--- /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) 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.
+ */
+package fr.orsay.lri.varna.views;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.imageio.IIOImage;
+import javax.imageio.ImageIO;
+import javax.imageio.ImageWriteParam;
+import javax.imageio.ImageWriter;
+import javax.imageio.stream.FileImageOutputStream;
+import javax.swing.JColorChooser;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.filechooser.FileFilter;
+import javax.swing.plaf.UIResource;
+import javax.swing.undo.UndoManager;
+import javax.swing.undo.UndoableEditSupport;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.applications.FileNameExtensionFilter;
+import fr.orsay.lri.varna.applications.VARNAPrinter;
+import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding;
+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.ExceptionPermissionDenied;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden;
+import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.models.FullBackup;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.VARNAEdits;
+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.rna.ModeleBP;
+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.RNA;
+
+
+public class VueUI {
+
+ /**
+ *
+ * BH SwingJS
+ *
+ * JavaScript cannot wait on a thread and so cannot wait for the result
+ * of a customized modal JOptionPane.
+ *
+ * Instead, we make any JPanel that is placed in the JOptionPane
+ * implement Runnable. In Java, we simply run that runnable here when an OK
+ * response is delivered; in JavaScript, we run the runnable within the
+ * JavaScript version of JOptionPane as an asynchronous callback.
+ *
+ * Same for a CANCEL, CLOSED, ERROR, or FINAL response.
+ *
+ * Note that for simple error or warning messages, this is not required; they will use simple HTML5 messages.
+ *
+ */
+ public Runnable okBtnCallback, cancelBtnCallback, closeBtnCallback, errorCallback, finalCallback, noBtnCallback, objectCallback;
+
+ public Object dialogReturnValue;
+
+ public Object getDialogReturnValue() {
+ return dialogReturnValue;
+ }
+
+ public Throwable dialogError;
+
+ /**
+ * BH SwingJS
+ *
+ *
+ * @return
+ */
+ public Throwable getDialogError() {
+ return dialogError;
+ }
+
+
+ /**
+ * BH SwingJS
+ *
+ * Initiate a message dialog with callback for OK and close.
+ *
+ * @param messagePanel
+ * @param title
+ * @param ok
+ * @param close
+ */
+ private void showMessageDialog(Object messagePanel, String title, int messageType, Runnable ok, Runnable close) {
+ okBtnCallback = ok;
+ closeBtnCallback = close;
+ JOptionPane.showMessageDialog(_vp, messagePanel, title, messageType);
+ }
+
+
+
+
+ /**
+ * BH SwingJS
+ *
+ * Initiate a confirm dialog with callbacks.
+ *
+ * @param optionPanel
+ * @param title
+ * @param ok
+ * @param cancel
+ * @param close_final_error optional close,finally,error
+ */
+ public void showConfirmDialog(JPanel optionPanel, String title, Runnable ok, Runnable cancel, Runnable... close_final_error) {
+ okBtnCallback = ok;
+ cancelBtnCallback = cancel;
+ closeBtnCallback = (close_final_error.length > 0 ? close_final_error[0] : null);
+ finalCallback = (close_final_error.length > 1 ? close_final_error[1] : null);
+ errorCallback = (close_final_error.length > 2 ? close_final_error[2] : null);
+ onDialogReturn(JOptionPane.showConfirmDialog(_vp, optionPanel, title, JOptionPane.OK_CANCEL_OPTION));
+ }
+
+ /**
+ * BH SwingJS
+ *
+ * Initiate an input dialog with callbacks.
+ *
+ * @param message
+ * @param initialValue
+ * @param input
+ * @param close_final_error optional [close,finally,error]
+ */
+ public void showInputDialog(String message, Object initialValue, Runnable input, Runnable... close_final_error) {
+ objectCallback = input;
+ closeBtnCallback = (close_final_error.length > 0 ? close_final_error[0] : null);
+ finalCallback = (close_final_error.length > 1 ? close_final_error[1] : null);
+ errorCallback = (close_final_error.length > 2 ? close_final_error[2] : null);
+ onDialogReturn(JOptionPane.showInputDialog(_vp, message, initialValue));
+ }
+
+ /**
+ * BH SwingJS
+ *
+ * Initiate an color chooser dialog with callbacks.
+ *
+ * @param message
+ * @param initialValue
+ * @param input
+ * @param close_final_error optional [close,finally,error]
+ */
+ public void showColorDialog(String message, Object initialValue, Runnable ret) {
+ objectCallback = ret;
+ onDialogReturn(JColorChooser.showDialog(_vp, message, (Color) initialValue));
+ }
+
+
+ /**
+ * BH SwingJS
+ *
+ * A general method to handle all the showInputDialog, JFileChooser, and JColorChooser callbacks from all the VueXXX classes.
+ *
+ * The initial return to be ignored is an object that is an instanceof UIResource.
+ *
+ */
+ public void onDialogReturn(Object value) {
+ dialogReturnValue = value;
+ if (objectCallback != null && !(value instanceof UIResource))
+ objectCallback.run();
+ }
+
+ /**
+ * BH SwingJS
+ *
+ * A general method to handle all the showConfirmDialog callbacks from all
+ * the VueXXX classes.
+ *
+ * The initial return to be ignored is NaN, testable as
+ * value != Math.floor(value).
+ *
+ */
+ public void onDialogReturn(int value) {
+ try {
+ switch (value) {
+ case JOptionPane.OK_OPTION | JOptionPane.YES_OPTION:
+ if (okBtnCallback != null)
+ okBtnCallback.run();
+ break;
+ case JOptionPane.NO_OPTION:
+ if (noBtnCallback != null)
+ noBtnCallback.run();
+ break;
+ case JOptionPane.CANCEL_OPTION:
+ if (cancelBtnCallback != null)
+ cancelBtnCallback.run();
+ break;
+ case JOptionPane.CLOSED_OPTION:
+ if (closeBtnCallback != null)
+ closeBtnCallback.run();
+ break;
+ }
+ } catch (Throwable e) {
+ dialogError = e;
+ if (errorCallback != null)
+ errorCallback.run();
+ } finally {
+ if (value != Math.floor(value)) {
+ // asynchronous deferred
+ return;
+ }
+ if (finalCallback != null)
+ finalCallback.run();
+ okBtnCallback = noBtnCallback = cancelBtnCallback = closeBtnCallback = errorCallback = objectCallback = null;
+ dialogError = null;
+ }
+ }
+
+
+ protected VARNAPanel _vp;
+ private File _fileChooserDirectory = null;
+ private UndoableEditSupport _undoableEditSupport;
+
+ public VueUI(VARNAPanel vp) {
+ _vp = vp;
+ _undoableEditSupport = new UndoableEditSupport(_vp);
+ }
+
+ public void addUndoableEditListener(UndoManager manager) {
+ _undoableEditSupport.addUndoableEditListener(manager);
+ }
+
+ public void UIToggleColorMap() {
+ if (_vp.isModifiable()) {
+ _vp.setColorMapVisible(!_vp.getColorMapVisible());
