() / 2.0);
- }
- // Draw RNA
- renderRNA(g2D, getClip(), true, _conf._autoCenter);
- }
- if (_selectionRectangle != null) {
- g2D.setColor(Color.BLACK);
- g2D.setSelectionStroke();
- g2D.drawRect(_selectionRectangle.x, _selectionRectangle.y,
- _selectionRectangle.width, _selectionRectangle.height);
- }
- if ((_linkOrigin != null) && (_linkDestination != null)) {
- g2D.setColor(_conf._bondColor);
- g2D.setPlainStroke();
- g2D.setStrokeThickness(3.0 * scaleFactor);
- Point2D.Double linkOrigin = (_linkOrigin);
- Point2D.Double linkDestination = (_linkDestination);
- g2D.drawLine(linkOrigin.x, linkOrigin.y, linkDestination.x,
- linkDestination.y);
- for (int i : getSelection().getIndices())
- drawBase(g2D, i, _realCoords, _realCenters, scaleFactor
- * _RNA.BASE_RADIUS, scaleFactor, true);
- }
-
- if (_debug) {
- g2D.setStrokeThickness(3.0 * scaleFactor);
- g2D.setColor(Color.black);
- Point2D.Double t = this.logicToPanel(_target);
- g2D.drawLine(t.x - 3, t.y - 3, t.x + 3, t.y + 3);
- g2D.drawLine(t.x - 3, t.y + 3, t.x + 3, t.y - 3);
- g2D.setColor(Color.red);
- t = this.logicToPanel(_target2);
- g2D.drawLine(t.x - 3, t.y - 3, t.x + 3, t.y + 3);
- g2D.drawLine(t.x - 3, t.y + 3, t.x + 3, t.y - 3);
- }
- }
-
- public void drawRegionHighlightsAnnotation(VueVARNAGraphics g2D,
- Point2D.Double[] realCoords, Point2D.Double[] realCenters,
- double scaleFactor) {
- g2D.setStrokeThickness(2.0 * scaleFactor);
- g2D.setPlainStroke();
- for (HighlightRegionAnnotation r : _RNA.getHighlightRegion()) {
- GeneralPath s = r.getShape(realCoords, realCenters, scaleFactor);
- g2D.setColor(r.getFillColor());
- g2D.fill(s);
- g2D.setColor(r.getOutlineColor());
- g2D.draw(s);
- }
- }
-
- private Rectangle2D.Double getClip() {
- return new Rectangle2D.Double(getLeftOffset(), getTopOffset(),
- this.getInnerWidth(), this.getInnerHeight());
- }
-
- public Rectangle2D.Double getViewClip() {
- return new Rectangle2D.Double(this.getLeftOffset(),
- this.getTopOffset(), this.getInnerWidth(),
- this.getInnerHeight());
- }
-
- /**
- * Returns the color used to draw backbone bounds.
- *
- * @return The color used to draw backbone bounds
- */
- public Color getBackboneColor() {
- return _conf._backboneColor;
- }
-
- /**
- * Sets the color to be used for drawing backbone interactions.
- *
- * @param backbone_color
- * The new color for the backbone bounds
- */
- public void setBackboneColor(Color backbone_color) {
- _conf._backboneColor = backbone_color;
- }
-
- /**
- * Returns the color used to display hydrogen bonds (base pairings)
- *
- * @return The color of hydrogen bonds
- */
- public Color getBondColor() {
- return _conf._bondColor;
- }
-
- /**
- * Returns the title of this panel
- *
- * @return The title
- */
- public String getTitle() {
- return _RNA.getName();
- }
-
- /**
- * Sets the new color to be used for hydrogen bonds (base pairings)
- *
- * @param bond_color
- * The new color for hydrogen bonds
- */
- public void setDefaultBPColor(Color bond_color) {
- _conf._bondColor = bond_color;
- }
-
- /**
- * Sets the size of the border, i.e. the empty space between the end of the
- * drawing area and the actual border.
- *
- * @param b
- * The new border size
- */
- public void setBorderSize(Dimension b) {
- _border = b;
- }
-
- /**
- * Returns the size of the border, i.e. the empty space between the end of
- * the drawing area
- *
- * @return The border size
- */
- public Dimension getBorderSize() {
- return _border;
- }
-
- /**
- * Sets the RNA to be displayed within this Panel. This method does not use
- * a drawing algorithm to reassigns base coordinates, rather assuming that
- * the RNA was previously drawn.
- *
- * @param r
- * An already drawn RNA to display in this panel
- */
- public synchronized void showRNA(RNA r) {
- fireUINewStructure(r);
- _RNA = r;
- }
-
- /**
- * Sets the RNA secondary structure to be drawn in this panel, using the
- * default layout algorithm. In addition to the raw nucleotides sequence,
- * the secondary structure is given in the so-called "Dot-bracket notation"
- * (DBN) format. This format is a well-parenthesized word over the alphabet
- * '(',')','.'.<br/>
- * Ex:<code>((((((((....))))..(((((...))).))))))</code><br />
- * Returns <code>true</code> if the sequence/structure couple could be
- * parsed into a valid secondary structure, and <code>false</code>
- * otherwise.
- *
- * @param seq
- * The raw nucleotides sequence
- * @param str
- * The secondary structure
- * @throws ExceptionNonEqualLength
- */
- public void drawRNA(String seq, String str) throws ExceptionNonEqualLength {
- drawRNA(seq, str, _RNA.get_drawMode());
- }
-
- /**
- * Sets the RNA secondary structure to be drawn in this panel, using a given
- * layout algorithm.
- *
- * @param r
- * The new secondary structure
- * @param drawMode
- * The drawing algorithm
- */
- public void drawRNA(RNA r, int drawMode) {
- r.setDrawMode(drawMode);
- drawRNA(r);
- }
-
- /**
- * Redraws the current RNA. This reassigns base coordinates to their default
- * value using the current drawing algorithm.
- */
-
- public void drawRNA() {
- try {
- _RNA.drawRNA(_RNA.get_drawMode(), _conf);
- } catch (ExceptionNAViewAlgorithm e) {
- errorDialog(e);
- e.printStackTrace();
- }
- repaint();
- }
-
- /**
- * Sets the RNA secondary structure to be drawn in this panel, using the
- * current drawing algorithm.
- *
- * @param r
- * The new secondary structure
- */
- public void drawRNA(RNA r) {
- if (r != null) {
- _RNA = r;
- drawRNA();
- }
- }
-
- /**
- * Sets the RNA secondary structure to be drawn in this panel, using a given
- * layout algorithm. In addition to the raw nucleotides sequence, the
- * secondary structure is given in the so-called "Dot-bracket notation"
- * (DBN) format. This format is a well-parenthesized word over the alphabet
- * '(',')','.'.<br/>
- * Ex: <code>((((((((....))))..(((((...))).))))))</code><br />
- * Returns <code>true</code> if the sequence/structure couple could be
- * parsed into a valid secondary structure, and <code>false</code>
- * otherwise.
- *
- * @param seq
- * The raw nucleotides sequence
- * @param str
- * The secondary structure
- * @param drawMode
- * The drawing algorithm
- * @throws ExceptionNonEqualLength
- */
- public void drawRNA(String seq, String str, int drawMode)
- throws ExceptionNonEqualLength {
- _RNA.setDrawMode(drawMode);
- try {
- _RNA.setRNA(seq, str);
- drawRNA();
- } catch (ExceptionUnmatchedClosingParentheses e) {
- errorDialog(e);
- } catch (ExceptionFileFormatOrSyntax e1) {
- errorDialog(e1);
- }
- }
-
- public void drawRNA(Reader r, int drawMode) throws ExceptionNonEqualLength,
- ExceptionFileFormatOrSyntax {
- _RNA.setDrawMode(drawMode);
- Collection<RNA> rnas = RNAFactory.loadSecStr(r);
- if (rnas.isEmpty()) {
- throw new ExceptionFileFormatOrSyntax(
- "No RNA could be parsed from that source.");
- }
- _RNA = rnas.iterator().next();
- drawRNA();
- }
-
- /**
- * Draws a secondary structure of RNA using the default drawing algorithm
- * and displays it, using an interpolated transition between the previous
- * one and the new one. Extra bases, resulting from a size difference
- * between the two successive RNAs, are assumed to initiate from the middle
- * of the sequence. In other words, both prefixes and suffixes of the RNAs
- * are assumed to match, and what remains is an insertion.
- *
- * @param seq
- * Sequence
- * @param str
- * Structure in dot bracket notation
- * @throws ExceptionNonEqualLength
- * If len(seq)!=len(str)
- */
- public void drawRNAInterpolated(String seq, String str)
- throws ExceptionNonEqualLength {
- drawRNAInterpolated(seq, str, _RNA.get_drawMode());
- }
-
- /**
- * Draws a secondary structure of RNA using a given algorithm and displays
- * it, using an interpolated transition between the previous one and the new
- * one. Extra bases, resulting from a size difference between the two
- * successive RNAs, are assumed to initiate from the middle of the sequence.
- * In other words, both prefixes and suffixes of the RNAs are assumed to
- * match, and what remains is an insertion.
- *
- * @param seq
- * Sequence
- * @param str
- * Structure in dot bracket notation
- * @param drawMode
- * The drawing algorithm to be used for the initial placement
- * @throws ExceptionNonEqualLength
- * If len(seq)!=len(str)
- */
- public void drawRNAInterpolated(String seq, String str, int drawMode) {
- drawRNAInterpolated(seq, str, drawMode,
- Mapping.DefaultOutermostMapping(_RNA.get_listeBases().size(),
- str.length()));
- }
-
- /**
- * Draws a secondary structure of RNA using the default drawing algorithm
- * and displays it, using an interpolated transition between the previous
- * one and the new one. Here, a mapping between those bases of the new
- * structure and the previous one is explicitly provided.
- *
- * @param seq
- * Sequence
- * @param str
- * Structure in dot bracket notation
- * @param m
- * A mapping between the currently rendered structure and its
- * successor (seq,str)
- * @throws ExceptionNonEqualLength
- * If len(seq)!=len(str)
- */
- public void drawRNAInterpolated(String seq, String str, Mapping m) {
- drawRNAInterpolated(seq, str, _RNA.get_drawMode(), m);
- }
-
- /**
- * Draws a secondary structure of RNA using a given drawing algorithm and
- * displays it, using an interpolated transition between the previous one
- * and the new one. Here, a mapping between those bases of the new structure
- * and the previous one is provided.
- *
- * @param seq
- * Sequence
- * @param str
- * Structure in dot bracket notation
- * @param drawMode
- * The drawing algorithm to be used for the initial placement
- * @param m
- * A mapping between the currently rendered structure and its
- * successor (seq,str)
- */
- public void drawRNAInterpolated(String seq, String str, int drawMode,
- Mapping m) {
- RNA target = new RNA();
- try {
- target.setRNA(seq, str);
- drawRNAInterpolated(target, drawMode, m);
- } catch (ExceptionUnmatchedClosingParentheses e) {
- errorDialog(e);
- } catch (ExceptionFileFormatOrSyntax e) {
- errorDialog(e);
- }
- }
-
- /**
- * Draws a secondary structure of RNA using the default drawing algorithm
- * and displays it, using an interpolated transition between the previous
- * one and the new one. Here, a mapping between those bases of the new
- * structure and the previous one is explicitly provided.
- *
- * @param target
- * Secondary structure
- */
- public void drawRNAInterpolated(RNA target) {
- drawRNAInterpolated(target, target.get_drawMode(),
- Mapping.DefaultOutermostMapping(_RNA.get_listeBases().size(),
- target.getSize()));
- }
-
- /**
- * Draws a secondary structure of RNA using the default drawing algorithm
- * and displays it, using an interpolated transition between the previous
- * one and the new one. Here, a mapping between those bases of the new
- * structure and the previous one is explicitly provided.
- *
- * @param target
- * Secondary structure
- * @param m
- * A mapping between the currently rendered structure and its
- * successor (seq,str)
- */
- public void drawRNAInterpolated(RNA target, Mapping m) {
- drawRNAInterpolated(target, target.get_drawMode(), m);
- }
-
- /**
- * Draws a secondary structure of RNA using a given drawing algorithm and
- * displays it, using an interpolated transition between the previous one
- * and the new one. Here, a mapping between those bases of the new structure
- * and the previous one is provided.
- *
- * @param target
- * Secondary structure of RNA
- * @param drawMode
- * The drawing algorithm to be used for the initial placement
- * @param m
- * A mapping between the currently rendered structure and its
- * successor (seq,str)
- */
- public void drawRNAInterpolated(RNA target, int drawMode, Mapping m) {
- try {
- target.drawRNA(drawMode, _conf);
- _conf._drawColorMap = false;
- _interpolator.addTarget(target, m);
- } catch (ExceptionNAViewAlgorithm e) {
- errorDialog(e);
- e.printStackTrace();
- }
- }
-
- /**
- * Returns the current algorithm used for drawing the structure
- *
- * @return The current drawing algorithm
- */
- public int getDrawMode() {
- return this._RNA.getDrawMode();
- }
-
- public void showRNA(RNA t, VARNAConfig cfg) {
- showRNA(t);
- if (cfg != null) {
- this.setConfig(cfg);
- }
- repaint();
- }
-
- /**
- * Checks whether an interpolated transition bewteen two RNAs is occurring.
- *
- * @return True if an interpolated transition is occurring, false otherwise
- */
-
- public boolean isInterpolationInProgress() {
- if (_interpolator == null) {
- return false;
- } else
- return _interpolator.isInterpolationInProgress();
- }
-
- /**
- * Simply displays (does not redraw) a secondary structure , using an
- * interpolated transition between the previous one and the new one. A
- * default mapping between those bases of the new structure and the previous
- * one is used.
- *
- * @param target
- * Secondary structure of RNA
- */
- public void showRNAInterpolated(RNA target) {
- showRNAInterpolated(target, Mapping.DefaultOutermostMapping(_RNA
- .get_listeBases().size(), target.getSize()));
- }
-
- /**
- * Simply displays (does not redraw) a secondary structure , using an
- * interpolated transition between the previous one and the new one. Here, a
- * mapping between bases of the new structure and the previous one is given.
- *
- * @param target
- * Secondary structure of RNA
- * @param m
- * A mapping between the currently rendered structure and its
- * successor (seq,str)
- * @throws ExceptionNonEqualLength
- * If len(seq)!=len(str)
- */
- public void showRNAInterpolated(RNA target, Mapping m) {
- showRNAInterpolated(target, null, m);
- }
-
- public void showRNAInterpolated(RNA target, VARNAConfig cfg, Mapping m) {
- _interpolator.addTarget(target, cfg, m);
- }
-
- /**
- * When comparison mode is ON, sets the two RNA secondary structure to be
- * drawn in this panel, using a given layout algorithm. In addition to the
- * raw nucleotides sequence, the secondary structure is given in the
- * so-called "Dot-bracket notation" (DBN) format. This format is a
- * well-parenthesized word over the alphabet '(',')','.'.<br/>
- * Ex: <code>((((((((....))))..(((((...))).))))))</code><br />
- *
- * @param firstSeq
- * The first RNA raw nucleotides sequence
- * @param firstStruct
- * The first RNA secondary structure
- * @param secondSeq
- * The second RNA raw nucleotides sequence
- * @param secondStruct
- * The second RNA secondary structure
- * @param drawMode
- * The drawing algorithm
- */
- public void drawRNA(String firstSeq, String firstStruct, String secondSeq,
- String secondStruct, int drawMode) {
- _RNA.setDrawMode(drawMode);
- /**
- * Checking the sequences and structures validities...
- */
-
- // This is a comparison, so the two RNA alignment past in parameters
- // must
- // have the same sequence and structure length.
- if (firstSeq.length() == secondSeq.length()
- && firstStruct.length() == secondStruct.length()) {
- // First RNA
- if (firstSeq.length() != firstStruct.length()) {
- if (_conf._showWarnings) {
- emitWarning("First sequence length " + firstSeq.length()
- + " differs from that of it's secondary structure "
- + firstStruct.length()
- + ". \nAdapting first sequence length ...");
- }
- if (firstSeq.length() < firstStruct.length()) {
- while (firstSeq.length() < firstStruct.length()) {
- firstSeq += " ";
- }
- } else {
- firstSeq = firstSeq.substring(0, firstStruct.length());
- }
- }
-
- // Second RNA
- if (secondSeq.length() != secondStruct.length()) {
- if (_conf._showWarnings) {
- emitWarning("Second sequence length " + secondSeq.length()
- + " differs from that of it's secondary structure "
- + secondStruct.length()
- + ". \nAdapting second sequence length ...");
- }
- if (secondSeq.length() < secondStruct.length()) {
- while (secondSeq.length() < secondStruct.length()) {
- secondSeq += " ";
- }
- } else {
- secondSeq = secondSeq.substring(0, secondStruct.length());
- }
- }
-
- int RNALength = firstSeq.length();
- String string_superStruct = new String("");
- String string_superSeq = new String("");
- /**
- * In this array, we'll have for each indexes of each characters of
- * the final super-structure, the RNA number which is own it.
- */
- ArrayList<Integer> array_rnaOwn = new ArrayList<Integer>();
-
- /**
- * Generating super-structure sequences and structures...
- */
-
- firstStruct = firstStruct.replace('-', '.');
- secondStruct = secondStruct.replace('-', '.');
- // First of all, we make the structure
- for (int i = 0; i < RNALength; i++) {
- // If both characters are the same, so it'll be in the super
- // structure
- if (firstStruct.charAt(i) == secondStruct.charAt(i)) {
- string_superStruct = string_superStruct
- + firstStruct.charAt(i);
- array_rnaOwn.add(0);
- }
- // Else if one of the characters is an opening parenthese, so
- // it'll be an opening parenthese in the super structure
- else if (firstStruct.charAt(i) == '('
- || secondStruct.charAt(i) == '(') {
- string_superStruct = string_superStruct + '(';
- array_rnaOwn.add((firstStruct.charAt(i) == '(') ? 1 : 2);
- }
- // Else if one of the characters is a closing parenthese, so
- // it'll be a closing parenthese in the super structure
- else if (firstStruct.charAt(i) == ')'
- || secondStruct.charAt(i) == ')') {
- string_superStruct = string_superStruct + ')';
- array_rnaOwn.add((firstStruct.charAt(i) == ')') ? 1 : 2);
- } else {
- string_superStruct = string_superStruct + '.';
- array_rnaOwn.add(-1);
- }
- }
-
- // Next, we make the sequence taking the characters at the same
- // index in the first and second sequence
- for (int i = 0; i < RNALength; i++) {
- string_superSeq = string_superSeq + firstSeq.charAt(i)
- + secondSeq.charAt(i);
- }
-
- // Now, we need to create the super-structure RNA with the owning
- // bases array
- // in order to color bases outer depending on the owning statement
- // of each bases.
- if (!string_superSeq.equals("") && !string_superStruct.equals("")) {
- try {
- _RNA.setRNA(string_superSeq, string_superStruct,
- array_rnaOwn);
- } catch (ExceptionUnmatchedClosingParentheses e) {
- errorDialog(e);
- } catch (ExceptionFileFormatOrSyntax e) {
- errorDialog(e);
- }
- } else {
- emitWarning("ERROR : The super-structure is NULL.");
- }
-
- switch (_RNA.get_drawMode()) {
- case RNA.DRAW_MODE_RADIATE:
- _RNA.drawRNARadiate(_conf);
- break;
- case RNA.DRAW_MODE_CIRCULAR:
- _RNA.drawRNACircle(_conf);
- break;
- case RNA.DRAW_MODE_LINEAR:
- _RNA.drawRNALine(_conf);
- break;
- case RNA.DRAW_MODE_NAVIEW:
- try {
- _RNA.drawRNANAView(_conf);
- } catch (ExceptionNAViewAlgorithm e) {
- errorDialog(e);
- }
- break;
- default:
- break;
- }
-
- }
- }
-
- /**
- * Returns the currently selected base index, obtained through a mouse-left
- * click
- *
- * @return Selected base
- *
- * public int getSelectedBaseIndex() { return _selectedBase; }
- *
- * /** Returns the currently selected base, obtained through a
- * mouse-left click
- *
- * @return Selected base
- *
- * public ModeleBase getSelectedBase() { return
- * _RNA.get_listeBases().get(_selectedBase); }
- *
- * /** Sets the selected base index
- *
- * @param base
- * New selected base index
- *
- * public void setSelectedBase(int base) { _selectedBase = base;
- * }
- */
-
- /**
- * Returns the coordinates of the currently displayed RNA
- *
- * @return Coordinates array
- */
- public Point2D.Double[] getRealCoords() {
- return _realCoords;
- }
-
- /**
- * Sets the coordinates of the currently displayed RNA
- *
- * @param coords
- * New coordinates
- */
- public void setRealCoords(Point2D.Double[] coords) {
- _realCoords = coords;
- }
-
- /**
- * Returns the popup menu used for user mouse iteractions
- *
- * @return Popup menu
- */
- public VueMenu getPopup() {
- return _popup;
- }
-
- /**
- * Sets the color used to display hydrogen bonds (base pairings)
- *
- * @param bond_color
- * The color of hydrogen bonds
- */
- public void setBondColor(Color bond_color) {
- _conf._bondColor = bond_color;
- }
-
- /**
- * Returns the color used to draw the title
- *
- * @return The color used to draw the title
- */
- public Color getTitleColor() {
- return _conf._titleColor;
- }
-
- /**
- * Sets the color used to draw the title
- *
- * @param title_color
- * The new color used to draw the title
- */
- public void setTitleColor(Color title_color) {
- _conf._titleColor = title_color;
- }
-
- /**
- * Returns the height taken by the title
- *
- * @return The height taken by the title
- */
- private int getTitleHeight() {
- return _titleHeight;
- }
-
- /**
- * Sets the height taken by the title
- *
- * @param title_height
- * The height taken by the title
- */
- @SuppressWarnings("unused")
- private void setTitleHeight(int title_height) {
- _titleHeight = title_height;
- }
-
- /**
- * Returns the current state of auto centering mode.
- *
- * @return True if autocentered, false otherwise
- */
- public boolean isAutoCentered() {
- return _conf._autoCenter;
- }
-
- /**
- * Sets the current state of auto centering mode.
- *
- * @param center
- * New auto-centered state
- */
- public void setAutoCenter(boolean center) {
- _conf._autoCenter = center;
- }
-
- /**
- * Returns the font currently used for rendering the title.
- *
- * @return Current title font
- */
- public Font getTitleFont() {
- return _conf._titleFont;
- }
-
- /**
- * Sets the font used for rendering the title.
- *
- * @param font
- * New title font
- */
- public void setTitleFont(Font font) {
- _conf._titleFont = font;
- updateTitleHeight();
- }
-
- /**
- * For the LINE_MODE drawing algorithm, sets the base pair height increment,
- * i.e. the vertical distance between two nested arcs.
- *
- * @return The current base pair increment
- */
- public double getBPHeightIncrement() {
- return _RNA._bpHeightIncrement;
- }
-
- /**
- * Sets the base pair height increment, i.e. the vertical distance between
- * two arcs to be used in LINE_MODE.
- *
- * @param inc
- * New height increment
- */
- public void setBPHeightIncrement(double inc) {
- _RNA._bpHeightIncrement = inc;
- }
-
- /**
- * Returns the shifting of the origin of the Panel in zoom mode
- *
- * @return The logical coordinate of the top-left panel point
- */
- public Point2D.Double getOffsetPanel() {
- return _offsetPanel;
- }
-
- /**
- * Returns the vector bringing the logical coordinate of left-top-most point
- * in the panel to the left-top-most point of the RNA.
- *
- * @return The logical coordinate of the top-left panel point
- */
- private Point2D.Double getRNAOffset() {
- return _offsetRNA;
- }
-
- /**
- * Returns this panel's UI menu
- *
- * @return Applet's UI popupmenu
- */
- public VueMenu getPopupMenu() {
- return _popup;
- }
-
- /**
- * Returns the atomic zoom factor step, or increment.
- *
- * @return Atomic zoom factor increment
- */
- public double getZoomIncrement() {
- return _conf._zoomAmount;
- }
-
- /**
- * Sets the atomic zoom factor step, or increment.
