From 1b277fdca45c13f59c3887780f14a37bb1beeb60 Mon Sep 17 00:00:00 2001 From: janengelhardt Date: Thu, 16 Jun 2011 00:42:55 +0200 Subject: [PATCH] JAL-842, Further creation of VARNA classes (probably to much), filled AppVarnaBinding with a main-method to test the varna call Change-Id: I075c9e61bba59fb416b63ff7c7656561eed88baf --- src/jalview/ext/varna/JalviewVarnaBinding.java | 6 + src/jalview/gui/AppVarna.java | 1256 +----------------------- src/jalview/gui/AppVarnaBinding.java | 228 +---- src/jalview/jbgui/GRnaStructureViewer.java | 42 + 4 files changed, 89 insertions(+), 1443 deletions(-) create mode 100644 src/jalview/jbgui/GRnaStructureViewer.java diff --git a/src/jalview/ext/varna/JalviewVarnaBinding.java b/src/jalview/ext/varna/JalviewVarnaBinding.java index 65a2665..089ee64 100644 --- a/src/jalview/ext/varna/JalviewVarnaBinding.java +++ b/src/jalview/ext/varna/JalviewVarnaBinding.java @@ -18,6 +18,7 @@ package jalview.ext.varna; import java.io.File; + import java.net.URL; import java.util.*; import java.applet.Applet; @@ -44,6 +45,9 @@ import org.jmol.viewer.Viewer; import jalview.schemes.*; +import fr.orsay.lri.varna.applications.*; + + public abstract class JalviewVarnaBinding implements StructureListener, JmolStatusListener, SequenceStructureBinding, JmolSelectionListener, ComponentListener, StructureSelectionManagerProvider @@ -103,6 +107,8 @@ public abstract class JalviewVarnaBinding implements StructureListener, int frameNo = 0; protected JmolPopup jmolpopup; + + protected VARNAGUI varnagui; String lastCommand; diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java index 7b388fc..3a67e10 100644 --- a/src/jalview/gui/AppVarna.java +++ b/src/jalview/gui/AppVarna.java @@ -25,1270 +25,54 @@ 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.*; -public class AppVarna extends GStructureViewer implements Runnable, - SequenceStructureBinding, ViewSetProvider +public class AppVarna extends JInternalFrame // implements Runnable,SequenceStructureBinding, ViewSetProvider { - AppJmolBinding jmb; + AppVarnaBinding vab; JPanel scriptWindow; JSplitPane splitPane; - RenderPanel renderPanel; + //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; - } - - /** - * 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; - } - - 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); - } - - 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); - } - } - - 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); - } - - 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; - } - - /** - * state flag for PDB retrieval thread - */ - private boolean _started = false; - - public void run() - { - _started = true; - String pdbid = ""; - // todo - record which pdbids were successfuly imported. - StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer(); - try - { - String[] curfiles = jmb.getPdbFile(); // files currently in viewer - // TODO: replace with reference fetching/transfer code (validate PDBentry - // as a DBRef?) - jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb(); - for (int pi = 0; pi < jmb.pdbentry.length; pi++) - { - String file = jmb.pdbentry[pi].getFile(); - if (file == null) - { - // retrieve the pdb and store it locally - AlignmentI pdbseq = null; - pdbid = jmb.pdbentry[pi].getId(); - long hdl = pdbid.hashCode() - System.currentTimeMillis(); - if (progressBar != null) - { - progressBar.setProgressBar("Fetching PDB " + pdbid, hdl); - } - try - { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi] - .getId()); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("Retrieving PDB id " + pdbid, oomerror); - } catch (Exception ex) - { - ex.printStackTrace(); - errormsgs.append("'" + pdbid + "'"); - } - if (progressBar != null) - { - progressBar.setProgressBar("Finished.", hdl); - } - if (pdbseq != null) - { - // just transfer the file name from the first sequence's first - // PDBEntry - jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq - .getSequenceAt(0).getPDBId().elementAt(0)).getFile()); - files.append(" \"" + file + "\""); - } - else - { - errormsgs.append("'" + pdbid + "' "); - } - } - else - { - if (curfiles != null && curfiles.length > 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 - { - 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 - { - // 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(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - 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()); - } - - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - strandColour.setSelected(true); - jmb.setJalviewColourScheme(new StrandColourScheme()); - } - - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - turnColour.setSelected(true); - jmb.setJalviewColourScheme(new TurnColourScheme()); - } - - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - buriedColour.setSelected(true); - jmb.setJalviewColourScheme(new BuriedColourScheme()); - } - public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new PurinePyrimidineColourScheme()); + void initVarna(){ + //vab.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,"test",300,300); } - 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; + private boolean _started = false; - for (AlignmentPanel ap : _alignwith) + public void run(){ + _started = true; + + try { - 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) + initVarna(); + } catch (OutOfMemoryError oomerror) { - 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) + new OOMWarning("When trying to open the Varna viewer!", oomerror); + } catch (Exception ex) { - return ap; + Cache.log.error("Couldn't open Varna viewer!", ex); } - } - 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(); - } } diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java index 105dd39..5b65b8c 100644 --- a/src/jalview/gui/AppVarnaBinding.java +++ b/src/jalview/gui/AppVarnaBinding.java @@ -17,214 +17,28 @@ */ package jalview.gui; -import java.awt.Container; -import java.awt.event.ComponentEvent; -import java.awt.event.ComponentListener; -import java.awt.event.ContainerEvent; -import java.awt.event.ContainerListener; -import java.util.BitSet; +import javax.swing.JFrame; -import javax.swing.JPanel; +import fr.orsay.lri.varna.applications.*; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.structure.StructureSelectionManager; - -import org.jmol.api.JmolAppConsoleInterface; -import org.jmol.api.JmolViewer; -import org.jmol.popup.JmolPopup; -import org.openscience.jmol.app.jmolpanel.AppConsole; - -public class AppVarnaBinding extends jalview.ext.jmol.JalviewJmolBinding +public class AppVarnaBinding// extends jalview.ext.jmol.JalviewJmolBinding { - - /** - * - */ - private AppJmol appJmolWindow; - - public AppVarnaBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry, - SequenceI[][] sequenceIs, String[][] chains, String protocol) - { - super(sSm, pdbentry, sequenceIs, chains, protocol); - appJmolWindow = appJmol; - } - - FeatureRenderer fr = null; - - @Override - public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) - { - AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment; - if (ap.av.showSequenceFeatures) - { - if (fr == null) - { - fr = new FeatureRenderer(ap); - } - - fr.transferSettings(ap. - seqPanel.seqCanvas.getFeatureRenderer()); - } - - return fr; - } - - @Override - public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) - { - return new SequenceRenderer(((AlignmentPanel)alignment).av); - } - - public void sendConsoleEcho(String strEcho) - { - if (console != null) - { - console.sendConsoleEcho(strEcho); - } - } - - public void sendConsoleMessage(String strStatus) - { - if (console != null && strStatus != null) - // && !strStatus.equals("Script completed")) - // should we squash the script completed string ? - { - console.sendConsoleMessage(strStatus); - } - } - - @Override - public void showUrl(String url, String target) - { - try - { - jalview.util.BrowserLauncher.openURL(url); - } catch (Exception e) - { - Cache.log.error("Failed to launch Jmol-associated url " + url, e); - // TODO: 2.6 : warn user if browser was not configured. - } - } - - @Override - public void refreshGUI() - { - // appJmolWindow.repaint(); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - appJmolWindow.updateTitleAndMenus(); - appJmolWindow.revalidate(); - } - }); - } - - public void updateColours(Object source) - { - AlignmentPanel ap = (AlignmentPanel) source,topap; - // ignore events from unrelated or non-user interactive frames - if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || !appJmolWindow.isUsedforcolourby(ap)) - return; - if (!isLoadingFromArchive()) { - colourBySequence(ap.av.getShowSequenceFeatures(), ap); - } - } - - public void notifyScriptTermination(String strStatus, int msWalltime) - { - // todo - script termination doesn't happen ? - // if (console != null) - // console.notifyScriptTermination(strStatus, - // msWalltime); - } - - public void showUrl(String url) - { - showUrl(url, "jmol"); - } - - public void newJmolPopup(boolean translateLocale, String menuName, - boolean asPopup) - { - - jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName, - asPopup); - } - - public void selectionChanged(BitSet arg0) - { - // TODO Auto-generated method stub - - } - - public void refreshPdbEntries() - { - // TODO Auto-generated method stub - - } - - public void showConsole(boolean b) - { - appJmolWindow.showConsole(b); - } - - /** - * add the given sequences to the mapping scope for the given pdb file handle - * - * @param pdbFile - * - pdbFile identifier - * @param seq - * - set of sequences it can be mapped to - */ - public void addSequenceForStructFile(String pdbFile, SequenceI[] seq) - { - for (int pe = 0; pe < pdbentry.length; pe++) - { - if (pdbentry[pe].getFile().equals(pdbFile)) - { - addSequence(pe, seq); - } - } - } - - @Override - protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2, - Container consolePanel, String buttonsToShow) - { - return new AppConsole(viewer, consolePanel, buttonsToShow); - } - - @Override - protected void releaseUIResources() - { - appJmolWindow = null; - if (console != null) - { - try - { - console.setVisible(false); - } catch (Error e) - { - } catch (Exception x) - { - } - ; - console = null; - } - - } - - @Override - public void releaseReferences(Object svl) - { - if (svl instanceof SeqPanel) { - appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap); - - }; - } + protected JFrame varnagui; + + public AppVarnaBinding(){ + newVarnaGui(); + } + + public void newVarnaGui(){ + varnagui=new VARNAGUI(); + } + + + public static void main(String[] args) + { + AppVarnaBinding vab = new AppVarnaBinding(); + vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + vab.varnagui.pack(); + vab.varnagui.setVisible(true); + } } diff --git a/src/jalview/jbgui/GRnaStructureViewer.java b/src/jalview/jbgui/GRnaStructureViewer.java new file mode 100644 index 0000000..efe6eb0 --- /dev/null +++ b/src/jalview/jbgui/GRnaStructureViewer.java @@ -0,0 +1,42 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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. + * + * Jalview 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 Jalview. If not, see . + */ +package jalview.jbgui; + +import javax.swing.*; +import java.awt.event.ActionListener; +import java.awt.event.ActionEvent; + +public class GRnaStructureViewer extends JInternalFrame +{ + public GRnaStructureViewer() + { + try + { + jbInit(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + private void jbInit() throws Exception + { + + } + +} -- 1.7.10.2