+ _vp.repaint();
+ }
+ }
+
+ public void UIToggleDrawBackbone() {
+ if (_vp.isModifiable()) {
+ _vp.setDrawBackbone(!_vp.getDrawBackbone());
+ _vp.repaint();
+ }
+ }
+
+ public Hashtable<Integer, Point2D.Double> backupAllCoords() {
+ Hashtable<Integer, Point2D.Double> tmp = new Hashtable<Integer, Point2D.Double>();
+ for (int i = 0; i < _vp.getRNA().getSize(); i++) {
+ tmp.put(i, _vp.getRNA().getCoords(i));
+ }
+ return tmp;
+ }
+
+ public void UIToggleFlatExteriorLoop() {
+ if (_vp.isModifiable()
+ && _vp.getRNA().get_drawMode() == RNA.DRAW_MODE_RADIATE) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(
+ RNA.DRAW_MODE_RADIATE, _vp, !_vp.getFlatExteriorLoop()));
+ _vp.setFlatExteriorLoop(!_vp.getFlatExteriorLoop());
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_RADIATE);
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ public void UIRadiate() {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(
+ RNA.DRAW_MODE_RADIATE, _vp));
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_RADIATE);
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ public void UIMOTIFView() {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(
+ RNA.DRAW_MODE_MOTIFVIEW, _vp));
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_MOTIFVIEW);
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ public void UILine() {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(
+ RNA.DRAW_MODE_LINEAR, _vp));
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_LINEAR);
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ public void UICircular() {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(
+ RNA.DRAW_MODE_CIRCULAR, _vp));
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_CIRCULAR);
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ public void UINAView() {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(
+ RNA.DRAW_MODE_NAVIEW, _vp));
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_NAVIEW);
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ public void UIVARNAView() {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(
+ RNA.DRAW_MODE_VARNA_VIEW, _vp));
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), RNA.DRAW_MODE_VARNA_VIEW);
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ public void UIReset() {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> bck = backupAllCoords();
+ _undoableEditSupport.postEdit(new VARNAEdits.RedrawEdit(_vp
+ .getRNA().get_drawMode(), _vp));
+ _vp.reset();
+ _vp.drawRNA(_vp.getRNA(), _vp.getRNA().get_drawMode());
+ _vp.repaint();
+ _vp.fireLayoutChanged(bck);
+ }
+ }
+
+ private void savePath(JFileChooser jfc) {
+ _fileChooserDirectory = jfc.getCurrentDirectory();
+ }
+
+ private void loadPath(JFileChooser jfc) {
+ if (_fileChooserDirectory != null) {
+ jfc.setCurrentDirectory(_fileChooserDirectory);
+ }
+ }
+
+ public void UIChooseRNAs(ArrayList<RNA> rnas) {
+ if (rnas.size() > 5) {
+ final VueRNAList vrna = new VueRNAList(rnas);
+ Runnable ok = new Runnable() {
+
+ @Override
+ public void run() {
+ for (RNA r : vrna.getSelectedRNAs()) {
+ try {
+ r.drawRNA(_vp.getConfig());
+ } catch (ExceptionNAViewAlgorithm e) {
+ e.printStackTrace();
+ }
+ _vp.showRNA(r);
+ }
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(vrna, "Select imported sequence/structures", ok, null);
+ } else {
+ for (RNA r : rnas) {
+ try {
+ r.drawRNA(_vp.getConfig());
+ } catch (ExceptionNAViewAlgorithm e) {
+ e.printStackTrace();
+ }
+ _vp.showRNA(r);
+ }
+ _vp.repaint();
+ }
+ }
+
+ public void UIFile() throws ExceptionNonEqualLength {
+ if (_vp.isModifiable()) {
+ JFileChooser fc = new JFileChooser();
+ fc.setFileSelectionMode(JFileChooser.OPEN_DIALOG);
+ fc.setDialogTitle("Open...");
+ loadPath(fc);
+ if (fc.showOpenDialog(_vp) == JFileChooser.APPROVE_OPTION) {
+ try {
+ savePath(fc);
+ String path = fc.getSelectedFile().getAbsolutePath();
+ if (!path.toLowerCase().endsWith(".varna")) {
+ ArrayList<RNA> rnas = RNAFactory.loadSecStr(path);
+ if (rnas.isEmpty()) {
+ throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from that source.");
+ } else {
+ UIChooseRNAs(rnas);
+ }
+ } else {
+ FullBackup bck = _vp.loadSession(fc.getSelectedFile()); // was path
+ }
+ } catch (ExceptionExportFailed e1) {
+ _vp.errorDialog(e1);
+ } catch (ExceptionPermissionDenied e1) {
+ _vp.errorDialog(e1);
+ } catch (ExceptionLoadingFailed e1) {
+ _vp.errorDialog(e1);
+ } catch (ExceptionFileFormatOrSyntax e1) {
+ _vp.errorDialog(e1);
+ } catch (ExceptionUnmatchedClosingParentheses e1) {
+ _vp.errorDialog(e1);
+ } catch (FileNotFoundException e) {
+ _vp.errorDialog(e);
+ }
+ }
+ }
+ }
+
+ public void UISetColorMapStyle() {
+ final VueColorMapStyle vcms = new VueColorMapStyle(_vp);
+ Runnable ok = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.setColorMap(vcms.getColorMap());
+ }
+
+ };
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ vcms.cancelChanges();
+ }
+
+ };
+ showConfirmDialog(vcms, "Choose color map style", ok, cancel, cancel, null, null);
+ }
+
+ public void UILoadColorMapValues() {
+ final VueLoadColorMapValues vcmv = new VueLoadColorMapValues(_vp);
+ Runnable ok = new Runnable(){
+
+ @Override
+ public void run() {
+ _vp.setColorMapVisible(true);
+ try {
+ _vp.readValues(vcmv.getReader());
+ } catch (IOException e) {
+ _vp.errorDialog((Exception) getDialogError());
+ }
+ }
+
+ };
+ showConfirmDialog(vcmv, "Load base values", ok, null);
+ }
+
+ public void UISetColorMapValues() {
+ final VueBaseValues vbv = new VueBaseValues(_vp);
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ vbv.cancelChanges();
+ }
+
+ };
+ showConfirmDialog(vbv, "Choose base values", null, cancel);
+ }
+
+ public void UIManualInput() throws ParseException, ExceptionNonEqualLength {
+ if (_vp.isModifiable()) {
+ final VueManualInput manualInput = new VueManualInput(_vp);
+ Runnable ok = new Runnable() {
+
+ @Override
+ public void run() {
+ if (_vp.getRNA().getSize() == 0) {
+
+ }
+ try {
+ RNA r = new RNA();
+ VARNAConfig cfg = new VARNAConfig();
+ r.setRNA(manualInput.getTseq().getText(), manualInput.getTstr().getText());
+ r.drawRNA(_vp.getRNA().get_drawMode(), cfg);
+ _vp.drawRNAInterpolated(r);
+ _vp.repaint();
+ } catch (ExceptionFileFormatOrSyntax e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionNAViewAlgorithm e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionUnmatchedClosingParentheses e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ };
+ showConfirmDialog(manualInput.getPanel(), "Input sequence/structure", ok, null);