- *
- * @param amount
- * Atomic zoom factor increment
- */
- public void setZoomIncrement(Object amount) {
- setZoomIncrement(Float.valueOf(amount.toString()));
- }
-
- /**
- * Sets the atomic zoom factor step, or increment.
- *
- * @param amount
- * Atomic zoom factor increment
- */
- public void setZoomIncrement(double amount) {
- _conf._zoomAmount = amount;
- }
-
- /**
- * Returns the current zoom factor
- *
- * @return Current zoom factor
- */
- public double getZoom() {
- return _conf._zoom;
- }
-
- /**
- * Sets the current zoom factor
- *
- * @param _zoom
- * New zoom factor
- */
- public void setZoom(Object _zoom) {
- double d = Float.valueOf(_zoom.toString());
- if (_conf._zoom != d) {
- _conf._zoom = d;
- fireZoomLevelChanged(d);
- }
- }
-
- /**
- * Returns the translation used for zooming in and out
- *
- * @return A vector describing the translation
- */
- public Point getTranslation() {
- return _translation;
- }
-
- /**
- * Sets the translation used for zooming in and out
- *
- * @param trans
- * A vector describing the new translation
- */
- public void setTranslation(Point trans) {
- _translation = trans;
- checkTranslation();
- fireTranslationChanged();
- }
-
- /**
- * Returns the current RNA model
- *
- * @return Current RNA model
- */
- public RNA getRNA() {
- return _RNA;
- }
-
- /**
- * Checks whether the drawn RNA is too large to be displayed, allowing for
- * shifting mouse interactions.
- *
- * @return true if the RNA is too large to be displayed, false otherwise
- */
- public boolean isOutOfFrame() {
- return _horsCadre;
- }
-
- /**
- * Pops up an error Dialog displaying an exception in an human-readable way.
- *
- * @param error
- * The exception to display within the Dialog
- */
- public void errorDialog(Exception error) {
- errorDialog(error, this);
- }
-
- /**
- * Pops up an error Dialog displaying an exception in an human-readable way
- * if errors are set to be displayed.
- *
- * @see #setErrorsOn(boolean)
- * @param error
- * The exception to display within the Dialog
- * @param c
- * Parent component for the dialog box
- */
- public void errorDialog(Exception error, Component c) {
- if (isErrorsOn()) {
- JOptionPane.showMessageDialog(c, error.getMessage(), "VARNA Error",
- JOptionPane.ERROR_MESSAGE);
- }
- }
-
- /**
- * Pops up an error Dialog displaying an exception in an human-readable way.
- *
- * @param error
- * The exception to display within the Dialog
- * @param c
- * Parent component for the dialog box
- */
- public static void errorDialogStatic(Exception error, Component c) {
- if (c != null) {
- JOptionPane.showMessageDialog(c, error.getMessage(),
- "VARNA Critical Error", JOptionPane.ERROR_MESSAGE);
- } else {
- System.err.println("Error: " + error.getMessage());
- }
- }
-
- /**
- * Displays a warning message through a modal dialog if warnings are set to
- * be displayed.
- *
- * @see #setShowWarnings(boolean)
- * @param warning
- * A message expliciting the warning
- */
- public void emitWarning(String warning) {
- if (_conf._showWarnings)
- JOptionPane.showMessageDialog(this, warning, "VARNA Warning",
- JOptionPane.WARNING_MESSAGE);
- }
-
- public static void emitWarningStatic(Exception e, Component c) {
- emitWarningStatic(e.getMessage(), c);
- }
-
- public static void emitWarningStatic(String warning, Component c) {
- if (c != null) {
- JOptionPane.showMessageDialog(c, warning, "VARNA Warning",
- JOptionPane.WARNING_MESSAGE);
- } else {
- System.err.println("Error: " + warning);
- }
- }
-
- /**
- * Toggles modifications on and off
- *
- * @param modifiable
- * Modification status
- */
- public void setModifiable(boolean modifiable) {
- _conf._modifiable = modifiable;
- }
-
- /**
- * Returns current modification status
- *
- * @return current modification status
- */
- public boolean isModifiable() {
- return _conf._modifiable;
- }
-
- /**
- * Resets the visual aspects (Zoom factor, shift) for the Panel.
- */
- public void reset() {
- this.setBorderSize(new Dimension(0, 0));
- this.setTranslation(new Point(0, (int) (-getTitleHeight() / 2.0)));
- this.setZoom(VARNAConfig.DEFAULT_ZOOM);
- this.setZoomIncrement(VARNAConfig.DEFAULT_AMOUNT);
- }
-
- /**
- * Returns the color used to draw non-standard bases
- *
- * @return The color used to draw non-standard bases
- */
- public Color getNonStandardBasesColor() {
- return _conf._specialBasesColor;
- }
-
- /**
- * Sets the color used to draw non-standard bases
- *
- * @param basesColor
- * The color used to draw non-standard bases
- */
- public void setNonStandardBasesColor(Color basesColor) {
- _conf._specialBasesColor = basesColor;
- }
-
- /**
- * Checks if the current translation doesn't "kick" the whole RNA out of the
- * panel, and corrects the situation if necessary.
- */
- public void checkTranslation() {
- // verification pour un zoom < 1
- if (this.getZoom() <= 1) {
- // verification sortie gauche
- if (this.getTranslation().x < -(int) ((this.getWidth() - this
- .getInnerWidth()) / 2.0)) {
- this.setTranslation(new Point(-(int) ((this.getWidth() - this
- .getInnerWidth()) / 2.0), this.getTranslation().y));
- }
- // verification sortie droite
- if (this.getTranslation().x > (int) ((this.getWidth() - this
- .getInnerWidth()) / 2.0)) {
- this.setTranslation(new Point((int) ((this.getWidth() - this
- .getInnerWidth()) / 2.0), this.getTranslation().y));
- }
- // verification sortie bas
- if (this.getTranslation().y > (int) ((this.getHeight()
- - getTitleHeight() * 2 - this.getInnerHeight()) / 2.0)) {
- this.setTranslation(new Point(this.getTranslation().x,
- (int) ((this.getHeight() - getTitleHeight() * 2 - this
- .getInnerHeight()) / 2.0)));
- }
- // verification sortie haut
- if (this.getTranslation().y < -(int) ((this.getHeight() - this
- .getInnerHeight()) / 2.0)) {
- this.setTranslation(new Point(
- this.getTranslation().x,
- -(int) ((this.getHeight() - this.getInnerHeight()) / 2.0)));
- }
- } else {
- // zoom > 1
- Rectangle r2 = getZoomedInTranslationBox();
- int LBoundX = r2.x;
- int UBoundX = r2.x + r2.width;
- int LBoundY = r2.y;
- int UBoundY = r2.y + r2.height;
- if (this.getTranslation().x < LBoundX) {
- this.setTranslation(new Point(LBoundX, getTranslation().y));
- } else if (this.getTranslation().x > UBoundX) {
- this.setTranslation(new Point(UBoundX, getTranslation().y));
- }
- if (this.getTranslation().y < LBoundY) {
- this.setTranslation(new Point(getTranslation().x, LBoundY));
- } else if (this.getTranslation().y > UBoundY) {
- this.setTranslation(new Point(getTranslation().x, UBoundY));
- }
- }
- }
-
- public Rectangle getZoomedInTranslationBox() {
- int LBoundX = -(int) ((this.getInnerWidth()) / 2.0);
- int UBoundX = (int) ((this.getInnerWidth()) / 2.0);
- int LBoundY = -(int) ((this.getInnerHeight()) / 2.0);
- int UBoundY = (int) ((this.getInnerHeight()) / 2.0);
- return new Rectangle(LBoundX, LBoundY, UBoundX - LBoundX, UBoundY
- - LBoundY);
-
- }
-
- /**
- * Returns the "real pixels" x-coordinate of the RNA.
- *
- * @return X-coordinate of the translation
- */
- public int getLeftOffset() {
- return _border.width
- + ((this.getWidth() - 2 * _border.width) - this.getInnerWidth())
- / 2 + _translation.x;
- }
-
- /**
- * Returns the "real pixels" width of the drawing surface for our RNA.
- *
- * @return Width of the drawing surface for our RNA
- */
- public int getInnerWidth() {
- // Largeur du dessin
- return (int) Math.round((this.getWidth() - 2 * _border.width)
- * _conf._zoom);
- }
-
- /**
- * Returns the "real pixels" y-coordinate of the RNA.
- *
- * @return Y-coordinate of the translation
- */
- public int getTopOffset() {
- return _border.height
- + ((this.getHeight() - 2 * _border.height) - this
- .getInnerHeight()) / 2 + _translation.y;
- }
-
- /**
- * Returns the "real pixels" height of the drawing surface for our RNA.
- *
- * @return Height of the drawing surface for our RNA
- */
- public int getInnerHeight() {
- // Hauteur du dessin
- return (int) Math.round((this.getHeight()) * _conf._zoom - 2
- * _border.height - getTitleHeight());
- }
-
- /**
- * Checks if the current mode is the "comparison" mode
- *
- * @return True if comparison, false otherwise
- */
- public boolean isComparisonMode() {
- return _conf._comparisonMode;
- }
-
- /**
- * Rotates the RNA coordinates by a certain angle
- *
- * @param angleDegres
- * Rotation angle, in degrees
- */
- public void globalRotation(Double angleDegres) {
- _RNA.globalRotation(angleDegres);
- fireLayoutChanged();
- repaint();
- }
-
- /**
- * Returns the index of the currently selected base, defaulting to the
- * closest base to the last mouse-click.
- *
- * @return Index of the currently selected base
- */
- public Integer getNearestBase() {
- return _nearestBase;
- }
-
- /**
- * Sets the index of the currently selected base.
- *
- * @param base
- * Index of the new selected base
- */
- public void setNearestBase(Integer base) {
- _nearestBase = base;
- }
-
- /**
- * Returns the color used to draw 'Gaps' bases in comparison mode
- *
- * @return Color used for 'Gaps'
- */
- public Color getGapsBasesColor() {
- return _conf._dashBasesColor;
- }
-
- /**
- * Sets the color to use for 'Gaps' bases in comparison mode
- *
- * @param c
- * Color used for 'Gaps'
- */
- public void setGapsBasesColor(Color c) {
- _conf._dashBasesColor = c;
- }
-
- @SuppressWarnings("unused")
- private void imprimer() {
- // PrintPanel canvas;
- // canvas = new PrintPanel();
- PrintRequestAttributeSet attributes;
- attributes = new HashPrintRequestAttributeSet();
- try {
- PrinterJob job = PrinterJob.getPrinterJob();
- // job.setPrintable(this);
- if (job.printDialog(attributes)) {
- job.print(attributes);
- }
- } catch (PrinterException exception) {
- errorDialog(exception);
- }
- }
-
- /**
- * Checks whether errors are to be displayed
- *
- * @return Error display status
- */
- public boolean isErrorsOn() {
- return _conf._errorsOn;
- }
-
- /**
- * Sets whether errors are to be displayed
- *
- * @param on
- * New error display status
- */
- public void setErrorsOn(boolean on) {
- _conf._errorsOn = on;
- }
-
- /**
- * Returns the view associated with user interactions
- *
- * @return A view associated with user interactions
- */
- public VueUI getVARNAUI() {
- return _UI;
- }
-
- /**
- * Toggles on/off using base inner color for drawing base-pairs
- *
- * @param on
- * True for using base inner color for drawing base-pairs, false
- * for classic mode
- */
- public void setUseBaseColorsForBPs(boolean on) {
- _conf._useBaseColorsForBPs = on;
- }
-
- /**
- * Returns true if current base color is used as inner color for drawing
- * base-pairs
- *
- * @return True for using base inner color for drawing base-pairs, false for
- * classic mode
- */
- public boolean getUseBaseColorsForBPs() {
- return _conf._useBaseColorsForBPs;
- }
-
- /**
- * Toggles on/off using a special color used for drawing "non-standard"
- * bases
- *
- * @param on
- * True for using a special color used for drawing "non-standard"
- * bases, false for classic mode
- */
- public void setColorNonStandardBases(boolean on) {
- _conf._colorSpecialBases = on;
- }
-
- /**
- * Returns true if a special color is used as inner color for non-standard
- * base
- *
- * @return True for using a special color used for drawing "non-standard"
- * bases, false for classic mode
- */
- public boolean getColorSpecialBases() {
- return _conf._colorSpecialBases;
- }
-
- /**
- * Toggles on/off using a special color used for drawing "Gaps" bases in
- * comparison mode
- *
- * @param on
- * True for using a special color used for drawing "Gaps" bases
- * in comparison mode, false for classic mode
- */
- public void setColorGapsBases(boolean on) {
- _conf._colorDashBases = on;
- }
-
- /**
- * Returns true if a special color is used for drawing "Gaps" bases in
- * comparison mode
- *
- * @return True for using a special color used for drawing "Gaps" bases in
- * comparison mode, false for classic mode
- */
- public boolean getColorGapsBases() {
- return _conf._colorDashBases;
- }
-
- /**
- * Toggles on/off displaying warnings
- *
- * @param on
- * True to display warnings, false otherwise
- */
- public void setShowWarnings(boolean on) {
- _conf._showWarnings = on;
- }
-
- /**
- * Get current warning display status
- *
- * @return True to display warnings, false otherwise
- */
- public boolean getShowWarnings() {
- return _conf._showWarnings;
- }
-
- /**
- * Toggles on/off displaying non-canonical base-pairs
- *
- * @param on
- * True to display NC base-pairs, false otherwise
- */
- public void setShowNonCanonicalBP(boolean on) {
- _conf._drawnNonCanonicalBP = on;
- }
-
- /**
- * Return the current display status for non-canonical base-pairs
- *
- * @return True if NC base-pairs are displayed, false otherwise
- */
- public boolean getShowNonCanonicalBP() {
- return _conf._drawnNonCanonicalBP;
- }
-
- /**
- * Toggles on/off displaying "non-planar" base-pairs
- *
- * @param on
- * True to display "non-planar" base-pairs, false otherwise
- */
- public void setShowNonPlanarBP(boolean on) {
- _conf._drawnNonPlanarBP = on;
- }
-
- /**
- * Return the current display status for non-planar base-pairs
- *
- * @return True if non-planars base-pairs are displayed, false otherwise
- */
- public boolean getShowNonPlanarBP() {
- return _conf._drawnNonPlanarBP;
- }
-
- /**
- * Sets the base-pair representation style
- *
- * @param st
- * The new base-pair style
- */
- public void setBPStyle(VARNAConfig.BP_STYLE st) {
- _conf._mainBPStyle = st;
- }
-
- /**
- * Returns the base-pair representation style
- *
- * @return The current base-pair style
- */
- public VARNAConfig.BP_STYLE getBPStyle() {
- return _conf._mainBPStyle;
- }
-
- /**
- * Returns the current VARNA Panel configuration. The returned instance
- * should not be modified directly, but rather through the getters/setters
- * from the VARNAPanel class.
- *
- * @return Current configuration
- */
- public VARNAConfig getConfig() {
- return _conf;
- }
-
- /**
- * Sets the background color
- *
- * @param c
- * New background color
- */
- public void setBackground(Color c) {
- if (_conf != null) {
- if (c != null) {
- _conf._backgroundColor = c;
- _conf._drawBackground = (!c
- .equals(VARNAConfig.DEFAULT_BACKGROUND_COLOR));
- } else {
- _conf._backgroundColor = VARNAConfig.DEFAULT_BACKGROUND_COLOR;
- _conf._drawBackground = false;
- }
- }
-
- }
-
- /**
- * Starts highlighting the selected base.
- */
- public void highlightSelectedBase(ModeleBase m) {
- ArrayList<Integer> v = new ArrayList<Integer>();
- int sel = m.getIndex();
- if (sel != -1) {
- v.add(sel);
- }
- setSelection(v);
- }
-
- /**
- * Starts highlighting the selected base.
- */
- public void highlightSelectedStem(ModeleBase m) {
- ArrayList<Integer> v = new ArrayList<Integer>();
- int sel = m.getIndex();
- if (sel != -1) {
- ArrayList<Integer> r = _RNA.findStem(sel);
- v.addAll(r);
- }
- setSelection(v);
- }
-
- public BaseList getSelection() {
- return _selectedBases;
- }
-
- public ArrayList<Integer> getSelectionIndices() {
- return _selectedBases.getIndices();
- }
-
- public void setSelection(ArrayList<Integer> indices) {
- setSelection(_RNA.getBasesAt(indices));
- }
-
- public void setSelection(Collection<? extends ModeleBase> mbs) {
- BaseList bck = new BaseList(_selectedBases);
- _selectedBases.clear();
- _selectedBases.addBases(mbs);
- _blink.setActive(true);
- fireSelectionChanged(bck, _selectedBases);
- }
-
- public ArrayList<Integer> getBasesInRectangleDiff(Rectangle recIn,
- Rectangle recOut) {
- ArrayList<Integer> result = new ArrayList<Integer>();
- for (int i = 0; i < _realCoords.length; i++) {
- if (recIn.contains(_realCoords[i])
- ^ recOut.contains(_realCoords[i]))
- result.add(i);
- }
- return result;
- }
-
- public ArrayList<Integer> getBasesInRectangle(Rectangle rec) {
- ArrayList<Integer> result = new ArrayList<Integer>();
- for (int i = 0; i < _realCoords.length; i++) {
- if (rec.contains(_realCoords[i]))
- result.add(i);
- }
- return result;
- }
-
- public void setSelectionRectangle(Rectangle rec) {
- ArrayList<Integer> result = new ArrayList<Integer>();
- if (_selectionRectangle != null) {
- result = getBasesInRectangleDiff(_selectionRectangle, rec);
- } else {
- result = getBasesInRectangle(rec);
- }
- _selectionRectangle = new Rectangle(rec);
- toggleSelection(result);
- repaint();
- }
-
- public void removeSelectionRectangle() {
- _selectionRectangle = null;
- }
-
- public void addToSelection(Collection<? extends Integer> indices) {
- for (int i : indices) {
- addToSelection(i);
- }
- }
-
- public void addToSelection(int i) {
- BaseList bck = new BaseList(_selectedBases);
- ModeleBase mb = _RNA.getBaseAt(i);
- _selectedBases.addBase(mb);
- _blink.setActive(true);
- fireSelectionChanged(bck, _selectedBases);
- }
-
- public void removeFromSelection(int i) {
- BaseList bck = new BaseList(_selectedBases);
- ModeleBase mb = _RNA.getBaseAt(i);
- _selectedBases.removeBase(mb);
- if (_selectedBases.size() == 0) {
- _blink.setActive(false);
- } else {
- _blink.setActive(true);
- }
- fireSelectionChanged(bck, _selectedBases);
- }
-
- public boolean isInSelection(int i) {
- return _selectedBases.contains(_RNA.getBaseAt(i));
- }
-
- public void toggleSelection(int i) {
- if (isInSelection(i))
- removeFromSelection(i);
- else
- addToSelection(i);
- }
-
- public void toggleSelection(Collection<? extends Integer> indices) {
- for (int i : indices) {
- toggleSelection(i);
- }
- }
-
- /**
- * Stops highlighting bases
- */
- public void clearSelection() {
- BaseList bck = new BaseList(_selectedBases);
- _selectedBases.clear();
- _blink.setActive(false);
- repaint();
- fireSelectionChanged(bck, _selectedBases);
- }
-
- public void saveSelection() {
- _backupSelection.clear();
- _backupSelection.addAll(_selectedBases.getBases());
- }
-
- public void restoreSelection() {
- setSelection(_backupSelection);
- }
-
- /**
- * Stops highlighting bases
- */
- public void resetAnnotationHighlight() {
- _highlightAnnotation = false;
- repaint();
- }
-
- /**
- * Toggles on/off a rectangular outline of the bounding box.
- *
- * @param on
- * True to draw the bounding box, false otherwise
- */
- public void drawBBox(boolean on) {
- _drawBBox = on;
- }
-
- /**
- * Toggles on/off a rectangular outline of the border.
- *
- * @param on
- * True to draw the bounding box, false otherwise
- */
- public void drawBorder(boolean on) {
- _drawBorder = on;
- }
-
- public void setBaseInnerColor(Color c) {
- _RNA.setBaseInnerColor(c);
- }
-
- public void setBaseNumbersColor(Color c) {
- _RNA.setBaseNumbersColor(c);
- }
-
- public void setBaseNameColor(Color c) {
- _RNA.setBaseNameColor(c);
- }
-
- public void setBaseOutlineColor(Color c) {
- _RNA.setBaseOutlineColor(c);
- }
-
- public ArrayList<TextAnnotation> getListeAnnotations() {
- return _RNA.getAnnotations();
- }
-
- public void resetListeAnnotations() {
- _RNA.clearAnnotations();
- repaint();
- }
-
- public void addAnnotation(TextAnnotation textAnnotation) {
- _RNA.addAnnotation(textAnnotation);
- repaint();
- }
-
- public boolean removeAnnotation(TextAnnotation textAnnotation) {
- boolean done = _RNA.removeAnnotation(textAnnotation);
- repaint();
- return done;
- }
-
- public TextAnnotation get_selectedAnnotation() {
- return _selectedAnnotation;
- }
-
- public void set_selectedAnnotation(TextAnnotation annotation) {
- _selectedAnnotation = annotation;
- }
-
- public void removeSelectedAnnotation() {
- _highlightAnnotation = false;
- _selectedAnnotation = null;
- }
-
- public void highlightSelectedAnnotation() {
- _highlightAnnotation = true;
- }
-
- public boolean getFlatExteriorLoop() {
- return _conf._flatExteriorLoop;
- }
-
- public void setFlatExteriorLoop(boolean on) {
- _conf._flatExteriorLoop = on;
- }
-
- public void setLastSelectedPosition(Point2D.Double p) {
- _lastSelectedCoord.x = p.x;
- _lastSelectedCoord.y = p.y;
- }
-
- public Point2D.Double getLastSelectedPosition() {
- return _lastSelectedCoord;
- }
-
- public void setSequence(String s) {
- _RNA.setSequence(s);
- repaint();
- }
-
- public void setColorMapVisible(boolean b) {
- _conf._drawColorMap = b;
- repaint();
- }
-
- public boolean getColorMapVisible() {
- return _conf._drawColorMap;
- }
-
- public void removeColorMap() {
- _conf._drawColorMap = false;
- repaint();
- }
-
- public void saveSession(String path) {
- /*
- * FileOutputStream fos = null; ObjectOutputStream out = null; try { fos
- * = new FileOutputStream(path); out = new ObjectOutputStream(fos);
- * out.writeObject(new FullBackup(_conf, _RNA, _conf._title));
- * out.close(); } catch (Exception ex) { ex.printStackTrace(); }
- */
- toXML(path);
- }
-
- public FullBackup loadSession(String path) throws ExceptionLoadingFailed {
- return loadSession(new File(path));
+public class VARNAPanel extends JPanel implements PropertyChangeListener
+{
+
+ /**
+ * SwingJS uses a PropertyChangeEvent to signal that a pseudo-modal dialog has
+ * been closed.
