X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=90542981d0351b1389a21b2019b0dfb6632a7e2d;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=7b388fc27dc3fa44b5245778ec669fab54785233;hpb=722f0bee96b96ceeb8ef69b3ccd1aeff13786b2b;p=jalview.git diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index 7b388fc..9054298 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -18,1277 +18,208 @@ package jalview.gui; import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import java.awt.*; + import javax.swing.*; import javax.swing.event.*; import java.awt.event.*; import java.io.*; -import jalview.jbgui.GStructureViewer; import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; import jalview.datamodel.*; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.structure.*; -import jalview.datamodel.PDBEntry; import jalview.io.*; import jalview.schemes.*; +import fr.orsay.lri.varna.VARNAPanel; +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; +import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; +import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener; +import fr.orsay.lri.varna.models.VARNAConfig; +import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation; +import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide; +import fr.orsay.lri.varna.models.rna.RNA; -public class AppVarna extends GStructureViewer implements Runnable, - SequenceStructureBinding, ViewSetProvider - -{ - AppJmolBinding jmb; - - JPanel scriptWindow; - - JSplitPane splitPane; - - RenderPanel renderPanel; - - AlignmentPanel ap; - - Vector atomsPicked = new Vector(); - - private boolean addingStructures = false; - - /** - * - * @param file - * @param id - * @param seq - * @param ap - * @param loadStatus - * @param bounds - * @deprecated defaults to AppJmol(String[] files, ... , viewid); - */ - public AppVarna(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds) - { - this(file, id, seq, ap, loadStatus, bounds, null); - } - - /** - * @deprecated - */ - public AppVarna(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds, - String viewid) - { - this(new String[] - { file }, new String[] - { id }, new SequenceI[][] - { seq }, ap, true, true, false, loadStatus, bounds, viewid); - } - - ViewSelectionMenu seqColourBy; - - /** - * - * @param files - * @param ids - * @param seqs - * @param ap - * @param usetoColour - * - add the alignment panel to the list used for colouring these - * structures - * @param useToAlign - * - add the alignment panel to the list used for aligning these - * structures - * @param leaveColouringToJmol - * - do not update the colours from any other source. Jmol is handling them - * @param loadStatus - * @param bounds - * @param viewid - */ - public AppVarna(String[] files, String[] ids, SequenceI[][] seqs, - AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol, - String loadStatus, Rectangle bounds, String viewid) - { - PDBEntry[] pdbentrys = new PDBEntry[files.length]; - for (int i = 0; i < pdbentrys.length; i++) - { - PDBEntry pdbentry = new PDBEntry(); - pdbentry.setFile(files[i]); - pdbentry.setId(ids[i]); - pdbentrys[i] = pdbentry; - } - // / TODO: check if protocol is needed to be set, and if chains are - // autodiscovered. - jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); - - jmb.setLoadingFromArchive(true); - addAlignmentPanel(ap); - if (useToAlign) - { - useAlignmentPanelForSuperposition(ap); - } - if (leaveColouringToJmol || !usetoColour) - { - jmb.setColourBySequence(false); - seqColour.setSelected(false); - jmolColour.setSelected(true); - } - if (usetoColour) - { - useAlignmentPanelForColourbyseq(ap); - jmb.setColourBySequence(true); - seqColour.setSelected(true); - jmolColour.setSelected(false); - } - this.setBounds(bounds); - initMenus(); - viewId = viewid; - // jalview.gui.Desktop.addInternalFrame(this, "Loading File", - // bounds.width,bounds.height); - - this.addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) - { - closeViewer(); - } - }); - initJmol(loadStatus); // pdbentry, seq, JBPCHECK! - - } - - private void initMenus() - { - seqColour.setSelected(jmb.isColourBySequence()); - jmolColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith==null) - { - _colourwith=new Vector(); - } - if (_alignwith==null) - { - _alignwith=new Vector(); - } - - seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith, - new ItemListener() - { - - @Override - public void itemStateChanged(ItemEvent e) - { - if (!seqColour.isSelected()) - { - seqColour.doClick(); - } - else - { - // update the jmol display now. - seqColour_actionPerformed(null); - } - } - }); - viewMenu.add(seqColourBy); - final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, - _alignwith, handler = new ItemListener() - { - - @Override - public void itemStateChanged(ItemEvent e) - { - alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText("Align structures using " - + _alignwith.size() + " linked alignment views"); - } - }); - handler.itemStateChanged(null); - jmolActionMenu.add(alpanels); - jmolActionMenu.addMenuListener(new MenuListener() - { - - @Override - public void menuSelected(MenuEvent e) - { - handler.itemStateChanged(null); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub - - } - }); - } - IProgressIndicator progressBar = null; - - public AppVarna(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap) - { - progressBar = ap.alignFrame; - // //////////////////////////////// - // Is the pdb file already loaded? - String alreadyMapped = jmb.ssm.alreadyMappedToFile( - pdbentry.getId()); - if (alreadyMapped != null) - { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - pdbentry.getId() + " is already displayed." - + "\nDo you want to re-use this viewer ?", - "Map Sequences to Visible Window: " + pdbentry.getId(), - JOptionPane.YES_NO_OPTION); - - if (option == JOptionPane.YES_OPTION) - { - jmb.ssm.setMapping(seq, chains, alreadyMapped, - AppletFormatAdapter.FILE); - if (ap.seqPanel.seqCanvas.fr != null) - { - ap.seqPanel.seqCanvas.fr.featuresAdded(); - ap.paintAlignment(true); - } - - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (int i = 0; i < frames.length; i++) - { - if (frames[i] instanceof AppVarna) - { - AppVarna topJmol = ((AppVarna) frames[i]); - // JBPNOTE: this looks like a binding routine, rather than a gui - // routine - for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++) - { - if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) - { - topJmol.jmb.addSequence(pe, seq); - topJmol.addAlignmentPanel(ap); - topJmol.buildJmolActionMenu(); - break; - } - } - } - } - - return; - } - } - // ///////////////////////////////// - // Check if there are other Jmol views involving this alignment - // and prompt user about adding this molecule to one of them - Vector existingViews = getJmolsFor(ap); - if (existingViews.size() > 0) - { - Enumeration jm = existingViews.elements(); - while (jm.hasMoreElements()) - { - AppVarna topJmol = (AppVarna) jm.nextElement(); - // TODO: highlight topJmol in view somehow - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "Do you want to add " + pdbentry.getId() - + " to the view called\n'" + topJmol.getTitle() - + "'\n", "Align to existing structure view", - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) - { - topJmol.useAlignmentPanelForSuperposition(ap); - topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } - } - } - // ///////////////////////////////// - - jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }, null, null); - addAlignmentPanel(ap); - useAlignmentPanelForColourbyseq(ap); - jmb.setColourBySequence(true); - setSize(400, 400); // probably should be a configurable/dynamic default here - initMenus(); - - if (pdbentry.getFile() != null) - { - initJmol("load \"" + pdbentry.getFile() + "\""); - } - else - { - addingStructures = false; - worker = new Thread(this); - worker.start(); - } - - this.addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) - { - closeViewer(); - } - }); - - } - - /** - * list of sequenceSet ids associated with the view - */ - ArrayList _aps = new ArrayList(); - - public AlignmentPanel[] getAllAlignmentPanels() - { - AlignmentPanel[] t, list = new AlignmentPanel[0]; - for (String setid : _aps) - { - AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); - if (panels != null) - { - t = new AlignmentPanel[list.length + panels.length]; - System.arraycopy(list, 0, t, 0, list.length); - System.arraycopy(panels, 0, t, list.length, panels.length); - list = t; - } - } - - return list; - } +public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider - /** - * list of alignment panels to use for superposition - */ - Vector _alignwith = new Vector(); - - /** - * list of alignment panels that are used for colouring structures by aligned - * sequences - */ - Vector _colourwith = new Vector(); - - /** - * set the primary alignmentPanel reference and add another alignPanel to the - * list of ones to use for colouring and aligning - * - * @param nap - */ - public void addAlignmentPanel(AlignmentPanel nap) - { - if (ap == null) - { - ap = nap; - } - if (!