+ }
+ }
+
+ public void UISetTitle() {
+ if (_vp.isModifiable()) {
+ Runnable input = new Runnable() {
+
+ @Override
+ public void run() {
+ String res = (String) getDialogReturnValue();
+ if (res != null) {
+ _vp.setTitle(res);
+ _vp.repaint();
+ }
+ }
+
+ };
+
+ showInputDialog("Input title", _vp.getTitle(), input);
+ }
+ }
+
+ public void UISetColorMapCaption() {
+ if (_vp.isModifiable()) {
+ Runnable input = new Runnable() {
+
+ @Override
+ public void run() {
+ String res = (String) getDialogReturnValue();
+ if (res != null) {
+ _vp.setColorMapCaption(res);
+ _vp.repaint();
+ }
+ }
+
+ };
+ showInputDialog("Input new color map caption", _vp.getColorMapCaption(), input);
+ }
+ }
+
+ public void UISetBaseCharacter() {
+ if (_vp.isModifiable()) {
+ final int i = _vp.getNearestBase();
+
+ if (_vp.isComparisonMode()) {
+
+ Runnable input = new Runnable() {
+
+ @Override
+ public void run() {
+ String res = (String) getDialogReturnValue();
+ if (res != null) {
+ ModeleBasesComparison mb = (ModeleBasesComparison) _vp.getRNA().get_listeBases().get(i);
+ String bck = mb.getBase1() + "|" + mb.getBase2();
+ mb.setBase1(((res.length() > 0) ? res.charAt(0) : ' '));
+ mb.setBase2(((res.length() > 1) ? res.charAt(1) : ' '));
+ _vp.repaint();
+ _vp.fireSequenceChanged(i, bck, res);
+ }
+ }
+
+ };
+
+
+
+ showInputDialog("Input base", ((ModeleBasesComparison) _vp.getRNA().get_listeBases().get(i)).getBases(), input);
+
+ } else {
+
+ Runnable input = new Runnable() {
+
+ @Override
+ public void run() {
+ String res = (String) getDialogReturnValue();
+ if (res != null) {
+ ModeleBaseNucleotide mb = (ModeleBaseNucleotide) _vp.getRNA().get_listeBases().get(i);
+ String bck = mb.getBase();
+ mb.setBase(res);
+ _vp.repaint();
+ _vp.fireSequenceChanged(i, bck, res);
+ }
+ }
+
+ };
+ showInputDialog("Input base", ((ModeleBaseNucleotide) _vp.getRNA().get_listeBases().get(i)).getBase(), input);
+ }
+ }
+ }
+
+ FileNameExtensionFilter _varnaFilter = new FileNameExtensionFilter(
+ "VARNA Session File", "varna", "VARNA");
+ FileNameExtensionFilter _bpseqFilter = new FileNameExtensionFilter(
+ "BPSeq (CRW) File", "bpseq", "BPSEQ");
+ FileNameExtensionFilter _ctFilter = new FileNameExtensionFilter(
+ "Connect (MFold) File", "ct", "CT");
+ FileNameExtensionFilter _dbnFilter = new FileNameExtensionFilter(
+ "Dot-bracket notation (Vienna) File", "dbn", "DBN", "faa", "FAA");
+
+ FileNameExtensionFilter _jpgFilter = new FileNameExtensionFilter(
+ "JPEG Picture", "jpeg", "jpg", "JPG", "JPEG");
+ FileNameExtensionFilter _pngFilter = new FileNameExtensionFilter(
+ "PNG Picture", "png", "PNG");
+ FileNameExtensionFilter _epsFilter = new FileNameExtensionFilter(
+ "EPS File", "eps", "EPS");
+ FileNameExtensionFilter _svgFilter = new FileNameExtensionFilter(
+ "SVG Picture", "svg", "SVG");
+ FileNameExtensionFilter _xfigFilter = new FileNameExtensionFilter(
+ "XFig Diagram", "fig", "xfig", "FIG", "XFIG");
+ FileNameExtensionFilter _tikzFilter = new FileNameExtensionFilter(
+ "PGF/Tikz diagram", "tex", "pgf");
+
+ public void UIExport() throws ExceptionExportFailed,
+ ExceptionPermissionDenied, ExceptionWritingForbidden,
+ ExceptionJPEGEncoding {
+ ArrayList<FileNameExtensionFilter> v = new ArrayList<FileNameExtensionFilter>();
+ v.add(_epsFilter);
+ v.add(_svgFilter);
+ v.add(_tikzFilter);
+ v.add(_xfigFilter);
+ v.add(_jpgFilter);
+ v.add(_pngFilter);
+ String dest = UIChooseOutputFile(v);
+ if (dest != null) {
+ String extLower = dest.substring(dest.lastIndexOf('.'))
+ .toLowerCase();
+ // System.out.println(extLower);
+ if (extLower.equals(".eps")) {
+ _vp.getRNA().saveRNAEPS(dest, _vp.getConfig());
+ } else if (extLower.equals(".svg")) {
+ _vp.getRNA().saveRNASVG(dest, _vp.getConfig());
+ } else if (extLower.equals(".fig") || extLower.equals(".xfig")) {
+ _vp.getRNA().saveRNAXFIG(dest, _vp.getConfig());
+ } else if (extLower.equals(".pgf") || extLower.equals(".tex")) {
+ _vp.getRNA().saveRNATIKZ(dest, _vp.getConfig());
+ } else if (extLower.equals(".png")) {
+ saveToPNG(dest);
+ } else if (extLower.equals(".jpg") || extLower.equals(".jpeg")) {
+ saveToJPEG(dest);
+ }
+ }
+ }
+
+ public void UIExportJPEG() throws ExceptionJPEGEncoding,
+ ExceptionExportFailed {
+ String dest = UIChooseOutputFile(_jpgFilter);
+ if (dest != null) {
+ saveToJPEG(dest);
+ }
+ }
+
+ public void UIPrint() {
+ VARNAPrinter.printComponent(_vp);
+ }
+
+ public void UIExportPNG() throws ExceptionExportFailed {
+ String dest = UIChooseOutputFile(_pngFilter);
+ if (dest != null) {
+ saveToPNG(dest);
+ }
+ }
+
+ public void UIExportXFIG() throws ExceptionExportFailed,
+ ExceptionWritingForbidden {
+ String dest = UIChooseOutputFile(_xfigFilter);
+ if (dest != null) {
+ _vp.getRNA().saveRNAXFIG(dest, _vp.getConfig());
+ }
+ }
+
+ public void UIExportTIKZ() throws ExceptionExportFailed,
+ ExceptionWritingForbidden {
+ String dest = UIChooseOutputFile(_tikzFilter);
+ if (dest != null) {
+ _vp.getRNA().saveRNATIKZ(dest, _vp.getConfig());
+ }
+ }
+
+ public void UIExportEPS() throws ExceptionExportFailed,
+ ExceptionWritingForbidden {
+ String dest = UIChooseOutputFile(_epsFilter);
+ if (dest != null) {
+ _vp.getRNA().saveRNAEPS(dest, _vp.getConfig());
+ }
+ }
+
+ public void UIExportSVG() throws ExceptionExportFailed,
+ ExceptionWritingForbidden {
+ String dest = UIChooseOutputFile(_svgFilter);
+ if (dest != null) {
+ _vp.getRNA().saveRNASVG(dest, _vp.getConfig());
+ }
+ }
+
+ public void UISaveAsDBN() throws ExceptionExportFailed,
+ ExceptionPermissionDenied {
+ String name = _vp.getVARNAUI().UIChooseOutputFile(_dbnFilter);
+ if (name != null)
+ _vp.getRNA().saveAsDBN(name, _vp.getTitle());
+ }
+
+ public void UISaveAsCT() throws ExceptionExportFailed,
+ ExceptionPermissionDenied {
+ String name = _vp.getVARNAUI().UIChooseOutputFile(_ctFilter);
+ if (name != null)
+ _vp.getRNA().saveAsCT(name, _vp.getTitle());
+ }
+
+ public void UISaveAsBPSEQ() throws ExceptionExportFailed,
+ ExceptionPermissionDenied {
+ String name = _vp.getVARNAUI().UIChooseOutputFile(_bpseqFilter);
+ if (name != null)
+ _vp.getRNA().saveAsBPSEQ(name, _vp.getTitle());
+ }
+
+ public void UISaveAs() throws ExceptionExportFailed,
+ ExceptionPermissionDenied {
+ ArrayList<FileNameExtensionFilter> v = new ArrayList<FileNameExtensionFilter>();
+ v.add(_bpseqFilter);
+ v.add(_dbnFilter);
+ v.add(_ctFilter);
+ v.add(_varnaFilter);
+ String dest = UIChooseOutputFile(v);
+ if (dest != null) {
+ String extLower = dest.substring(dest.lastIndexOf('.'))
