X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=c5273dd0b86fdcb90666a984e43cf86028e76e3b;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=4379c20b628261f29e16650553225d59c55f5ea5;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 4379c20..c5273dd 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -26,7 +26,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; +import jalview.gui.StructureViewer.ViewerType; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemes.BuriedColourScheme; @@ -56,8 +56,10 @@ import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; +import java.io.IOException; import java.io.PrintWriter; -import java.util.Enumeration; +import java.util.ArrayList; +import java.util.List; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; @@ -83,41 +85,6 @@ public class AppJmol extends StructureViewerBase RenderPanel renderPanel; - 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); - */ - @Deprecated - public AppJmol(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds) - { - this(file, id, seq, ap, loadStatus, bounds, null); - } - - /** - * @deprecated - */ - @Deprecated - public AppJmol(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; /** @@ -147,7 +114,9 @@ public class AppJmol extends StructureViewerBase PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) { - PDBEntry pdbentry = new PDBEntry(files[i], ids[i]); + // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]); + PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB, + files[i]); pdbentrys[i] = pdbentry; } // / TODO: check if protocol is needed to be set, and if chains are @@ -182,9 +151,10 @@ public class AppJmol extends StructureViewerBase this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! @@ -204,7 +174,8 @@ public class AppJmol extends StructureViewerBase _alignwith = new Vector(); } - seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith, + seqColourBy = new ViewSelectionMenu( + MessageManager.getString("label.colour_by"), this, _colourwith, new ItemListener() { @@ -224,7 +195,8 @@ public class AppJmol extends StructureViewerBase }); viewMenu.add(seqColourBy); final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this, + JMenu alpanels = new ViewSelectionMenu( + MessageManager.getString("label.superpose_with"), this, _alignwith, handler = new ItemListener() { @@ -235,8 +207,8 @@ public class AppJmol extends StructureViewerBase alignStructs.setToolTipText(MessageManager .formatMessage( "label.align_structures_using_linked_alignment_views", - new String[] - { new Integer(_alignwith.size()).toString() })); + new String[] { new Integer(_alignwith + .size()).toString() })); } }); handler.itemStateChanged(null); @@ -280,104 +252,39 @@ public class AppJmol extends StructureViewerBase final AlignmentPanel ap) { progressBar = ap.alignFrame; - // //////////////////////////////// - // Is the pdb file already loaded? - String alreadyMapped = ap.getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); + String pdbId = pdbentry.getId(); - if (alreadyMapped != null) + /* + * If the PDB file is already loaded, the user may just choose to add to an + * existing viewer (or cancel) + */ + if (addAlreadyLoadedFile(seq, chains, ap, pdbId)) { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - 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_CANCEL_OPTION); - - if (option == JOptionPane.CANCEL_OPTION) - { - return; - } - if (option == JOptionPane.YES_OPTION) - { - // TODO : Fix multiple seq to one chain issue here. - ap.getStructureSelectionManager().setMapping(seq, chains, - alreadyMapped, AppletFormatAdapter.FILE); - if (ap.getSeqPanel().seqCanvas.fr != null) - { - ap.getSeqPanel().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 AppJmol) - { - 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.getPdbCount(); pe++) - { - if (topJmol.jmb.getPdbEntry(pe).getFile() - .equals(alreadyMapped)) - { - topJmol.jmb.addSequence(pe, seq); - topJmol.addAlignmentPanel(ap); - // add it to the set used for colouring - topJmol.useAlignmentPanelForColourbyseq(ap); - topJmol.buildActionMenu(); - ap.getStructureSelectionManager() - .sequenceColoursChanged(ap); - break; - } - } - } - } - - return; - } + 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) + + /* + * Check if there are other Jmol views involving this alignment and prompt + * user about adding this molecule to one of them + */ + if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId)) { - Enumeration jm = existingViews.elements(); - while (jm.hasMoreElements()) - { - AppJmol topJmol = (AppJmol) jm.nextElement(); - // TODO: highlight topJmol in view somehow - 