+ *
+ * @param event
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent event)
+ {
+ Object val = event.getNewValue();
+ switch (event.getPropertyName())
+ {
+ case "value":
+ _UI.onDialogReturn(val == null ? JOptionPane.CLOSED_OPTION
+ : ((Integer) val).intValue());
+ return;
+ case "SelectedFile":
+ case "SelectedColor":
+ case "inputValue":
+ _UI.onDialogReturn(val);
+ break;
+ }
+ }
+
+ private static final long serialVersionUID = 8194421570308956001L;
+
+ private RNA _RNA = new RNA();
+
+ private boolean _debug = false;
+
+ private VARNAConfig _conf = new VARNAConfig();
+
+ private ArrayList<InterfaceVARNAListener> _VARNAListeners = new ArrayList<InterfaceVARNAListener>();
+
+ private ArrayList<InterfaceVARNASelectionListener> _selectionListeners = new ArrayList<InterfaceVARNASelectionListener>();
+
+ private ArrayList<InterfaceVARNARNAListener> _RNAListeners = new ArrayList<InterfaceVARNARNAListener>();
+
+ private ArrayList<InterfaceVARNABasesListener> _basesListeners = new ArrayList<InterfaceVARNABasesListener>();
+
+ UndoManager _manager;
+
+ // private boolean _foldMode = true;
+
+ private Point2D.Double[] _realCoords = new Point2D.Double[0];
+
+ private Point2D.Double[] _realCenters = new Point2D.Double[0];
+
+ private double _scaleFactor = 1.0;
+
+ private Point2D.Double _offsetPanel = new Point2D.Double();
+
+ private Point2D.Double _offsetRNA = new Point2D.Double();
+
+ private double _offX;
+
+ private double _offY;
+
+ private ControleurBlinkingThread _blink;
+
+ private BaseList _selectedBases = new BaseList("selection");
+
+ private ArrayList<ModeleBase> _backupSelection = new ArrayList<ModeleBase>();
+
+ private Integer _nearestBase = null;
+
+ private Point2D.Double _lastSelectedCoord = new Point2D.Double(0.0, 0.0);
+
+ private Point2D.Double _linkOrigin = null;
+
+ private Point2D.Double _linkDestination = null;
+
+ private Rectangle _selectionRectangle = null;
+
+ private boolean _highlightAnnotation = false;
+
+ private int _titleHeight;
+
+ // BH SwingJS issue here is that we are using _border already. Hmm.
+ private Dimension _border = new Dimension(0, 0);
+
+ private boolean _drawBBox = false;
+
+ private boolean _drawBorder = false;
+
+ // private Point _positionRelativeSouris;
+ private Point _translation;
+
+ private boolean _horsCadre;
+
+ private boolean _premierAffichage;
+
+ private ControleurInterpolator _interpolator;
+
+ /**
+ * If comparison mode is TRUE (ON), then the application will be used to
+ * display a super-structure resulting on an RNA secondary structure
+ * comparison. Else, the application is used by default.
+ */
+
+ private VueMenu _popup = new VueMenu(this);
+
+ private VueUI _UI = new VueUI(this);
+
+ private TextAnnotation _selectedAnnotation;
+
+ /**
+ * Creates an RNA 2D panel with initially displays the empty structure.
+ *
+ * @throws ExceptionNonEqualLength
+ *
+ */
+ public VARNAPanel()
+ {
+ init();
+ drawRNA();
+ }
+
+ /**
+ * Creates an RNA 2D panel, and creates and displays an RNA coupled with its
+ * secondary structure formatted as a well-balanced parenthesis with dots word
+ * (DBN format).
+ *
+ * @param seq
+ * The raw nucleotide sequence
+ * @param str
+ * The secondary structure in DBN format
+ * @throws ExceptionNonEqualLength
+ */
+
+ public VARNAPanel(String seq, String str) throws ExceptionNonEqualLength
+ {
+ this(seq, str, RNA.DRAW_MODE_RADIATE);
+ }
+
+ /**
+ * Creates a VARNAPanel instance, and creates and displays an RNA coupled with
+ * its secondary structure formatted as a well-balanced parenthesis with dots
+ * word (DBN format). Allows the user to choose the drawing algorithm to be
+ * used.
+ *
+ * @param seq
+ * The raw nucleotide sequence
+ * @param str
+ * The secondary structure in DBN format
+ * @param drawMode
+ * The drawing mode
+ * @throws ExceptionNonEqualLength
+ * @see RNA#DRAW_MODE_RADIATE
+ * @see RNA#DRAW_MODE_CIRCULAR
+ * @see RNA#DRAW_MODE_NAVIEW
+ */
+ public VARNAPanel(String seq, String str, int drawMode)
+ throws ExceptionNonEqualLength
+ {
+ this(seq, str, drawMode, "");
+ }
+
+ public VARNAPanel(Reader r)
+ throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax
+ {
+ this(r, RNA.DRAW_MODE_RADIATE);
+ }
+
+ public VARNAPanel(Reader r, int drawMode)
+ throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax
+ {
+ this(r, drawMode, "");
+ }
+
+ public VARNAPanel(Reader r, int drawMode, String title)
+ throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax
+ {
+ init();
+ drawRNA(r, drawMode);
+ setTitle(title);
+ }
+
+ public void setOriginLink(Point2D.Double p)
+ {
+ _linkOrigin = (p);
+ }
+
+ public void setDestinationLink(Point2D.Double p)
+ {
+ _linkDestination = (p);
+ }
+
+ public void removeLink()
+ {
+ _linkOrigin = null;
+ _linkDestination = null;
+ }
+
+ /**
+ * Creates a VARNAPanel instance, and displays an RNA.
+ *
+ * @param r
+ * The RNA to be displayed within this panel
+ */
+
+ public VARNAPanel(RNA r)
+ {
+ showRNA(r);
+ init();
+ }
+
+ /**
+ * Creates a VARNAPanel instance, and creates and displays an RNA coupled with
+ * its secondary structure formatted as a well-balanced parenthesis with dots
+ * word (DBN format). Allows the user to choose the drawing algorithm to be
+ * used. Additionally, sets the panel's title.
+ *
+ * @param seq
+ * The raw nucleotide sequence
+ * @param str
+ * The secondary structure in DBN format
+ * @param drawMode
+ * The drawing mode
+ * @param title
+ * The panel title
+ * @throws ExceptionNonEqualLength
+ * @see RNA#DRAW_MODE_CIRCULAR
+ * @see RNA#DRAW_MODE_RADIATE
+ * @see RNA#DRAW_MODE_NAVIEW
+ */
+
+ public VARNAPanel(String seq, String str, int drawMode, String title)
+ throws ExceptionNonEqualLength
+ {
+ drawRNA(seq, str, drawMode);
+ init();
+ setTitle(title);
+ // VARNASecDraw._vp = this;
+ }
+
+ public VARNAPanel(String seq1, String struct1, String seq2,
+ String struct2, int drawMode, String title)
+ {
+ _conf._comparisonMode = true;
+ drawRNA(seq1, struct1, seq2, struct2, drawMode);
+ init();
+ setTitle(title);
+ }
+
+ private void init()
+ {
+ _popup.buildPopupMenu();
+ this.add(_popup);
+ setBackground(VARNAConfig.DEFAULT_BACKGROUND_COLOR);
+ _manager = new UndoManager();
+ _manager.setLimit(10000);
+ _UI.addUndoableEditListener(_manager);
+
+ _blink = new ControleurBlinkingThread(this,
+ ControleurBlinkingThread.DEFAULT_FREQUENCY, 0, 1.0, 0.0, 0.2);
+ _blink.start();
+
+ _premierAffichage = true;
+ _translation = new Point(0, 0);
+
+ _horsCadre = false;
+ this.setFont(_conf._fontBasesGeneral);
+
+ // ajout des controleurs au VARNAPanel
+ ControleurClicMovement controleurClicMovement = new ControleurClicMovement(
+ this);
+ this.addMouseListener(controleurClicMovement);
+ this.addMouseMotionListener(controleurClicMovement);
+ this.addMouseWheelListener(new ControleurMolette(this));
+
+ ControleurDraggedMolette ctrlDraggedMolette = new ControleurDraggedMolette(
+ this);
+ this.addMouseMotionListener(ctrlDraggedMolette);
+ this.addMouseListener(ctrlDraggedMolette);
+
+ ControleurVARNAPanelKeys ctrlKey = new ControleurVARNAPanelKeys(this);
+ this.addKeyListener(ctrlKey);
+ this.addFocusListener(ctrlKey);
+
+ _interpolator = new ControleurInterpolator(this);
+ /**
+ *
+ * BH SwingJS do not start this thread
+ *
+ * @j2sNative
+ */
+ {
+ _interpolator.start();
+ }
+
+ }
+
+ public void undo()
+ {
+ if (_manager.canUndo())
+ _manager.undo();
+ }
+
+ public void redo()
+ {
+ if (_manager.canRedo())
+ _manager.redo();
+ }
+
+ /**
+ * Sets the new style of the title font.
+ *
+ * @param newStyle
+ * An int that describes the new font style ("PLAIN","BOLD",
+ * "BOLDITALIC", or "ITALIC")
+ */
+ public void setTitleFontStyle(int newStyle)
+ {
+ _conf._titleFont = _conf._titleFont.deriveFont(newStyle);
+ updateTitleHeight();
+ }
+
+ /**
+ * Sets the new size of the title font.
+ *
+ * @param newSize
+ * The new size of the title font
+ */
+ public void setTitleFontSize(float newSize)
+ {
+ // System.err.println("Applying title size "+newSize);
+ _conf._titleFont = _conf._titleFont.deriveFont(newSize);
+ updateTitleHeight();
+ }
+
+ /**
+ * Sets the new font family to be used for the title. Available fonts are
+ * system-specific, yet it seems that "Arial", "Dialog", and "MonoSpaced" are
+ * almost always available.
+ *
+ * @param newFamily
+ * New font family used for the title
+ */
+ public void setTitleFontFamily(String newFamily)
+ {
+ _conf._titleFont = new Font(newFamily, _conf._titleFont.getStyle(),
+ _conf._titleFont.getSize());
+ updateTitleHeight();
+ }
+
+ /**
+ * Sets the color to be used for the title.
+ *
+ * @param newColor
+ * A color used to draw the title
+ */
+ public void setTitleFontColor(Color newColor)
+ {
+ _conf._titleColor = newColor;
+ updateTitleHeight();
+ }
+
+ /**
+ * Sets the font size for displaying bases
+ *
+ * @param size
+ * Font size for base caption
+ */
+
+ public void setBaseFontSize(Float size)
+ {
+ _conf._fontBasesGeneral = _conf._fontBasesGeneral.deriveFont(size);
+ }
+
+ /**
+ * Sets the font size for displaying base numbers
+ *
+ * @param size
+ * Font size for base numbers
+ */
+
+ public void setNumbersFontSize(Float size)
+ {
+ _conf._numbersFont = _conf._numbersFont.deriveFont(size);
+ }
+
+ /**
+ * Sets the font style for displaying bases
+ *
+ * @param style
+ * An int that describes the new font style ("PLAIN","BOLD",
+ * "BOLDITALIC", or "ITALIC")
+ */
+
+ public void setBaseFontStyle(int style)
+ {
+ _conf._fontBasesGeneral = _conf._fontBasesGeneral.deriveFont(style);
+ }
+
+ private void updateTitleHeight()
+ {
+ if (!getTitle().equals(""))
+ {
+ _titleHeight = (int) (_conf._titleFont.getSize() * 1.5);
+ }
+ else
+ {
+ _titleHeight = 0;
+ }
+ if (Math.abs(this.getZoom() - 1) < .02)
+ {
+ _translation.y = (int) (-getTitleHeight() / 2.0);
+ }
+ }
+
+ /**
+ * Sets the panel's title, giving a short description of the RNA secondary
+ * structure.
+ *
+ * @param title
+ * The new title
+ */
+ public void setTitle(String title)
+ {
+ _RNA.setName(title);
+ updateTitleHeight();
+ }
+
+ /**
+ * Sets the distance between consecutive base numbers. Please notice that :
+ * <ul>
+ * <li>The first and last base are always numbered</li>
+ * <li>The numbering is based on the base numbers, not on the indices. So base
+ * numbers may appear more frequently than expected if bases are skipped</li>
+ * <li>The periodicity is measured starting from 0. This means that for a
+ * period of 10 and bases numbered from 1 to 52, the base numbers
+ * [1,10,20,30,40,50,52] will be drawn.</li>
+ * </ul>
+ *
+ * @param n
+ * New numbering period
+ */
+ public void setNumPeriod(int n)
+ {
+ _conf._numPeriod = n;
+ }
+
+ /**
+ * Returns the current numbering period. Please notice that :
+ * <ul>
+ * <li>The first and last base are always numbered</li>
+ * <li>The numbering is based on the base numbers, not on the indices. So base
+ * numbers may appear more frequently than expected if bases are skipped</li>
+ * <li>The periodicity is measured starting from 0. This means that for a
+ * period of 10 and bases numbered from 1 to 52, the base numbers
+ * [1,10,20,30,40,50,52] will be drawn.</li>
+ * </ul>
+ *
+ * @return Current numbering period
+ */
+ public int getNumPeriod()
+ {
+ return _conf._numPeriod;
+ }
+
+ private void setScaleFactor(double d)
+ {
+ _scaleFactor = d;
+ }
+
+ private double getScaleFactor()
+ {
+ return _scaleFactor;
+ }
+
+ private void setAutoFit(boolean fit)
+ {
+ _conf._autoFit = fit;
+ repaint();
+ }
+
+ public void lockScrolling()
+ {
+ setAutoFit(false);
+ setAutoCenter(false);
+ }
+
+ public void unlockScrolling()
+ {
+ setAutoFit(true);
+ setAutoCenter(true);
+ }
+
+ private void drawStringOutline(VueVARNAGraphics g2D, String res, double x,
+ double y, double margin)
+ {
+ Dimension d = g2D.getStringDimension(res);
+ x -= (double) d.width / 2.0;
+ y += (double) d.height / 2.0;
+ g2D.setColor(Color.GRAY);
+ g2D.setSelectionStroke();
+ g2D.drawRect((x - margin), (y - d.height - margin),
+ (d.width + 2.0 * margin), (d.height + 2.0 * margin));
+ }
+
+ private void drawSymbol(VueVARNAGraphics g2D, double posx, double posy,
+ double normx, double normy, double radius, boolean isCIS,
+ ModeleBP.Edge e)
+ {
+ Color bck = g2D.getColor();
+ switch (e)
+ {
+ case WC:
+ if (isCIS)
+ {
+ g2D.setColor(bck);
+ g2D.fillCircle((posx - (radius) / 2.0), (posy - (radius) / 2.0),
+ radius);
+ g2D.drawCircle((posx - (radius) / 2.0), (posy - (radius) / 2.0),
+ radius);
+ }
+ else
+ {
+ g2D.setColor(Color.white);
+ g2D.fillCircle(posx - (radius) / 2.0, (posy - (radius) / 2.0),
+ (radius));
+ g2D.setColor(bck);
+ g2D.drawCircle((posx - (radius) / 2.0), (posy - (radius) / 2.0),
+ (radius));
+ }
+ break;
+ case HOOGSTEEN:
+ {
+ GeneralPath p2 = new GeneralPath();
+ radius /= 1.05;
+ p2.moveTo(
+ (float) (posx - radius * normx / 2.0 - radius * normy / 2.0),
+ (float) (posy - radius * normy / 2.0 + radius * normx / 2.0));
+ p2.lineTo(
+ (float) (posx + radius * normx / 2.0 - radius * normy / 2.0),
+ (float) (posy + radius * normy / 2.0 + radius * normx / 2.0));
+ p2.lineTo(
+ (float) (posx + radius * normx / 2.0 + radius * normy / 2.0),
+ (float) (posy + radius * normy / 2.0 - radius * normx / 2.0));
+ p2.lineTo(
+ (float) (posx - radius * normx / 2.0 + radius * normy / 2.0),
+ (float) (posy - radius * normy / 2.0 - radius * normx / 2.0));
+ p2.closePath();
+
+ if (isCIS)
+ {
+ g2D.setColor(bck);
+ g2D.fill(p2);
+ g2D.draw(p2);
+ }
+ else
+ {
+ g2D.setColor(Color.white);
+ g2D.fill(p2);
+ g2D.setColor(bck);
+ g2D.draw(p2);
+ }
+ }
+ break;
+ case SUGAR:
+ {
+ double ix = radius * normx / 2.0;
+ double iy = radius * normy / 2.0;
+ double jx = radius * normy / 2.0;
+ double jy = -radius * normx / 2.0;
+
+ GeneralPath p2 = new GeneralPath();
+ p2.moveTo((float) (posx - ix + jx), (float) (posy - iy + jy));
+ p2.lineTo((float) (posx + ix + jx), (float) (posy + iy + jy));
+ p2.lineTo((float) (posx - jx), (float) (posy - jy));
+ p2.closePath();
+
+ if (isCIS)
+ {
+ g2D.setColor(bck);
+ g2D.fill(p2);
+ g2D.draw(p2);
+ }
+ else
+ {
+ g2D.setColor(Color.white);
+ g2D.fill(p2);
+ g2D.setColor(bck);
+ g2D.draw(p2);
+ }
+ }
+ break;
+ }
+ g2D.setColor(bck);
+ }
+
+ private void drawBasePairArc(VueVARNAGraphics g2D, int i, int j,
+ Point2D.Double orig, Point2D.Double dest, double scaleFactor,
+ ModeleBP style, double newRadius)
+ {
+ double distance, coef;
+ if (j - i == 1)
+ coef = getBPHeightIncrement() * 1.75;
+ else
+ coef = getBPHeightIncrement();
+ distance = dest.x - orig.x;
+ switch (_conf._mainBPStyle)
+ {
+ case LW:
+ {
+ double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS)
+ / 5.0) * scaleFactor;
+ if (style.isCanonical())
+ {
+ if (style.isCanonicalGC())
+ {
+ if ((orig.x != dest.x) || (orig.y != dest.y))
+ {
+ g2D.drawArc((dest.x + orig.x) / 2.,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0,
+ (distance - scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ (distance * coef
+ - scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ 0, 180);
+ g2D.drawArc((dest.x + orig.x) / 2.,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0,
+ (distance + scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ (distance * coef
+ + scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ 0, 180);
+ }
+ }
+ else if (style.isCanonicalAU())
+ {
+ g2D.drawArc((dest.x + orig.x) / 2.,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance),
+ (distance * coef), 0, 180);
+ }
+ else if (style.isWobbleUG())
+ {
+ Point2D.Double midtop = new Point2D.Double((dest.x + orig.x) / 2.,
+ dest.y - distance * coef / 2.
+ - scaleFactor * _RNA.BASE_RADIUS / 2.0);
+ g2D.drawArc(midtop.x,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance),
+ (distance * coef), 0, 180);
+ drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle, false,
+ ModeleBP.Edge.WC);
+ }
+ else
+ {
+ Point2D.Double midtop = new Point2D.Double((dest.x + orig.x) / 2.,
+ dest.y - distance * coef / 2.
+ - scaleFactor * _RNA.BASE_RADIUS / 2.0);
+ g2D.drawArc(midtop.x,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance),
+ (distance * coef), 0, 180);
+ drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle,
+ style.isCIS(), style.getEdgePartner5());
+ }
+ }
+ else
+ {
+ ModeleBP.Edge p1 = style.getEdgePartner5();
+ ModeleBP.Edge p2 = style.getEdgePartner3();
+ Point2D.Double midtop = new Point2D.Double((dest.x + orig.x) / 2.,
+ dest.y - distance * coef / 2.
+ - scaleFactor * _RNA.BASE_RADIUS / 2.0);
+ g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0,
+ (distance), (distance * coef), 0, 180);
+ if (p1 == p2)
+ {
+ drawSymbol(g2D, midtop.x, midtop.y, 1., 0., radiusCircle, false,
+ style.getEdgePartner5());
+ }
+ else
+ {
+ drawSymbol(g2D, midtop.x - scaleFactor * _RNA.BASE_RADIUS,
+ midtop.y, 1., 0., radiusCircle, style.isCIS(), p1);
+ drawSymbol(g2D, midtop.x + scaleFactor * _RNA.BASE_RADIUS,
+ midtop.y, -1., 0., radiusCircle, style.isCIS(), p2);
+ }
+ }
+ }
+ break;
+ case LW_ALT:
+ {
+ double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS)
+ / 5.0) * scaleFactor;
+ double distFromBaseCenter = DISTANCE_FACT * scaleFactor;
+ orig = new Point2D.Double(orig.x,
+ orig.y - (distFromBaseCenter + newRadius));
+ dest = new Point2D.Double(dest.x,
+ dest.y - (distFromBaseCenter + newRadius));
+ if (style.isCanonical())
+ {
+ if (style.isCanonicalGC())
+ {
+ if ((orig.x != dest.x) || (orig.y != dest.y))
+ {
+ g2D.drawArc((dest.x + orig.x) / 2.,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0,
+ (distance - scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ (distance * coef
+ - scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ 0, 180);
+ g2D.drawArc((dest.x + orig.x) / 2.,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0,
+ (distance + scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ (distance * coef
+ + scaleFactor * _RNA.BASE_RADIUS / 3.0),
+ 0, 180);
+ }
+ }
+ else if (style.isCanonicalAU())
+ {
+ g2D.drawArc((dest.x + orig.x) / 2.,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance),
+ (distance * coef), 0, 180);
+ }
+ }
+ else
+ {
+ ModeleBP.Edge p1 = style.getEdgePartner5();
+ ModeleBP.Edge p2 = style.getEdgePartner3();
+ Point2D.Double midtop = new Point2D.Double((dest.x + orig.x) / 2.,
+ dest.y - distance * coef / 2.
