X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=a16ea68b94d1774ef5af3239b0be085239c1ec20;hb=83d955d73ec9236ce46af494fc4242909763bbc5;hp=90d3b153c190c99fd9e8c008c96071ae0c195f75;hpb=c66902a9536b10a5477b58aaf7c2d75772890a5d;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 90d3b15..a16ea68 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 2.8.2) - * 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. * @@ -26,11 +26,10 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.gui.StructureViewer.ViewerType; import jalview.io.AppletFormatAdapter; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; -import jalview.jbgui.GStructureViewer; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; @@ -46,7 +45,6 @@ import jalview.util.Platform; import java.awt.BorderLayout; import java.awt.Color; -import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; @@ -59,8 +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; @@ -76,9 +74,7 @@ import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; -public class AppJmol extends GStructureViewer implements Runnable, - ViewSetProvider - +public class AppJmol extends StructureViewerBase { AppJmolBinding jmb; @@ -88,43 +84,8 @@ public class AppJmol extends GStructureViewer implements Runnable, RenderPanel renderPanel; - AlignmentPanel ap; - - 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; /** @@ -154,9 +115,9 @@ public class AppJmol extends GStructureViewer implements Runnable, PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) { - PDBEntry pdbentry = new PDBEntry(); - pdbentry.setFile(files[i]); - pdbentry.setId(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 @@ -176,7 +137,7 @@ public class AppJmol extends GStructureViewer implements Runnable, seqColour.setSelected(false); viewerColour.setSelected(true); } - if (usetoColour) + else if (usetoColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); @@ -191,9 +152,10 @@ public class AppJmol extends GStructureViewer implements Runnable, this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! @@ -339,7 +301,7 @@ public class AppJmol extends GStructureViewer implements Runnable, topJmol.addAlignmentPanel(ap); // add it to the set used for colouring topJmol.useAlignmentPanelForColourbyseq(ap); - topJmol.buildJmolActionMenu(); + topJmol.buildActionMenu(); ap.getStructureSelectionManager() .sequenceColoursChanged(ap); break; @@ -351,36 +313,30 @@ public class AppJmol extends GStructureViewer implements Runnable, 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; } } // ///////////////////////////////// @@ -413,9 +369,10 @@ public class AppJmol extends GStructureViewer implements Runnable, } this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); @@ -434,117 +391,6 @@ public class AppJmol extends GStructureViewer implements Runnable, openNewJmol(ap, pe, seqs); } - public AlignmentPanel[] getAllAlignmentPanels() - { - AlignmentPanel[] t, list = new AlignmentPanel[0]; - for (String setid : _aps) - { - AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); - if (panels != null) - { - t = new AlignmentPanel[list.length + panels.length]; - System.arraycopy(list, 0, t, 0, list.length); - System.arraycopy(panels, 0, t, list.length, panels.length); - list = t; - } - } - - return list; - } - - /** - * set the primary alignmentPanel reference and add another alignPanel to the - * list of ones to use for colouring and aligning - * - * @param nap - */ - public void addAlignmentPanel(AlignmentPanel nap) - { - if (ap == null) - { - ap = nap; - } - if (!_aps.contains(nap.av.getSequenceSetId())) - { - _aps.add(nap.av.getSequenceSetId()); - } - } - - /** - * remove any references held to the given alignment panel - * - * @param nap - */ - public void removeAlignmentPanel(AlignmentPanel nap) - { - try - { - _alignwith.remove(nap); - _colourwith.remove(nap); - if (ap == nap) - { - ap = null; - for (AlignmentPanel aps : getAllAlignmentPanels()) - { - if (aps != nap) - { - ap = aps; - break; - } - } - } - } catch (Exception ex) - { - } - if (ap != null) - { - buildJmolActionMenu(); - } - } - - public void useAlignmentPanelForSuperposition(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_alignwith.contains(nap)) - { - _alignwith.add(nap); - } - } - - public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) - { - if (_alignwith.contains(nap)) - { - _alignwith.remove(nap); - } - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, - boolean enableColourBySeq) - { - useAlignmentPanelForColourbyseq(nap); - jmb.setColourBySequence(enableColourBySeq); - seqColour.setSelected(enableColourBySeq); - viewerColour.setSelected(!enableColourBySeq); - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_colourwith.contains(nap)) - { - _colourwith.add(nap); - } - } - - public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - if (_colourwith.contains(nap)) - { - _colourwith.remove(nap); - } - } - /** * pdb