/*
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) 2008 Kevin Darty, Alain Denise and Yann Ponty.
electronic mail : Yann.Ponty@lri.fr
paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France
This file is part of VARNA version 3.1.
VARNA version 3.1 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 3.1 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.
*/
/*
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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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.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.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
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 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.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.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.ModeleBP;
import fr.orsay.lri.varna.models.rna.RNA;
import fr.orsay.lri.varna.views.VueMenu;
import fr.orsay.lri.varna.views.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 {
/**
*
*/
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>();
UndoManager _manager;
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() throws ExceptionNonEqualLength {
this("", "", RNA.DRAW_MODE_RADIATE);
}
/**
* 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);
_interpolator.start();
}
public void undo()
{
//System.out.println(_manager.getUndoOrRedoPresentationName());
_manager.undo();
}
public void redo()
{
_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) {
_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 caption
*/
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 (_translation.x==0)
{_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);
_conf._title = 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 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.setDashedStroke();
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) {
switch (e) {
case WATSON_CRICK:
if (isCIS) {
g2D.fillCircle( (posx - (radius) / 2.0),
(posy - (radius) / 2.0), radius);
} else {
Color bck = g2D.getColor();
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();
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.fill(p2);
} else {
Color bck = g2D.getColor();
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.fill(p2);
} else {
Color bck = g2D.getColor();
g2D.setColor(Color.white);
g2D.fill(p2);
g2D.setColor(bck);
g2D.draw(p2);
}
}
break;
}
}
private void drawBasePair(VueVARNAGraphics g2D,Point2D.Double orig,
Point2D.Double dest, ModeleBP style, double newRadius) {
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);
if (_conf._mainBPStyle == VARNAConfig.BP_STYLE.BP_STYLE_LW)
{
double radiusCircle = ((RNA.BASE_PAIR_DISTANCE - _RNA.BASE_RADIUS) / 5.0)
* this._scaleFactor;
if (style.isCanonical())
{
if (style.isCanonicalGC())
{
if ((orig.x != dest.x) || (orig.y != dest.y)) {
nx *= this._scaleFactor * _RNA.BASE_RADIUS / 4.0;
ny *= this._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.WATSON_CRICK);
}
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);
}
}
} else if (_conf._mainBPStyle == VARNAConfig.BP_STYLE.BP_STYLE_SIMPLE) {
g2D.drawLine( orig.x, orig.y,dest.x, dest.y);
} else if (_conf._mainBPStyle == VARNAConfig.BP_STYLE.BP_STYLE_RNAVIZ) {
double xcenter = (orig.x + dest.x) / 2.0;
double ycenter = (orig.y + dest.y) / 2.0;
double radius = Math.max(4.0 * this._scaleFactor, 1.0);
g2D.fillCircle( (xcenter - radius), (ycenter - radius), (2.0 * radius));
}
}
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) {
if (_selectedBases.contains(_RNA.getBaseAt(index))) {
return getHighlightedVersion(c1, c2);
} else
return initialColor;
}
private 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
{
return byCenter;
}
}
private void drawBase(VueVARNAGraphics g2D,int i, Point2D.Double[] points,
Point2D.Double[] centers, double newRadius) {
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));
Color baseOuterColor = highlightFilter(i, _RNA.getBaseOuterColor(i,
_conf), _RNA.getBaseOuterColor(i, _conf), Color.white);
Color baseNameColor = highlightFilter(i, _RNA.getBaseNameColor(i, _conf), _RNA.getBaseNameColor(i, _conf),Color.white);
if (mb instanceof ModeleBaseNucleotide)
{
ModeleBaseNucleotide mbn = (ModeleBaseNucleotide) mb;
String res = mbn.get_c();
if (_hoveredBase== mb)
{
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._fillBase)
{
// Filling inner circle
g2D.setColor(baseInnerColor);
g2D.fillCircle(p.getX()-newRadius, p.getY()-newRadius,2.0 * newRadius);
}
if (_conf._drawOutlineBase)
{
// 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() - 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() - newRadius),
(p.getY() - newRadius), (3 * newRadius),
(2 * newRadius), 10*_scaleFactor, 10*_scaleFactor);
// On le dessine au centre de l'étiquette.