_aps.contains(nap.av.getSequenceSetId())) - { - _aps.add(nap.av.getSequenceSetId()); - } - } - - /** - * remove any references held to the given alignment panel - * - * @param nap - */ - public void removeAlignmentPanel(AlignmentPanel nap) - { - try - { - _alignwith.remove(nap); - _colourwith.remove(nap); - if (ap == nap) - { - ap = null; - for (AlignmentPanel aps : getAllAlignmentPanels()) - { - if (aps != nap) - { - ap = aps; - break; - } - } - } - } catch (Exception ex) - { - } - if (ap != null) - { - buildJmolActionMenu(); - } - } - - public void useAlignmentPanelForSuperposition(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_alignwith.contains(nap)) - { - _alignwith.add(nap); - } - } - - public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) - { - if (_alignwith.contains(nap)) - { - _alignwith.remove(nap); - } - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq) - { - useAlignmentPanelForColourbyseq(nap); - jmb.setColourBySequence(enableColourBySeq); - seqColour.setSelected(enableColourBySeq); - jmolColour.setSelected(!enableColourBySeq); - } - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_colourwith.contains(nap)) - { - _colourwith.add(nap); - } - } - - public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - if (_colourwith.contains(nap)) - { - _colourwith.remove(nap); - } - } - - /** - * pdb retrieval thread. - */ - private Thread worker = null; - - /** - * add a new structure (with associated sequences and chains) to this viewer, - * retrieving it if necessary first. - * - * @param pdbentry - * @param seq - * @param chains - * @param alignFrame - * @param align - * if true, new structure(s) will be align using associated alignment - */ - private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, - final String[] chains, final boolean b, - final IProgressIndicator alignFrame) - { - if (pdbentry.getFile() == null) - { - if (worker != null && worker.isAlive()) - { - // a retrieval is in progress, wait around and add ourselves to the - // queue. - new Thread(new Runnable() - { - public void run() - { - while (worker != null && worker.isAlive() && _started) - { - try - { - Thread.sleep(100 + ((int) Math.random() * 100)); - - } catch (Exception e) - { - } - - } - // and call ourselves again. - addStructure(pdbentry, seq, chains, b, alignFrame); - } - }).start(); - return; - } - } - // otherwise, start adding the structure. - jmb.addSequenceAndChain(new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }, new String[][] - { chains }); - addingStructures = true; - _started = false; - alignAddedStructures = b; - progressBar = alignFrame; // visual indication happens on caller frame. - (worker = new Thread(this)).start(); - return; - } - - private Vector getJmolsFor(AlignmentPanel ap2) - { - Vector otherJmols = new Vector(); - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (int i = 0; i < frames.length; i++) - { - if (frames[i] instanceof AppVarna) - { - AppVarna topJmol = ((AppVarna) frames[i]); - if (topJmol.isLinkedWith(ap2)) - { - otherJmols.addElement(topJmol); - } - } - } - return otherJmols; - } +{ + AppVarnaBinding vab; - void initJmol(String command) - { - jmb.setFinishedInit(false); - renderPanel = new RenderPanel(); - // TODO: consider waiting until the structure/view is fully loaded before - // displaying - this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); - jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(), - getBounds().width, getBounds().height); - if (scriptWindow == null) - { - BorderLayout bl = new BorderLayout(); - bl.setHgap(0); - bl.setVgap(0); - scriptWindow = new