retrieval thread. */ @@ -606,18 +452,18 @@ public class AppJmol extends GStructureViewer implements Runnable, 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 (((GStructureViewer) frame).isLinkedWith(apanel)) + if (((AppJmol) frame).isLinkedWith(apanel)) { - result.addElement(frame); + result.addElement((AppJmol) frame); } } } @@ -641,10 +487,10 @@ public class AppJmol extends GStructureViewer implements Runnable, 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 = ""; @@ -653,7 +499,7 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(Vector chains) { chainMenu.removeAll(); if (chains == null) @@ -681,9 +527,9 @@ public class AppJmol extends GStructureViewer implements Runnable, 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) @@ -705,9 +551,7 @@ public class AppJmol extends GStructureViewer implements Runnable, 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) @@ -722,10 +566,11 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.centerViewer(toshow); } - public void closeViewer() + public void closeViewer(boolean closeExternalViewer) { + // JMol does not use an external viewer jmb.closeViewer(); - ap = null; + setAlignmentPanel(null); _aps.clear(); _alignwith.clear(); _colourwith.clear(); @@ -766,9 +611,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } try { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry( - pi) - .getId()); + pdbseq = pdbclient.getSequenceRecords(pdbid); } catch (OutOfMemoryError oomerror) { new OOMWarning("Retrieving PDB id " + pdbid, oomerror); @@ -785,8 +628,8 @@ 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(pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0).getFile()).getAbsolutePath(); jmb.getPdbEntry(pi).setFile(file); files.append(" \"" + Platform.escapeString(file) + "\""); @@ -881,7 +724,7 @@ public class AppJmol extends GStructureViewer implements Runnable, // 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 @@ -892,6 +735,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { } } + // refresh the sequence colours for the new structure(s) for (AlignmentPanel ap : _colourwith) { @@ -931,10 +775,11 @@ public class AppJmol extends GStructureViewer implements Runnable, 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(); @@ -951,6 +796,18 @@ public class AppJmol extends GStructureViewer implements Runnable, } catch (Exception ex) { ex.printStackTrace(); + } finally + { + if (in != null) + { + try + { + in.close(); + } catch (IOException e) + { + // ignore + } + } } } } @@ -961,11 +818,7 @@ public class AppJmol extends GStructureViewer implements Runnable, 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( @@ -1021,8 +874,7 @@ public class AppJmol extends GStructureViewer implements Runnable, 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(); } } @@ -1049,16 +901,16 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (!jmb.isLoadingFromArchive()) { - if (_colourwith.size() == 0 && ap != null) + if (_colourwith.size() == 0 && getAlignmentPanel() != null) { // Make the currently displayed alignment panel the associated view - _colourwith.add(ap.alignFrame.alignPanel); + _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); } } // Set the colour using the current view for the associated alignframe for (AlignmentPanel ap : _colourwith) { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + jmb.colourBySequence(ap); } } } @@ -1199,14 +1051,12 @@ public class AppJmol extends GStructureViewer implements Runnable, { 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); @@ -1243,7 +1093,8 @@ public class AppJmol extends GStructureViewer implements Runnable, } else { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } } @@ -1268,27 +1119,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - protected void buildJmolActionMenu() - { - if (_alignwith == null) - { - _alignwith = new Vector(); - } - if (_alignwith.size() == 0 && ap != null) - { - _alignwith.add(ap); - } - ; - for (Component c : viewerActionMenu.getMenuComponents()) - { - if (c != alignStructs) - { - viewerActionMenu.remove((JMenuItem) c); - } - } - final ItemListener handler; - } - /* * (non-Javadoc) * @@ -1304,14 +1134,14 @@ public class AppJmol extends GStructureViewer implements Runnable, private void alignStructs_withAllAlignPanels() { - if (ap == null) + if (getAlignmentPanel() == null) { return; } ; if (_alignwith.size() == 0) { - _alignwith.add(ap); + _alignwith.add(getAlignmentPanel()); } ; try @@ -1363,7 +1193,7 @@ public class AppJmol extends GStructureViewer implements Runnable, return ap; } } - return ap; + return getAlignmentPanel(); } @Override @@ -1378,4 +1208,10 @@ public class AppJmol extends GStructureViewer implements Runnable, return jmb == null ? null : jmb.viewer.getStateInfo(); } + @Override + public ViewerType getViewerType() + { + return ViewerType.JMOL; + } + }