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_CANCEL_OPTION); - if (option == JOptionPane.CANCEL_OPTION) - { - return; - } - if (option == JOptionPane.YES_OPTION) - { - topJmol.useAlignmentPanelForSuperposition(ap); - topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } - } + return; } - // ///////////////////////////////// - openNewJmol(ap, new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }); + + /* + * If the options above are declined or do not apply, open a new viewer + */ + openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); + } + + /** + * Answers true if this viewer already involves the given PDB ID + */ + @Override + protected boolean hasPdbId(String pdbId) + { + return jmb.hasPdbId(pdbId); } private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, @@ -404,9 +311,10 @@ public class AppJmol extends StructureViewerBase } this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); @@ -426,78 +334,23 @@ public class AppJmol extends StructureViewerBase } /** - * pdb retrieval thread. + * Returns a list of any Jmol viewers. The list is restricted to those linked + * to the given alignment panel if it is not null. */ - 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 apanel) + @Override + protected List getViewersFor(AlignmentPanel apanel) { - Vector result = new Vector(); + List result = new ArrayList(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof AppJmol) { - if (((StructureViewerBase) frame).isLinkedWith(apanel)) + if (apanel == null + || ((StructureViewerBase) frame).isLinkedWith(apanel)) { - result.addElement(frame); + result.add((StructureViewerBase) frame); } } } @@ -521,19 +374,20 @@ public class AppJmol extends StructureViewerBase scriptWindow = new JPanel(bl); scriptWindow.setVisible(false); } - ; + jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); - jmb.newJmolPopup(true, "Jmol", true); + // jmb.newJmolPopup("Jmol"); if (command == null) { command = ""; } jmb.evalStateCommand(command); + jmb.evalStateCommand("set hoverDelay=0.1"); jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(Vector chains) { chainMenu.removeAll(); if (chains == null) @@ -561,9 +415,9 @@ public class AppJmol extends StructureViewerBase chainMenu.add(menuItem); - for (int c = 0; c < chains.size(); c++) + for (String chain : chains) { - menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true); + menuItem = new JCheckBoxMenuItem(chain, true); menuItem.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent evt) @@ -581,13 +435,9 @@ public class AppJmol extends StructureViewerBase boolean allChainsSelected = false; - private boolean alignAddedStructures = false; - void centerViewer() { - Vector toshow = new Vector(); - String lbl; - int mlength, p, mnum; + Vector toshow = new Vector(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) @@ -602,9 +452,13 @@ public class AppJmol extends StructureViewerBase jmb.centerViewer(toshow); } - public void closeViewer() + public void closeViewer(boolean closeExternalViewer) { - jmb.closeViewer(); + // Jmol does not use an external viewer + if (jmb != null) + { + jmb.closeViewer(); + } setAlignmentPanel(null); _aps.clear(); _alignwith.clear(); @@ -614,11 +468,6 @@ public class AppJmol extends StructureViewerBase jmb = null; } - /** - * state flag for PDB retrieval thread - */ - private boolean _started = false; - public void run() { _started = true; @@ -642,13 +491,12 @@ public class AppJmol extends StructureViewerBase long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { - progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl); + progressBar.setProgressBar(MessageManager.formatMessage( + "status.fetching_pdb", new String[] { pdbid }), hdl); } try { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry( - pi) - .getId()); + pdbseq = pdbclient.getSequenceRecords(pdbid); } catch (OutOfMemoryError oomerror) { new OOMWarning("Retrieving PDB id " + pdbid, oomerror); @@ -659,14 +507,15 @@ public class AppJmol extends StructureViewerBase } if (progressBar != null) { - progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl); + progressBar.setProgressBar( + MessageManager.getString("label.state_completed"), hdl); } if (pdbseq != null) { // 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(pdbseq.getSequenceAt(0).getAllPDBEntries() + .elementAt(0).getFile()).getAbsolutePath(); jmb.getPdbEntry(pi).setFile(file); files.append(" \"" + Platform.escapeString(file) + "\""); @@ -710,9 +559,8 @@ public class AppJmol extends StructureViewerBase JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new String[] - { errormsgs.toString() }), MessageManager - .getString("label.couldnt_load_file"), + new