X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=3b4b7389fd5c5e0e5ff2c36db079bdb6dd0bc415;hb=21c29b20790ac555b2e2a124a034f6c6b4486270;hp=fdf00c0fa867e603d542489166509c336dff9b3c;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index fdf00c0..3b4b738 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,13 +1,13 @@ /* - * 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) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 @@ -30,10 +30,11 @@ 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 jalview.util.MessageManager; +import jalview.util.Platform; public class AppJmol extends GStructureViewer implements Runnable, SequenceStructureBinding, ViewSetProvider @@ -97,14 +98,16 @@ public class AppJmol extends GStructureViewer implements Runnable, * - 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 + * - 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, boolean leaveColouringToJmol, - String loadStatus, Rectangle bounds, String viewid) + 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++) @@ -116,7 +119,8 @@ 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, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), + pdbentrys, seqs, null, null); jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); @@ -158,15 +162,15 @@ 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, new ItemListener() { @@ -225,29 +229,38 @@ 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 = jmb.ssm.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(), + 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) { - jmb.ssm.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(); @@ -262,7 +275,7 @@ 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++) @@ -271,7 +284,11 @@ 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; } } @@ -293,9 +310,8 @@ 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", + 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) { @@ -306,27 +322,33 @@ public class AppJmol extends GStructureViewer implements Runnable, } } // ///////////////////////////////// - - jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), 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) @@ -338,6 +360,19 @@ 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(); @@ -438,13 +473,15 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq) + 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); @@ -565,9 +602,9 @@ 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); @@ -699,9 +736,11 @@ 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 { @@ -724,7 +763,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } if (file != null) { - files.append(" \"" + file + "\""); + files.append(" \"" + Platform.escapeString(file) + "\""); } } } @@ -741,12 +780,11 @@ public class AppJmol extends GStructureViewer implements Runnable, { 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); + 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) @@ -772,7 +810,8 @@ 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); @@ -786,37 +825,40 @@ 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().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; @@ -866,8 +908,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) { - cap.appendText(jmb.printMapping( - jmb.pdbentry[pdbe].getFile())); + cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); cap.appendText("\n"); } } catch (OutOfMemoryError e) @@ -930,13 +971,16 @@ 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()); @@ -948,7 +992,8 @@ 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); } @@ -1015,6 +1060,11 @@ 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); @@ -1092,7 +1142,7 @@ 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++) @@ -1117,7 +1167,7 @@ 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 { @@ -1283,7 +1333,6 @@ public class AppJmol extends GStructureViewer implements Runnable, public boolean isColouredByJmol() { return !jmb.isColourBySequence(); - } - + } }