+ - scaleFactor * _RNA.BASE_RADIUS / 2.0);
+ g2D.drawArc(midtop.x, dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0,
+ (distance), (distance * coef), 0, 180);
+ drawSymbol(g2D, orig.x, orig.y - radiusCircle * .95, 1., 0.,
+ radiusCircle, style.isCIS(), p1);
+ drawSymbol(g2D, dest.x, dest.y - radiusCircle * .95, -1., 0.,
+ radiusCircle, style.isCIS(), p2);
+ }
+ }
+ break;
+ default:
+ g2D.drawArc((dest.x + orig.x) / 2.,
+ dest.y - scaleFactor * _RNA.BASE_RADIUS / 2.0, (distance),
+ (distance * coef), 0, 180);
+ break;
+ }
+
+ }
+
+ public static double DISTANCE_FACT = 2.;
+
+ private void drawBasePair(VueVARNAGraphics g2D, Point2D.Double orig,
+ Point2D.Double dest, ModeleBP style, double newRadius,
+ double scaleFactor)
+ {
+
+ double dx = dest.x - orig.x;
+ double dy = dest.y - orig.y;
+ double dist = Math.sqrt((dest.x - orig.x) * (dest.x - orig.x)
+ + (dest.y - orig.y) * (dest.y - orig.y));
+ dx /= dist;
+ dy /= dist;
+ double nx = -dy;
+ double ny = dx;
+ orig = new Point2D.Double(orig.x + newRadius * dx,
+ orig.y + newRadius * dy);
+ dest = new Point2D.Double(dest.x - newRadius * dx,
+ dest.y - newRadius * dy);
+ switch (_conf._mainBPStyle)
+ {
+ case LW:
+ {
+ double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS)
+ / 5.0) * scaleFactor;
+ if (style.isCanonical())
+ {
+ if (style.isCanonicalGC())
+ {
+ if ((orig.x != dest.x) || (orig.y != dest.y))
+ {
+ nx *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
+ ny *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
+ g2D.drawLine((orig.x + nx), (orig.y + ny), (dest.x + nx),
+ (dest.y + ny));
+ g2D.drawLine((orig.x - nx), (orig.y - ny), (dest.x - nx),
+ (dest.y - ny));
+ }
+ }
+ else if (style.isCanonicalAU())
+ {
+ g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
+ }
+ else if (style.isWobbleUG())
+ {
+ double cx = (dest.x + orig.x) / 2.0;
+ double cy = (dest.y + orig.y) / 2.0;
+ g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
+ drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, false,
+ ModeleBP.Edge.WC);
+ }
+ else
+ {
+ double cx = (dest.x + orig.x) / 2.0;
+ double cy = (dest.y + orig.y) / 2.0;
+ g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
+ drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(),
+ style.getEdgePartner5());
+ }
+ }
+ else
+ {
+ ModeleBP.Edge p1 = style.getEdgePartner5();
+ ModeleBP.Edge p2 = style.getEdgePartner3();
+ double cx = (dest.x + orig.x) / 2.0;
+ double cy = (dest.y + orig.y) / 2.0;
+ g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
+ if (p1 == p2)
+ {
+ drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(), p1);
+
+ }
+ else
+ {
+ double vdx = (dest.x - orig.x);
+ double vdy = (dest.y - orig.y);
+ vdx /= 6.0;
+ vdy /= 6.0;
+ drawSymbol(g2D, cx + vdx, cy + vdy, -nx, -ny, radiusCircle,
+ style.isCIS(), p2);
+ drawSymbol(g2D, cx - vdx, cy - vdy, nx, ny, radiusCircle,
+ style.isCIS(), p1);
+ }
+ }
+ }
+ break;
+ case LW_ALT:
+ {
+ double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS)
+ / 5.0) * scaleFactor;
+ double distFromBaseCenter = DISTANCE_FACT * scaleFactor;
+ Point2D.Double norig = new Point2D.Double(
+ orig.x + (distFromBaseCenter + .5 * newRadius) * dx,
+ orig.y + (distFromBaseCenter + .5 * newRadius) * dy);
+ Point2D.Double ndest = new Point2D.Double(
+ dest.x - (distFromBaseCenter + .5 * newRadius) * dx,
+ dest.y - (distFromBaseCenter + .5 * newRadius) * dy);
+ if (style.isCanonical())
+ {
+ if (style.isCanonicalGC())
+ {
+ if ((norig.x != ndest.x) || (norig.y != ndest.y))
+ {
+ nx *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
+ ny *= scaleFactor * _RNA.BASE_RADIUS / 4.0;
+ g2D.drawLine((norig.x + nx), (norig.y + ny), (ndest.x + nx),
+ (ndest.y + ny));
+ g2D.drawLine((norig.x - nx), (norig.y - ny), (ndest.x - nx),
+ (ndest.y - ny));
+ }
+ }
+ else if (style.isCanonicalAU())
+ {
+ g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
+ }
+ else if (style.isWobbleUG())
+ {
+ double cx = (ndest.x + norig.x) / 2.0;
+ double cy = (ndest.y + norig.y) / 2.0;
+ g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
+ drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, false,
+ ModeleBP.Edge.WC);
+ }
+ else
+ {
+ double cx = (ndest.x + norig.x) / 2.0;
+ double cy = (ndest.y + norig.y) / 2.0;
+ g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
+ drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(),
+ style.getEdgePartner5());
+ }
+ }
+ else
+ {
+ ModeleBP.Edge p1 = style.getEdgePartner5();
+ ModeleBP.Edge p2 = style.getEdgePartner3();
+ double cx = (ndest.x + norig.x) / 2.0;
+ double cy = (ndest.y + norig.y) / 2.0;
+ g2D.drawLine(norig.x, norig.y, ndest.x, ndest.y);
+ if (p1 == p2)
+ {
+ drawSymbol(g2D, cx, cy, nx, ny, radiusCircle, style.isCIS(), p1);
+
+ }
+ else
+ {
+ double fac = .4;
+ drawSymbol(g2D, ndest.x - fac * radiusCircle * dx,
+ ndest.y - fac * radiusCircle * dy, -nx, -ny, radiusCircle,
+ style.isCIS(), p2);
+ drawSymbol(g2D, norig.x + fac * radiusCircle * dx,
+ norig.y + fac * radiusCircle * dy, nx, ny, radiusCircle,
+ style.isCIS(), p1);
+ }
+ }
+ }
+ break;
+ case SIMPLE:
+ g2D.drawLine(orig.x, orig.y, dest.x, dest.y);
+ break;
+ case RNAVIZ:
+ double xcenter = (orig.x + dest.x) / 2.0;
+ double ycenter = (orig.y + dest.y) / 2.0;
+ double radius = Math.max(4.0 * scaleFactor, 1.0);
+ g2D.fillCircle((xcenter - radius), (ycenter - radius),
+ (2.0 * radius));
+ break;
+ case NONE:
+ break;
+ }
+ }
+
+ private Color getHighlightedVersion(Color c1, Color c2)
+ {
+ int r1 = c1.getRed();
+ int g1 = c1.getGreen();
+ int b1 = c1.getBlue();
+ int r2 = c2.getRed();
+ int g2 = c2.getGreen();
+ int b2 = c2.getBlue();
+ double val = _blink.getVal();
+ int nr = Math.max(0,
+ Math.min((int) ((r1 * val + r2 * (1.0 - val))), 255));
+ int ng = Math.max(0,
+ Math.min((int) ((g1 * val + g2 * (1.0 - val))), 255));
+ int nb = Math.max(0,
+ Math.min((int) ((b1 * val + b2 * (1.0 - val))), 255));
+ return new Color(nr, ng, nb);
+ }
+
+ private Color highlightFilter(int index, Color initialColor, Color c1,
+ Color c2, boolean localView)
+ {
+ if (_selectedBases.contains(_RNA.getBaseAt(index)) && localView)
+ {
+ return getHighlightedVersion(c1, c2);
+ }
+ else
+ return initialColor;
+ }
+
+ public static Point2D.Double computeExcentricUnitVector(int i,
+ Point2D.Double[] points, Point2D.Double[] centers)
+ {
+ double dist = points[i].distance(centers[i]);
+ Point2D.Double byCenter = new Point2D.Double(
+ (points[i].x - centers[i].x) / dist,
+ (points[i].y - centers[i].y) / dist);
+ if ((i > 0) && (i < points.length - 1))
+ {
+ Point2D.Double p0 = points[i - 1];
+ Point2D.Double p1 = points[i];
+ Point2D.Double p2 = points[i + 1];
+ double dist1 = p2.distance(p1);
+ Point2D.Double v1 = new Point2D.Double((p2.x - p1.x) / dist1,
+ (p2.y - p1.y) / dist1);
+ Point2D.Double vn1 = new Point2D.Double(v1.y, -v1.x);
+ double dist2 = p1.distance(p0);
+ Point2D.Double v2 = new Point2D.Double((p1.x - p0.x) / dist2,
+ (p1.y - p0.y) / dist2);
+ Point2D.Double vn2 = new Point2D.Double(v2.y, -v2.x);
+ Point2D.Double vn = new Point2D.Double((vn1.x + vn2.x) / 2.0,
+ (vn1.y + vn2.y) / 2.0);
+ double D = vn.distance(new Point2D.Double(0.0, 0.0));
+ vn.x /= D;
+ vn.y /= D;
+ if (byCenter.x * vn.x + byCenter.y * vn.y < 0)
+ {
+ vn.x = -vn.x;
+ vn.y = -vn.y;
+ }
+ return vn;
+ }
+ else if (((i == 0) || (i == points.length - 1)) && (points.length > 1))
+ {
+ int a = (i == 0) ? 0 : points.length - 1;
+ int b = (i == 0) ? 1 : points.length - 2;
+ double D = points[a].distance(points[b]);
+ return new Point2D.Double((points[a].x - points[b].x) / D,
+ (points[a].y - points[b].y) / D);
+ }
+ else
+ {
+ return byCenter;
+ }
+ }
+
+ private void drawBase(VueVARNAGraphics g2D, int i,
+ Point2D.Double[] points, Point2D.Double[] centers,
+ double newRadius, double _scaleFactor, boolean localView)
+ {
+ Point2D.Double p = points[i];
+ ModeleBase mb = _RNA.get_listeBases().get(i);
+ g2D.setFont(_conf._fontBasesGeneral);
+ Color baseInnerColor = highlightFilter(i,
+ _RNA.getBaseInnerColor(i, _conf), Color.white,
+ _RNA.getBaseInnerColor(i, _conf), localView);
+ Color baseOuterColor = highlightFilter(i,
+ _RNA.getBaseOuterColor(i, _conf),
+ _RNA.getBaseOuterColor(i, _conf), Color.white, localView);
+ Color baseNameColor = highlightFilter(i,
+ _RNA.getBaseNameColor(i, _conf),
+ _RNA.getBaseNameColor(i, _conf), Color.white, localView);
+ if (RNA.whiteLabelPreferrable(baseInnerColor))
+ {
+ baseNameColor = Color.white;
+ }
+
+ if (mb instanceof ModeleBaseNucleotide)
+ {
+ ModeleBaseNucleotide mbn = (ModeleBaseNucleotide) mb;
+ String res = mbn.getBase();
+ if (_hoveredBase == mb && localView && isModifiable())
+ {
+ g2D.setColor(_conf._hoverColor);
+ g2D.fillCircle(p.getX() - 1.5 * newRadius,
+ p.getY() - 1.5 * newRadius, 3.0 * newRadius);
+ g2D.setColor(_conf._hoverColor.darker());
+ g2D.drawCircle(p.getX() - 1.5 * newRadius,
+ p.getY() - 1.5 * newRadius, 3.0 * newRadius);
+ g2D.setPlainStroke();
+ }
+ if (_conf._fillBases)
+ {
+ // Filling inner circle
+ g2D.setColor(baseInnerColor);
+ g2D.fillCircle(p.getX() - newRadius, p.getY() - newRadius,
+ 2.0 * newRadius);
+ }
+
+ if (_conf._drawOutlineBases)
+ {
+ // Drawing outline
+ g2D.setColor(baseOuterColor);
+ g2D.setStrokeThickness(_conf._baseThickness * _scaleFactor);
+ g2D.drawCircle(p.getX() - newRadius, p.getY() - newRadius,
+ 2.0 * newRadius);
+ }
+ // Drawing label
+ g2D.setColor(baseNameColor);
+ g2D.drawStringCentered(String.valueOf(res), p.getX(), p.getY());
+ }
+ else if (mb instanceof ModeleBasesComparison)
+ {
+
+ ModeleBasesComparison mbc = (ModeleBasesComparison) mb;
+
+ // On lui donne l'aspect voulue (on a un trait droit)
+ g2D.setPlainStroke(); // On doit avoir un trait droit, sans arrondit
+ g2D.setStrokeThickness(_conf._baseThickness * _scaleFactor);
+
+ // On dessine l'étiquette, rectangle aux bords arrondies.
+ g2D.setColor(baseInnerColor);
+ g2D.fillRoundRect((p.getX() - 1.5 * newRadius),
+ (p.getY() - newRadius), (3.0 * newRadius), (2.0 * newRadius),
+ 10 * _scaleFactor, 10 * _scaleFactor);
+
+ /* Dessin du rectangle exterieur (bords) */
+ g2D.setColor(baseOuterColor);
+ g2D.drawRoundRect((p.getX() - 1.5 * newRadius),
+ (p.getY() - newRadius), (3 * newRadius), (2 * newRadius),
+ 10 * _scaleFactor, 10 * _scaleFactor);
+
+ // On le dessine au centre de l'étiquette.
+ g2D.drawLine((p.getX()), (p.getY() + newRadius) - 1, (p.getX()),
+ (p.getY() - newRadius) + 1);
+
+ /* Dessin du nom de la base (A,C,G,U,etc...) */
+ // On créer le texte des étiquettes
+ String label1 = String.valueOf(mbc.getBase1());
+ String label2 = String.valueOf(mbc.getBase2());
+
+ // On leur donne une couleur
+ g2D.setColor(getRNA().get_listeBases().get(i).getStyleBase()
+ .getBaseNameColor());
+
+ // Et on les dessine.
+ g2D.drawStringCentered(label1, p.getX() - (.75 * newRadius),
+ p.getY());
+ g2D.drawStringCentered(label2, p.getX() + (.75 * newRadius),
+ p.getY());
+ }
+
+ // Drawing base number
+ if (_RNA.isNumberDrawn(mb, getNumPeriod()))
+ {
+
+ Point2D.Double vn = computeExcentricUnitVector(i, points, centers);
+ g2D.setColor(mb.getStyleBase().getBaseNumberColor());
+ g2D.setFont(_conf._numbersFont);
+ double factorMin = Math.min(.5, _conf._distNumbers);
+ double factorMax = Math.min(_conf._distNumbers - 1.5,
+ _conf._distNumbers);
+ g2D.drawLine(p.x + vn.x * ((1 + factorMin) * newRadius),
+ p.y + vn.y * ((1 + factorMin) * newRadius),
+ p.x + vn.x * ((1 + factorMax) * newRadius),
+ p.y + vn.y * ((1 + factorMax) * newRadius));
+ g2D.drawStringCentered(mb.getLabel(),
+ p.x + vn.x * ((1 + _conf._distNumbers) * newRadius),
+ p.y + vn.y * ((1 + _conf._distNumbers) * newRadius));
+
+ }
+ }
+
+ void drawChemProbAnnotation(VueVARNAGraphics g2D, ChemProbAnnotation cpa,
+ Point2D.Double anchor, double scaleFactor)
+ {
+ g2D.setColor(cpa.getColor());
+ g2D.setStrokeThickness(RNA.CHEM_PROB_ARROW_THICKNESS * scaleFactor
+ * cpa.getIntensity());
+ g2D.setPlainStroke();
+ Point2D.Double v = cpa.getDirVector();
+ Point2D.Double vn = cpa.getNormalVector();
+ Point2D.Double base = new Point2D.Double(
+ (anchor.x + _RNA.CHEM_PROB_DIST * scaleFactor * v.x),
+ (anchor.y + _RNA.CHEM_PROB_DIST * scaleFactor * v.y));
+ Point2D.Double edge = new Point2D.Double(
+ (base.x + _RNA.CHEM_PROB_BASE_LENGTH * cpa.getIntensity()
+ * scaleFactor * v.x),
+ (base.y + _RNA.CHEM_PROB_BASE_LENGTH * cpa.getIntensity()
+ * scaleFactor * v.y));
+ switch (cpa.getType())
+ {
+ case ARROW:
+ {
+ Point2D.Double arrowTip1 = new Point2D.Double(
+ (base.x + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_ARROW_WIDTH * vn.x
+ + _RNA.CHEM_PROB_ARROW_HEIGHT * v.x)),
+ (base.y + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_ARROW_WIDTH * vn.y
+ + _RNA.CHEM_PROB_ARROW_HEIGHT * v.y)));
+ Point2D.Double arrowTip2 = new Point2D.Double(
+ (base.x + cpa.getIntensity() * scaleFactor
+ * (-_RNA.CHEM_PROB_ARROW_WIDTH * vn.x
+ + _RNA.CHEM_PROB_ARROW_HEIGHT * v.x)),
+ (base.y + cpa.getIntensity() * scaleFactor
+ * (-_RNA.CHEM_PROB_ARROW_WIDTH * vn.y
+ + _RNA.CHEM_PROB_ARROW_HEIGHT * v.y)));
+ g2D.drawLine(base.x, base.y, edge.x, edge.y);
+ g2D.drawLine(base.x, base.y, arrowTip1.x, arrowTip1.y);
+ g2D.drawLine(base.x, base.y, arrowTip2.x, arrowTip2.y);
+ }
+ break;
+ case PIN:
+ {
+ Point2D.Double side1 = new Point2D.Double(
+ (edge.x - cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.x)),
+ (edge.y - cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.y)));
+ Point2D.Double side2 = new Point2D.Double(
+ (edge.x - cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.x)),
+ (edge.y - cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.y)));
+ Point2D.Double side3 = new Point2D.Double(
+ (edge.x + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.x)),
+ (edge.y + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * v.y)));
+ Point2D.Double side4 = new Point2D.Double(
+ (edge.x + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.x)),
+ (edge.y + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_PIN_SEMIDIAG * vn.y)));
+ GeneralPath p2 = new GeneralPath();
+ p2.moveTo((float) side1.x, (float) side1.y);
+ p2.lineTo((float) side2.x, (float) side2.y);
+ p2.lineTo((float) side3.x, (float) side3.y);
+ p2.lineTo((float) side4.x, (float) side4.y);
+ p2.closePath();
+ g2D.fill(p2);
+ g2D.drawLine(base.x, base.y, edge.x, edge.y);
+ }
+ break;
+ case TRIANGLE:
+ {
+ Point2D.Double arrowTip1 = new Point2D.Double(
+ (edge.x + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.x)),
+ (edge.y + cpa.getIntensity() * scaleFactor
+ * (_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.y)));
+ Point2D.Double arrowTip2 = new Point2D.Double(
+ (edge.x + cpa.getIntensity() * scaleFactor
+ * (-_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.x)),
+ (edge.y + cpa.getIntensity() * scaleFactor
+ * (-_RNA.CHEM_PROB_TRIANGLE_WIDTH * vn.y)));
+ GeneralPath p2 = new GeneralPath();
+ p2.moveTo((float) base.x, (float) base.y);
+ p2.lineTo((float) arrowTip1.x, (float) arrowTip1.y);
+ p2.lineTo((float) arrowTip2.x, (float) arrowTip2.y);
+ p2.closePath();
+ g2D.fill(p2);
+ }
+ break;
+ case DOT:
+ {
+ Double radius = scaleFactor * _RNA.CHEM_PROB_DOT_RADIUS
+ * cpa.getIntensity();
+ Point2D.Double center = new Point2D.Double((base.x + radius * v.x),
+ (base.y + radius * v.y));
+ g2D.fillCircle((center.x - radius), (center.y - radius),
+ (2 * radius));
+ }
+ break;
+ }
+ }
+
+ Point2D.Double buildCaptionPosition(ModeleBase mb, double scaleFactor,
+ double heightEstimate)
+ {
+ double radius = 2.0;
+ if (_RNA.isNumberDrawn(mb, getNumPeriod()))
+ {
+ radius += _conf._distNumbers;
+ }
+ Point2D.Double center = mb.getCenter();
+ Point2D.Double p = mb.getCoords();
+ double realDistance = _RNA.BASE_RADIUS * radius + heightEstimate;
+ return new Point2D.Double(center.getX() + (p.getX() - center.getX())
+ * ((p.distance(center) + realDistance) / p.distance(center)),
+ center.getY() + (p.getY() - center.getY())
+ * ((p.distance(center) + realDistance)
+ / p.distance(center)));
+ }
+
+ private void renderAnnotations(VueVARNAGraphics g2D, double offX,
+ double offY, double rnaBBoxX, double rnaBBoxY, double scaleFactor)
+ {
+ for (TextAnnotation textAnnotation : _RNA.getAnnotations())
+ {
+ g2D.setColor(textAnnotation.getColor());
+ g2D.setFont(textAnnotation.getFont().deriveFont((float) (2.0
+ * textAnnotation.getFont().getSize() * scaleFactor)));
+ Point2D.Double position = textAnnotation.getCenterPosition();
+ if (textAnnotation.getType() == TextAnnotation.AnchorType.BASE)
+ {
+ ModeleBase mb = (ModeleBase) textAnnotation.getAncrage();
+ double fontHeight = Math.ceil(textAnnotation.getFont().getSize());
+ position = buildCaptionPosition(mb, scaleFactor, fontHeight);
+ }
+ position = transformCoord(position, offX, offY, rnaBBoxX, rnaBBoxY,
+ scaleFactor);
+ g2D.drawStringCentered(textAnnotation.getTexte(), position.x,
+ position.y);
+ if ((_selectedAnnotation == textAnnotation) && (_highlightAnnotation))
+ {
+ drawStringOutline(g2D, textAnnotation.getTexte(), position.x,
+ position.y, 5);
+ }
+ }
+ for (ChemProbAnnotation cpa : _RNA.getChemProbAnnotations())
+ {
+ Point2D.Double anchor = transformCoord(cpa.getAnchorPosition(), offX,
+ offY, rnaBBoxX, rnaBBoxY, scaleFactor);
+ drawChemProbAnnotation(g2D, cpa, anchor, scaleFactor);
+ }
+
+ }
+
+ public Rectangle2D.Double getExtendedRNABBox()
+ {
+ // We get the logical bounding box
+ Rectangle2D.Double rnabbox = _RNA.getBBox();
+ rnabbox.y -= _conf._distNumbers * _RNA.BASE_RADIUS;
+ rnabbox.height += 2.0 * _conf._distNumbers * _RNA.BASE_RADIUS;
+ rnabbox.x -= _conf._distNumbers * _RNA.BASE_RADIUS;
+ rnabbox.width += 2.0 * _conf._distNumbers * _RNA.BASE_RADIUS;
+ if (_RNA.hasVirtualLoops())
+ {
+ rnabbox.y -= RNA.VIRTUAL_LOOP_RADIUS;
+ rnabbox.height += 2.0 * RNA.VIRTUAL_LOOP_RADIUS;
+ rnabbox.x -= RNA.VIRTUAL_LOOP_RADIUS;
+ rnabbox.width += 2.0 * RNA.VIRTUAL_LOOP_RADIUS;
+ }
+ return rnabbox;
+ }
+
+ public void drawBackbone(VueVARNAGraphics g2D, Point2D.Double[] newCoords,
+ double newRadius, double _scaleFactor)
+ {
+ // Drawing backbone
+ if (getDrawBackbone())
+ {
+ g2D.setStrokeThickness(1.5 * _scaleFactor);
+ g2D.setColor(_conf._backboneColor);
+
+ ModeleBackbone bck = _RNA.getBackbone();
+
+ for (int i = 1; i < _RNA.get_listeBases().size(); i++)
+ {
+ Point2D.Double p1 = newCoords[i - 1];
+ Point2D.Double p2 = newCoords[i];
+ double dist = p1.distance(p2);
+ int a = _RNA.getBaseAt(i - 1).getElementStructure();
+ int b = _RNA.getBaseAt(i).getElementStructure();
+ boolean consecutivePair = (a == i) && (b == i - 1);
+
+ if ((dist > 0))
+ {
+ Point2D.Double vbp = new Point2D.Double();
+ vbp.x = (p2.x - p1.x) / dist;
+ vbp.y = (p2.y - p1.y) / dist;
+
+ BackboneType bt = bck.getTypeBefore(i);
+ if (bt != BackboneType.DISCONTINUOUS_TYPE)
+ {
+ if (bt == BackboneType.MISSING_PART_TYPE)
+ {
+ g2D.setSelectionStroke();
+ }
+ else
+ {
+ g2D.setPlainStroke();
+ }
+ g2D.setColor(bck.getColorBefore(i, _conf._backboneColor));
+
+ if (consecutivePair
+ && (_RNA.getDrawMode() != RNA.DRAW_MODE_LINEAR)
+ && (_RNA.getDrawMode() != RNA.DRAW_MODE_CIRCULAR))
+ {
+ int dir = 0;
+ if (i + 1 < newCoords.length)
+ {
+ dir = (_RNA.testDirectionality(i - 1, i, i + 1) ? -1 : 1);
+ }
+ else if (i - 2 >= 0)
+ {
+ dir = (_RNA.testDirectionality(i - 2, i - 1, i) ? -1 : 1);
+ }
+ Point2D.Double vn = new Point2D.Double(dir * vbp.y,
+ -dir * vbp.x);
+ Point2D.Double centerSeg = new Point2D.Double(
+ (p1.x + p2.x) / 2.0, (p1.y + p2.y) / 2.0);
+ double distp1CenterSeq = p1.distance(centerSeg);
+ double centerDist = Math
+ .sqrt((RNA.VIRTUAL_LOOP_RADIUS * _scaleFactor
+ * RNA.VIRTUAL_LOOP_RADIUS * _scaleFactor)
+ - distp1CenterSeq * distp1CenterSeq);
+ Point2D.Double centerLoop = new Point2D.Double(
+ centerSeg.x + centerDist * vn.x,
+ centerSeg.y + centerDist * vn.y);
+ double radius = centerLoop.distance(p1);
+ double a1 = 360. * (Math.atan2(-(p1.y - centerLoop.y),
+ (p1.x - centerLoop.x))) / (2. * Math.PI);
+ double a2 = 360. * (Math.atan2(-(p2.y - centerLoop.y),
+ (p2.x - centerLoop.x))) / (2. * Math.PI);
+ double angle = (a2 - a1);
+ if (-dir * angle < 0)
+ {
+ angle += -dir * 360.;
+ }
+ // if (angle<0.) angle += 360.;
+ // angle = -dir*(360-dir*angle);
+ g2D.drawArc(centerLoop.x + .8 * newRadius * vn.x,
+ centerLoop.y + .8 * newRadius * vn.y, 2 * radius,
+ 2 * radius, a1, angle);
+ }
+ else
+ {
+ g2D.drawLine((newCoords[i - 1].x + newRadius * vbp.x),
+ (newCoords[i - 1].y + newRadius * vbp.y),
+ (newCoords[i].x - newRadius * vbp.x),
+ (newCoords[i].y - newRadius * vbp.y));
+ }
+ }
+ }
+ }
+ }
+ }
+
+ public Point2D.Double logicToPanel(Point2D.Double logicPoint)
+ {
+ return new Point2D.Double(
+ _offX + (getScaleFactor() * (logicPoint.x - _offsetRNA.x)),
+ _offY + (getScaleFactor() * (logicPoint.y - _offsetRNA.y)));
+
+ }
+
+ public Rectangle2D.Double renderRNA(VueVARNAGraphics g2D,
+ Rectangle2D.Double bbox)
+ {
+ return renderRNA(g2D, bbox, false, true);
+ }
+
+ private double computeScaleFactor(Rectangle2D.Double bbox,
+ boolean localView, boolean autoCenter)
+ {
+ Rectangle2D.Double rnabbox = getExtendedRNABBox();
+ double scaleFactor = Math.min(
+ (double) bbox.width / (double) rnabbox.width,
+ (double) bbox.height / (double) rnabbox.height);
+
+ // Use it to get an estimate of the font size for numbers ...
