+++ /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?
- AffineTransform AF = new AffineTransform();
- AF.setToScale(scale, scale);
- Graphics2D g2 = myImage.createGraphics();
- 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);
- AffineTransform AF = new AffineTransform();
- AF.setToScale(scale, scale);
- Graphics2D g2 = myImage.createGraphics();
- 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