String[] { errormsgs.toString() }), + MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE); } @@ -761,7 +609,7 @@ public class AppJmol extends StructureViewerBase // need to wait around until script has finished while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() - : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb + : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb .getPdbFile().length != jmb.getPdbCount())) { try @@ -772,20 +620,35 @@ public class AppJmol extends StructureViewerBase { } } + // refresh the sequence colours for the new structure(s) for (AlignmentPanel ap : _colourwith) { jmb.updateColours(ap); } // do superposition if asked to - if (alignAddedStructures) + if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) { javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { - alignStructs_withAllAlignPanels(); - // jmb.superposeStructures(ap.av.getAlignment(), -1, null); + if (jmb.viewer.isScriptExecuting()) + { + javax.swing.SwingUtilities.invokeLater(this); + try + { + Thread.sleep(5); + } catch (InterruptedException q) + { + } + ; + return; + } + else + { + alignStructs_withAllAlignPanels(); + } } }); alignAddedStructures = false; @@ -811,11 +674,11 @@ public class AppJmol extends StructureViewerBase if (value == JalviewFileChooser.APPROVE_OPTION) { + BufferedReader in = null; try { // TODO: cope with multiple PDB files in view - BufferedReader in = new BufferedReader(new FileReader( - jmb.getPdbFile()[0])); + in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); File outFile = chooser.getSelectedFile(); PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); @@ -831,6 +694,18 @@ public class AppJmol extends StructureViewerBase } catch (Exception ex) { ex.printStackTrace(); + } finally + { + if (in != null) + { + try + { + in.close(); + } catch (IOException e) + { + // ignore + } + } } } } @@ -841,11 +716,7 @@ public class AppJmol extends StructureViewerBase jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); try { - for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++) - { - cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile())); - cap.appendText("\n"); - } + cap.appendText(jmb.printMappings()); } catch (OutOfMemoryError e) { new OOMWarning( @@ -881,15 +752,14 @@ public class AppJmol extends StructureViewerBase if (type == jalview.util.ImageMaker.TYPE.PNG) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, - "Make PNG image from view", width, height, null, null); + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", + width, height, null, null); } else if (type == jalview.util.ImageMaker.TYPE.EPS) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, - "Make EPS file from view", width, height, null, - this.getTitle()); + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", + width, height, null, this.getTitle()); } else { @@ -901,8 +771,7 @@ public class AppJmol extends StructureViewerBase if (im.getGraphics() != null) { - Rectangle rect = new Rectangle(width, height); - jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); + jmb.viewer.renderScreenImage(im.getGraphics(), width, height); im.writeImage(); } } @@ -938,7 +807,7 @@ public class AppJmol extends StructureViewerBase // Set the colour using the current view for the associated alignframe for (AlignmentPanel ap : _colourwith) { - jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap); + jmb.colourBySequence(ap); } } } @@ -1022,8 +891,9 @@ public class AppJmol extends StructureViewerBase @Override public void backGround_actionPerformed(ActionEvent actionEvent) { - java.awt.Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_backgroud_colour"), null); + java.awt.Color col = JColorChooser + .showDialog(this, MessageManager + .getString("label.select_backgroud_colour"), null); if (col != null) { jmb.setBackgroundColour(col); @@ -1079,14 +949,12 @@ public class AppJmol extends StructureViewerBase { final Dimension currentSize = new Dimension(); - final Rectangle rectClip = new Rectangle(); - + @Override public void paintComponent(Graphics g) { getSize(currentSize); - g.getClipBounds(rectClip); - if (jmb.fileLoadingError != null) + if (jmb != null && jmb.fileLoadingError != null) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1123,7 +991,8 @@ public class AppJmol extends StructureViewerBase } else { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } } @@ -1237,4 +1106,16 @@ public class AppJmol extends StructureViewerBase return jmb == null ? null : jmb.viewer.getStateInfo(); } + @Override + public ViewerType getViewerType() + { + return ViewerType.JMOL; + } + + @Override + protected AAStructureBindingModel getBindingModel() + { + return jmb; + } + }