+ float newFontSize = Math.max(1,
+ (int) ((1.7 * _RNA.BASE_RADIUS) * scaleFactor));
+ // ... and increase bounding box accordingly
+ rnabbox.y -= newFontSize;
+ rnabbox.height += newFontSize;
+ if (_conf._drawColorMap)
+ {
+ rnabbox.height += getColorMapHeight();
+ }
+ rnabbox.x -= newFontSize;
+ rnabbox.width += newFontSize;
+
+ // Now, compute the final scaling factor and corresponding font size
+ scaleFactor = Math.min((double) bbox.width / (double) rnabbox.width,
+ (double) bbox.height / (double) rnabbox.height);
+ if (localView)
+ {
+ if (_conf._autoFit)
+ setScaleFactor(scaleFactor);
+ scaleFactor = getScaleFactor();
+ }
+ return scaleFactor;
+ }
+
+ public synchronized Rectangle2D.Double renderRNA(VueVARNAGraphics g2D,
+ Rectangle2D.Double bbox, boolean localView, boolean autoCenter)
+ {
+ Rectangle2D.Double rnaMultiBox = new Rectangle2D.Double(0, 0, 1, 1);
+ double scaleFactor = computeScaleFactor(bbox, localView, autoCenter);
+ float newFontSize = Math.max(1,
+ (int) ((1.7 * _RNA.BASE_RADIUS) * scaleFactor));
+ double newRadius = Math.max(1.0, (scaleFactor * _RNA.BASE_RADIUS));
+ setBaseFontSize(newFontSize);
+ setNumbersFontSize(newFontSize);
+ double offX = bbox.x;
+ double offY = bbox.y;
+ Rectangle2D.Double rnabbox = getExtendedRNABBox();
+
+ if (_RNA.getSize() != 0)
+ {
+
+ Point2D.Double offsetRNA = new Point2D.Double(rnabbox.x, rnabbox.y);
+
+ if (autoCenter)
+ {
+ offX = (bbox.x
+ + (bbox.width - Math.round(rnabbox.width * scaleFactor))
+ / 2.0);
+ offY = (bbox.y
+ + (bbox.height - Math.round(rnabbox.height * scaleFactor))
+ / 2.0);
+ if (localView)
+ {
+ _offX = offX;
+ _offY = offY;
+ _offsetPanel = new Point2D.Double(_offX, _offY);
+ _offsetRNA = new Point2D.Double(rnabbox.x, rnabbox.y);
+ }
+ }
+
+ if (localView)
+ {
+ offX = _offX;
+ offY = _offY;
+ offsetRNA = _offsetRNA;
+ }
+
+ // Re-scaling once and for all
+ Point2D.Double[] newCoords = new Point2D.Double[_RNA.get_listeBases()
+ .size()];
+ Point2D.Double[] newCenters = new Point2D.Double[_RNA.get_listeBases()
+ .size()];
+ for (int i = 0; i < _RNA.get_listeBases().size(); i++)
+ {
+ ModeleBase mb = _RNA.getBaseAt(i);
+ newCoords[i] = new Point2D.Double(
+ offX + (scaleFactor * (mb.getCoords().x - offsetRNA.x)),
+ offY + (scaleFactor * (mb.getCoords().y - offsetRNA.y)));
+
+ Point2D.Double centerBck = _RNA.getCenter(i);
+ // si la base est dans un angle entre une boucle et une helice
+ if (_RNA.get_drawMode() == RNA.DRAW_MODE_NAVIEW
+ || _RNA.get_drawMode() == RNA.DRAW_MODE_RADIATE)
+ {
+ if ((mb.getElementStructure() != -1)
+ && i < _RNA.get_listeBases().size() - 1 && i > 1)
+ {
+ ModeleBase b1 = _RNA.get_listeBases().get(i - 1);
+ ModeleBase b2 = _RNA.get_listeBases().get(i + 1);
+ int j1 = b1.getElementStructure();
+ int j2 = b2.getElementStructure();
+ if ((j1 == -1) ^ (j2 == -1))
+ {
+ // alors la position du nombre associé doit etre
+ Point2D.Double a1 = b1.getCoords();
+ Point2D.Double a2 = b2.getCoords();
+ Point2D.Double c1 = b1.getCenter();
+ Point2D.Double c2 = b2.getCenter();
+
+ centerBck.x = mb.getCoords().x
+ + (c1.x - a1.x) / c1.distance(a1)
+ + (c2.x - a2.x) / c2.distance(a2);
+ centerBck.y = mb.getCoords().y
+ + (c1.y - a1.y) / c1.distance(a1)
+ + (c2.y - a2.y) / c2.distance(a2);
+ }
+ }
+ }
+ newCenters[i] = new Point2D.Double(
+ offX + (scaleFactor * (centerBck.x - offsetRNA.x)),
+ offY + (scaleFactor * (centerBck.y - offsetRNA.y)));
+ }
+ // Keep track of coordinates for mouse interactions
+ if (localView)
+ {
+ _realCoords = newCoords;
+ _realCenters = newCenters;
+ }
+
+ g2D.setStrokeThickness(1.5 * scaleFactor);
+ g2D.setPlainStroke();
+ g2D.setFont(_conf._fontBasesGeneral);
+
+ // Drawing region highlights Annotation
+ drawRegionHighlightsAnnotation(g2D, _realCoords, _realCenters,
+ scaleFactor);
+ drawBackbone(g2D, newCoords, newRadius, scaleFactor);
+
+ // Drawing base-pairs
+ // pour chaque base
+ for (int i = 0; i < _RNA.get_listeBases().size(); i++)
+ {
+ int j = _RNA.get_listeBases().get(i).getElementStructure();
+ // si c'est une parenthese ouvrante (premiere base du
+ // couple)
+ if (j > i)
+ {
+ ModeleBP msbp = _RNA.get_listeBases().get(i).getStyleBP();
+ // System.err.println(msbp);
+ if (msbp.isCanonical() || _conf._drawnNonCanonicalBP)
+ {
+ if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR)
+ {
+ g2D.setStrokeThickness(_RNA.getBasePairThickness(msbp, _conf)
+ * 2.0 * scaleFactor * _conf._bpThickness);
+ }
+ else
+ {
+ g2D.setStrokeThickness(_RNA.getBasePairThickness(msbp, _conf)
+ * 1.5 * scaleFactor);
+ }
+ g2D.setColor(_RNA.getBasePairColor(msbp, _conf));
+
+ if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR)
+ {
+ drawBasePairArc(g2D, i, j, newCoords[i], newCoords[j],
+ scaleFactor, msbp, newRadius);
+ }
+ else
+ {
+ drawBasePair(g2D, newCoords[i], newCoords[j], msbp, newRadius,
+ scaleFactor);
+ }
+ }
+ }
+ }
+
+ // Liaisons additionelles (non planaires)
+ if (_conf._drawnNonPlanarBP)
+ {
+ ArrayList<ModeleBP> bpaux = _RNA.getStructureAux();
+ for (int k = 0; k < bpaux.size(); k++)
+ {
+ ModeleBP msbp = bpaux.get(k);
+ if (msbp.isCanonical() || _conf._drawnNonCanonicalBP)
+ {
+ int i = msbp.getPartner5().getIndex();
+ int j = msbp.getPartner3().getIndex();
+ if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR)
+ {
+ g2D.setStrokeThickness(_RNA.getBasePairThickness(msbp, _conf)
+ * 2.5 * scaleFactor * _conf._bpThickness);
+ g2D.setPlainStroke();
+ }
+ else
+ {
+ g2D.setStrokeThickness(_RNA.getBasePairThickness(msbp, _conf)
+ * 1.5 * scaleFactor);
+ g2D.setPlainStroke();
+ }
+
+ g2D.setColor(_RNA.getBasePairColor(msbp, _conf));
+ if (j > i)
+ {
+ if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR)
+ {
+ drawBasePairArc(g2D, i, j, newCoords[i], newCoords[j],
+ scaleFactor, msbp, newRadius);
+ }
+ else
+ {
+ drawBasePair(g2D, newCoords[i], newCoords[j], msbp,
+ newRadius, scaleFactor);
+ }
+ }
+ }
+ }
+ }
+
+ // Drawing bases
+ g2D.setPlainStroke();
+ for (int i = 0; i < Math.min(_RNA.get_listeBases().size(),
+ newCoords.length); i++)
+ {
+ drawBase(g2D, i, newCoords, newCenters, newRadius, scaleFactor,
+ localView);
+ }
+
+ rnaMultiBox = new Rectangle2D.Double(offX, offY,
+ (scaleFactor * rnabbox.width) - 1,
+ (scaleFactor * rnabbox.height) - 1);
+
+ if (localView)
+ {
+ // Drawing bbox
+ if (_debug || _drawBBox)
+ {
+ g2D.setColor(Color.RED);
+ g2D.setSelectionStroke();
+ g2D.drawRect(rnaMultiBox.x, rnaMultiBox.y, rnaMultiBox.width,
+ rnaMultiBox.height);
+ }
+
+ // Draw color map
+ if (_conf._drawColorMap)
+ {
+ drawColorMap(g2D, scaleFactor, rnabbox);
}
- public FullBackup loadSession(File path) throws ExceptionLoadingFailed {
-
- FullBackup bck = importSession(path);
- Mapping map = Mapping.DefaultOutermostMapping(getRNA().getSize(),
- bck.rna.getSize());
- showRNAInterpolated(bck.rna, map);
- _conf = bck.config;
- repaint();
- return bck;
- }
-
- public static String VARNA_SESSION_EXTENSION = "varna";
-
- public static FullBackup importSession(Object path) // BH was String
- throws ExceptionLoadingFailed {
- try {
- FileInputStream fis = (path instanceof File ? new FileInputStream((File) path) : new FileInputStream(path.toString()));
- // ZipInputStream zis = new
- // ZipInputStream(new BufferedInputStream(fis));
- // zis.getNextEntry();
- FullBackup h = importSession(fis, path.toString());
- // zis.close();
- return h;
- } catch (FileNotFoundException e) {
- throw (new ExceptionLoadingFailed("File not found.", path.toString()));
- } catch (IOException e) {
- // TODO Auto-generated catch block
- throw (new ExceptionLoadingFailed(
- "I/O error while loading session.", path.toString()));
- }
- }
-
- public static FullBackup importSession(InputStream fis, String path)
- throws ExceptionLoadingFailed {
- System.setProperty("javax.xml.parsers.SAXParserFactory",
- "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
- SAXParserFactory saxFact = javax.xml.parsers.SAXParserFactory
- .newInstance();
- saxFact.setValidating(false);
- saxFact.setXIncludeAware(false);
- saxFact.setNamespaceAware(false);
- try {
- SAXParser sp = saxFact.newSAXParser();
- VARNASessionParser sessionData = new VARNASessionParser();
- sp.parse(fis, sessionData);
- FullBackup res = new FullBackup(sessionData.getVARNAConfig(),
- sessionData.getRNA(), "test");
- return res;
- } catch (ParserConfigurationException e) {
- throw new ExceptionLoadingFailed("Bad XML parser configuration",
- path);
- } catch (SAXException e) {
- throw new ExceptionLoadingFailed("XML parser Exception", path);
- } catch (IOException e) {
- throw new ExceptionLoadingFailed("I/O error", path);
- }
- }
-
- public void loadFile(File path) {
- loadFile(path, false);
- }
-
- public boolean getDrawBackbone() {
- return _conf._drawBackbone;
- }
-
- public void setDrawBackbone(boolean b) {
- _conf._drawBackbone = b;
- }
-
- public void addHighlightRegion(HighlightRegionAnnotation n) {
- _RNA.addHighlightRegion(n);
- }
-
- public void removeHighlightRegion(HighlightRegionAnnotation n) {
- _RNA.removeHighlightRegion(n);
- }
-
- public void addHighlightRegion(int i, int j) {
- _RNA.addHighlightRegion(i, j);
- }
-
- public void addHighlightRegion(int i, int j, Color fill, Color outline,
- double radius) {
- _RNA.addHighlightRegion(i, j, fill, outline, radius);
- }
-
- public void loadRNA(String path) {
- loadRNA(path, false);
- }
-
- public void loadRNA(Object path, boolean interpolate) { // BH was String
- try {
- Collection<RNA> rnas = (path instanceof File ? RNAFactory.loadSecStr(new FileReader((File) path)) : RNAFactory.loadSecStr(path.toString()));
- if (rnas.isEmpty()) {
- throw new ExceptionFileFormatOrSyntax(
- "No RNA could be parsed from that source.");
- }
- RNA rna = rnas.iterator().next();
- try {
- rna.drawRNA(_conf);
- } catch (ExceptionNAViewAlgorithm e) {
- e.printStackTrace();
- }
- if (!interpolate) {
- showRNA(rna);
- } else {
- this.showRNAInterpolated(rna);
- }
-
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- } catch (ExceptionFileFormatOrSyntax e) {
- e.printStackTrace();
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- public void loadFile(File path, boolean interpolate) { // was String BH StringJS
- try {
- loadSession(path);
- } catch (Exception e1) {
- loadRNA(path, interpolate);
- }
- }
-
- public void setConfig(VARNAConfig cfg) {
- _conf = cfg;
- }
-
- public void toggleDrawOutlineBases() {
- _conf._drawOutlineBases = !_conf._drawOutlineBases;
- }
-
- public void toggleFillBases() {
- _conf._fillBases = !_conf._fillBases;
- }
-
- public void setDrawOutlineBases(boolean drawn) {
- _conf._drawOutlineBases = drawn;
- }
-
- public void setFillBases(boolean drawn) {
- _conf._fillBases = drawn;
- }
-
- public void readValues(Reader r) {
- this._RNA.readValues(r, _conf._cm);
- }
-
- public void addVARNAListener(InterfaceVARNAListener v) {
- _VARNAListeners.add(v);
- }
-
- public void fireLayoutChanged() {
- for (InterfaceVARNAListener v : _VARNAListeners) {
- v.onStructureRedrawn();
- }
- }
-
- public void fireUINewStructure(RNA r) {
- for (InterfaceVARNAListener v : _VARNAListeners) {
- v.onUINewStructure(_conf, r);
- }
- }
-
- public void fireZoomLevelChanged(double d) {
- for (InterfaceVARNAListener v : _VARNAListeners) {
- v.onZoomLevelChanged();
- }
- }
-
- public void fireTranslationChanged() {
- for (InterfaceVARNAListener v2 : _VARNAListeners) {
- v2.onTranslationChanged();
- }
- }
-
- public void addSelectionListener(InterfaceVARNASelectionListener v) {
- _selectionListeners.add(v);
- }
-
- public void fireSelectionChanged(BaseList mold, BaseList mnew) {
- BaseList addedBases = mnew.removeAll(mold);
- BaseList removedBases = mold.removeAll(mnew);
- for (InterfaceVARNASelectionListener v2 : _selectionListeners) {
- v2.onSelectionChanged(mnew, addedBases, removedBases);
- }
- }
-
- public void fireHoverChanged(ModeleBase mold, ModeleBase mnew) {
- for (InterfaceVARNASelectionListener v2 : _selectionListeners) {
- v2.onHoverChanged(mold, mnew);
- }
- }
-
- public void addRNAListener(InterfaceVARNARNAListener v) {
- _RNAListeners.add(v);
- }
-
- public void addVARNABasesListener(InterfaceVARNABasesListener l) {
- _basesListeners.add(l);
- }
-
- public void fireSequenceChanged(int index, String oldseq, String newseq) {
- for (InterfaceVARNARNAListener v2 : _RNAListeners) {
- v2.onSequenceModified(index, oldseq, newseq);
- }
- }
-
- public void fireStructureChanged(Set<ModeleBP> current,
- Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs) {
- for (InterfaceVARNARNAListener v2 : _RNAListeners) {
- v2.onStructureModified(current, addedBasePairs, removedBasePairs);
- }
- }
-
- public void fireLayoutChanged(
- Hashtable<Integer, Point2D.Double> movedPositions) {
- for (InterfaceVARNARNAListener v2 : _RNAListeners) {
- v2.onRNALayoutChanged(movedPositions);
- }
- }
-
- public void fireBaseClicked(ModeleBase mb, MouseEvent me) {
- if (mb != null) {
- for (InterfaceVARNABasesListener v2 : _basesListeners) {
- v2.onBaseClicked(mb, me);
- }
- }
- }
-
- public double getOrientation() {
- return _RNA.getOrientation();
- }
-
- public ModeleBase _hoveredBase = null;
-
- public void setHoverBase(ModeleBase m) {
- if (m != _hoveredBase) {
- ModeleBase bck = _hoveredBase;
- _hoveredBase = m;
- repaint();
- fireHoverChanged(bck, m);
- }
- }
-
- public void toXML(String path) {
- FileOutputStream fis;
- try {
- fis = new FileOutputStream(path);
- // ZipOutputStream zis = new ZipOutputStream(new
- // BufferedOutputStream(fis));
- // ZipEntry entry = new ZipEntry("VARNASession");
- // zis.putNextEntry(entry);
- PrintWriter pw = new PrintWriter(fis);
- toXML(pw);
- pw.flush();
- // zis.closeEntry();
- // zis.close();
- fis.close();
- } catch (FileNotFoundException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- public void toXML(PrintWriter out) {
- try {
-
- // out = new PrintWriter(System.out);
- StreamResult streamResult = new StreamResult(out);
- SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory
- .newInstance();
- // SAX2.0 ContentHandler.