+ .toLowerCase();
+ if (extLower.endsWith("bpseq")) {
+ _vp.getRNA().saveAsBPSEQ(dest, _vp.getTitle());
+ } else if (extLower.endsWith("ct")) {
+ _vp.getRNA().saveAsCT(dest, _vp.getTitle());
+ } else if (extLower.endsWith("dbn") || extLower.endsWith("faa")) {
+ _vp.getRNA().saveAsDBN(dest, _vp.getTitle());
+ } else if (extLower.endsWith("varna")) {
+ _vp.saveSession(dest);
+ }
+ }
+ }
+
+ public String UIChooseOutputFile(FileNameExtensionFilter filtre) {
+ ArrayList<FileNameExtensionFilter> v = new ArrayList<FileNameExtensionFilter>();
+ v.add(filtre);
+ return UIChooseOutputFile(v);
+ }
+
+ /**
+ * Opens a save dialog with right extensions and return the absolute path
+ *
+ * @param filtre
+ * Allowed extensions
+ * @return <code>null</code> if the user doesn't approve the save dialog,<br>
+ * <code>absolutePath</code> if the user approve the save dialog
+ */
+ public String UIChooseOutputFile(ArrayList<FileNameExtensionFilter> filtre) {
+ JFileChooser fc = new JFileChooser();
+ loadPath(fc);
+ String absolutePath = null;
+ // applique le filtre
+ for (int i = 0; i < filtre.size(); i++) {
+ fc.addChoosableFileFilter(filtre.get(i));
+ }
+ // en mode open dialog pour voir les autres fichiers avec la meme
+ // extension
+ fc.setFileSelectionMode(JFileChooser.OPEN_DIALOG);
+ fc.setDialogTitle("Save...");
+ // Si l'utilisateur a valider
+ if (fc.showSaveDialog(_vp) == JFileChooser.APPROVE_OPTION) {
+ savePath(fc);
+ absolutePath = fc.getSelectedFile().getAbsolutePath();
+ String extension = _vp.getPopupMenu().get_controleurMenu()
+ .getExtension(fc.getSelectedFile());
+ FileFilter f = fc.getFileFilter();
+ if (f instanceof FileNameExtensionFilter) {
+ ArrayList<String> listeExtension = new ArrayList<String>();
+ listeExtension.addAll(Arrays
+ .asList(((FileNameExtensionFilter) f).getExtensions()));
+ // si l'extension du fichier ne fait pas partie de la liste
+ // d'extensions acceptées
+ if (!listeExtension.contains(extension)) {
+ absolutePath += "." + listeExtension.get(0);
+ }
+ }
+ }
+ return absolutePath;
+ }
+
+ public void UISetBorder() {
+ VueBorder border = new VueBorder(_vp);
+ final Dimension oldBorder = _vp.getBorderSize();
+ _vp.drawBBox(true);
+ _vp.drawBorder(true);
+ _vp.repaint();
+ Runnable cancel = new Runnable () {
+
+ @Override
+ public void run() {
+ _vp.setBorderSize(oldBorder);
+ }
+
+ };
+ Runnable final_ = new Runnable () {
+
+ @Override
+ public void run() {
+ _vp.drawBorder(false);
+ _vp.drawBBox(false);
+ _vp.repaint();
+ }
+
+ };
+
+ showConfirmDialog(border.getPanel(), "Set new border size", null, cancel, cancel, final_);
+ }
+
+ public void UISetBackground() {
+ showColorDialog("Choose new background color", _vp.getBackground(), new Runnable() {
+
+ @Override
+ public void run() {
+ if (dialogReturnValue != null) {
+ _vp.setBackground((Color) dialogReturnValue);
+ _vp.repaint();
+ }
+ }
+
+ });
+ }
+
+ public void UIZoomIn() {
+ double _actualZoom = _vp.getZoom();
+ double _actualAmount = _vp.getZoomIncrement();
+ Point _actualTranslation = _vp.getTranslation();
+ double newZoom = Math.min(VARNAConfig.MAX_ZOOM, _actualZoom
+ * _actualAmount);
+ double ratio = newZoom / _actualZoom;
+ Point newTrans = new Point((int) (_actualTranslation.x * ratio),
+ (int) (_actualTranslation.y * ratio));
+ _vp.setZoom(newZoom);
+ _vp.setTranslation(newTrans);
+ // verification que la translation ne pose pas de problemes
+ _vp.checkTranslation();
+ // System.out.println("Zoom in");
+ _vp.repaint();
+ }
+
+ public void UIZoomOut() {
+ double _actualZoom = _vp.getZoom();
+ double _actualAmount = _vp.getZoomIncrement();
+ Point _actualTranslation = _vp.getTranslation();
+ double newZoom = Math.max(_actualZoom / _actualAmount,
+ VARNAConfig.MIN_ZOOM);
+ double ratio = newZoom / _actualZoom;
+ Point newTrans = new Point((int) (_actualTranslation.x * ratio),
+ (int) (_actualTranslation.y * ratio));
+ _vp.setZoom(newZoom);
+ _vp.setTranslation(newTrans);
+ // verification que la translation ne pose pas de problemes
+ _vp.checkTranslation();
+ _vp.repaint();
+ }
+
+ public void UICustomZoom() {
+ VueZoom zoom = new VueZoom(_vp);
+ final double oldZoom = _vp.getZoom();
+ final double oldZoomAmount = _vp.getZoomIncrement();
+ _vp.drawBBox(true);
+ _vp.repaint();
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.setZoom(oldZoom);
+ _vp.setZoomIncrement(oldZoomAmount);
+ }
+
+ };
+ Runnable final_ = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.drawBBox(false);
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(zoom.getPanel(), "Set zoom", null, cancel, cancel, final_);
+ }
+
+ public void UIGlobalRescale() {
+ if (_vp.isModifiable()) {
+ if (_vp.getRNA().get_listeBases().size() > 0) {
+ final VueGlobalRescale rescale = new VueGlobalRescale(_vp);
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ UIGlobalRescale(1. / rescale.getScale());
+ }
+
+ };
+ Runnable final_ = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.drawBBox(false);
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(rescale.getPanel(), "Rescales the whole RNA (No redraw)", null, cancel, cancel, final_);
+ }
+ }
+ }
+
+ public void UIGlobalRescale(double d) {
+ if (_vp.isModifiable()) {
+ if (_vp.getRNA().get_listeBases().size() > 0) {
+ _vp.globalRescale(d);
+ _undoableEditSupport.postEdit(new VARNAEdits.RescaleRNAEdit(d,
+ _vp));
+ }
+ }
+ }
+
+ public void UIGlobalRotation() {
+ if (_vp.isModifiable()) {
+ if (_vp.getRNA().get_listeBases().size() > 0) {
+ _vp.drawBBox(true);
+ _vp.repaint();
+ final VueGlobalRotation rotation = new VueGlobalRotation(_vp);
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ UIGlobalRotation(-rotation.getAngle());
+ }
+
+ };
+ Runnable final_ = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.drawBBox(false);
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(rotation.getPanel(), "Rotates the whole RNA", null, cancel, cancel, final_, null);
+ }
+ }
+ }
+
+ public void UIGlobalRotation(double d) {
+ if (_vp.isModifiable()) {
+ if (_vp.getRNA().get_listeBases().size() > 0) {
+ _vp.globalRotation(d);
+ _undoableEditSupport.postEdit(new VARNAEdits.RotateRNAEdit(d,
+ _vp));
+ }
+ }
+ }
+
+ public void UISetBPStyle() {
+ if (_vp.getRNA().get_listeBases().size() > 0) {
+ VueStyleBP bpstyle = new VueStyleBP(_vp);
+ final VARNAConfig.BP_STYLE bck = _vp.getBPStyle();
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.setBPStyle(bck);
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(bpstyle.getPanel(), "Set main base pair style", null, cancel, cancel);
+ }
+ }
+
+ public void UISetTitleColor() {
+ if (_vp.isModifiable()) {