g2D.drawLine((p.getX() + (newRadius) / 2.0),
(p.getY() + newRadius)-1,
(p.getX() + (newRadius / 2.0)),
(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.get_base1());
String label2 = String.valueOf(mbc.get_base2());
// On leur donne une couleur
g2D.setColor(getRNA().get_listeBases().get(i).getStyleBase()
.get_base_name_color());
// Et on les dessine.
g2D.drawStringCentered( label1, p.getX() - (newRadius * 0.15), p.getY());
g2D.drawStringCentered( label2, p.getX() + (newRadius * 1.2), p.getY());
}
// Drawing base number
if (_RNA.isNumberDrawn(mb,getNumPeriod()))
{
Point2D.Double vn = computeExcentricUnitVector(i,points,centers);
g2D.setColor(mb.getStyleBase().get_base_number_color());
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.getBaseNumber()),
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_TYPE:
{
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_TYPE:
{
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_TYPE:
{
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_TYPE:
{
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.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)
{
// Drawing backbone
if (getDrawBackbone())
{
g2D.setStrokeThickness(1.5 * _scaleFactor);
g2D.setColor(_conf._backboneColor);
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);
boolean discontinuous = (_RNA.getBaseNumber(i)-_RNA.getBaseNumber(i-1)!=1);
int a = _RNA.getBaseAt(i-1).getElementStructure();
int b = _RNA.getBaseAt(i).getElementStructure();
boolean consecutive = (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;
if (!discontinuous)
{ g2D.setPlainStroke(); }
else
{ g2D.setDashedStroke(); }
if (consecutive && (_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 + (_scaleFactor * (logicPoint.x - _offsetRNA.x)),
_offY + (_scaleFactor * (logicPoint.y - _offsetRNA.y)));
}
private void renderRNA(VueVARNAGraphics g2D, Rectangle2D.Double bbox) {
if (_RNA.get_listeBases().size() != 0) {
//_conf._autoCenter = (_RNA.get_drawMode() != RNA.DRAW_MODE_LINEAR);
Rectangle2D.Double rnabbox = getExtendedRNABBox();
// Then compute an estimate of the scaling factor
if (_conf._autoFit) {
setScaleFactor(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
if (_conf._autoFit) {
setScaleFactor(Math.min((double) bbox.width
/ (double) rnabbox.width, (double) bbox.height
/ (double) rnabbox.height));
}
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);
if (_conf._autoCenter) {
_offX = bbox.x;
_offY = bbox.y;
_offX = (bbox.x + (bbox.width - Math.round(rnabbox.width
* _scaleFactor)) / 2.0);
_offY = (bbox.y + (bbox.height - Math.round(rnabbox.height
* _scaleFactor)) / 2.0);
_offsetPanel = new Point2D.Double(_offX, _offY);
_offsetRNA = new Point2D.Double(rnabbox.x, rnabbox.y);
}
// 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 décalé
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
_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);
// Drawing base-pairs
double distance, coef;
// 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) {
if (j - i == 1)
coef = getBPHeightIncrement() * 1.75;
else
coef = getBPHeightIncrement();
distance = newCoords[j].x - newCoords[i].x;
g2D.drawArc((newCoords[j].x + newCoords[i].x)/2.,
newCoords[j].y-_scaleFactor * _RNA.BASE_RADIUS / 2.0,
(distance), (distance * coef), 0, 180);
} else {
drawBasePair(g2D, newCoords[i], newCoords[j], msbp, newRadius);
}
}
}
}
// Liaisons additionelles (non planaires)
if (_conf._drawnNonPlanarBP) {
ArrayList<ModeleBP> bpaux = _RNA.getStructureAux();
for (int k = 0; k < bpaux.size(); k++) {
ModeleBP bp = bpaux.get(k);
if (bp.isCanonical() || _conf._drawnNonCanonicalBP) {
int i = bp.getPartner5().getIndex();
int j = bp.getPartner3().getIndex();
if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR) {