JPanel(bl); - scriptWindow.setVisible(false); - } - ; - jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, - null); - jmb.newJmolPopup(true, "Jmol", true); - if (command==null) - { - command=""; - } - jmb.evalStateCommand(command); - jmb.setFinishedInit(true); + VARNAPanel varnaPanel; + + public String name; + + public StructureSelectionManager ssm; + + /*public AppVarna(){ + vab = new AppVarnaBinding(); + initVarna(); + }*/ + + + + public AppVarna(String seq,String struc,String name,AlignmentPanel ap){ + ArrayList rnaList = new ArrayList(); + RNA rna1 = new RNA(name); + try { + rna1.setRNA(seq,replaceOddGaps(struc)); + } catch (ExceptionUnmatchedClosingParentheses e2) { + e2.printStackTrace(); + } catch (ExceptionFileFormatOrSyntax e3) { + e3.printStackTrace(); + } + rnaList.add(trimRNA(rna1)); + rnaList.add(rna1); + rna1.setName("consenus_"+rna1.getName()); + + + vab = new AppVarnaBinding(rnaList); + //vab = new AppVarnaBinding(seq,struc); + //System.out.println("Hallo: "+name); + this.name=name; + initVarna(); + ssm = ap.getStructureSelectionManager(); + ssm.addStructureViewerListener(this); } - - void setChainMenuItems(Vector chains) - { - chainMenu.removeAll(); - if (chains == null) - { - return; - } - JMenuItem menuItem = new JMenuItem("All"); - menuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - allChainsSelected = true; - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); - } - centerViewer(); - allChainsSelected = false; - } - }); - - chainMenu.add(menuItem); - - for (int c = 0; c < chains.size(); c++) - { - menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true); - menuItem.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent evt) - { - if (!allChainsSelected) - centerViewer(); - } - }); - - chainMenu.add(menuItem); - } + + public void initVarna(){ + //vab.setFinishedInit(false); + varnaPanel=vab.get_varnaPanel(); + setBackground(Color.white); + JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel); + getContentPane().setLayout(new BorderLayout()); + getContentPane().add(split, BorderLayout.CENTER); + //getContentPane().add(vab.getTools(), BorderLayout.NORTH); + varnaPanel.addVARNAListener(this); + jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height); + this.pack(); + showPanel(true); } - - boolean allChainsSelected = false; - - private boolean alignAddedStructures = false; - - void centerViewer() - { - Vector toshow = new Vector(); - String lbl; - int mlength, p, mnum; - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - { - JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); - if (item.isSelected()) - { - toshow.addElement(item.getText()); - } - } - } - jmb.centerViewer(toshow); + + public String replaceOddGaps(String oldStr){ + String patternStr = "[^([{<>}])]"; + String replacementStr = "."; + Pattern pattern = Pattern.compile(patternStr); + Matcher matcher = pattern.matcher(oldStr); + String newStr=matcher.replaceAll(replacementStr); + return newStr; } - - void closeViewer() - { - jmb.closeViewer(); - ap = null; - _aps.clear(); - _alignwith.clear(); - _colourwith.clear(); - // TODO: check for memory leaks where instance isn't finalised because jmb - // holds a reference to the window - jmb = null; + + public RNA trimRNA(RNA rna){ + RNA rnaTrim = new RNA("trim_"+rna.getName()); + try { + rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN())); + } catch (ExceptionUnmatchedClosingParentheses e2) { + e2.printStackTrace(); + } catch (ExceptionFileFormatOrSyntax e3) { + e3.printStackTrace(); + } + + StringBuffer seq=new StringBuffer(rnaTrim.getSeq()); + StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN()); + for(int i=0;i 0) - { - addingStructures = true; // already files loaded. - for (int c = 0; c < curfiles.length; c++) - { - if (curfiles[c].equals(file)) - { - file = null; - break; - } - } - } - if (file != null) - { - files.append(" \"" + file + "\""); - } - } - } - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); - } catch (Exception ex) - { - ex.printStackTrace(); - errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid - + "'"); - } - if (errormsgs.length() > 0) - { - - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "The following pdb entries could not be retrieved from the PDB:\n" - + errormsgs.toString() - + "\nPlease