+ showColorDialog("Choose new title color", _vp.getTitleColor(), new Runnable() {
+
+ @Override
+ public void run() {
+ if (dialogReturnValue != null) {
+ _vp.setTitleColor((Color) dialogReturnValue);
+ _vp.repaint();
+ }
+ }
+
+ });
+ }
+ }
+
+ public void UISetBackboneColor() {
+ if (_vp.isModifiable()) {
+ showColorDialog("Choose new backbone color", _vp.getBackboneColor(), new Runnable() {
+
+ @Override
+ public void run() {
+ if (dialogReturnValue != null) {
+ _vp.setBackboneColor((Color) dialogReturnValue);
+ _vp.repaint();
+ }
+ }
+
+ });
+ }
+ }
+
+ public void UISetTitleFont() {
+ if (_vp.isModifiable()) {
+ final VueFont font = new VueFont(_vp);
+ Runnable ok = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.setTitleFont(font.getFont());
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(font.getPanel(), "New Title font", ok, null);
+ }
+ }
+
+ public void UISetSpaceBetweenBases() {
+ if (_vp.isModifiable()) {
+
+ final VueSpaceBetweenBases vsbb = new VueSpaceBetweenBases(_vp);
+ final Double oldSpace = _vp.getSpaceBetweenBases();
+ Runnable cancel = new Runnable () {
+
+ @Override
+ public void run() {
+ _vp.setSpaceBetweenBases(oldSpace);
+ _vp.drawRNA(_vp.getRNA());
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(vsbb.getPanel(), "Set the space between each base", null, cancel, cancel);
+ }
+ }
+
+ public void UISetBPHeightIncrement() {
+ if (_vp.isModifiable()) {
+
+ VueBPHeightIncrement v = new VueBPHeightIncrement(_vp);
+ final Double oldSpace = _vp.getBPHeightIncrement();
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.setBPHeightIncrement(oldSpace);
+ _vp.drawRNA(_vp.getRNA());
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(v.getPanel(), "Set the vertical increment in linear mode", null, cancel, cancel);
+ }
+ }
+
+ public void UISetNumPeriod() {
+ if (_vp.getRNA().get_listeBases().size() != 0) {
+ final int oldNumPeriod = _vp.getNumPeriod();
+ VueNumPeriod vnp = new VueNumPeriod(_vp);
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ _vp.setNumPeriod(oldNumPeriod);
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(vnp.getPanel(), "Set new numbering period", null, cancel, cancel);
+ }
+ }
+
+ public void UIEditBasePair() {
+ if (_vp.isModifiable()) {
+ ModeleBase mb = _vp.getRNA().get_listeBases().get(_vp.getNearestBase());
+ if (mb.getElementStructure() != -1) {
+ final ModeleBP msbp = mb.getStyleBP();
+ final ModeleBP.Edge bck5 = msbp.getEdgePartner5();
+ final ModeleBP.Edge bck3 = msbp.getEdgePartner3();
+ final ModeleBP.Stericity bcks = msbp.getStericity();
+
+ VueBPType vbpt = new VueBPType(_vp, msbp);
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ msbp.setEdge5(bck5);
+ msbp.setEdge3(bck3);
+ msbp.setStericity(bcks);
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(vbpt.getPanel(), "Set base pair L/W type", null, cancel, cancel);
+ }
+ }
+ }
+
+ public void UIColorBasePair() {
+ if (_vp.isModifiable()) {
+ ModeleBase mb = _vp.getRNA().get_listeBases().get(_vp.getNearestBase());
+ if (mb.getElementStructure() != -1) {
+ final ModeleBP msbp = mb.getStyleBP();
+ showColorDialog("Choose custom base pair color",
+ msbp.getStyle().getColor(_vp.getConfig()._bondColor), new Runnable() {
+
+ @Override
+ public void run() {
+ if (dialogReturnValue != null) {
+ msbp.getStyle().setCustomColor((Color) dialogReturnValue);
+ _vp.repaint();
+ }
+ }
+
+ });
+ }
+ }
+ }
+
+ public void UIThicknessBasePair() {
+ if (_vp.isModifiable()) {
+ ModeleBase mb = _vp.getRNA().get_listeBases()
+ .get(_vp.getNearestBase());
+ if (mb.getElementStructure() != -1) {
+ ModeleBP msbp = mb.getStyleBP();
+ ArrayList<ModeleBP> bases = new ArrayList<ModeleBP>();
+ bases.add(msbp);
+ UIThicknessBasePairs(bases);
+ }
+ }
+ }
+
+ public void saveToPNG(final String filename) {
+ final VueJPEG jpeg = new VueJPEG(true, false);
+ Runnable ok = new Runnable() {
+
+ @Override
+ public void run() {
+ Double scale = jpeg.getScaleSlider().getValue() / 100.0;
+ BufferedImage myImage = new BufferedImage((int) Math.round(_vp.getWidth() * scale),
+ (int) Math.round(_vp.getHeight() * scale), BufferedImage.TYPE_INT_ARGB);
+ // BH j2s SwingJS: was BufferedImage.TRANSLUCENT, which is TYPE_INT_ARGB_PRE ?? no transparent background?
+ Graphics2D g2 = myImage.createGraphics();
+ AffineTransform AF = new AffineTransform();
+ AF.setToScale(scale, scale);
+ g2.setTransform(AF);
+ _vp.paintComponent(g2, !_vp.getConfig()._drawBackground);
+ g2.dispose();
+ try {
+ ImageIO.write(myImage, "PNG", new File(filename));
+ } catch (IOException e) {
+ // cannot throw an exception from Runnable.run()
+ _vp.errorDialog(new ExceptionExportFailed(e.getMessage(), filename));
+ }
+ }
+
+ };
+ showConfirmDialog(jpeg.getPanel(), "Set resolution", ok, null);
+ }
+
+ public void saveToJPEG(final String filename) {
+ final VueJPEG jpeg = new VueJPEG(true, true);
+ Runnable ok = new Runnable() {
+
+ @Override
+ public void run() {
+ Double scale;
+ if (jpeg.getScaleSlider().getValue() == 0)
+ scale = 1. / 100.;
+ else
+ scale = jpeg.getScaleSlider().getValue() / 100.;
+ BufferedImage myImage = new BufferedImage((int) Math.round(_vp
+ .getWidth() * scale), (int) Math.round(_vp.getHeight()
+ * scale), BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = myImage.createGraphics();
+ AffineTransform AF = new AffineTransform();
+ AF.setToScale(scale, scale);
+ g2.setTransform(AF);
+ _vp.paintComponent(g2);
+ try {
+ FileImageOutputStream out = new FileImageOutputStream(new File(
+ filename));
+ ImageWriter writer = ImageIO
+ .getImageWritersByFormatName("jpeg").next();
+ ImageWriteParam params = writer.getDefaultWriteParam();
+ params.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+ params.setCompressionQuality(jpeg.getQualitySlider().getValue() / 100.0f);
+ writer.setOutput(out);
+ IIOImage myIIOImage = new IIOImage(myImage, null, null);
+ writer.write(null, myIIOImage, params);
+ out.close();
+ } catch (IOException e) {
+ // cannot throw an exception from Runnable.run()
+ _vp.errorDialog(new ExceptionExportFailed(e.getMessage(), filename));
+ }
+ }
+
+ };
+ showConfirmDialog(jpeg.getPanel(), "Set resolution/quality", ok, null);
+ }
+
+ public void UIToggleShowNCBP() {
+ if (_vp.isModifiable()) {
+ _vp.setShowNonCanonicalBP(!_vp.getShowNonCanonicalBP());
+ _vp.repaint();
+ }
+ }
+
+ public void UIToggleColorSpecialBases() {
+ _vp.setColorNonStandardBases(!_vp.getColorSpecialBases());
+ _vp.repaint();
+ }
+
+ public void UIToggleColorGapsBases() {
+ _vp.setColorGapsBases(!_vp.getColorGapsBases());
+ _vp.repaint();
+ }
+
+ public void UIToggleShowNonPlanar() {
+ if (_vp.isModifiable()) {