- TransformerHandler hd = tf.newTransformerHandler();
- Transformer serializer = hd.getTransformer();
- serializer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1");
- serializer
- .setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "users.dtd");
- serializer.setOutputProperty(OutputKeys.INDENT, "yes");
- hd.setResult(streamResult);
- hd.startDocument();
- toXML(hd);
- hd.endDocument();
- } catch (TransformerConfigurationException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (SAXException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- }
-
- public static String XML_ELEMENT_NAME = "VARNASession";
-
- public void toXML(TransformerHandler hd) throws SAXException {
- AttributesImpl atts = new AttributesImpl();
- hd.startElement("", "", XML_ELEMENT_NAME, atts);
- _RNA.toXML(hd);
- _conf.toXML(hd);
- hd.endElement("", "", XML_ELEMENT_NAME);
- }
-
- public TextAnnotation getNearestAnnotation(int x, int y) {
- TextAnnotation t = null;
- if (getListeAnnotations().size() != 0) {
- double dist = Double.MAX_VALUE;
- double d2;
- Point2D.Double position;
- for (TextAnnotation textAnnot : getListeAnnotations()) {
- // calcul de la distance
- position = textAnnot.getCenterPosition();
- position = transformCoord(position);
- d2 = Math.sqrt(Math.pow((position.x - x), 2)
- + Math.pow((position.y - y), 2));
- // si la valeur est inferieur au minimum actuel
- if ((dist > d2)
- && (d2 < getScaleFactor()
- * ControleurClicMovement.MIN_SELECTION_DISTANCE)) {
- t = textAnnot;
- dist = d2;
- }
- }
- }
- return t;
- }
-
- public ModeleBase getNearestBase(int x, int y, boolean always,
- boolean onlyPaired) {
- int i = getNearestBaseIndex(x, y, always, onlyPaired);
- if (i == -1)
- return null;
- return getRNA().get_listeBases().get(i);
- }
-
- public ModeleBase getNearestBase(int x, int y) {
- return getNearestBase(x, y, false, false);
- }
-
- public int getNearestBaseIndex(int x, int y, boolean always,
- boolean onlyPaired) {
- double d2, dist = Double.MAX_VALUE;
- int mb = -1;
- for (int i = 0; i < getRealCoords().length; i++) {
- if (!onlyPaired
- || (getRNA().get_listeBases().get(i).getElementStructure() != -1)) {
- d2 = Math.sqrt(Math.pow((getRealCoords()[i].x - x), 2)
- + Math.pow((getRealCoords()[i].y - y), 2));
- if ((dist > d2)
- && ((d2 < getScaleFactor()
- * ControleurClicMovement.MIN_SELECTION_DISTANCE) || always)) {
- dist = d2;
- mb = i;
- }
- }
- }
- return mb;
- }
-
- public void globalRescale(double factor) {
- _RNA.rescale(factor);
- fireLayoutChanged();
- repaint();
- }
-
- public void setSpaceBetweenBases(double sp) {
- _conf._spaceBetweenBases = sp;
- }
-
- public double getSpaceBetweenBases() {
- return _conf._spaceBetweenBases;
- }
+ if (_debug || _drawBBox)
+ {
+ g2D.setColor(Color.GRAY);
+ g2D.setSelectionStroke();
+ g2D.drawRect(0, 0, getWidth() - 1,
+ getHeight() - getTitleHeight() - 1);
+ }
+ }
+ // Draw annotations
+ renderAnnotations(g2D, offX, offY, offsetRNA.x, offsetRNA.y,
+ scaleFactor);
+ // Draw additional debug shape
+ if (_RNA._debugShape != null)
+ {
+ Color c = new Color(255, 0, 0, 50);
+ g2D.setColor(c);
+ AffineTransform at = new AffineTransform();
+ at.translate(offX - scaleFactor * rnabbox.x,
+ offY - scaleFactor * rnabbox.y);
+ at.scale(scaleFactor, scaleFactor);
+ Shape s = at.createTransformedShape(_RNA._debugShape);
+ if (s instanceof GeneralPath)
+ {
+ g2D.fill((GeneralPath) s);
+ }
+ }
+ }
+ else
+ {
+ g2D.setColor(VARNAConfig.DEFAULT_MESSAGE_COLOR);
+ g2D.setFont(VARNAConfig.DEFAULT_MESSAGE_FONT);
+ rnaMultiBox = new Rectangle2D.Double(0, 0, 10, 10);
+ g2D.drawStringCentered("No RNA here", bbox.getCenterX(),
+ bbox.getCenterY());
+ }
+ return rnaMultiBox;
+ }
+
+ public void centerViewOn(double x, double y)
+ {
+ Rectangle2D.Double r = _RNA.getBBox();
+ _target = new Point2D.Double(x, y);
+ Point2D.Double q = logicToPanel(_target);
+ Point p = new Point((int) (-q.x), (int) (-q.y));
+ setTranslation(p);
+ repaint();
+ }
+
+ Point2D.Double _target = new Point2D.Double(0, 0);
+
+ Point2D.Double _target2 = new Point2D.Double(0, 0);
+
+ public ModeleBase getBaseAt(Point2D.Double po)
+ {
+ ModeleBase mb = null;
+ Point2D.Double p = panelToLogicPoint(po);
+ double dist = Double.MAX_VALUE;
+ for (ModeleBase tmp : _RNA.get_listeBases())
+ {
+ double ndist = tmp.getCoords().distance(p);
+ if (dist > ndist)
+ {
+ mb = tmp;
+ dist = ndist;
+ }
+ }
+ return mb;
+ }
+
+ public void setColorMapValues(Double[] values)
+ {
+ _RNA.setColorMapValues(values, _conf._cm, true);
+ _conf._drawColorMap = true;
+ repaint();
+ }
+
+ public void setColorMapMaxValue(double d)
+ {
+ _conf._cm.setMaxValue(d);
+ }
+
+ public void setColorMapMinValue(double d)
+ {
+ _conf._cm.setMinValue(d);
+ }
+
+ public ModeleColorMap getColorMap()
+ {
+ return _conf._cm;
+ }
+
+ public void setColorMap(ModeleColorMap cm)
+ {
+ // _RNA.adaptColorMapToValues(cm);
+ _conf._cm = cm;
+ repaint();
+ }
+
+ public void setColorMapCaption(String caption)
+ {
+ _conf._colorMapCaption = caption;
+ repaint();
+ }
+
+ public String getColorMapCaption()
+ {
+ return _conf._colorMapCaption;
+ }
+
+ public void drawColorMap(boolean draw)
+ {
+ _conf._drawColorMap = draw;
+ }
+
+ private double getColorMapHeight()
+ {
+ double result = VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE
+ + _conf._colorMapHeight;
+ if (!_conf._colorMapCaption.equals(""))
+ result += VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE;
+ return result;
+ }
+
+ private void drawColorMap(VueVARNAGraphics g2D, double scaleFactor,
+ Rectangle2D.Double rnabbox)
+ {
+ double v1 = _conf._cm.getMinValue();
+ double v2 = _conf._cm.getMaxValue();
+ double x, y;
+ g2D.setPlainStroke();
+
+ double xSpaceAvail = 0;
+ double ySpaceAvail = Math.min(
+ (getHeight() - rnabbox.height * scaleFactor - getTitleHeight())
+ / 2.0,
+ scaleFactor * (_conf._colorMapHeight
+ + VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE));
+ if ((int) ySpaceAvail == 0)
+ {
+ xSpaceAvail = Math.min((getWidth() - rnabbox.width * scaleFactor) / 2,
+ scaleFactor * (_conf._colorMapWidth)
+ + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH);
+ }
+ double xBase = (xSpaceAvail + _offX + scaleFactor * (rnabbox.width
+ - _conf._colorMapWidth - _conf._colorMapXOffset));
+ double hcaption = VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE;
+ double yBase = (ySpaceAvail + _offY + scaleFactor * (rnabbox.height
+ - _conf._colorMapHeight - _conf._colorMapYOffset - hcaption));
+
+ for (int i = 0; i < _conf._colorMapWidth; i++)
+ {
+ double ratio = (((double) i) / ((double) _conf._colorMapWidth));
+ double val = v1 + (v2 - v1) * ratio;
+ g2D.setColor(_conf._cm.getColorForValue(val));
+ x = (xBase + scaleFactor * i);
+ y = yBase;
+ g2D.fillRect(x, y,
+ scaleFactor * VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH,
+ (scaleFactor * _conf._colorMapHeight));
+ }
+ g2D.setColor(VARNAConfig.DEFAULT_COLOR_MAP_OUTLINE);
+ g2D.drawRect(xBase, yBase,
+ (VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH - 1
+ + scaleFactor * _conf._colorMapWidth),
+ ((scaleFactor * _conf._colorMapHeight)));
+ g2D.setFont(getFont().deriveFont((float) (scaleFactor
+ * VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE)));
+ g2D.setColor(VARNAConfig.DEFAULT_COLOR_MAP_FONT_COLOR);
+ NumberFormat nf = NumberFormat.getInstance();
+ nf.setMaximumFractionDigits(2);
+ nf.setMinimumFractionDigits(0);
+ g2D.drawStringCentered(nf.format(_conf._cm.getMinValue()), xBase,
+ yBase + scaleFactor * (_conf._colorMapHeight
+ + (VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7)));
+ g2D.drawStringCentered(nf.format(_conf._cm.getMaxValue()),
+ xBase + VARNAConfig.DEFAULT_COLOR_MAP_STRIPE_WIDTH
+ + scaleFactor * _conf._colorMapWidth,
+ yBase + scaleFactor * (_conf._colorMapHeight
+ + (VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7)));
+ if (!_conf._colorMapCaption.equals(""))
+ g2D.drawStringCentered("" + _conf._colorMapCaption,
+ xBase + scaleFactor * _conf._colorMapWidth / 2.0,
+ yBase + scaleFactor
+ * (VARNAConfig.DEFAULT_COLOR_MAP_FONT_SIZE / 1.7
+ + _conf._colorMapHeight));
+
+ }
+
+ public Point2D.Double panelToLogicPoint(Point2D.Double p)
+ {
+ return new Point2D.Double(
+ ((p.x - getOffsetPanel().x) / getScaleFactor())
+ + getRNAOffset().x,
+ ((p.y - getOffsetPanel().y) / getScaleFactor())
+ + getRNAOffset().y);
+ }
+
+ public Point2D.Double transformCoord(Point2D.Double coordDebut,
+ double offX, double offY, double rnaBBoxX, double rnaBBoxY,
+ double scaleFactor)
+ {
+ return new Point2D.Double(
+ offX + (scaleFactor * (coordDebut.x - rnaBBoxX)),
+ offY + (scaleFactor * (coordDebut.y - rnaBBoxY)));
+ }
+
+ public void eraseSequence()
+ {
+ _RNA.eraseSequence();
+ }
+
+ public Point2D.Double transformCoord(Point2D.Double coordDebut)
+ {
+ Rectangle2D.Double rnabbox = getExtendedRNABBox();
+ return new Point2D.Double(
+ _offX + (getScaleFactor() * (coordDebut.x - rnabbox.x)),
+ _offY + (getScaleFactor() * (coordDebut.y - rnabbox.y)));
+ }
+
+ public void paintComponent(Graphics g)
+ {
+ paintComponent(g, false);
+ }
+
+ public void paintComponent(Graphics g, boolean transparentBackground)
+ {
+ if (_premierAffichage)
+ {
+ // _border = new Dimension(0, 0);
+ _translation.x = 0;
+ _translation.y = (int) (-getTitleHeight() / 2.0);
+ _premierAffichage = false;
+ }
+
+ Graphics2D g2 = (Graphics2D) g;
+ Stroke dflt = g2.getStroke();
+ VueVARNAGraphics g2D = new SwingGraphics(g2);
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ this.removeAll();
+ super.paintComponent(g2);
+ renderComponent(g2D, transparentBackground, getScaleFactor());
+ if (isFocusOwner())
+ {
+ g2.setStroke(new BasicStroke(1.5f));
+ g2.setColor(Color.decode("#C0C0C0"));
+ g2.drawRect(0, 0, getWidth() - 1, getHeight() - 1);
+
+ }
+ g2.setStroke(dflt);
+ /*
+ * PSExport e = new PSExport(); SecStrProducerGraphics export = new
+ * SecStrProducerGraphics(e); renderRNA(export, getExtendedRNABBox());
+ * try { export.saveToDisk("./out.ps"); } catch
+ * (ExceptionWritingForbidden e1) { e1.printStackTrace(); }
+ */
+ }
+
+ /**
+ * Draws current RNA structure in a given Graphics "device".
+ *
+ * @param g2D
+ * A graphical device
+ * @param transparentBackground
+ * Whether the background should be transparent, or drawn.
+ */
+ public synchronized void renderComponent(VueVARNAGraphics g2D,
+ boolean transparentBackground, double scaleFactor)
+ {
+
+ updateTitleHeight();
+
+ if (!transparentBackground)
+ {
+ g2D.setColor(_conf._backgroundColor);
+ g2D.fillRect(0, 0, getWidth(), getHeight());
+ }
+ else
+ {
+ super.setBackground(new Color(0, 0, 0, 120));
+ }
+
+ if (_debug || _drawBorder)
+ {
+ g2D.setColor(Color.BLACK);
+ g2D.setPlainStroke();
+ g2D.drawRect(getLeftOffset(), getTopOffset(), getInnerWidth(),
+ getInnerHeight());
+
+ }
+
+ // if (!transparentBackground) {
+ // super.setBackground(_conf._backgroundColor);
+ // } else {
+ // super.setBackground(new Color(0, 0, 0, 120));
+ // }
+
+ if (getMinimumSize().height < getSize().height
+ && getMinimumSize().width < getSize().width)
+ {
+ // Draw Title
+ if (!getTitle().equals(""))
+ {
+ g2D.setColor(_conf._titleColor);
+ g2D.setFont(_conf._titleFont);
+ g2D.drawStringCentered(getTitle(), this.getWidth() / 2,
+ this.getHeight() - getTitleHeight() / 2.0);
+ }
+ // Draw RNA
+ renderRNA(g2D, getClip(), true, _conf._autoCenter);
+ }
+ if (_selectionRectangle != null)
+ {
+ g2D.setColor(Color.BLACK);
+ g2D.setSelectionStroke();
+ g2D.drawRect(_selectionRectangle.x, _selectionRectangle.y,
+ _selectionRectangle.width, _selectionRectangle.height);
+ }
+ if ((_linkOrigin != null) && (_linkDestination != null))
+ {
+ g2D.setColor(_conf._bondColor);
+ g2D.setPlainStroke();
+ g2D.setStrokeThickness(3.0 * scaleFactor);
+ Point2D.Double linkOrigin = (_linkOrigin);
+ Point2D.Double linkDestination = (_linkDestination);
+ g2D.drawLine(linkOrigin.x, linkOrigin.y, linkDestination.x,
+ linkDestination.y);
+ for (int i : getSelection().getIndices())
+ drawBase(g2D, i, _realCoords, _realCenters,
+ scaleFactor * _RNA.BASE_RADIUS, scaleFactor, true);
+ }
+
+ if (_debug)
+ {
+ g2D.setStrokeThickness(3.0 * scaleFactor);
+ g2D.setColor(Color.black);
+ Point2D.Double t = this.logicToPanel(_target);
+ g2D.drawLine(t.x - 3, t.y - 3, t.x + 3, t.y + 3);
+ g2D.drawLine(t.x - 3, t.y + 3, t.x + 3, t.y - 3);
+ g2D.setColor(Color.red);
+ t = this.logicToPanel(_target2);
+ g2D.drawLine(t.x - 3, t.y - 3, t.x + 3, t.y + 3);
+ g2D.drawLine(t.x - 3, t.y + 3, t.x + 3, t.y - 3);
+ }
+ }
+
+ public void drawRegionHighlightsAnnotation(VueVARNAGraphics g2D,
+ Point2D.Double[] realCoords, Point2D.Double[] realCenters,
+ double scaleFactor)
+ {
+ g2D.setStrokeThickness(2.0 * scaleFactor);
+ g2D.setPlainStroke();
+ for (HighlightRegionAnnotation r : _RNA.getHighlightRegion())
+ {
+ GeneralPath s = r.getShape(realCoords, realCenters, scaleFactor);
+ g2D.setColor(r.getFillColor());
+ g2D.fill(s);
+ g2D.setColor(r.getOutlineColor());
+ g2D.draw(s);
+ }
+ }
+
+ private Rectangle2D.Double getClip()
+ {
+ return new Rectangle2D.Double(getLeftOffset(), getTopOffset(),
+ this.getInnerWidth(), this.getInnerHeight());
+ }
+
+ public Rectangle2D.Double getViewClip()
+ {
+ return new Rectangle2D.Double(this.getLeftOffset(), this.getTopOffset(),
+ this.getInnerWidth(), this.getInnerHeight());
+ }
+
+ /**
+ * Returns the color used to draw backbone bounds.
+ *
+ * @return The color used to draw backbone bounds
+ */
+ public Color getBackboneColor()
+ {
+ return _conf._backboneColor;
+ }
+
+ /**
+ * Sets the color to be used for drawing backbone interactions.
+ *
+ * @param backbone_color
+ * The new color for the backbone bounds
+ */
+ public void setBackboneColor(Color backbone_color)
+ {
+ _conf._backboneColor = backbone_color;
+ }
+
+ /**
+ * Returns the color used to display hydrogen bonds (base pairings)
+ *
+ * @return The color of hydrogen bonds
+ */
+ public Color getBondColor()
+ {
+ return _conf._bondColor;
+ }
+
+ /**
+ * Returns the title of this panel
+ *
+ * @return The title
+ */
+ public String getTitle()
+ {
+ return _RNA.getName();
+ }
+
+ /**
+ * Sets the new color to be used for hydrogen bonds (base pairings)
+ *
+ * @param bond_color
+ * The new color for hydrogen bonds
+ */
+ public void setDefaultBPColor(Color bond_color)
+ {
+ _conf._bondColor = bond_color;
+ }
+
+ /**
+ * Sets the size of the border, i.e. the empty space between the end of the
+ * drawing area and the actual border.
+ *
+ * @param b
+ * The new border size
+ */
+ public void setBorderSize(Dimension b)
+ {
+ _border = b;
+ }
+
+ /**
+ * Returns the size of the border, i.e. the empty space between the end of the
+ * drawing area
+ *
+ * @return The border size
+ */
+ public Dimension getBorderSize()
+ {
+ return _border;
+ }
+
+ /**
+ * Sets the RNA to be displayed within this Panel. This method does not use a
+ * drawing algorithm to reassigns base coordinates, rather assuming that the
+ * RNA was previously drawn.
+ *
+ * @param r
+ * An already drawn RNA to display in this panel
+ */
+ public synchronized void showRNA(RNA r)
+ {
+ fireUINewStructure(r);
+ _RNA = r;
+ }
+
+ /**
+ * Sets the RNA secondary structure to be drawn in this panel, using the
+ * default layout algorithm. In addition to the raw nucleotides sequence, the
+ * secondary structure is given in the so-called "Dot-bracket notation" (DBN)
+ * format. This format is a well-parenthesized word over the alphabet
+ * '(',')','.'.<br/>
+ * Ex:<code>((((((((....))))..(((((...))).))))))</code><br />
+ * Returns <code>true</code> if the sequence/structure couple could be parsed
+ * into a valid secondary structure, and <code>false</code> otherwise.
+ *
+ * @param seq
+ * The raw nucleotides sequence
+ * @param str
+ * The secondary structure
+ * @throws ExceptionNonEqualLength
+ */
+ public void drawRNA(String seq, String str) throws ExceptionNonEqualLength
+ {
+ drawRNA(seq, str, _RNA.get_drawMode());
+ }
+
+ /**
+ * Sets the RNA secondary structure to be drawn in this panel, using a given
+ * layout algorithm.
+ *
+ * @param r
+ * The new secondary structure
+ * @param drawMode
+ * The drawing algorithm
+ */
+ public void drawRNA(RNA r, int drawMode)
+ {
+ r.setDrawMode(drawMode);
+ drawRNA(r);
+ }
+
+ /**
+ * Redraws the current RNA. This reassigns base coordinates to their default
+ * value using the current drawing algorithm.
+ */
+
+ public void drawRNA()
+ {
+ try
+ {
+ _RNA.drawRNA(_RNA.get_drawMode(), _conf);
+ } catch (ExceptionNAViewAlgorithm e)
+ {
+ errorDialog(e);
+ e.printStackTrace();
+ }
+ repaint();
+ }
+
+ /**
+ * Sets the RNA secondary structure to be drawn in this panel, using the
+ * current drawing algorithm.
+ *
+ * @param r
+ * The new secondary structure
+ */
+ public void drawRNA(RNA r)
+ {
+ if (r != null)
+ {
+ _RNA = r;
+ drawRNA();
+ }
+ }
+
+ /**
+ * Sets the RNA secondary structure to be drawn in this panel, using a given
+ * layout algorithm. In addition to the raw nucleotides sequence, the
+ * secondary structure is given in the so-called "Dot-bracket notation" (DBN)
+ * format. This format is a well-parenthesized word over the alphabet
+ * '(',')','.'.<br/>
+ * Ex: <code>((((((((....))))..(((((...))).))))))</code><br />
+ * Returns <code>true</code> if the sequence/structure couple could be parsed
+ * into a valid secondary structure, and <code>false</code> otherwise.
+ *
+ * @param seq
+ * The raw nucleotides sequence
+ * @param str
+ * The secondary structure
+ * @param drawMode
+ * The drawing algorithm
+ * @throws ExceptionNonEqualLength
+ */
+ public void drawRNA(String seq, String str, int drawMode)
+ throws ExceptionNonEqualLength
+ {
+ _RNA.setDrawMode(drawMode);
+ try
+ {
+ _RNA.setRNA(seq, str);
+ drawRNA();
+ } catch (ExceptionUnmatchedClosingParentheses e)
+ {
+ errorDialog(e);
+ } catch (ExceptionFileFormatOrSyntax e1)
+ {
+ errorDialog(e1);
+ }
+ }
+
+ public void drawRNA(Reader r, int drawMode)
+ throws ExceptionNonEqualLength, ExceptionFileFormatOrSyntax
+ {
+ _RNA.setDrawMode(drawMode);
+ Collection<RNA> rnas = RNAFactory.loadSecStr(r);
+ if (rnas.isEmpty())
+ {
+ throw new ExceptionFileFormatOrSyntax(
+ "No RNA could be parsed from that source.");
+ }
+ _RNA = rnas.iterator().next();
+ drawRNA();
+ }
+
+ /**
+ * Draws a secondary structure of RNA using the default drawing algorithm and
+ * displays it, using an interpolated transition between the previous one and
+ * the new one. Extra bases, resulting from a size difference between the two
+ * successive RNAs, are assumed to initiate from the middle of the sequence.
+ * In other words, both prefixes and suffixes of the RNAs are assumed to
+ * match, and what remains is an insertion.
+ *
+ * @param seq
+ * Sequence
+ * @param str
+ * Structure in dot bracket notation
+ * @throws ExceptionNonEqualLength
+ * If len(seq)!=len(str)
+ */
+ public void drawRNAInterpolated(String seq, String str)
+ throws ExceptionNonEqualLength
+ {
+ drawRNAInterpolated(seq, str, _RNA.get_drawMode());
+ }
+
+ /**
+ * Draws a secondary structure of RNA using a given algorithm and displays it,
+ * using an interpolated transition between the previous one and the new one.
+ * Extra bases, resulting from a size difference between the two successive
+ * RNAs, are assumed to initiate from the middle of the sequence. In other
+ * words, both prefixes and suffixes of the RNAs are assumed to match, and
+ * what remains is an insertion.
+ *
+ * @param seq
+ * Sequence
+ * @param str
+ * Structure in dot bracket notation
+ * @param drawMode
+ * The drawing algorithm to be used for the initial placement
+ * @throws ExceptionNonEqualLength
+ * If len(seq)!=len(str)
+ */
+ public void drawRNAInterpolated(String seq, String str, int drawMode)
+ {
+ drawRNAInterpolated(seq, str, drawMode, Mapping.DefaultOutermostMapping(
+ _RNA.get_listeBases().size(), str.length()));
+ }
+
+ /**
+ * Draws a secondary structure of RNA using the default drawing algorithm and
+ * displays it, using an interpolated transition between the previous one and
+ * the new one. Here, a mapping between those bases of the new structure and
+ * the previous one is explicitly provided.
+ *
+ * @param seq
+ * Sequence
+ * @param str
+ * Structure in dot bracket notation
+ * @param m
+ * A mapping between the currently rendered structure and its
+ * successor (seq,str)
+ * @throws ExceptionNonEqualLength
+ * If len(seq)!=len(str)
+ */
+ public void drawRNAInterpolated(String seq, String str, Mapping m)
+ {
+ drawRNAInterpolated(seq, str, _RNA.get_drawMode(), m);
+ }
+
+ /**
+ * Draws a secondary structure of RNA using a given drawing algorithm and
+ * displays it, using an interpolated transition between the previous one and
+ * the new one. Here, a mapping between those bases of the new structure and
+ * the previous one is provided.
+ *
+ * @param seq
+ * Sequence
+ * @param str
+ * Structure in dot bracket notation
+ * @param drawMode
+ * The drawing algorithm to be used for the initial placement
+ * @param m
+ * A mapping between the currently rendered structure and its
+ * successor (seq,str)
+ */
+ public void drawRNAInterpolated(String seq, String str, int drawMode,
+ Mapping m)
+ {
+ RNA target = new RNA();
+ try
+ {
+ target.setRNA(seq, str);
+ drawRNAInterpolated(target, drawMode, m);
+ } catch (ExceptionUnmatchedClosingParentheses e)
+ {
+ errorDialog(e);
+ } catch (ExceptionFileFormatOrSyntax e)
+ {
+ errorDialog(e);
+ }
+ }
+
+ /**
+ * Draws a secondary structure of RNA using the default drawing algorithm and
+ * displays it, using an interpolated transition between the previous one and
+ * the new one. Here, a mapping between those bases of the new structure and
+ * the previous one is explicitly provided.
+ *
+ * @param target
+ * Secondary structure
+ */
+ public void drawRNAInterpolated(RNA target)
+ {
+ drawRNAInterpolated(target, target.get_drawMode(),
+ Mapping.DefaultOutermostMapping(_RNA.get_listeBases().size(),
+ target.getSize()));
+ }
+
+ /**
+ * Draws a secondary structure of RNA using the default drawing algorithm and
+ * displays it, using an interpolated transition between the previous one and
+ * the new one. Here, a mapping between those bases of the new structure and
+ * the previous one is explicitly provided.
+ *
+ * @param target
+ * Secondary structure
+ * @param m
+ * A mapping between the currently rendered structure and its
+ * successor (seq,str)
+ */
+ public void drawRNAInterpolated(RNA target, Mapping m)
+ {
+ drawRNAInterpolated(target, target.get_drawMode(), m);
+ }
+
+ /**
+ * Draws a secondary structure of RNA using a given drawing algorithm and
+ * displays it, using an interpolated transition between the previous one and
+ * the new one. Here, a mapping between those bases of the new structure and
+ * the previous one is provided.
+ *
+ * @param target
+ * Secondary structure of RNA
+ * @param drawMode
+ * The drawing algorithm to be used for the initial placement
+ * @param m
+ * A mapping between the currently rendered structure and its
+ * successor (seq,str)
+ */
+ public void drawRNAInterpolated(RNA target, int drawMode, Mapping m)
+ {
+ try
+ {
+ target.drawRNA(drawMode, _conf);
+ _conf._drawColorMap = false;
+ _interpolator.addTarget(target, m);
+ } catch (ExceptionNAViewAlgorithm e)
+ {
+ errorDialog(e);
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Returns the current algorithm used for drawing the structure
+ *
+ * @return The current drawing algorithm
+ */
+ public int getDrawMode()
+ {
+ return this._RNA.getDrawMode();
+ }
+
+ public void showRNA(RNA t, VARNAConfig cfg)
+ {
+ showRNA(t);
+ if (cfg != null)
+ {
+ this.setConfig(cfg);
+ }
+ repaint();
+ }
+
+ /**
+ * Checks whether an interpolated transition bewteen two RNAs is occurring.
+ *
+ * @return True if an interpolated transition is occurring, false otherwise
+ */
+
+ public boolean isInterpolationInProgress()
+ {
+ if (_interpolator == null)
+ {
+ return false;
+ }
+ else
+ return _interpolator.isInterpolationInProgress();
+ }
+
+ /**
+ * Simply displays (does not redraw) a secondary structure , using an
+ * interpolated transition between the previous one and the new one. A default
+ * mapping between those bases of the new structure and the previous one is
+ * used.
+ *
+ * @param target
+ * Secondary structure of RNA
+ */
+ public void showRNAInterpolated(RNA target)
+ {
+ showRNAInterpolated(target, Mapping.DefaultOutermostMapping(
+ _RNA.get_listeBases().size(), target.getSize()));
+ }
+
+ /**
+ * Simply displays (does not redraw) a secondary structure , using an
+ * interpolated transition between the previous one and the new one. Here, a
+ * mapping between bases of the new structure and the previous one is given.
+ *
+ * @param target
+ * Secondary structure of RNA
+ * @param m
+ * A mapping between the currently rendered structure and its
+ * successor (seq,str)
+ * @throws ExceptionNonEqualLength
+ * If len(seq)!=len(str)
+ */
+ public void showRNAInterpolated(RNA target, Mapping m)
+ {
+ showRNAInterpolated(target, null, m);
+ }
+
+ public void showRNAInterpolated(RNA target, VARNAConfig cfg, Mapping m)
+ {
+ _interpolator.addTarget(target, cfg, m);
+ }
+
+ /**
+ * When comparison mode is ON, sets the two RNA secondary structure to be
+ * drawn in this panel, using a given layout algorithm. In addition to the raw
+ * nucleotides sequence, the secondary structure is given in the so-called
+ * "Dot-bracket notation" (DBN) format. This format is a well-parenthesized
+ * word over the alphabet '(',')','.'.<br/>
+ * Ex: <code>((((((((....))))..(((((...))).))))))</code><br />
+ *
+ * @param firstSeq
+ * The first RNA raw nucleotides sequence
+ * @param firstStruct
+ * The first RNA secondary structure
+ * @param secondSeq
+ * The second RNA raw nucleotides sequence
+ * @param secondStruct
+ * The second RNA secondary structure
+ * @param drawMode
+ * The drawing algorithm
+ */
+ public void drawRNA(String firstSeq, String firstStruct, String secondSeq,
+ String secondStruct, int drawMode)
+ {
+ _RNA.setDrawMode(drawMode);
+ /**
+ * Checking the sequences and structures validities...
