X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=bab8a2d7fc145b9a577425674a6d5f0c6933746b;hb=58afea88095280d807e5c2ac8b9155de5ba3503c;hp=f71cd3077ee666176e11d98e472016cd44b2d9cb;hpb=6aae80a714d6cf5c2d28d02f74fbbf5296a0b71a;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index f71cd30..bab8a2d 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,24 +1,28 @@ /* - * 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 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.util.*; import java.awt.*; + import javax.swing.*; import javax.swing.event.*; @@ -27,16 +31,19 @@ import java.io.*; import jalview.jbgui.GStructureViewer; import jalview.api.SequenceStructureBinding; +import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.*; import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.structure.*; import jalview.datamodel.PDBEntry; +import jalview.ext.jmol.JalviewJmolBinding; import jalview.io.*; import jalview.schemes.*; +import jalview.util.MessageManager; +import jalview.util.Platform; public class AppJmol extends GStructureViewer implements Runnable, - SequenceStructureBinding, ViewSetProvider + ViewSetProvider, JalviewStructureDisplayI { AppJmolBinding jmb; @@ -79,7 +86,7 @@ public class AppJmol extends GStructureViewer implements Runnable, this(new String[] { file }, new String[] { id }, new SequenceI[][] - { seq }, ap, true, true, loadStatus, bounds, viewid); + { seq }, ap, true, true, false, loadStatus, bounds, viewid); } ViewSelectionMenu seqColourBy; @@ -96,13 +103,17 @@ public class AppJmol extends GStructureViewer implements Runnable, * @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 AppJmol(String[] files, String[] ids, SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour, boolean useToAlign, - String loadStatus, Rectangle bounds, String viewid) + boolean leaveColouringToJmol, String loadStatus, + Rectangle bounds, String viewid) { PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) @@ -114,7 +125,8 @@ public class AppJmol extends GStructureViewer implements Runnable, } // / TODO: check if protocol is needed to be set, and if chains are // autodiscovered. - jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null); + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), + pdbentrys, seqs, null, null); jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); @@ -122,15 +134,18 @@ public class AppJmol extends GStructureViewer implements Runnable, { useAlignmentPanelForSuperposition(ap); } + if (leaveColouringToJmol || !usetoColour) + { + jmb.setColourBySequence(false); + seqColour.setSelected(false); + jmolColour.setSelected(true); + } if (usetoColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); seqColour.setSelected(true); - } else { - jmb.setColourBySequence(false); - seqColour.setSelected(false); - jmolColour.setSelected(true); + jmolColour.setSelected(false); } this.setBounds(bounds); initMenus(); @@ -153,16 +168,16 @@ public class AppJmol extends GStructureViewer implements Runnable, { seqColour.setSelected(jmb.isColourBySequence()); jmolColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith==null) + if (_colourwith == null) { - _colourwith=new Vector(); + _colourwith = new Vector(); } - if (_alignwith==null) + if (_alignwith == null) { - _alignwith=new Vector(); + _alignwith = new Vector(); } - - seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith, + + seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith, new ItemListener() { @@ -182,7 +197,7 @@ public class AppJmol extends GStructureViewer implements Runnable, }); viewMenu.add(seqColourBy); final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, + JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this, _alignwith, handler = new ItemListener() { @@ -190,8 +205,11 @@ public class AppJmol extends GStructureViewer implements Runnable, public void itemStateChanged(ItemEvent e) { alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText("Align structures using " - + _alignwith.size() + " linked alignment views"); + alignStructs.setToolTipText(MessageManager + .formatMessage( + "label.align_structures_using_linked_alignment_views", + new String[] + { new Integer(_alignwith.size()).toString() })); } }); handler.itemStateChanged(null); @@ -220,31 +238,40 @@ public class AppJmol extends GStructureViewer implements Runnable, } }); } + IProgressIndicator progressBar = null; + /** + * add a single PDB structure to a new or existing Jmol view + * + * @param pdbentry + * @param seq + * @param chains + * @param ap + */ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap) + final AlignmentPanel ap) { progressBar = ap.alignFrame; // //////////////////////////////// // Is the pdb file already loaded? - String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager().alreadyMappedToFile( - pdbentry.getId()); + String alreadyMapped = ap.getStructureSelectionManager() + .