X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=fd740b1361caad356d99283d1b1d1a02960e41ea;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=e942b88d9f1a93807891429d49ecf47209356a6a;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index e942b88..fd740b1 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -99,14 +99,16 @@ 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++) @@ -118,7 +120,8 @@ 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); @@ -160,15 +163,15 @@ 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() { @@ -227,10 +230,12 @@ 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 @@ -242,8 +247,8 @@ public class AppJmol extends GStructureViewer implements Runnable, 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) { @@ -256,8 +261,8 @@ public class AppJmol extends GStructureViewer implements Runnable, if (option == JOptionPane.YES_OPTION) { // TODO : Fix multiple seq to one chain issue here. - ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped, - AppletFormatAdapter.FILE); + ap.getStructureSelectionManager().setMapping(seq, chains, + alreadyMapped, AppletFormatAdapter.FILE); if (ap.seqPanel.seqCanvas.fr != null) { ap.seqPanel.seqCanvas.fr.featuresAdded(); @@ -284,7 +289,8 @@ public class AppJmol extends GStructureViewer implements Runnable, // add it to the set used for colouring topJmol.useAlignmentPanelForColourbyseq(ap); topJmol.buildJmolActionMenu(); - ap.getStructureSelectionManager().sequenceColoursChanged(ap); + ap.getStructureSelectionManager() + .sequenceColoursChanged(ap); break; } } @@ -319,27 +325,33 @@ 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) { + + 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; - { - addingStructures = false; - worker = new Thread(this); - worker.start(); - } + worker = null; + { + addingStructures = false; + worker = new Thread(this); + worker.start(); + } this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) @@ -351,7 +363,9 @@ 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 @@ -462,13 +476,15 @@ 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); @@ -589,9 +605,9 @@ 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); @@ -723,10 +739,10 @@ public class AppJmol extends GStructureViewer implements Runnable, { // just transfer the file name from the first sequence's first // PDBEntry - file = new File(((PDBEntry) pdbseq - .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).getAbsolutePath(); + file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0)).getFile()).getAbsolutePath(); jmb.pdbentry[pi].setFile(file); - + files.append(" \"" + Platform.escapeString(file) + "\""); } else @@ -800,7 +816,7 @@ public class AppJmol extends GStructureViewer implements Runnable, final String command = cmd.toString(); cmd = null; lastnotify = jmb.getLoadNotifiesHandled(); - + try { jmb.evalStateCommand(command); @@ -815,10 +831,10 @@ 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 { @@ -897,8 +913,7 @@ 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) @@ -961,13 +976,16 @@ 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()); @@ -979,7 +997,8 @@ 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); } @@ -1045,12 +1064,12 @@ public class AppJmol extends GStructureViewer implements Runnable, buriedColour.setSelected(true); jmb.setJalviewColourScheme(new BuriedColourScheme()); } - + public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new PurinePyrimidineColourScheme()); } - + public void userColour_actionPerformed(ActionEvent actionEvent) { userColour.setSelected(true); @@ -1319,7 +1338,6 @@ public class AppJmol extends GStructureViewer implements Runnable, public boolean isColouredByJmol() { return !jmb.isColourBySequence(); - } - + } }