try downloading them manually.", - "Couldn't load file", JOptionPane.ERROR_MESSAGE); - - } - if (files.length() > 0) - { - if (!addingStructures) - { - - try - { - initJmol("load FILES " + files.toString()); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("When trying to open the Jmol viewer!", oomerror); - Cache.log.debug("File locations are " + files); - } catch (Exception ex) - { - Cache.log.error("Couldn't open Jmol viewer!", ex); - } - } - else + public void run(){ + _started = true; + + try { - StringBuffer cmd = new StringBuffer(); - cmd.append("loadingJalviewdata=true\nload APPEND "); - cmd.append(files.toString()); - cmd.append("\nloadingJalviewdata=null"); - final String command = cmd.toString(); - cmd = null; - long lastnotify = jmb.getLoadNotifiesHandled(); - try - { - jmb.evalStateCommand(command); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning( - "When trying to add structures to the Jmol viewer!", - oomerror); - Cache.log.debug("File locations are " + files); - } catch (Exception ex) - { - Cache.log.error("Couldn't add files to Jmol viewer!", ex); - } - // need to wait around until script has finished - while (lastnotify >= jmb.getLoadNotifiesHandled()) - ; - { - try - { - Thread.sleep(35); - } catch (Exception e) - { - } - } - // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) - { - jmb.updateColours(ap); - } - // do superposition if asked to - if (alignAddedStructures) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - alignStructs_withAllAlignPanels(); - // jmb.superposeStructures(ap.av.getAlignment(), -1, null); - } - }); - alignAddedStructures = false; - } - addingStructures = false; - } - } - _started = false; - worker = null; - } - - public void pdbFile_actionPerformed(ActionEvent actionEvent) - { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save PDB File"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - try + initVarna(); + } catch (OutOfMemoryError oomerror) { - // TODO: cope with multiple PDB files in view - BufferedReader in = new BufferedReader(new FileReader( - jmb.getPdbFile()[0])); - File outFile = chooser.getSelectedFile(); - - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ((data = in.readLine()) != null) - { - if (!(data.indexOf("
") > -1 || data.indexOf("
") > -1)) - { - out.println(data); - } - } - out.close(); + new OOMWarning("When trying to open the Varna viewer!", oomerror); } catch (Exception ex) { - ex.printStackTrace(); + Cache.log.error("Couldn't open Varna viewer!", ex); } - } - } - - public void viewMapping_actionPerformed(ActionEvent actionEvent) - { - jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); - try - { - for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) - { - cap.appendText(jmb.printMapping( - jmb.pdbentry[pdbe].getFile())); - cap.appendText("\n"); - } - } catch (OutOfMemoryError e) - { - new OOMWarning( - "composing sequence-structure alignments for display in text box.", - e); - cap.dispose(); - return; - } - jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", - 550, 600); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - public void eps_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.EPS); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - public void png_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.PNG); - } - - void makePDBImage(int type) - { - int width = getWidth(); - int height = getHeight(); - - jalview.util.ImageMaker im; - - if (type == jalview.util.ImageMaker.PNG) - { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Make PNG image from view", width, height, null, null); - } - else - { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Make EPS file from view", width, height, null, - this.getTitle()); - } - - if (im.getGraphics() != null) - { - Rectangle rect = new Rectangle(width, height); - jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); - im.writeImage(); - } - } - public void jmolColour_actionPerformed(ActionEvent actionEvent) - { - if (jmolColour.isSelected()) { - // disable automatic sequence colouring. - jmb.setColourBySequence(false); - } - } - public void seqColour_actionPerformed(ActionEvent actionEvent) - { - jmb.setColourBySequence(seqColour.isSelected()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (jmb.isColourBySequence()) - { - if (!jmb.isLoadingFromArchive()) - { - if (_colourwith.size()==0 && ap!