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); + MessageManager.formatMessage( + "label.pdb_entry_is_already_displayed", new String[] + { pdbentry.getId() }), MessageManager.formatMessage( + "label.map_sequences_to_visible_window", new String[] + { pdbentry.getId() }), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, chains, alreadyMapped, - AppletFormatAdapter.FILE); + // TODO : Fix multiple seq to one chain issue here. + ap.getStructureSelectionManager().setMapping(seq, chains, + alreadyMapped, AppletFormatAdapter.FILE); if (ap.seqPanel.seqCanvas.fr != null) { ap.seqPanel.seqCanvas.fr.featuresAdded(); @@ -259,7 +286,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (frames[i] instanceof AppJmol) { - AppJmol topJmol = ((AppJmol) frames[i]); + final AppJmol topJmol = ((AppJmol) frames[i]); // JBPNOTE: this looks like a binding routine, rather than a gui // routine for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++) @@ -268,7 +295,11 @@ public class AppJmol extends GStructureViewer implements Runnable, { topJmol.jmb.addSequence(pe, seq); topJmol.addAlignmentPanel(ap); + // add it to the set used for colouring + topJmol.useAlignmentPanelForColourbyseq(ap); topJmol.buildJmolActionMenu(); + ap.getStructureSelectionManager() + .sequenceColoursChanged(ap); break; } } @@ -289,11 +320,15 @@ public class AppJmol extends GStructureViewer implements Runnable, { AppJmol topJmol = (AppJmol) 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); + int option = JOptionPane + .showInternalConfirmDialog( + Desktop.desktop, + MessageManager.formatMessage( + "label.add_pdbentry_to_view", new String[] + { pdbentry.getId(), topJmol.getTitle() }), + MessageManager + .getString("label.align_to_existing_structure_view"), + JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { topJmol.useAlignmentPanelForSuperposition(ap); @@ -303,27 +338,33 @@ public class AppJmol extends GStructureViewer implements Runnable, } } // ///////////////////////////////// - - jmb = new AppJmolBinding(this, new PDBEntry[] + openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] - { seq }, null, null); + { seq }); + } + + private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, + SequenceI[][] seqs) + { + progressBar = ap.alignFrame; + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), + pdbentrys, seqs, null, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) + { + alignAddedStructures = true; + useAlignmentPanelForSuperposition(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 + worker = null; { addingStructures = false; worker = new Thread(this); worker.start(); } - this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) @@ -335,6 +376,19 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** + * create a new Jmol containing several structures superimposed using the + * given alignPanel. + * + * @param ap + * @param pe + * @param seqs + */ + public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs) + { + openNewJmol(ap, pe, seqs); + } + + /** * list of sequenceSet ids associated with the view */ ArrayList _aps = new ArrayList(); @@ -435,6 +489,15 @@ public class AppJmol extends GStructureViewer implements Runnable, } } + 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); @@ -555,9 +618,9 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); jmb.newJmolPopup(true, "Jmol", true); - if (command==null) + if (command == null) { - command=""; + command = ""; } jmb.evalStateCommand(command); jmb.setFinishedInit(true); @@ -570,7 +633,8 @@ public class AppJmol extends GStructureViewer implements Runnable, { return; } - JMenuItem menuItem = new JMenuItem("All"); + JMenuItem menuItem = new JMenuItem( + MessageManager.getString("label.all")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) @@ -627,7 +691,7 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.centerViewer(toshow); } - void closeViewer() + public void closeViewer() { jmb.closeViewer(); ap = null; @@ -689,9 +753,11 @@ public class AppJmol extends GStructureViewer implements Runnable, { // 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 + "\""); + file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0)).getFile()).getAbsolutePath(); + jmb.pdbentry[pi].setFile(file); + + files.append(" \"" + Platform.escapeString(file) + "\""); } else { @@ -714,7 +780,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } if (file != null) { - files.append(" \"" + file + "\""); + files.append(" \"" + Platform.escapeString(file) + "\""); } } } @@ -730,13 +796,15 @@ public class AppJmol extends GStructureViewer implements Runnable, 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); + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .formatMessage("label.pdb_entries_couldnt_be_retrieved", + new