X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=b1f7e4c5d3ea61a5b46d11a7ef735e44835f4648;hb=e280466ffa0b7103da4a8ebe85aacbad354fd278;hp=a269860f804ded1d084016cad27d284906867c42;hpb=ad07946b57c7e3d85d6d2e6dc060fc5af5536cd1;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index a269860..b1f7e4c 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 @@ -26,15 +26,14 @@ import java.awt.event.*; import java.io.*; import jalview.jbgui.GStructureViewer; -import jalview.api.AlignmentViewPanel; 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.Platform; public class AppJmol extends GStructureViewer implements Runnable, SequenceStructureBinding, ViewSetProvider @@ -98,14 +97,16 @@ 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++) @@ -117,7 +118,8 @@ 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); @@ -159,15 +161,15 @@ 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() { @@ -226,23 +228,25 @@ 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 = ap.getStructureSelectionManager().alreadyMappedToFile( - pdbentry.getId()); + String alreadyMapped = ap.getStructureSelectionManager() + .alreadyMappedToFile(pdbentry.getId()); if (alreadyMapped != null) { @@ -254,8 +258,9 @@ public class AppJmol extends GStructureViewer implements Runnable, if (option == JOptionPane.YES_OPTION) { - ap.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(); @@ -270,7 +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++) @@ -279,7 +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; } } @@ -314,41 +323,33 @@ public class AppJmol extends GStructureViewer implements Runnable, } } // ///////////////////////////////// - openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); + openNewJmol(ap, new PDBEntry[] + { pdbentry }, new SequenceI[][] + { seq }); } - private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { - boolean promptUser=pdbentrys.length==1; + + private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, + SequenceI[][] seqs) + { progressBar = ap.alignFrame; - jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), + pdbentrys, seqs, null, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); - if (pdbentrys.length>1) + if (pdbentrys.length > 1) { - alignAddedStructures=true; + alignAddedStructures = true; useAlignmentPanelForSuperposition(ap); } jmb.setColourBySequence(true); setSize(400, 400); // probably should be a configurable/dynamic default here initMenus(); - worker=null; - String filelist=""; -// for (PDBEntry pe: pdbentrys) -// { -// if (pe.getFile()==null) - { - addingStructures = false; - worker = new Thread(this); - worker.start(); -// break; - } -// filelist+=" \""+pe.getFile()+"\""; - -/* } - if (worker==null) + worker = null; { - initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist); + addingStructures = false; + worker = new Thread(this); + worker.start(); } -*/ this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) @@ -360,7 +361,9 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** - * create a new Jmol containing several structures superimposed using the given alignPanel. + * create a new Jmol containing several structures superimposed using the + * given alignPanel. + * * @param ap * @param pe * @param seqs @@ -471,13 +474,15 @@ 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); @@ -598,9 +603,9 @@ 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); @@ -732,9 +737,11 @@ 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 { @@ -757,7 +764,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } if (file != null) { - files.append(" \"" + file + "\""); + files.append(" \"" + Platform.escapeString(file) + "\""); } } } @@ -807,7 +814,7 @@ public class AppJmol extends GStructureViewer implements Runnable, final String command = cmd.toString(); cmd = null; lastnotify = jmb.getLoadNotifiesHandled(); - + try { jmb.evalStateCommand(command); @@ -822,10 +829,10 @@ 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 (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() - : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length)) + : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length)) { try { @@ -904,8 +911,7 @@ 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) @@ -968,13 +974,16 @@ 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()); @@ -986,7 +995,8 @@ 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); } @@ -1053,6 +1063,11 @@ 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); @@ -1321,7 +1336,6 @@ public class AppJmol extends GStructureViewer implements Runnable, public boolean isColouredByJmol() { return !jmb.isColourBySequence(); - } - + } }