+ _vp.setShowNonPlanarBP(!_vp.getShowNonPlanarBP());
+ _vp.repaint();
+ }
+ }
+
+ public void UIToggleShowWarnings() {
+ _vp.setShowWarnings(!_vp.getShowWarnings());
+ _vp.repaint();
+ }
+
+ public void UIPickSpecialBasesColor() {
+ showColorDialog("Choose new special bases color", _vp.getNonStandardBasesColor(), new Runnable() {
+
+ @Override
+ public void run() {
+ if (dialogReturnValue != null) {
+ _vp.setNonStandardBasesColor((Color) dialogReturnValue);
+ _vp.setColorNonStandardBases(true);
+ _vp.repaint();
+ }
+ }
+
+ });
+ }
+
+ public void UIPickGapsBasesColor() {
+ showColorDialog("Choose new gaps bases color", _vp.getGapsBasesColor(), new Runnable() {
+
+ @Override
+ public void run() {
+ if (dialogReturnValue != null) {
+ _vp.setGapsBasesColor((Color) dialogReturnValue);
+ _vp.setColorGapsBases(true);
+ _vp.repaint();
+ }
+ }
+
+ });
+ }
+
+ public void UIBaseTypeColor() {
+ if (_vp.isModifiable()) {
+ new VueBases(_vp, VueBases.KIND_MODE);
+ }
+ }
+
+ public void UIToggleModifiable() {
+ _vp.setModifiable(!_vp.isModifiable());
+ }
+
+ public void UIBasePairTypeColor() {
+ if (_vp.isModifiable()) {
+ new VueBases(_vp, VueBases.COUPLE_MODE);
+ }
+ }
+
+ public void UIBaseAllColor() {
+ if (_vp.isModifiable()) {
+ new VueBases(_vp, VueBases.ALL_MODE);
+ }
+ }
+
+ public void UIAbout() {
+ final VueAboutPanel about = new VueAboutPanel();
+ Runnable ok = new Runnable() {
+
+ @Override
+ public void run() {
+ about.gracefulStop();
+ }
+
+ };
+ showMessageDialog(about, "About VARNA " + VARNAConfig.MAJOR_VERSION + "." + VARNAConfig.MINOR_VERSION,
+ JOptionPane.PLAIN_MESSAGE, ok, ok);
+ }
+
+ public void UIAutoAnnotateHelices() {
+ if (_vp.isModifiable()) {
+ _vp.getRNA().autoAnnotateHelices();
+ _vp.repaint();
+ }
+ }
+
+ public void UIAutoAnnotateStrandEnds() {
+ if (_vp.isModifiable()) {
+ _vp.getRNA().autoAnnotateStrandEnds();
+ _vp.repaint();
+ }
+ }
+
+ public void UIAutoAnnotateInteriorLoops() {
+ if (_vp.isModifiable()) {
+ _vp.getRNA().autoAnnotateInteriorLoops();
+ _vp.repaint();
+ }
+ }
+
+ public void UIAutoAnnotateTerminalLoops() {
+ if (_vp.isModifiable()) {
+ _vp.getRNA().autoAnnotateTerminalLoops();
+ _vp.repaint();
+ }
+ }
+
+ public void UIAnnotationRemoveFromAnnotation(TextAnnotation textAnnotation) {
+ if (_vp.isModifiable()) {
+ _vp.set_selectedAnnotation(null);
+ _vp.getListeAnnotations().remove(textAnnotation);
+ _vp.repaint();
+ }
+ }
+
+ public void UIAnnotationEditFromAnnotation(TextAnnotation textAnnotation) {
+ VueAnnotation vue;
+ if (textAnnotation.getType() == TextAnnotation.AnchorType.POSITION)
+ vue = new VueAnnotation(_vp, textAnnotation, false);
+ else
+ vue = new VueAnnotation(_vp, textAnnotation, true, false);
+ vue.show();
+ }
+
+ public void UIAnnotationAddFromStructure(TextAnnotation.AnchorType type, ArrayList<Integer> listeIndex)
+ throws Exception {
+ TextAnnotation textAnnot;
+ ArrayList<ModeleBase> listeBase;
+ VueAnnotation vue;
+ switch (type) {
+ case BASE:
+ textAnnot = new TextAnnotation("", _vp.getRNA().get_listeBases()
+ .get(listeIndex.get(0)));
+ vue = new VueAnnotation(_vp, textAnnot, true);
+ vue.show();
+ break;
+ case LOOP:
+ listeBase = new ArrayList<ModeleBase>();
+ for (Integer i : listeIndex) {
+ listeBase.add(_vp.getRNA().get_listeBases().get(i));
+ }
+ textAnnot = new TextAnnotation("", listeBase, type);
+ vue = new VueAnnotation(_vp, textAnnot, true);
+ vue.show();
+ break;
+ case HELIX:
+ listeBase = new ArrayList<ModeleBase>();
+ for (Integer i : listeIndex) {
+ listeBase.add(_vp.getRNA().get_listeBases().get(i));
+ }
+ textAnnot = new TextAnnotation("", listeBase, type);
+ vue = new VueAnnotation(_vp, textAnnot, true);
+ vue.show();
+ break;
+ default:
+ _vp.errorDialog(new Exception("Unknown structure type"));
+ break;
+ }
+ }
+
+ public void UIAnnotationEditFromStructure(TextAnnotation.AnchorType type,
+ ArrayList<Integer> listeIndex) {
+ if (_vp.isModifiable()) {
+ ModeleBase mb = _vp.getRNA().get_listeBases()
+ .get(listeIndex.get(0));
+ TextAnnotation ta = _vp.getRNA().getAnnotation(type, mb);
+ if (ta != null)
+ UIAnnotationEditFromAnnotation(ta);
+ }
+ }
+
+ public void UIAnnotationRemoveFromStructure(TextAnnotation.AnchorType type,
+ ArrayList<Integer> listeIndex) {
+ if (_vp.isModifiable()) {
+ ModeleBase mb = _vp.getRNA().get_listeBases()
+ .get(listeIndex.get(0));
+ TextAnnotation ta = _vp.getRNA().getAnnotation(type, mb);
+ if (ta != null)
+ UIAnnotationRemoveFromAnnotation(ta);
+ }
+ }
+
+ public void UIAnnotationsAddPosition(int x, int y) {
+ if (_vp.isModifiable()) {
+ Point2D.Double p = _vp.panelToLogicPoint(new Point2D.Double(x, y));
+ VueAnnotation annotationAdd = new VueAnnotation(_vp, (int) p.x,
+ (int) p.y);
+ annotationAdd.show();
+ }
+ }
+
+ public void UIAnnotationsAddBase(int x, int y) {
+ if (_vp.isModifiable()) {
+ ModeleBase mb = _vp.getBaseAt(new Point2D.Double(x, y));
+ if (mb != null) {
+ _vp.highlightSelectedBase(mb);
+ TextAnnotation textAnnot = new TextAnnotation("", mb);
+ VueAnnotation annotationAdd = new VueAnnotation(_vp, textAnnot,
+ true);
+ annotationAdd.show();
+ }
+ }
+ }
+
+ public void UIAnnotationsAddLoop(int x, int y) {
+ if (_vp.isModifiable()) {
+ try {
+ ModeleBase mb = _vp.getBaseAt(new Point2D.Double(x, y));
+ if (mb != null) {
+ Vector<Integer> v = _vp.getRNA()
+ .getLoopBases(mb.getIndex());
+ ArrayList<ModeleBase> mbs = _vp.getRNA().getBasesAt(v);
+ TextAnnotation textAnnot;
+ textAnnot = new TextAnnotation("", mbs,
+ TextAnnotation.AnchorType.LOOP);
+ _vp.setSelection(mbs);
+ VueAnnotation annotationAdd = new VueAnnotation(_vp,
+ textAnnot, true);
+ annotationAdd.show();
+ }
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ }
+
+ private ArrayList<ModeleBase> extractMaxContiguousPortion(
+ ArrayList<ModeleBase> m) {
+ ModeleBase[] tab = new ModeleBase[_vp.getRNA().getSize()];
+ for (int i = 0; i < tab.length; i++) {
+ tab[i] = null;
+ }
+ for (ModeleBase mb : m) {
+ tab[mb.getIndex()] = mb;
+ }
+ ArrayList<ModeleBase> best = new ArrayList<ModeleBase>();
+ ArrayList<ModeleBase> current = new ArrayList<ModeleBase>();
+ for (int i = 0; i < tab.length; i++) {
+ if (tab[i] != null) {
+ current.add(tab[i]);
+ } else {
+ if (current.size() > best.size())
+ best = current;
+ current = new ArrayList<ModeleBase>();
+ }
+ }
+ if (current.size() > best.size()) {
+ best = current;
+ }
+ return best;
+ }
+
+ public void UIAnnotationsAddRegion(int x, int y) {
+ if (_vp.isModifiable()) {
+ ArrayList<ModeleBase> mb = _vp.getSelection().getBases();
+ if (mb.size() == 0) {
+ ModeleBase m = _vp.getBaseAt(new Point2D.Double(x, y));
+ mb.add(m);