String[] + { errormsgs.toString() }), MessageManager + .getString("label.couldnt_load_file"), + JOptionPane.ERROR_MESSAGE); } + long lastnotify = jmb.getLoadNotifiesHandled(); if (files.length() > 0) { if (!addingStructures) @@ -762,7 +830,8 @@ public class AppJmol extends GStructureViewer implements Runnable, cmd.append("\nloadingJalviewdata=null"); final String command = cmd.toString(); cmd = null; - long lastnotify = jmb.getLoadNotifiesHandled(); + lastnotify = jmb.getLoadNotifiesHandled(); + try { jmb.evalStateCommand(command); @@ -776,37 +845,41 @@ public class AppJmol extends GStructureViewer implements Runnable, { Cache.log.error("Couldn't add files to Jmol viewer!", ex); } - // need to wait around until script has finished - while (lastnotify >= jmb.getLoadNotifiesHandled()) - ; + } + + // need to wait around until script has finished + while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() + : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb + .getPdbFile().length != jmb.pdbentry.length)) + { + try { - try - { - Thread.sleep(35); - } catch (Exception e) - { - } - } - // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) + Cache.log.debug("Waiting around for jmb notify."); + Thread.sleep(35); + } catch (Exception e) { - jmb.updateColours(ap); } - // do superposition if asked to - if (alignAddedStructures) + } + // 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() { - javax.swing.SwingUtilities.invokeLater(new Runnable() + public void run() { - public void run() - { - alignStructs_withAllAlignPanels(); - // jmb.superposeStructures(ap.av.getAlignment(), -1, null); - } - }); - alignAddedStructures = false; - } - addingStructures = false; + alignStructs_withAllAlignPanels(); + // jmb.superposeStructures(ap.av.getAlignment(), -1, null); + } + }); + alignAddedStructures = false; } + addingStructures = false; + } _started = false; worker = null; @@ -819,7 +892,7 @@ public class AppJmol extends GStructureViewer implements Runnable, chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save PDB File"); - chooser.setToolTipText("Save"); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -856,9 +929,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) { - cap.appendText(StructureSelectionManager - .getStructureSelectionManager().printMapping( - jmb.pdbentry[pdbe].getFile())); + cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); cap.appendText("\n"); } } catch (OutOfMemoryError e) @@ -869,8 +940,9 @@ public class AppJmol extends GStructureViewer implements Runnable, cap.dispose(); return; } - jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", - 550, 600); + jalview.gui.Desktop.addInternalFrame(cap, + MessageManager.getString("label.pdb_sequence_mapping"), 550, + 600); } /** @@ -921,13 +993,16 @@ public class AppJmol extends GStructureViewer implements Runnable, im.writeImage(); } } + public void jmolColour_actionPerformed(ActionEvent actionEvent) { - if (jmolColour.isSelected()) { + if (jmolColour.isSelected()) + { // disable automatic sequence colouring. jmb.setColourBySequence(false); } } + public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); @@ -939,7 +1014,8 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (!jmb.isLoadingFromArchive()) { - if (_colourwith.size()==0 && ap!=null) { + if (_colourwith.size() == 0 && ap != null) + { // Make the currently displayed alignment panel the associated view _colourwith.add(ap.alignFrame.alignPanel); } @@ -1006,6 +1082,11 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.setJalviewColourScheme(new BuriedColourScheme()); } + public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new PurinePyrimidineColourScheme()); + } + public void userColour_actionPerformed(ActionEvent actionEvent) { userColour.setSelected(true); @@ -1083,7 +1164,8 @@ public class AppJmol extends GStructureViewer implements Runnable, 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); + g.drawString(MessageManager.getString("label.error_loading_file") + + "...", 20, currentSize.height / 2); StringBuffer sb = new StringBuffer(); int lines = 0; for (int e = 0; e < jmb.pdbentry.length; e++) @@ -1108,7 +1190,8 @@ public class AppJmol extends GStructureViewer implements Runnable, 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); + g.drawString(MessageManager.getString("label.retrieving_pdb_data"), + 20, currentSize.height / 2); } else { @@ -1267,4 +1350,18 @@ public class AppJmol extends GStructureViewer implements Runnable, return (_colourwith != null) && _colourwith.contains(ap2); } + /** + * + * @return TRUE if the view is NOT being coloured by sequence associations. + */ + public boolean isColouredByJmol() + { + return !jmb.isColourBySequence(); + } + + public JalviewJmolBinding getBinding() + { + return jmb; + } + }