+ */
+
+ // This is a comparison, so the two RNA alignment past in parameters
+ // must
+ // have the same sequence and structure length.
+ if (firstSeq.length() == secondSeq.length()
+ && firstStruct.length() == secondStruct.length())
+ {
+ // First RNA
+ if (firstSeq.length() != firstStruct.length())
+ {
+ if (_conf._showWarnings)
+ {
+ emitWarning("First sequence length " + firstSeq.length()
+ + " differs from that of it's secondary structure "
+ + firstStruct.length()
+ + ". \nAdapting first sequence length ...");
+ }
+ if (firstSeq.length() < firstStruct.length())
+ {
+ while (firstSeq.length() < firstStruct.length())
+ {
+ firstSeq += " ";
+ }
+ }
+ else
+ {
+ firstSeq = firstSeq.substring(0, firstStruct.length());
+ }
+ }
+
+ // Second RNA
+ if (secondSeq.length() != secondStruct.length())
+ {
+ if (_conf._showWarnings)
+ {
+ emitWarning("Second sequence length " + secondSeq.length()
+ + " differs from that of it's secondary structure "
+ + secondStruct.length()
+ + ". \nAdapting second sequence length ...");
+ }
+ if (secondSeq.length() < secondStruct.length())
+ {
+ while (secondSeq.length() < secondStruct.length())
+ {
+ secondSeq += " ";
+ }
+ }
+ else
+ {
+ secondSeq = secondSeq.substring(0, secondStruct.length());
+ }
+ }
+
+ int RNALength = firstSeq.length();
+ String string_superStruct = new String("");
+ String string_superSeq = new String("");
+ /**
+ * In this array, we'll have for each indexes of each characters of the
+ * final super-structure, the RNA number which is own it.
+ */
+ ArrayList<Integer> array_rnaOwn = new ArrayList<Integer>();
+
+ /**
+ * Generating super-structure sequences and structures...
+ */
+
+ firstStruct = firstStruct.replace('-', '.');
+ secondStruct = secondStruct.replace('-', '.');
+ // First of all, we make the structure
+ for (int i = 0; i < RNALength; i++)
+ {
+ // If both characters are the same, so it'll be in the super
+ // structure
+ if (firstStruct.charAt(i) == secondStruct.charAt(i))
+ {
+ string_superStruct = string_superStruct + firstStruct.charAt(i);
+ array_rnaOwn.add(0);
+ }
+ // Else if one of the characters is an opening parenthese, so
+ // it'll be an opening parenthese in the super structure
+ else if (firstStruct.charAt(i) == '('
+ || secondStruct.charAt(i) == '(')
+ {
+ string_superStruct = string_superStruct + '(';
+ array_rnaOwn.add((firstStruct.charAt(i) == '(') ? 1 : 2);
+ }
+ // Else if one of the characters is a closing parenthese, so
+ // it'll be a closing parenthese in the super structure
+ else if (firstStruct.charAt(i) == ')'
+ || secondStruct.charAt(i) == ')')
+ {
+ string_superStruct = string_superStruct + ')';
+ array_rnaOwn.add((firstStruct.charAt(i) == ')') ? 1 : 2);
+ }
+ else
+ {
+ string_superStruct = string_superStruct + '.';
+ array_rnaOwn.add(-1);
+ }
+ }
+
+ // Next, we make the sequence taking the characters at the same
+ // index in the first and second sequence
+ for (int i = 0; i < RNALength; i++)
+ {
+ string_superSeq = string_superSeq + firstSeq.charAt(i)
+ + secondSeq.charAt(i);
+ }
+
+ // Now, we need to create the super-structure RNA with the owning
+ // bases array
+ // in order to color bases outer depending on the owning statement
+ // of each bases.
+ if (!string_superSeq.equals("") && !string_superStruct.equals(""))
+ {
+ try
+ {
+ _RNA.setRNA(string_superSeq, string_superStruct, array_rnaOwn);
+ } catch (ExceptionUnmatchedClosingParentheses e)
+ {
+ errorDialog(e);
+ } catch (ExceptionFileFormatOrSyntax e)
+ {
+ errorDialog(e);
+ }
+ }
+ else
+ {
+ emitWarning("ERROR : The super-structure is NULL.");
+ }
+
+ switch (_RNA.get_drawMode())
+ {
+ case RNA.DRAW_MODE_RADIATE:
+ _RNA.drawRNARadiate(_conf);
+ break;
+ case RNA.DRAW_MODE_CIRCULAR:
+ _RNA.drawRNACircle(_conf);
+ break;
+ case RNA.DRAW_MODE_LINEAR:
+ _RNA.drawRNALine(_conf);
+ break;
+ case RNA.DRAW_MODE_NAVIEW:
+ try
+ {
+ _RNA.drawRNANAView(_conf);
+ } catch (ExceptionNAViewAlgorithm e)
+ {
+ errorDialog(e);
+ }
+ break;
+ default:
+ break;
+ }
+
+ }
+ }
+
+ /**
+ * Returns the currently selected base index, obtained through a mouse-left
+ * click
+ *
+ * @return Selected base
+ *
+ * public int getSelectedBaseIndex() { return _selectedBase; }
+ *
+ * /** Returns the currently selected base, obtained through a
+ * mouse-left click
+ *
+ * @return Selected base
+ *
+ * public ModeleBase getSelectedBase() { return
+ * _RNA.get_listeBases().get(_selectedBase); }
+ *
+ * /** Sets the selected base index
+ *
+ * @param base
+ * New selected base index
+ *
+ * public void setSelectedBase(int base) { _selectedBase = base; }
+ */
+
+ /**
+ * Returns the coordinates of the currently displayed RNA
+ *
+ * @return Coordinates array
+ */
+ public Point2D.Double[] getRealCoords()
+ {
+ return _realCoords;
+ }
+
+ /**
+ * Sets the coordinates of the currently displayed RNA
+ *
+ * @param coords
+ * New coordinates
+ */
+ public void setRealCoords(Point2D.Double[] coords)
+ {
+ _realCoords = coords;
+ }
+
+ /**
+ * Returns the popup menu used for user mouse iteractions
+ *
+ * @return Popup menu
+ */
+ public VueMenu getPopup()
+ {
+ return _popup;
+ }
+
+ /**
+ * Sets the color used to display hydrogen bonds (base pairings)
+ *
+ * @param bond_color
+ * The color of hydrogen bonds
+ */
+ public void setBondColor(Color bond_color)
+ {
+ _conf._bondColor = bond_color;
+ }
+
+ /**
+ * Returns the color used to draw the title
+ *
+ * @return The color used to draw the title
+ */
+ public Color getTitleColor()
+ {
+ return _conf._titleColor;
+ }
+
+ /**
+ * Sets the color used to draw the title
+ *
+ * @param title_color
+ * The new color used to draw the title
+ */
+ public void setTitleColor(Color title_color)
+ {
+ _conf._titleColor = title_color;
+ }
+
+ /**
+ * Returns the height taken by the title
+ *
+ * @return The height taken by the title
+ */
+ private int getTitleHeight()
+ {
+ return _titleHeight;
+ }
+
+ /**
+ * Sets the height taken by the title
+ *
+ * @param title_height
+ * The height taken by the title
+ */
+ @SuppressWarnings("unused")
+ private void setTitleHeight(int title_height)
+ {
+ _titleHeight = title_height;
+ }
+
+ /**
+ * Returns the current state of auto centering mode.
+ *
+ * @return True if autocentered, false otherwise
+ */
+ public boolean isAutoCentered()
+ {
+ return _conf._autoCenter;
+ }
+
+ /**
+ * Sets the current state of auto centering mode.
+ *
+ * @param center
+ * New auto-centered state
+ */
+ public void setAutoCenter(boolean center)
+ {
+ _conf._autoCenter = center;
+ }
+
+ /**
+ * Returns the font currently used for rendering the title.
+ *
+ * @return Current title font
+ */
+ public Font getTitleFont()
+ {
+ return _conf._titleFont;
+ }
+
+ /**
+ * Sets the font used for rendering the title.
+ *
+ * @param font
+ * New title font
+ */
+ public void setTitleFont(Font font)
+ {
+ _conf._titleFont = font;
+ updateTitleHeight();
+ }
+
+ /**
+ * For the LINE_MODE drawing algorithm, sets the base pair height increment,
+ * i.e. the vertical distance between two nested arcs.
+ *
+ * @return The current base pair increment
+ */
+ public double getBPHeightIncrement()
+ {
+ return _RNA._bpHeightIncrement;
+ }
+
+ /**
+ * Sets the base pair height increment, i.e. the vertical distance between two
+ * arcs to be used in LINE_MODE.
+ *
+ * @param inc
+ * New height increment
+ */
+ public void setBPHeightIncrement(double inc)
+ {
+ _RNA._bpHeightIncrement = inc;
+ }
+
+ /**
+ * Returns the shifting of the origin of the Panel in zoom mode
+ *
+ * @return The logical coordinate of the top-left panel point
+ */
+ public Point2D.Double getOffsetPanel()
+ {
+ return _offsetPanel;
+ }
+
+ /**
+ * Returns the vector bringing the logical coordinate of left-top-most point
+ * in the panel to the left-top-most point of the RNA.
+ *
+ * @return The logical coordinate of the top-left panel point
+ */
+ private Point2D.Double getRNAOffset()
+ {
+ return _offsetRNA;
+ }
+
+ /**
+ * Returns this panel's UI menu
+ *
+ * @return Applet's UI popupmenu
+ */
+ public VueMenu getPopupMenu()
+ {
+ return _popup;
+ }
+
+ /**
+ * Returns the atomic zoom factor step, or increment.
+ *
+ * @return Atomic zoom factor increment
+ */
+ public double getZoomIncrement()
+ {
+ return _conf._zoomAmount;
+ }
+
+ /**
+ * Sets the atomic zoom factor step, or increment.
+ *
+ * @param amount
+ * Atomic zoom factor increment
+ */
+ public void setZoomIncrement(Object amount)
+ {
+ setZoomIncrement(Float.valueOf(amount.toString()));
+ }
+
+ /**
+ * Sets the atomic zoom factor step, or increment.
+ *
+ * @param amount
+ * Atomic zoom factor increment
+ */
+ public void setZoomIncrement(double amount)
+ {
+ _conf._zoomAmount = amount;
+ }
+
+ /**
+ * Returns the current zoom factor
+ *
+ * @return Current zoom factor
+ */
+ public double getZoom()
+ {
+ return _conf._zoom;
+ }
+
+ /**
+ * Sets the current zoom factor
+ *
+ * @param _zoom
+ * New zoom factor
+ */
+ public void setZoom(Object _zoom)
+ {
+ double d = Float.valueOf(_zoom.toString());
+ if (_conf._zoom != d)
+ {
+ _conf._zoom = d;
+ fireZoomLevelChanged(d);
+ }
+ }
+
+ /**
+ * Returns the translation used for zooming in and out
+ *
+ * @return A vector describing the translation
+ */
+ public Point getTranslation()
+ {
+ return _translation;
+ }
+
+ /**
+ * Sets the translation used for zooming in and out
+ *
+ * @param trans
+ * A vector describing the new translation
+ */
+ public void setTranslation(Point trans)
+ {
+ _translation = trans;
+ checkTranslation();
+ fireTranslationChanged();
+ }
+
+ /**
+ * Returns the current RNA model
+ *
+ * @return Current RNA model
+ */
+ public RNA getRNA()
+ {
+ return _RNA;
+ }
+
+ /**
+ * Checks whether the drawn RNA is too large to be displayed, allowing for
+ * shifting mouse interactions.
+ *
+ * @return true if the RNA is too large to be displayed, false otherwise
+ */
+ public boolean isOutOfFrame()
+ {
+ return _horsCadre;
+ }
+
+ /**
+ * Pops up an error Dialog displaying an exception in an human-readable way.
+ *
+ * @param error
+ * The exception to display within the Dialog
+ */
+ public void errorDialog(Exception error)
+ {
+ errorDialog(error, this);
+ }
+
+ /**
+ * Pops up an error Dialog displaying an exception in an human-readable way if
+ * errors are set to be displayed.
+ *
+ * @see #setErrorsOn(boolean)
+ * @param error
+ * The exception to display within the Dialog
+ * @param c
+ * Parent component for the dialog box
+ */
+ public void errorDialog(Exception error, Component c)
+ {
+ if (isErrorsOn())
+ {
+ JOptionPane.showMessageDialog(c, error.getMessage(), "VARNA Error",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * Pops up an error Dialog displaying an exception in an human-readable way.
+ *
+ * @param error
+ * The exception to display within the Dialog
+ * @param c
+ * Parent component for the dialog box
+ */
+ public static void errorDialogStatic(Exception error, Component c)
+ {
+ if (c != null)
+ {
+ JOptionPane.showMessageDialog(c, error.getMessage(),
+ "VARNA Critical Error", JOptionPane.ERROR_MESSAGE);
+ }
+ else
+ {
+ System.err.println("Error: " + error.getMessage());
+ }
+ }
+
+ /**
+ * Displays a warning message through a modal dialog if warnings are set to be
+ * displayed.
+ *
+ * @see #setShowWarnings(boolean)
+ * @param warning
+ * A message expliciting the warning
+ */
+ public void emitWarning(String warning)
+ {
+ if (_conf._showWarnings)
+ JOptionPane.showMessageDialog(this, warning, "VARNA Warning",
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ public static void emitWarningStatic(Exception e, Component c)
+ {
+ emitWarningStatic(e.getMessage(), c);
+ }
+
+ public static void emitWarningStatic(String warning, Component c)
+ {
+ if (c != null)
+ {
+ JOptionPane.showMessageDialog(c, warning, "VARNA Warning",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ System.err.println("Error: " + warning);
+ }
+ }
+
+ /**
+ * Toggles modifications on and off
+ *
+ * @param modifiable
+ * Modification status
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ _conf._modifiable = modifiable;
+ }
+
+ /**
+ * Returns current modification status
+ *
+ * @return current modification status
+ */
+ public boolean isModifiable()
+ {
+ return _conf._modifiable;
+ }
+
+ /**
+ * Resets the visual aspects (Zoom factor, shift) for the Panel.
+ */
+ public void reset()
+ {
+ this.setBorderSize(new Dimension(0, 0));
+ this.setTranslation(new Point(0, (int) (-getTitleHeight() / 2.0)));
+ this.setZoom(VARNAConfig.DEFAULT_ZOOM);
+ this.setZoomIncrement(VARNAConfig.DEFAULT_AMOUNT);
+ }
+
+ /**
+ * Returns the color used to draw non-standard bases
+ *
+ * @return The color used to draw non-standard bases
+ */
+ public Color getNonStandardBasesColor()
+ {
+ return _conf._specialBasesColor;
+ }
+
+ /**
+ * Sets the color used to draw non-standard bases
+ *
+ * @param basesColor
+ * The color used to draw non-standard bases
+ */
+ public void setNonStandardBasesColor(Color basesColor)
+ {
+ _conf._specialBasesColor = basesColor;
+ }
+
+ /**
+ * Checks if the current translation doesn't "kick" the whole RNA out of the
+ * panel, and corrects the situation if necessary.
+ */
+ public void checkTranslation()
+ {
+ // verification pour un zoom < 1
+ if (this.getZoom() <= 1)
+ {
+ // verification sortie gauche
+ if (this.getTranslation().x < -(int) ((this.getWidth()
+ - this.getInnerWidth()) / 2.0))
+ {
+ this.setTranslation(new Point(
+ -(int) ((this.getWidth() - this.getInnerWidth()) / 2.0),
+ this.getTranslation().y));
+ }
+ // verification sortie droite
+ if (this.getTranslation().x > (int) ((this.getWidth()
+ - this.getInnerWidth()) / 2.0))
+ {
+ this.setTranslation(new Point(
+ (int) ((this.getWidth() - this.getInnerWidth()) / 2.0),
+ this.getTranslation().y));
+ }
+ // verification sortie bas
+ if (this.getTranslation().y > (int) ((this.getHeight()
+ - getTitleHeight() * 2 - this.getInnerHeight()) / 2.0))
+ {
+ this.setTranslation(new Point(this.getTranslation().x,
+ (int) ((this.getHeight() - getTitleHeight() * 2
+ - this.getInnerHeight()) / 2.0)));
+ }
+ // verification sortie haut
+ if (this.getTranslation().y < -(int) ((this.getHeight()
+ - this.getInnerHeight()) / 2.0))
+ {
+ this.setTranslation(new Point(this.getTranslation().x,
+ -(int) ((this.getHeight() - this.getInnerHeight()) / 2.0)));
+ }
+ }
+ else
+ {
+ // zoom > 1
+ Rectangle r2 = getZoomedInTranslationBox();
+ int LBoundX = r2.x;
+ int UBoundX = r2.x + r2.width;
+ int LBoundY = r2.y;
+ int UBoundY = r2.y + r2.height;
+ if (this.getTranslation().x < LBoundX)
+ {
+ this.setTranslation(new Point(LBoundX, getTranslation().y));
+ }
+ else if (this.getTranslation().x > UBoundX)
+ {
+ this.setTranslation(new Point(UBoundX, getTranslation().y));
+ }
+ if (this.getTranslation().y < LBoundY)
+ {
+ this.setTranslation(new Point(getTranslation().x, LBoundY));
+ }
+ else if (this.getTranslation().y > UBoundY)
+ {
+ this.setTranslation(new Point(getTranslation().x, UBoundY));
+ }
+ }
+ }
+
+ public Rectangle getZoomedInTranslationBox()
+ {
+ int LBoundX = -(int) ((this.getInnerWidth()) / 2.0);
+ int UBoundX = (int) ((this.getInnerWidth()) / 2.0);
+ int LBoundY = -(int) ((this.getInnerHeight()) / 2.0);
+ int UBoundY = (int) ((this.getInnerHeight()) / 2.0);
+ return new Rectangle(LBoundX, LBoundY, UBoundX - LBoundX,
+ UBoundY - LBoundY);
+
+ }
+
+ /**
+ * Returns the "real pixels" x-coordinate of the RNA.
+ *
+ * @return X-coordinate of the translation
+ */
+ public int getLeftOffset()
+ {
+ return _border.width + ((this.getWidth() - 2 * _border.width)
+ - this.getInnerWidth()) / 2 + _translation.x;
+ }
+
+ /**
+ * Returns the "real pixels" width of the drawing surface for our RNA.
+ *
+ * @return Width of the drawing surface for our RNA
+ */
+ public int getInnerWidth()
+ {
+ // Largeur du dessin
+ return (int) Math
+ .round((this.getWidth() - 2 * _border.width) * _conf._zoom);
+ }
+
+ /**
+ * Returns the "real pixels" y-coordinate of the RNA.
+ *
+ * @return Y-coordinate of the translation
+ */
+ public int getTopOffset()
+ {
+ return _border.height + ((this.getHeight() - 2 * _border.height)
+ - this.getInnerHeight()) / 2 + _translation.y;
+ }
+
+ /**
+ * Returns the "real pixels" height of the drawing surface for our RNA.
+ *
+ * @return Height of the drawing surface for our RNA
+ */
+ public int getInnerHeight()
+ {
+ // Hauteur du dessin
+ return (int) Math.round((this.getHeight()) * _conf._zoom
+ - 2 * _border.height - getTitleHeight());
+ }
+
+ /**
+ * Checks if the current mode is the "comparison" mode
+ *
+ * @return True if comparison, false otherwise
+ */
+ public boolean isComparisonMode()
+ {
+ return _conf._comparisonMode;
+ }
+
+ /**
+ * Rotates the RNA coordinates by a certain angle
+ *
+ * @param angleDegres
+ * Rotation angle, in degrees
+ */
+ public void globalRotation(Double angleDegres)
+ {
+ _RNA.globalRotation(angleDegres);
+ fireLayoutChanged();
+ repaint();
+ }
+
+ /**
+ * Returns the index of the currently selected base, defaulting to the closest
+ * base to the last mouse-click.
+ *
+ * @return Index of the currently selected base
+ */
+ public Integer getNearestBase()
+ {
+ return _nearestBase;
+ }
+
+ /**
+ * Sets the index of the currently selected base.
+ *
+ * @param base
+ * Index of the new selected base
+ */
+ public void setNearestBase(Integer base)
+ {
+ _nearestBase = base;
+ }
+
+ /**
+ * Returns the color used to draw 'Gaps' bases in comparison mode
+ *
+ * @return Color used for 'Gaps'
+ */
+ public Color getGapsBasesColor()
+ {
+ return _conf._dashBasesColor;
+ }
+
+ /**
+ * Sets the color to use for 'Gaps' bases in comparison mode
+ *
+ * @param c
+ * Color used for 'Gaps'
+ */
+ public void setGapsBasesColor(Color c)
+ {
+ _conf._dashBasesColor = c;
+ }
+
+ @SuppressWarnings("unused")
+ private void imprimer()
+ {
+ // PrintPanel canvas;
+ // canvas = new PrintPanel();
+ PrintRequestAttributeSet attributes;
+ attributes = new HashPrintRequestAttributeSet();
+ try
+ {
+ PrinterJob job = PrinterJob.getPrinterJob();
+ // job.setPrintable(this);
+ if (job.printDialog(attributes))
+ {
+ job.print(attributes);
+ }
+ } catch (PrinterException exception)
+ {
+ errorDialog(exception);
+ }
+ }
+
+ /**
+ * Checks whether errors are to be displayed
+ *
+ * @return Error display status
+ */
+ public boolean isErrorsOn()
+ {
+ return _conf._errorsOn;
+ }
+
+ /**
+ * Sets whether errors are to be displayed
+ *
+ * @param on
+ * New error display status
+ */
+ public void setErrorsOn(boolean on)
+ {
+ _conf._errorsOn = on;
+ }
+
+ /**
+ * Returns the view associated with user interactions
+ *
+ * @return A view associated with user interactions
+ */
+ public VueUI getVARNAUI()
+ {
+ return _UI;
+ }
+
+ /**
+ * Toggles on/off using base inner color for drawing base-pairs
+ *
+ * @param on
+ * True for using base inner color for drawing base-pairs, false for
+ * classic mode
+ */
+ public void setUseBaseColorsForBPs(boolean on)
+ {
+ _conf._useBaseColorsForBPs = on;
+ }
+
+ /**
+ * Returns true if current base color is used as inner color for drawing
+ * base-pairs
+ *
+ * @return True for using base inner color for drawing base-pairs, false for
+ * classic mode
+ */
+ public boolean getUseBaseColorsForBPs()
+ {
+ return _conf._useBaseColorsForBPs;
+ }
+
+ /**
+ * Toggles on/off using a special color used for drawing "non-standard" bases
+ *
+ * @param on
+ * True for using a special color used for drawing "non-standard"
+ * bases, false for classic mode
+ */
+ public void setColorNonStandardBases(boolean on)
+ {
+ _conf._colorSpecialBases = on;
+ }
+
+ /**
+ * Returns true if a special color is used as inner color for non-standard
+ * base
+ *
+ * @return True for using a special color used for drawing "non-standard"
+ * bases, false for classic mode
+ */
+ public boolean getColorSpecialBases()
+ {
+ return _conf._colorSpecialBases;
+ }
+
+ /**
+ * Toggles on/off using a special color used for drawing "Gaps" bases in
+ * comparison mode
+ *
+ * @param on
+ * True for using a special color used for drawing "Gaps" bases in
+ * comparison mode, false for classic mode
+ */
+ public void setColorGapsBases(boolean on)
+ {
+ _conf._colorDashBases = on;
+ }
+
+ /**
+ * Returns true if a special color is used for drawing "Gaps" bases in
+ * comparison mode
+ *
+ * @return True for using a special color used for drawing "Gaps" bases in
+ * comparison mode, false for classic mode
+ */
+ public boolean getColorGapsBases()
+ {
+ return _conf._colorDashBases;
+ }
+
+ /**
+ * Toggles on/off displaying warnings
+ *
+ * @param on
+ * True to display warnings, false otherwise
+ */
+ public void setShowWarnings(boolean on)
+ {
+ _conf._showWarnings = on;
+ }
+
+ /**
+ * Get current warning display status
+ *
+ * @return True to display warnings, false otherwise
+ */
+ public boolean getShowWarnings()
+ {
+ return _conf._showWarnings;
+ }
+
+ /**
+ * Toggles on/off displaying non-canonical base-pairs
+ *
+ * @param on
+ * True to display NC base-pairs, false otherwise
+ */
+ public void setShowNonCanonicalBP(boolean on)
+ {
+ _conf._drawnNonCanonicalBP = on;
+ }
+
+ /**
+ * Return the current display status for non-canonical base-pairs
+ *
+ * @return True if NC base-pairs are displayed, false otherwise
+ */
+ public boolean getShowNonCanonicalBP()
+ {
+ return _conf._drawnNonCanonicalBP;
+ }
+
+ /**
+ * Toggles on/off displaying "non-planar" base-pairs
+ *
+ * @param on
+ * True to display "non-planar" base-pairs, false otherwise
+ */
+ public void setShowNonPlanarBP(boolean on)
+ {
+ _conf._drawnNonPlanarBP = on;
+ }
+
+ /**
+ * Return the current display status for non-planar base-pairs
+ *
+ * @return True if non-planars base-pairs are displayed, false otherwise
+ */
+ public boolean getShowNonPlanarBP()
+ {
+ return _conf._drawnNonPlanarBP;
+ }
+
+ /**
+ * Sets the base-pair representation style
+ *
+ * @param st
+ * The new base-pair style
+ */
+ public void setBPStyle(VARNAConfig.BP_STYLE st)
+ {
+ _conf._mainBPStyle = st;
+ }
+
+ /**
+ * Returns the base-pair representation style
+ *
+ * @return The current base-pair style
+ */
+ public VARNAConfig.BP_STYLE getBPStyle()
+ {
+ return _conf._mainBPStyle;
+ }
+
+ /**
+ * Returns the current VARNA Panel configuration. The returned instance should
+ * not be modified directly, but rather through the getters/setters from the
+ * VARNAPanel class.
