X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=787634694f2689c41c8b792842441dee0cac3ac6;hb=215cda864f5b16592196795281a622b57c493a04;hp=4379c20b628261f29e16650553225d59c55f5ea5;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 4379c20..7876346 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; import jalview.io.AppletFormatAdapter; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -56,8 +57,8 @@ 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.Vector; import javax.swing.JCheckBoxMenuItem; @@ -83,41 +84,8 @@ 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 +115,9 @@ 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 +152,10 @@ public class AppJmol extends StructureViewerBase this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! @@ -342,36 +313,30 @@ public class AppJmol extends StructureViewerBase 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 + */ + for (AppJmol topJmol : getJmolsFor(ap)) { - Enumeration jm = existingViews.elements(); - while (jm.hasMoreElements()) + // 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) { - 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; + } + if (option == JOptionPane.YES_OPTION) + { + topJmol.useAlignmentPanelForSuperposition(ap); + topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); + return; } } // ///////////////////////////////// @@ -404,9 +369,10 @@ public class AppJmol extends StructureViewerBase } this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); @@ -486,18 +452,18 @@ public class AppJmol extends StructureViewerBase return; } - private Vector getJmolsFor(AlignmentPanel apanel) + private Vector getJmolsFor(AlignmentPanel apanel) { - Vector result = new Vector(); + Vector result = new Vector(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof AppJmol) { - if (((StructureViewerBase) frame).isLinkedWith(apanel)) + if (((AppJmol) frame).isLinkedWith(apanel)) { - result.addElement(frame); + result.addElement((AppJmol) frame); } } } @@ -521,10 +487,10 @@ 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 = ""; @@ -533,7 +499,7 @@ public class AppJmol extends StructureViewerBase jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(Vector chains) { chainMenu.removeAll(); if (chains == null) @@ -561,9 +527,9 @@ 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) @@ -585,9 +551,7 @@ public class AppJmol extends StructureViewerBase 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) @@ -602,8 +566,9 @@ public class AppJmol extends StructureViewerBase jmb.centerViewer(toshow); } - public void closeViewer() + public void closeViewer(boolean closeExternalViewer) { + // JMol does not use an external viewer jmb.closeViewer(); setAlignmentPanel(null); _aps.clear(); @@ -646,9 +611,7 @@ public class AppJmol extends StructureViewerBase } try { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry( - pi) - .getId()); + pdbseq = pdbclient.getSequenceRecords(pdbid); } catch (OutOfMemoryError oomerror) { new OOMWarning("Retrieving PDB id " + pdbid, oomerror); @@ -665,8 +628,8 @@ public class AppJmol extends StructureViewerBase { // 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).getPDBId() + .elementAt(0).getFile()).getAbsolutePath(); jmb.getPdbEntry(pi).setFile(file); files.append(" \"" + Platform.escapeString(file) + "\""); @@ -761,7 +724,7 @@ 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 @@ -772,6 +735,7 @@ public class AppJmol extends StructureViewerBase { } } + // refresh the sequence colours for the new structure(s) for (AlignmentPanel ap : _colourwith) { @@ -784,8 +748,22 @@ public class AppJmol extends StructureViewerBase { 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; @@ -811,10 +789,11 @@ 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( + in = new BufferedReader(new FileReader( jmb.getPdbFile()[0])); File outFile = chooser.getSelectedFile(); @@ -831,6 +810,18 @@ public class AppJmol extends StructureViewerBase } catch (Exception ex) { ex.printStackTrace(); + } finally + { + if (in != null) + { + try + { + in.close(); + } catch (IOException e) + { + // ignore + } + } } } } @@ -841,11 +832,7 @@ 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( @@ -901,8 +888,7 @@ 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 +924,7 @@ 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); } } } @@ -1079,14 +1065,12 @@ 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 +1107,8 @@ public class AppJmol extends StructureViewerBase } else { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } } @@ -1237,4 +1222,10 @@ public class AppJmol extends StructureViewerBase return jmb == null ? null : jmb.viewer.getStateInfo(); } + @Override + public ViewerType getViewerType() + { + return ViewerType.JMOL; + } + }