=null) { - // Make the currently displayed alignment panel the associated view - _colourwith.add(ap.alignFrame.alignPanel); - } - } - // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) - { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); - } - } - } - - public void chainColour_actionPerformed(ActionEvent actionEvent) - { - chainColour.setSelected(true); - jmb.colourByChain(); - } - - public void chargeColour_actionPerformed(ActionEvent actionEvent) - { - chargeColour.setSelected(true); - jmb.colourByCharge(); - } - - public void zappoColour_actionPerformed(ActionEvent actionEvent) - { - zappoColour.setSelected(true); - jmb.setJalviewColourScheme(new ZappoColourScheme()); - } - - public void taylorColour_actionPerformed(ActionEvent actionEvent) - { - taylorColour.setSelected(true); - jmb.setJalviewColourScheme(new TaylorColourScheme()); } - public void hydroColour_actionPerformed(ActionEvent actionEvent) - { - hydroColour.setSelected(true); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); - } - - public void helixColour_actionPerformed(ActionEvent actionEvent) - { - helixColour.setSelected(true); - jmb.setJalviewColourScheme(new HelixColourScheme()); - } +@Override +public void onUINewStructure(VARNAConfig v, RNA r) { + // TODO Auto-generated method stub + +} - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - strandColour.setSelected(true); - jmb.setJalviewColourScheme(new StrandColourScheme()); - } +@Override +public void onWarningEmitted(String s) { + // TODO Auto-generated method stub + +} +/** + * If a mouseOver event from the AlignmentPanel + * is noticed the currently selected RNA in the + * VARNA window is highlighted at the specific position. + * To be able to remove it before the next highlight + * it is saved in _lastHighlight + */ +private HighlightRegionAnnotation _lastHighlight; +@Override +public void mouseOverSequence(SequenceI sequence, int index) { + // TODO Auto-generated method stub + RNA rna=vab.getSelectedRNA(); + rna.removeHighlightRegion(_lastHighlight); + + HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(index,index)); + rna.addHighlightRegion(highlight); + _lastHighlight=highlight; + vab.updateSelectedRNA(rna); +} - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - turnColour.setSelected(true); - jmb.setJalviewColourScheme(new TurnColourScheme()); - } +@Override +public void mouseOverStructure(int atomIndex, String strInfo) { + // TODO Auto-generated method stub + +} - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - buriedColour.setSelected(true); - jmb.setJalviewColourScheme(new BuriedColourScheme()); - } - - public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new PurinePyrimidineColourScheme()); - } +@Override +public void onStructureRedrawn() +{ + // TODO Auto-generated method stub - public void userColour_actionPerformed(ActionEvent actionEvent) - { - userColour.setSelected(true); - new UserDefinedColours(this, null); - } - - public void backGround_actionPerformed(ActionEvent actionEvent) - { - java.awt.Color col = JColorChooser.showDialog(this, - "Select Background Colour", null); - if (col != null) - { - jmb.setBackgroundColour(col); - } - } - - public void jmolHelp_actionPerformed(ActionEvent actionEvent) - { - try - { - jalview.util.BrowserLauncher - .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); - } catch (Exception ex) - { - } - } - - public void showConsole(boolean showConsole) - { - - if (showConsole) - { - if (splitPane == null) - { - splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT); - splitPane.setTopComponent(renderPanel); - splitPane.setBottomComponent(scriptWindow); - this.getContentPane().add(splitPane, BorderLayout.CENTER); - splitPane.setDividerLocation(getHeight() - 200); - scriptWindow.setVisible(true); - scriptWindow.validate(); - splitPane.validate(); - } - - } - else - { - if (splitPane != null) - { - splitPane.setVisible(false); - } - - splitPane = null; - - this.getContentPane().add(renderPanel, BorderLayout.CENTER); - } - - validate(); - } - - class RenderPanel extends JPanel - { - final Dimension