g2D.setStrokeThickness(_RNA
.getBasePairThickness(bp, _conf)
* 2.5 * _scaleFactor * _conf._bpThickness);
g2D.setPlainStroke();
} else {
g2D.setStrokeThickness(_RNA.getBasePairThickness(bp, _conf) * 1.5 * _scaleFactor);
g2D.setPlainStroke();
}
g2D.setColor(_RNA.getBasePairColor(bp, _conf));
if (j > i) {
if (_RNA.get_drawMode() == RNA.DRAW_MODE_LINEAR ) {
if (j - i == 1)
coef = getBPHeightIncrement() * 1.75;
else
coef = getBPHeightIncrement();
distance = newCoords[j].x - newCoords[i].x;
g2D.drawArc((newCoords[j].x + newCoords[i].x)/2.,
newCoords[j].y-_scaleFactor * _RNA.BASE_RADIUS / 2.0,
(distance), (distance * coef), 0, 180);
} else {
drawBasePair(g2D, newCoords[i], newCoords[j],
bp, newRadius);
}
}
}
}
}
// Drawing bases
g2D.setPlainStroke();
for (int i = 0; i < Math.min(_RNA.get_listeBases().size(),
newCoords.length); i++) {
/*if (mb instanceof ModeleBasesComparison)
{
ModeleBasesComparison mbc = (ModeleBasesComparison)mb;
drawBaseComparison(g2D, i,
mbc.get_base1(),
mbc.get_base2(), newCoords[i],
newCenters[i], newRadius);
}
else if (mb instanceof ModeleBaseNucleotide)*/
{
drawBase(g2D, i, newCoords, newCenters, newRadius);
}
}
// Drawing bbox
if (_debug || _drawBBox) {
g2D.setColor(Color.RED);
g2D.setDashedStroke();
g2D.drawRect(_offX, _offY,
(_scaleFactor * rnabbox.width)-1,
(_scaleFactor * rnabbox.height)-1);
}
// Draw color map
if (_conf._drawColorMap)
{ drawColorMap(g2D, _scaleFactor,rnabbox); }
if (_debug || _drawBBox) {
g2D.setColor(Color.GRAY);
g2D.setDashedStroke();
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); }
}
}
}
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, 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(2);
g2D.drawStringCentered(nf.format(_conf._cm.getMinValue()),xBase,yBase-scaleFactor*(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*(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 + (_scaleFactor * (coordDebut.x - rnabbox.x)),
_offY+ (_scaleFactor * (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;
VueVARNAGraphics g2D = new SwingGraphics(g2);
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
//renderComponent(g2D,transparentBackground);
this.removeAll();
super.paintComponent(g2);
renderComponent(g2D, transparentBackground);
if (isFocusOwner())
{
g2.setStroke(new BasicStroke(1.5f));
g2.setColor(Color.decode("#C0C0C0"));
g2.drawRect(0, 0, getWidth()-1, getHeight()-1);
}
/*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) {
updateTitleHeight();
if (_debug || _drawBorder) {
g2D.setColor(Color.BLACK);
g2D.setPlainStroke();
g2D.drawRect(this.getLeftOffset(), this.getTopOffset(), this.getInnerWidth(), this.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());
}
if (_selectionRectangle!=null)
{
g2D.setColor(Color.BLACK);
g2D.setDashedStroke();
g2D.drawRect(_selectionRectangle.x,_selectionRectangle.y,_selectionRectangle.width,_selectionRectangle.height);
}
if ((_linkOrigin != null) && (_linkDestination!=null))
{
g2D.setColor(_conf._bondColor);
g2D.setPlainStroke();
g2D.setStrokeThickness(4.0 * _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);
}
}
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(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() {
if (!_RNA.getName().equals(""))
return _RNA.getName();
else
return _conf._title;
}
/**
* 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) {
_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();
break;
case RNA.DRAW_MODE_LINEAR:
_RNA.drawRNALine();
break;
case RNA.DRAW_MODE_NAVIEW:
try {
_RNA.drawRNANAView();
} 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;
}
/**
* Gets the scale factor used by the autofitting function
*
* @return Current scale factor
*/
public double getScaleFactor() {