+ }
+ mb = extractMaxContiguousPortion(extractMaxContiguousPortion(mb));
+ _vp.setSelection(mb);
+ HighlightRegionAnnotation regionAnnot = new HighlightRegionAnnotation(
+ mb);
+ _vp.addHighlightRegion(regionAnnot);
+ VueHighlightRegionEdit annotationAdd = new VueHighlightRegionEdit(
+ _vp, regionAnnot);
+ if (!annotationAdd.show()) {
+ _vp.removeHighlightRegion(regionAnnot);
+ }
+ _vp.clearSelection();
+ }
+ }
+
+ public void UIAnnotationsAddChemProb(int x, int y) {
+ if (_vp.isModifiable() && _vp.getRNA().getSize() > 1) {
+ Point2D.Double p = _vp.panelToLogicPoint(new Point2D.Double(x, y));
+ ModeleBase m1 = _vp.getBaseAt(new Point2D.Double(x, y));
+ ModeleBase best = null;
+ if (m1.getIndex() - 1 >= 0) {
+ best = _vp.getRNA().getBaseAt(m1.getIndex() - 1);
+ }
+ if (m1.getIndex() + 1 < _vp.getRNA().getSize()) {
+ ModeleBase m2 = _vp.getRNA().getBaseAt(m1.getIndex() + 1);
+ if (best == null) {
+ best = m2;
+ } else {
+ if (best.getCoords().distance(p) > m2.getCoords().distance(
+ p)) {
+ best = m2;
+ }
+ }
+ }
+ ArrayList<ModeleBase> tab = new ArrayList<ModeleBase>();
+ tab.add(m1);
+ tab.add(best);
+ _vp.setSelection(tab);
+ ChemProbAnnotation regionAnnot = new ChemProbAnnotation(m1, best);
+ _vp.getRNA().addChemProbAnnotation(regionAnnot);
+ VueChemProbAnnotation annotationAdd = new VueChemProbAnnotation(
+ _vp, regionAnnot);
+ if (!annotationAdd.show()) {
+ _vp.getRNA().removeChemProbAnnotation(regionAnnot);
+ }
+ _vp.clearSelection();
+ }
+ }
+
+ public void UIAnnotationsAddHelix(int x, int y) {
+ if (_vp.isModifiable()) {
+ try {
+ ModeleBase mb = _vp.getBaseAt(new Point2D.Double(x, y));
+ if (mb != null) {
+ ArrayList<Integer> v = _vp.getRNA().findHelix(mb.getIndex());
+ ArrayList<ModeleBase> mbs = _vp.getRNA().getBasesAt(v);
+ TextAnnotation textAnnot;
+ textAnnot = new TextAnnotation("", mbs,
+ TextAnnotation.AnchorType.HELIX);
+ _vp.setSelection(mbs);
+ VueAnnotation annotationAdd = new VueAnnotation(_vp,
+ textAnnot, true);
+ annotationAdd.show();
+ }
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ }
+
+ public void UIToggleGaspinMode() {
+ if (_vp.isModifiable()) {
+ _vp.toggleDrawOutlineBases();
+ _vp.toggleFillBases();
+ _vp.repaint();
+ }
+ }
+
+ public void UIAnnotationsAdd() {
+ if (_vp.isModifiable()) {
+ VueAnnotation annotationAdd = new VueAnnotation(_vp);
+ annotationAdd.show();
+ }
+ }
+
+ public void UIEditAllBasePairs() {
+ if (_vp.isModifiable()) {
+ new VueBPList(_vp);
+ }
+ }
+
+ public void UIEditAllBases() {
+ if (_vp.isModifiable()) {
+ new VueBases(_vp, VueBases.ALL_MODE);
+ }
+ }
+
+ public void UIAnnotationsRemove() {
+ if (_vp.isModifiable()) {
+ new VueListeAnnotations(_vp, VueListeAnnotations.REMOVE);
+ }
+ }
+
+ public void UIAnnotationsEdit() {
+ if (_vp.isModifiable()) {
+ new VueListeAnnotations(_vp, VueListeAnnotations.EDIT);
+ }
+ }
+
+ public void UIAddBP(int i, int j, ModeleBP ms) {
+ if (_vp.isModifiable()) {
+ _vp.getRNA().addBP(i, j, ms);
+ _undoableEditSupport.postEdit(new VARNAEdits.AddBPEdit(i, j, ms,
+ _vp));
+ _vp.repaint();
+
+ HashSet<ModeleBP> tmp = new HashSet<ModeleBP>();
+ tmp.add(ms);
+ _vp.fireStructureChanged(new HashSet<ModeleBP>(_vp.getRNA()
+ .getAllBPs()), tmp, new HashSet<ModeleBP>());
+ }
+ }
+
+ public void UIRemoveBP(ModeleBP ms) {
+ if (_vp.isModifiable()) {
+ _undoableEditSupport.postEdit(new VARNAEdits.RemoveBPEdit(ms
+ .getIndex5(), ms.getIndex3(), ms, _vp));
+ _vp.getRNA().removeBP(ms);
+ _vp.repaint();
+
+ HashSet<ModeleBP> tmp = new HashSet<ModeleBP>();
+ tmp.add(ms);
+ _vp.fireStructureChanged(new HashSet<ModeleBP>(_vp.getRNA()
+ .getAllBPs()), new HashSet<ModeleBP>(), tmp);
+ }
+ }
+
+ public void UIShiftBaseCoord(ArrayList<Integer> indices, double dx, double dy) {
+ if (_vp.isModifiable()) {
+ Hashtable<Integer, Point2D.Double> backupPos = new Hashtable<Integer, Point2D.Double>();
+
+ for (int index : indices) {
+ ModeleBase mb = _vp.getRNA().getBaseAt(index);
+ Point2D.Double d = mb.getCoords();
+ backupPos.put(index, d);
+ _vp.getRNA().setCoord(index, d.x + dx, d.y + dy);
+ _vp.getRNA().setCenter(index, mb.getCenter().x + dx, mb.getCenter().y + dy);
+ }
+ _undoableEditSupport.postEdit(new VARNAEdits.BasesShiftEdit(
+ indices, dx, dy, _vp));
+ _vp.repaint();
+ _vp.fireLayoutChanged(backupPos);
+ }
+ }
+
+ public void UIShiftBaseCoord(ArrayList<Integer> indices, Point2D.Double dv) {
+ UIShiftBaseCoord(indices, dv.x, dv.y);
+ }
+
+ public void UIMoveSingleBase(int index, double nx, double ny) {
+ if (_vp.isModifiable()) {
+ ModeleBase mb = _vp.getRNA().getBaseAt(index);
+ Point2D.Double d = mb.getCoords();
+ Hashtable<Integer, Point2D.Double> backupPos = new Hashtable<Integer, Point2D.Double>();
+ backupPos.put(index, d);
+ _undoableEditSupport.postEdit(new VARNAEdits.SingleBaseMoveEdit(
+ index, nx, ny, _vp));
+ _vp.getRNA().setCoord(index, nx, ny);
+ _vp.repaint();
+ _vp.fireLayoutChanged(backupPos);
+ }
+ }
+
+ public void UIMoveSingleBase(int index, Point2D.Double dv) {
+ UIMoveSingleBase(index, dv.x, dv.y);
+ }
+
+ public void UISetBaseCenter(int index, double x, double y) {
+ UISetBaseCenter(index, new Point2D.Double(x, y));
+ }
+
+ public void UISetBaseCenter(int index, Point2D.Double p) {
+ if (_vp.isModifiable()) {
+ _vp.getRNA().setCenter(index, p);
+ }
+ }
+
+ public void UIUndo() {
+ _vp.undo();
+ }
+
+ public void UIRedo() {
+ _vp.redo();
+ }
+
+ /**
+ * Move a helix of the rna
+ *
+ * @param index
+ * :the index of the selected base
+ * @param newPos
+ * :the new xy coordinate, within the logical system of
+ * coordinates
+ */
+ public void UIMoveHelixAtom(int index, Point2D.Double newPos) {
+ if (_vp.isModifiable() && (index >= 0)
+ && (index < _vp.getRNA().get_listeBases().size())) {
+ int indexTo = _vp.getRNA().get_listeBases().get(index)
+ .getElementStructure();
+ Point h = _vp.getRNA().getHelixInterval(index);
+ Point ml = _vp.getRNA().getMultiLoop(h.x);
+ int i = ml.x;
+ if (indexTo != -1) {
+ if (i == 0) {
+ if (shouldFlip(index, newPos)) {
+ UIFlipHelix(h);
+ _undoableEditSupport
+ .postEdit(new VARNAEdits.HelixFlipEdit(h, _vp));
+ }
+ } else {
+ UIRotateHelixAtom(index, newPos);
+ }
+
+ }
+ _vp.fireLayoutChanged();
+ }
+ }
+
+ /**
+ * Flip an helix around its supporting base
+ */
+ public void UIFlipHelix(Point h) {
+ int hBeg = h.x;
+ int hEnd = h.y;
+ Point2D.Double A = _vp.getRNA().getCoords(hBeg);
+ Point2D.Double B = _vp.getRNA().getCoords(hEnd);
+ Point2D.Double AB = new Point2D.Double(B.x - A.x, B.y - A.y);
+ double normAB = Math.sqrt(AB.x * AB.x + AB.y * AB.y);
+ // Creating a coordinate system centered on A and having
+ // unit x-vector Ox.