+ *
+ * @return Current configuration
+ */
+ public VARNAConfig getConfig()
+ {
+ return _conf;
+ }
+
+ /**
+ * Sets the background color
+ *
+ * @param c
+ * New background color
+ */
+ public void setBackground(Color c)
+ {
+ if (_conf != null)
+ {
+ if (c != null)
+ {
+ _conf._backgroundColor = c;
+ _conf._drawBackground = (!c
+ .equals(VARNAConfig.DEFAULT_BACKGROUND_COLOR));
+ }
+ else
+ {
+ _conf._backgroundColor = VARNAConfig.DEFAULT_BACKGROUND_COLOR;
+ _conf._drawBackground = false;
+ }
+ }
+
+ }
+
+ /**
+ * Starts highlighting the selected base.
+ */
+ public void highlightSelectedBase(ModeleBase m)
+ {
+ ArrayList<Integer> v = new ArrayList<Integer>();
+ int sel = m.getIndex();
+ if (sel != -1)
+ {
+ v.add(sel);
+ }
+ setSelection(v);
+ }
+
+ /**
+ * Starts highlighting the selected base.
+ */
+ public void highlightSelectedStem(ModeleBase m)
+ {
+ ArrayList<Integer> v = new ArrayList<Integer>();
+ int sel = m.getIndex();
+ if (sel != -1)
+ {
+ ArrayList<Integer> r = _RNA.findStem(sel);
+ v.addAll(r);
+ }
+ setSelection(v);
+ }
+
+ public BaseList getSelection()
+ {
+ return _selectedBases;
+ }
+
+ public ArrayList<Integer> getSelectionIndices()
+ {
+ return _selectedBases.getIndices();
+ }
+
+ public void setSelection(ArrayList<Integer> indices)
+ {
+ setSelection(_RNA.getBasesAt(indices));
+ }
+
+ public void setSelection(Collection<? extends ModeleBase> mbs)
+ {
+ BaseList bck = new BaseList(_selectedBases);
+ _selectedBases.clear();
+ _selectedBases.addBases(mbs);
+ _blink.setActive(true);
+ fireSelectionChanged(bck, _selectedBases);
+ }
+
+ public ArrayList<Integer> getBasesInRectangleDiff(Rectangle recIn,
+ Rectangle recOut)
+ {
+ ArrayList<Integer> result = new ArrayList<Integer>();
+ for (int i = 0; i < _realCoords.length; i++)
+ {
+ if (recIn.contains(_realCoords[i]) ^ recOut.contains(_realCoords[i]))
+ result.add(i);
+ }
+ return result;
+ }
+
+ public ArrayList<Integer> getBasesInRectangle(Rectangle rec)
+ {
+ ArrayList<Integer> result = new ArrayList<Integer>();
+ for (int i = 0; i < _realCoords.length; i++)
+ {
+ if (rec.contains(_realCoords[i]))
+ result.add(i);
+ }
+ return result;
+ }
+
+ public void setSelectionRectangle(Rectangle rec)
+ {
+ ArrayList<Integer> result = new ArrayList<Integer>();
+ if (_selectionRectangle != null)
+ {
+ result = getBasesInRectangleDiff(_selectionRectangle, rec);
+ }
+ else
+ {
+ result = getBasesInRectangle(rec);
+ }
+ _selectionRectangle = new Rectangle(rec);
+ toggleSelection(result);
+ repaint();
+ }
+
+ public void removeSelectionRectangle()
+ {
+ _selectionRectangle = null;
+ }
+
+ public void addToSelection(Collection<? extends Integer> indices)
+ {
+ for (int i : indices)
+ {
+ addToSelection(i);
+ }
+ }
+
+ public void addToSelection(int i)
+ {
+ BaseList bck = new BaseList(_selectedBases);
+ ModeleBase mb = _RNA.getBaseAt(i);
+ _selectedBases.addBase(mb);
+ _blink.setActive(true);
+ fireSelectionChanged(bck, _selectedBases);
+ }
+
+ public void removeFromSelection(int i)
+ {
+ BaseList bck = new BaseList(_selectedBases);
+ ModeleBase mb = _RNA.getBaseAt(i);
+ _selectedBases.removeBase(mb);
+ if (_selectedBases.size() == 0)
+ {
+ _blink.setActive(false);
+ }
+ else
+ {
+ _blink.setActive(true);
+ }
+ fireSelectionChanged(bck, _selectedBases);
+ }
+
+ public boolean isInSelection(int i)
+ {
+ return _selectedBases.contains(_RNA.getBaseAt(i));
+ }
+
+ public void toggleSelection(int i)
+ {
+ if (isInSelection(i))
+ removeFromSelection(i);
+ else
+ addToSelection(i);
+ }
+
+ public void toggleSelection(Collection<? extends Integer> indices)
+ {
+ for (int i : indices)
+ {
+ toggleSelection(i);
+ }
+ }
+
+ /**
+ * Stops highlighting bases
+ */
+ public void clearSelection()
+ {
+ BaseList bck = new BaseList(_selectedBases);
+ _selectedBases.clear();
+ _blink.setActive(false);
+ repaint();
+ fireSelectionChanged(bck, _selectedBases);
+ }
+
+ public void saveSelection()
+ {
+ _backupSelection.clear();
+ _backupSelection.addAll(_selectedBases.getBases());
+ }
+
+ public void restoreSelection()
+ {
+ setSelection(_backupSelection);
+ }
+
+ /**
+ * Stops highlighting bases
+ */
+ public void resetAnnotationHighlight()
+ {
+ _highlightAnnotation = false;
+ repaint();
+ }
+
+ /**
+ * Toggles on/off a rectangular outline of the bounding box.
+ *
+ * @param on
+ * True to draw the bounding box, false otherwise
+ */
+ public void drawBBox(boolean on)
+ {
+ _drawBBox = on;
+ }
+
+ /**
+ * Toggles on/off a rectangular outline of the border.
+ *
+ * @param on
+ * True to draw the bounding box, false otherwise
+ */
+ public void drawBorder(boolean on)
+ {
+ _drawBorder = on;
+ }
+
+ public void setBaseInnerColor(Color c)
+ {
+ _RNA.setBaseInnerColor(c);
+ }
+
+ public void setBaseNumbersColor(Color c)
+ {
+ _RNA.setBaseNumbersColor(c);
+ }
+
+ public void setBaseNameColor(Color c)
+ {
+ _RNA.setBaseNameColor(c);
+ }
+
+ public void setBaseOutlineColor(Color c)
+ {
+ _RNA.setBaseOutlineColor(c);
+ }
+
+ public ArrayList<TextAnnotation> getListeAnnotations()
+ {
+ return _RNA.getAnnotations();
+ }
+
+ public void resetListeAnnotations()
+ {
+ _RNA.clearAnnotations();
+ repaint();
+ }
+
+ public void addAnnotation(TextAnnotation textAnnotation)
+ {
+ _RNA.addAnnotation(textAnnotation);
+ repaint();
+ }
+
+ public boolean removeAnnotation(TextAnnotation textAnnotation)
+ {
+ boolean done = _RNA.removeAnnotation(textAnnotation);
+ repaint();
+ return done;
+ }
+
+ public TextAnnotation get_selectedAnnotation()
+ {
+ return _selectedAnnotation;
+ }
+
+ public void set_selectedAnnotation(TextAnnotation annotation)
+ {
+ _selectedAnnotation = annotation;
+ }
+
+ public void removeSelectedAnnotation()
+ {
+ _highlightAnnotation = false;
+ _selectedAnnotation = null;
+ }
+
+ public void highlightSelectedAnnotation()
+ {
+ _highlightAnnotation = true;
+ }
+
+ public boolean getFlatExteriorLoop()
+ {
+ return _conf._flatExteriorLoop;
+ }
+
+ public void setFlatExteriorLoop(boolean on)
+ {
+ _conf._flatExteriorLoop = on;
+ }
+
+ public void setLastSelectedPosition(Point2D.Double p)
+ {
+ _lastSelectedCoord.x = p.x;
+ _lastSelectedCoord.y = p.y;
+ }
+
+ public Point2D.Double getLastSelectedPosition()
+ {
+ return _lastSelectedCoord;
+ }
+
+ public void setSequence(String s)
+ {
+ _RNA.setSequence(s);
+ repaint();
+ }
+
+ public void setColorMapVisible(boolean b)
+ {
+ _conf._drawColorMap = b;
+ repaint();
+ }
+
+ public boolean getColorMapVisible()
+ {
+ return _conf._drawColorMap;
+ }
+
+ public void removeColorMap()
+ {
+ _conf._drawColorMap = false;
+ repaint();
+ }
+
+ public void saveSession(String path)
+ {
+ /*
+ * FileOutputStream fos = null; ObjectOutputStream out = null; try { fos
+ * = new FileOutputStream(path); out = new ObjectOutputStream(fos);
+ * out.writeObject(new FullBackup(_conf, _RNA, _conf._title));
+ * out.close(); } catch (Exception ex) { ex.printStackTrace(); }
+ */
+ toXML(path);
+ }
+
+ /** Added for Jalview */
+
+ public FullBackup loadSession(String path) throws ExceptionLoadingFailed
+ {
+ return loadSession(new File(path));
+ }
+
+ public FullBackup loadSession(File path) throws ExceptionLoadingFailed
+ {
+
+ FullBackup bck = importSession(path);
+ Mapping map = Mapping.DefaultOutermostMapping(getRNA().getSize(),
+ bck.rna.getSize());
+ showRNAInterpolated(bck.rna, map);
+ _conf = bck.config;
+ repaint();
+ return bck;
+ }
+
+ public static String VARNA_SESSION_EXTENSION = "varna";
+
+ public static FullBackup importSession(Object path) // BH was String
+ throws ExceptionLoadingFailed
+ {
+ try
+ {
+ FileInputStream fis = (path instanceof File
+ ? new FileInputStream((File) path)
+ : new FileInputStream(path.toString()));
+ // ZipInputStream zis = new
+ // ZipInputStream(new BufferedInputStream(fis));
+ // zis.getNextEntry();
+ FullBackup h = importSession(fis, path.toString());
+ // zis.close();
+ return h;
+ } catch (FileNotFoundException e)
+ {
+ throw (new ExceptionLoadingFailed("File not found.",
+ path.toString()));
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ throw (new ExceptionLoadingFailed("I/O error while loading session.",
+ path.toString()));
+ }
+ }
+
+ public static FullBackup importSession(InputStream fis, String path)
+ throws ExceptionLoadingFailed
+ {
+ System.setProperty("javax.xml.parsers.SAXParserFactory",
+ "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
+ SAXParserFactory saxFact = javax.xml.parsers.SAXParserFactory
+ .newInstance();
+ saxFact.setValidating(false);
+ saxFact.setXIncludeAware(false);
+ saxFact.setNamespaceAware(false);
+ try
+ {
+ SAXParser sp = saxFact.newSAXParser();
+ VARNASessionParser sessionData = new VARNASessionParser();
+ sp.parse(fis, sessionData);
+ FullBackup res = new FullBackup(sessionData.getVARNAConfig(),
+ sessionData.getRNA(), "test");
+ return res;
+ } catch (ParserConfigurationException e)
+ {
+ throw new ExceptionLoadingFailed("Bad XML parser configuration",
+ path);
+ } catch (SAXException e)
+ {
+ throw new ExceptionLoadingFailed("XML parser Exception", path);
+ } catch (IOException e)
+ {
+ throw new ExceptionLoadingFailed("I/O error", path);
+ }
+ }
+
+ public void loadFile(File path)
+ {
+ loadFile(path, false);
+ }
+
+ public boolean getDrawBackbone()
+ {
+ return _conf._drawBackbone;
+ }
+
+ public void setDrawBackbone(boolean b)
+ {
+ _conf._drawBackbone = b;
+ }
+
+ public void addHighlightRegion(HighlightRegionAnnotation n)
+ {
+ _RNA.addHighlightRegion(n);
+ }
+
+ public void removeHighlightRegion(HighlightRegionAnnotation n)
+ {
+ _RNA.removeHighlightRegion(n);
+ }
+
+ public void addHighlightRegion(int i, int j)
+ {
+ _RNA.addHighlightRegion(i, j);
+ }
+
+ public void addHighlightRegion(int i, int j, Color fill, Color outline,
+ double radius)
+ {
+ _RNA.addHighlightRegion(i, j, fill, outline, radius);
+ }
+
+ public void loadRNA(String path)
+ {
+ loadRNA(path, false);
+ }
+
+ public void loadRNA(Object path, boolean interpolate)
+ { // BH was String
+ try
+ {
+ Collection<RNA> rnas = (path instanceof File
+ ? RNAFactory.loadSecStr(new FileReader((File) path))
+ : RNAFactory.loadSecStr(path.toString()));
+ if (rnas.isEmpty())
+ {
+ throw new ExceptionFileFormatOrSyntax(
+ "No RNA could be parsed from that source.");
+ }
+ RNA rna = rnas.iterator().next();
+ try
+ {
+ rna.drawRNA(_conf);
+ } catch (ExceptionNAViewAlgorithm e)
+ {
+ e.printStackTrace();
+ }
+ if (!interpolate)
+ {
+ showRNA(rna);
+ }
+ else
+ {
+ this.showRNAInterpolated(rna);
+ }
+
+ } catch (FileNotFoundException e)
+ {
+ e.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e)
+ {
+ e.printStackTrace();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ public void loadFile(File path, boolean interpolate)
+ { // was String BH StringJS
+ try
+ {
+ loadSession(path);
+ } catch (Exception e1)
+ {
+ loadRNA(path, interpolate);
+ }
+ }
+
+ public void setConfig(VARNAConfig cfg)
+ {
+ _conf = cfg;
+ }
+
+ public void toggleDrawOutlineBases()
+ {
+ _conf._drawOutlineBases = !_conf._drawOutlineBases;
+ }
+
+ public void toggleFillBases()
+ {
+ _conf._fillBases = !_conf._fillBases;
+ }
+
+ public void setDrawOutlineBases(boolean drawn)
+ {
+ _conf._drawOutlineBases = drawn;
+ }
+
+ public void setFillBases(boolean drawn)
+ {
+ _conf._fillBases = drawn;
+ }
+
+ public void readValues(Reader r)
+ {
+ this._RNA.readValues(r, _conf._cm);
+ }
+
+ public void addVARNAListener(InterfaceVARNAListener v)
+ {
+ _VARNAListeners.add(v);
+ }
+
+ public void fireLayoutChanged()
+ {
+ for (InterfaceVARNAListener v : _VARNAListeners)
+ {
+ v.onStructureRedrawn();
+ }
+ }
+
+ public void fireUINewStructure(RNA r)
+ {
+ for (InterfaceVARNAListener v : _VARNAListeners)
+ {
+ v.onUINewStructure(_conf, r);
+ }
+ }
+
+ public void fireZoomLevelChanged(double d)
+ {
+ for (InterfaceVARNAListener v : _VARNAListeners)
+ {
+ v.onZoomLevelChanged();
+ }
+ }
+
+ public void fireTranslationChanged()
+ {
+ for (InterfaceVARNAListener v2 : _VARNAListeners)
+ {
+ v2.onTranslationChanged();
+ }
+ }
+
+ public void addSelectionListener(InterfaceVARNASelectionListener v)
+ {
+ _selectionListeners.add(v);
+ }
+
+ public void fireSelectionChanged(BaseList mold, BaseList mnew)
+ {
+ BaseList addedBases = mnew.removeAll(mold);
+ BaseList removedBases = mold.removeAll(mnew);
+ for (InterfaceVARNASelectionListener v2 : _selectionListeners)
+ {
+ v2.onSelectionChanged(mnew, addedBases, removedBases);
+ }
+ }
+
+ public void fireHoverChanged(ModeleBase mold, ModeleBase mnew)
+ {
+ for (InterfaceVARNASelectionListener v2 : _selectionListeners)
+ {
+ v2.onHoverChanged(mold, mnew);
+ }
+ }
+
+ public void addRNAListener(InterfaceVARNARNAListener v)
+ {
+ _RNAListeners.add(v);
+ }
+
+ public void addVARNABasesListener(InterfaceVARNABasesListener l)
+ {
+ _basesListeners.add(l);
+ }
+
+ public void fireSequenceChanged(int index, String oldseq, String newseq)
+ {
+ for (InterfaceVARNARNAListener v2 : _RNAListeners)
+ {
+ v2.onSequenceModified(index, oldseq, newseq);
+ }
+ }
+
+ public void fireStructureChanged(Set<ModeleBP> current,
+ Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
+ {
+ for (InterfaceVARNARNAListener v2 : _RNAListeners)
+ {
+ v2.onStructureModified(current, addedBasePairs, removedBasePairs);
+ }
+ }
+
+ public void fireLayoutChanged(
+ Hashtable<Integer, Point2D.Double> movedPositions)
+ {
+ for (InterfaceVARNARNAListener v2 : _RNAListeners)
+ {
+ v2.onRNALayoutChanged(movedPositions);
+ }
+ }
+
+ public void fireBaseClicked(ModeleBase mb, MouseEvent me)
+ {
+ if (mb != null)
+ {
+ for (InterfaceVARNABasesListener v2 : _basesListeners)
+ {
+ v2.onBaseClicked(mb, me);
+ }
+ }
+ }
+
+ public double getOrientation()
+ {
+ return _RNA.getOrientation();
+ }
+
+ public ModeleBase _hoveredBase = null;
+
+ public void setHoverBase(ModeleBase m)
+ {
+ if (m != _hoveredBase)
+ {
+ ModeleBase bck = _hoveredBase;
+ _hoveredBase = m;
+ repaint();
+ fireHoverChanged(bck, m);
+ }
+ }
+
+ public void toXML(String path)
+ {
+ FileOutputStream fis;
+ try
+ {
+ fis = new FileOutputStream(path);
+ // ZipOutputStream zis = new ZipOutputStream(new
+ // BufferedOutputStream(fis));
+ // ZipEntry entry = new ZipEntry("VARNASession");
+ // zis.putNextEntry(entry);
+ PrintWriter pw = new PrintWriter(fis);
+ toXML(pw);
+ pw.flush();
+ // zis.closeEntry();
+ // zis.close();
+ fis.close();
+ } catch (FileNotFoundException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ public void toXML(PrintWriter out)
+ {
+ try
+ {
+
+ // out = new PrintWriter(System.out);
+ StreamResult streamResult = new StreamResult(out);
+ SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory
+ .newInstance();
+ // SAX2.0 ContentHandler.
+ TransformerHandler hd = tf.newTransformerHandler();
+ Transformer serializer = hd.getTransformer();
+ serializer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1");
+ serializer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "users.dtd");
+ serializer.setOutputProperty(OutputKeys.INDENT, "yes");
+ hd.setResult(streamResult);
+ hd.startDocument();
+ toXML(hd);
+ hd.endDocument();
+ } catch (TransformerConfigurationException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (SAXException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+
+ public static String XML_ELEMENT_NAME = "VARNASession";
+
+ public void toXML(TransformerHandler hd) throws SAXException
+ {
+ AttributesImpl atts = new AttributesImpl();
+ hd.startElement("", "", XML_ELEMENT_NAME, atts);
+ _RNA.toXML(hd);
+ _conf.toXML(hd);
+ hd.endElement("", "", XML_ELEMENT_NAME);
+ }
+
+ public TextAnnotation getNearestAnnotation(int x, int y)
+ {
+ TextAnnotation t = null;
+ if (getListeAnnotations().size() != 0)
+ {
+ double dist = Double.MAX_VALUE;
+ double d2;
+ Point2D.Double position;
+ for (TextAnnotation textAnnot : getListeAnnotations())
+ {
+ // calcul de la distance
+ position = textAnnot.getCenterPosition();
+ position = transformCoord(position);
+ d2 = Math.sqrt(Math.pow((position.x - x), 2)
+ + Math.pow((position.y - y), 2));
+ // si la valeur est inferieur au minimum actuel
+ if ((dist > d2) && (d2 < getScaleFactor()
+ * ControleurClicMovement.MIN_SELECTION_DISTANCE))
+ {
+ t = textAnnot;
+ dist = d2;
+ }
+ }
+ }
+ return t;
+ }
+
+ public ModeleBase getNearestBase(int x, int y, boolean always,
+ boolean onlyPaired)
+ {
+ int i = getNearestBaseIndex(x, y, always, onlyPaired);
+ if (i == -1)
+ return null;
+ return getRNA().get_listeBases().get(i);
+ }
+
+ public ModeleBase getNearestBase(int x, int y)
+ {
+ return getNearestBase(x, y, false, false);
+ }
+
+ public int getNearestBaseIndex(int x, int y, boolean always,
+ boolean onlyPaired)
+ {
+ double d2, dist = Double.MAX_VALUE;
+ int mb = -1;
+ for (int i = 0; i < getRealCoords().length; i++)
+ {
+ if (!onlyPaired || (getRNA().get_listeBases().get(i)
+ .getElementStructure() != -1))
+ {
+ d2 = Math.sqrt(Math.pow((getRealCoords()[i].x - x), 2)
+ + Math.pow((getRealCoords()[i].y - y), 2));
+ if ((dist > d2) && ((d2 < getScaleFactor()
+ * ControleurClicMovement.MIN_SELECTION_DISTANCE) || always))
+ {
+ dist = d2;
+ mb = i;
+ }
+ }
+ }
+ return mb;
+ }
+
+ public void globalRescale(double factor)
+ {
+ _RNA.rescale(factor);
+ fireLayoutChanged();
+ repaint();
+ }
+
+ public void setSpaceBetweenBases(double sp)
+ {
+ _conf._spaceBetweenBases = sp;
+ }
+
+ public double getSpaceBetweenBases()
+ {
+ return _conf._spaceBetweenBases;
+ }
}
git://source.jalview.org / jalview.git / commitdiff