return _scaleFactor;
}
/**
* Sets the scale factor used by the autofitting function
*
* @param factor
* New scale factor
*/
public void setScaleFactor(double factor) {
_scaleFactor = factor;
}
/**
* 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
*/
public 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) {
_conf._zoom = Float.valueOf(_zoom.toString());
}
/**
* 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) {
this._translation = trans;
}
/**
* 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) {
JOptionPane.showMessageDialog(c, error.getMessage(), "VARNA Critical Error",
JOptionPane.ERROR_MESSAGE);
}
/**
* 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);
}
/**
* 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
if (this.getTranslation().x < -(int) ((this.getInnerWidth()) / 2.0)) {
this.setTranslation(new Point(
-(int) ((this.getInnerWidth()) / 2.0), this
.getTranslation().y));
}
if (this.getTranslation().x > (int) ((this.getInnerWidth()) / 2.0)) {
this.setTranslation(new Point(
(int) ((this.getInnerWidth()) / 2.0), this
.getTranslation().y));
}
if (this.getTranslation().y < -(int) ((this.getInnerHeight()) / 2.0)) {
this.setTranslation(new Point(this.getTranslation().x,
-(int) ((this.getInnerHeight()) / 2.0)));
}
if (this.getTranslation().y > (int) ((this.getInnerHeight()) / 2.0)) {
this.setTranslation(new Point(this.getTranslation().x,
(int) ((this.getInnerHeight()) / 2.0)));
}
}
}
/**
* 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<this._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<this._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();
}
}
public FullBackup loadSession(String 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(String path) throws ExceptionLoadingFailed
{
try {
return importSession(new FileInputStream(path),path);
} catch (FileNotFoundException e) {
throw (new ExceptionLoadingFailed("File not found.",path));
}
}
public static FullBackup importSession(InputStream fis, String path) throws ExceptionLoadingFailed
{
FullBackup bck = null;
ObjectInputStream in = null;
try
{
in = new ObjectInputStream(fis);
bck = (FullBackup) in.readObject();
in.close();
return bck;
}
catch(IOException ex)
{
throw new ExceptionLoadingFailed("I/O error while reading VARNA session", path);
}
catch(ClassNotFoundException ex)
{
throw new ExceptionLoadingFailed("Bad format while reading VARNA session", path);
}
}
public void loadFile(String 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 loadFile(String path, boolean interpolate)
{
try{
loadSession(path);
}
catch(Exception e1)
{
try {
Collection<RNA> rnas = RNAFactory.loadSecStr(path);
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 setConfig(VARNAConfig cfg)
{
_conf = cfg;
}
public void toggleDrawOutlineBase()
{
_conf._drawOutlineBase = !_conf._drawOutlineBase;
}
public void toggleFillBase()
{
_conf._fillBase =!_conf._fillBase;
}
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()
{
for(InterfaceVARNAListener v: _VARNAListeners)
{ v.onUINewStructure(_conf,_RNA ); }
}
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 fireSequenceChanged(int index, String oldseq, String newseq)
{
for(InterfaceVARNARNAListener v2: _RNAListeners)
{ v2.onSequenceChanged(index,oldseq,newseq); }
}
public void fireStructureChanged(Set<ModeleBP> current, Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs)
{
for(InterfaceVARNARNAListener v2: _RNAListeners)
{ v2.onStructureChanged(current, addedBasePairs, removedBasePairs); }
}
public void fireLayoutChanged(Hashtable<Integer,Point2D.Double> movedPositions)
{
for(InterfaceVARNARNAListener v2: _RNAListeners)
{ v2.onLayoutChanged(movedPositions); }
}
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);
}
}
}