--- /dev/null
+/*
+ VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
+ Copyright (C) 2012 Kevin Darty, Alain Denise and Yann Ponty.
+ electronic mail : Yann.Ponty@lri.fr
+ paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
+
+ This file is part of VARNA version 3.9.
+ VARNA version 3.9 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
+ as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+ VARNA version 3.9 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
+ without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ See the GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along with VARNA version 3.1.
+ If not, see http://www.gnu.org/licenses.
+ */
+
+/*
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+ WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+ THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+ GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+ USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+ DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+ PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+ EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+ above cannot be given local legal effect according to their terms,
+ reviewing courts shall apply local law that most closely approximates
+ an absolute waiver of all civil liability in connection with the
+ Program, unless a warranty or assumption of liability accompanies a
+ copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+ */
+
+package fr.orsay.lri.varna;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.event.MouseEvent;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintWriter;
+import java.io.Reader;
+import java.text.NumberFormat;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Hashtable;
+import java.util.Set;
+
+import javax.print.attribute.HashPrintRequestAttributeSet;
+import javax.print.attribute.PrintRequestAttributeSet;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.undo.UndoManager;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.sax.SAXTransformerFactory;
+import javax.xml.transform.sax.TransformerHandler;
+import javax.xml.transform.stream.StreamResult;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.AttributesImpl;
+
+import fr.orsay.lri.varna.controlers.ControleurBlinkingThread;
+import fr.orsay.lri.varna.controlers.ControleurClicMovement;
+import fr.orsay.lri.varna.controlers.ControleurDraggedMolette;
+import fr.orsay.lri.varna.controlers.ControleurInterpolator;
+import fr.orsay.lri.varna.controlers.ControleurMolette;
+import fr.orsay.lri.varna.controlers.ControleurVARNAPanelKeys;
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
+import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
+import fr.orsay.lri.varna.models.BaseList;
+import fr.orsay.lri.varna.models.FullBackup;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation;
+import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
+import fr.orsay.lri.varna.models.annotations.TextAnnotation;
+import fr.orsay.lri.varna.models.export.SwingGraphics;
+import fr.orsay.lri.varna.models.export.VueVARNAGraphics;
+import fr.orsay.lri.varna.models.rna.Mapping;
+import fr.orsay.lri.varna.models.rna.ModeleBP;
+import fr.orsay.lri.varna.models.rna.ModeleBackbone;
+import fr.orsay.lri.varna.models.rna.ModeleBackboneElement.BackboneType;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
+import fr.orsay.lri.varna.models.rna.ModeleBasesComparison;
+import fr.orsay.lri.varna.models.rna.ModeleColorMap;
+import fr.orsay.lri.varna.models.rna.RNA;
+import fr.orsay.lri.varna.utils.VARNASessionParser;
+import fr.orsay.lri.varna.views.VueMenu;
+import fr.orsay.lri.varna.views.VueUI;
+
+/**
+ *
+ * BH j2s SwingJS Added PropertyChangeListener for returns from VueUI.
+ *
+ *
+ *
+ *
+ * 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
+ * ensure a non-overlapping drawing of helices, thus it is possible to "spin the
+ * helices" through a click-and-drag approach. A typical usage of the class from
+ * within the constructor of a <code>JFrame</code> would be the following:<br/>
+ * <code>
+ * VARNAPanel _rna = new VARNAPanel("CCCCAUAUGGGGACC","((((....))))...");<br />
+ * this.getContentPane().add(_rna);
+ * </code>
+ *
+ * @version 3.4
+ * @author Yann Ponty & Kevin Darty
+ *
+ */
+
+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));
+ }
+
+ 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 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 / blobdiff