+ Point2D.Double O = A;
+ Point2D.Double Ox = new Point2D.Double(AB.x / normAB, AB.y / normAB);
+ Hashtable<Integer, Point2D.Double> old = new Hashtable<Integer, Point2D.Double>();
+ for (int i = hBeg + 1; i < hEnd; i++) {
+ Point2D.Double P = _vp.getRNA().getCoords(i);
+ Point2D.Double nP = RNA.project(O, Ox, P);
+ old.put(i, nP);
+ }
+ _vp.getRNA().flipHelix(h);
+ _vp.fireLayoutChanged(old);
+ }
+
+ /**
+ * Tests if an helix needs to be flipped.
+ */
+ boolean shouldFlip(int index, Point2D.Double P) {
+ Point h = _vp.getRNA().getHelixInterval(index);
+
+ Point2D.Double A = _vp.getRNA().getCoords(h.x);
+ Point2D.Double B = _vp.getRNA().getCoords(h.y);
+ Point2D.Double C = _vp.getRNA().getCoords(h.x + 1);
+ // Creating a vector that is orthogonal to AB
+ Point2D.Double hAB = new Point2D.Double(B.y - A.y, -(B.x - A.x));
+ Point2D.Double AC = new Point2D.Double(C.x - A.x, C.y - A.y);
+ Point2D.Double AP = new Point2D.Double(P.x - A.x, P.y - A.y);
+ double signC = (hAB.x * AC.x + hAB.y * AC.y);
+ double signP = (hAB.x * AP.x + hAB.y * AP.y);
+ // Now, the product signC*signP is negative iff the mouse and the first
+ // base inside
+ // the helix are on different sides of the end of the helix => Flip the
+ // helix!
+ return (signC * signP < 0.0);
+ }
+
+ public void UIRotateHelixAtom(int index, Point2D.Double newPos) {
+ Point h = _vp.getRNA().getHelixInterval(index);
+ Point ml = _vp.getRNA().getMultiLoop(h.x);
+ int i = ml.x;
+ int prevIndex = h.x;
+ int nextIndex = h.y;
+ while (i <= ml.y) {
+ int j = _vp.getRNA().get_listeBases().get(i).getElementStructure();
+ if ((j != -1) && (i < h.x)) {
+ prevIndex = i;
+ }
+ if ((j != -1) && (i > h.y) && (nextIndex == h.y)) {
+ nextIndex = i;
+ }
+ if ((j > i) && (j < ml.y)) {
+ i = _vp.getRNA().get_listeBases().get(i).getElementStructure();
+ } else {
+ i++;
+ }
+ }
+ Point2D.Double oldPos = _vp.getRNA().getCoords(index);
+ Point2D.Double limitLoopLeft, limitLoopRight, limitLeft, limitRight, helixStart, helixStop;
+ boolean isDirect = _vp.getRNA().testDirectionality(ml.x, ml.y, h.x);
+ if (isDirect) {
+ limitLoopLeft = _vp.getRNA().getCoords(ml.y);
+ limitLoopRight = _vp.getRNA().getCoords(ml.x);
+ limitLeft = _vp.getRNA().getCoords(prevIndex);
+ limitRight = _vp.getRNA().getCoords(nextIndex);
+ helixStart = _vp.getRNA().getCoords(h.x);
+ helixStop = _vp.getRNA().getCoords(h.y);
+ } else {
+ limitLoopLeft = _vp.getRNA().getCoords(ml.x);
+ limitLoopRight = _vp.getRNA().getCoords(ml.y);
+ limitLeft = _vp.getRNA().getCoords(nextIndex);
+ limitRight = _vp.getRNA().getCoords(prevIndex);
+ helixStart = _vp.getRNA().getCoords(h.y);
+ helixStop = _vp.getRNA().getCoords(h.x);
+ }
+
+ Point2D.Double center = _vp.getRNA().get_listeBases().get(h.x)
+ .getCenter();
+ double base = (RNA.computeAngle(center, limitLoopRight) + RNA
+ .computeAngle(center, limitLoopLeft)) / 2.0;
+ double pLimR = RNA.computeAngle(center, limitLeft) - base;
+ double pHelR = RNA.computeAngle(center, helixStart) - base;
+ double pNew = RNA.computeAngle(center, newPos) - base;
+ double pOld = RNA.computeAngle(center, oldPos) - base;
+ double pHelL = RNA.computeAngle(center, helixStop) - base;
+ double pLimL = RNA.computeAngle(center, limitRight) - base;
+
+ while (pLimR < 0.0)
+ pLimR += 2.0 * Math.PI;
+ while (pHelR < pLimR)
+ pHelR += 2.0 * Math.PI;
+ while ((pNew < pHelR))
+ pNew += 2.0 * Math.PI;
+ while ((pOld < pHelR))
+ pOld += 2.0 * Math.PI;
+ while ((pHelL < pOld))
+ pHelL += 2.0 * Math.PI;
+ while ((pLimL < pHelL))
+ pLimL += 2.0 * Math.PI;
+
+ double minDelta = normalizeAngle((pLimR - pHelR) + 0.25);
+ double maxDelta = normalizeAngle((pLimL - pHelL) - 0.25);
+ while (maxDelta < minDelta)
+ maxDelta += 2.0 * Math.PI;
+ double delta = normalizeAngle(pNew - pOld);
+ while (delta < minDelta)
+ delta += 2.0 * Math.PI;
+
+ if (delta > maxDelta) {
+ double distanceMax = delta - maxDelta;
+ double distanceMin = minDelta - (delta - 2.0 * Math.PI);
+ if (distanceMin < distanceMax) {
+ delta = minDelta;
+ } else {
+ delta = maxDelta;
+ }
+ }
+ double corrected = RNA
+ .correctHysteresis((delta + base + (pHelR + pHelL) / 2.));
+ delta = corrected - (base + (pHelR + pHelL) / 2.);
+ _undoableEditSupport.postEdit(new VARNAEdits.HelixRotateEdit(delta,
+ base, pLimL, pLimR, h, ml, _vp));
+ UIRotateEverything(delta, base, pLimL, pLimR, h, ml);
+ }
+
+ public void UIRotateEverything(double delta, double base, double pLimL,
+ double pLimR, Point h, Point ml) {
+ Hashtable<Integer, Point2D.Double> backupPos = new Hashtable<Integer, Point2D.Double>();
+ _vp.getRNA().rotateEverything(delta, base, pLimL, pLimR, h, ml,
+ backupPos);
+ _vp.fireLayoutChanged(backupPos);
+ }
+
+ private double normalizeAngle(double angle) {
+ return normalizeAngle(angle, 0.0);
+ }
+
+ private double normalizeAngle(double angle, double base) {
+ while (angle < base) {
+ angle += 2.0 * Math.PI;
+ }
+ while (angle >= (2.0 * Math.PI) - base) {
+ angle -= 2.0 * Math.PI;
+ }
+ return angle;
+ }
+
+ public void UIThicknessBasePairs(ArrayList<ModeleBP> bases) {
+ final VueBPThickness vbpt = new VueBPThickness(_vp, bases);
+ Runnable cancel = new Runnable() {
+
+ @Override
+ public void run() {
+ vbpt.restoreThicknesses();
+ _vp.repaint();
+ }
+
+ };
+ showConfirmDialog(vbpt.getPanel(), "Set base pair(s) thickness", null, cancel, cancel);
+ }
+
+
+
+}
git://source.jalview.org / jalview.git / blobdiff