currentSize = new Dimension(); - - final Rectangle rectClip = new Rectangle(); - - public void paintComponent(Graphics g) - { - getSize(currentSize); - g.getClipBounds(rectClip); - - if (jmb.fileLoadingError != null) - { - g.setColor(Color.black); - g.fillRect(0, 0, currentSize.width, currentSize.height); - g.setColor(Color.white); - g.setFont(new Font("Verdana", Font.BOLD, 14)); - g.drawString("Error loading file...", 20, currentSize.height / 2); - StringBuffer sb = new StringBuffer(); - int lines = 0; - for (int e = 0; e < jmb.pdbentry.length; e++) - { - sb.append(jmb.pdbentry[e].getId()); - if (e < jmb.pdbentry.length - 1) - { - sb.append(","); - } - - if (e == jmb.pdbentry.length - 1 || sb.length() > 20) - { - lines++; - g.drawString(sb.toString(), 20, currentSize.height / 2 - lines - * g.getFontMetrics().getHeight()); - } - } - } - else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit()) - { - g.setColor(Color.black); - g.fillRect(0, 0, currentSize.width, currentSize.height); - g.setColor(Color.white); - g.setFont(new Font("Verdana", Font.BOLD, 14)); - g.drawString("Retrieving PDB data....", 20, currentSize.height / 2); - } - else - { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); - } - } - } - - String viewId = null; - - public String getViewId() - { - if (viewId == null) - { - viewId = System.currentTimeMillis() + "." + this.hashCode(); - } - return viewId; - } - - public void updateTitleAndMenus() - { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) - { - repaint(); - return; - } - setChainMenuItems(jmb.chainNames); - - this.setTitle(jmb.getViewerTitle()); - if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) - { - jmolActionMenu.setVisible(true); - } - if (!jmb.isLoadingFromArchive()) - { - seqColour_actionPerformed(null); - } - } - - protected void buildJmolActionMenu() - { - if (_alignwith == null) - { - _alignwith = new Vector(); - } - if (_alignwith.size() == 0 && ap != null) - { - _alignwith.add(ap); - } - ; - for (Component c : jmolActionMenu.getMenuComponents()) - { - if (c != alignStructs) - { - jmolActionMenu.remove((JMenuItem) c); - } - } - final ItemListener handler; - } - - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event - * .ActionEvent) - */ - @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) - { - alignStructs_withAllAlignPanels(); - } - - private void alignStructs_withAllAlignPanels() - { - if (ap == null) - { - return; - } - ; - if (_alignwith.size() == 0) - { - _alignwith.add(ap); - } - ; - try - { - AlignmentI[] als = new Alignment[_alignwith.size()]; - ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; - int[] alm = new int[_alignwith.size()]; - int a = 0; - - for (AlignmentPanel ap : _alignwith) - { - als[a] = ap.av.getAlignment(); - alm[a] = -1; - alc[a++] = ap.av.getColumnSelection(); - } - jmb.superposeStructures(als, alm, alc); - } catch (Exception e) - { - StringBuffer sp = new StringBuffer(); - for (AlignmentPanel ap : _alignwith) - { - sp.append("'" + ap.alignFrame.getTitle() + "' "); - } - Cache.log.info("Couldn't align structures with the " + sp.toString() - + "associated alignment panels.", e); - - } - - } - - public void setJalviewColourScheme(ColourSchemeI ucs) - { - jmb.setJalviewColourScheme(ucs); - - } - - /** - * - * @param alignment - * @return first alignment panel displaying given alignment, or the default - * alignment panel - */ - public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) - { - for (AlignmentPanel ap : getAllAlignmentPanels()) - { - if (ap.av.getAlignment() == alignment) - { - return ap; - } - } - return ap; - } - - /** - * - * @param ap2 - * @return true if this Jmol instance is linked with the given alignPanel - */ - public boolean isLinkedWith(AlignmentPanel ap2) - { - return _aps.contains(ap2.av.getSequenceSetId()); - } - - public boolean isUsedforaligment(AlignmentPanel ap2) - { - - return (_alignwith != null) && _alignwith.contains(ap2); - } - - public boolean isUsedforcolourby(AlignmentPanel ap2) - { - return (_colourwith != null) && _colourwith.contains(ap2); - } +} - /** - * - * @return TRUE if the view is NOT being coloured by sequence associations. - */ - public boolean isColouredByJmol() - { - return !jmb.isColourBySequence(); - } - }