From 75dcf03278eac69e3dafbbf7c0d839e9087734f8 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 18 Feb 2011 17:33:41 +0000 Subject: [PATCH] JAL-777/JAL-641 debugging --- src/jalview/gui/AppJmol.java | 323 +++++++++++++++++++++++++++++++++-- src/jalview/gui/AppJmolBinding.java | 36 ++-- 2 files changed, 331 insertions(+), 28 deletions(-) diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 19178f2..723b5f4 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -19,9 +19,11 @@ package jalview.gui; import java.util.regex.*; import java.util.*; +import java.util.List; import java.awt.*; import javax.swing.*; import javax.swing.event.*; + import java.awt.event.*; import java.io.*; @@ -30,6 +32,7 @@ import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; import jalview.datamodel.*; import jalview.gui.*; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.structure.*; import jalview.datamodel.PDBEntry; import jalview.io.*; @@ -42,8 +45,11 @@ import org.jmol.popup.*; import org.jmol.viewer.JmolConstants; import org.openscience.jmol.app.jmolpanel.AppConsole; +import com.sun.org.apache.xml.internal.security.Init; +import com.sun.xml.internal.bind.v2.runtime.unmarshaller.XsiNilLoader.Array; + public class AppJmol extends GStructureViewer implements Runnable, - SequenceStructureBinding + SequenceStructureBinding, ViewSetProvider { AppJmolBinding jmb; @@ -86,21 +92,25 @@ public class AppJmol extends GStructureViewer implements Runnable, this(new String[] { file }, new String[] { id }, new SequenceI[][] - { seq }, ap, loadStatus, bounds, viewid); + { seq }, ap, true,true, loadStatus, bounds, viewid); } + ViewSelectionMenu seqColourBy; + /** * * @param files * @param ids * @param seqs * @param ap + * @param usetoColour - add the alignment panel to the list used for colouring these structures + * @param useToAlign - add the alignment panel to the list used for aligning these structures * @param loadStatus * @param bounds * @param viewid */ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs, - AlignmentPanel ap, String loadStatus, Rectangle bounds, + AlignmentPanel ap, boolean usetoColour,boolean useToAlign, String loadStatus, Rectangle bounds, String viewid) { PDBEntry[] pdbentrys = new PDBEntry[files.length]; @@ -116,10 +126,19 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null); jmb.setLoadingFromArchive(true); - this.ap = ap; + addAlignmentPanel(ap); + if (useToAlign) + { + useAlignmentPanelForSuperposition(ap); + } + if (usetoColour) + { + useAlignmentPanelForColourbyseq(ap); + } this.setBounds(bounds); jmb.setColourBySequence(false); seqColour.setSelected(false); + initMenus(); viewId = viewid; // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); @@ -134,7 +153,66 @@ public class AppJmol extends GStructureViewer implements Runnable, initJmol(loadStatus); // pdbentry, seq, JBPCHECK! } + private void initMenus() { + seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith, + new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + if (!seqColour.isSelected()) + { + seqColour.doClick(); + } + else + { + // update the jmol display now. + seqColour_actionPerformed(null); + } + } + }); + viewMenu.add(seqColourBy); + final ItemListener handler; + JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, + _alignwith, handler=new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + alignStructs.setEnabled(_alignwith.size() > 0); + alignStructs.setToolTipText("Align structures using " + + _alignwith.size() + " linked alignment views"); + } + }); + handler.itemStateChanged(null); + jmolActionMenu.add(alpanels); + jmolActionMenu.addMenuListener(new MenuListener() + { + + @Override + public void menuSelected(MenuEvent e) + { + handler.itemStateChanged(null); + } + + @Override + public void menuDeselected(MenuEvent e) + { + // TODO Auto-generated method stub + + } + + @Override + public void menuCanceled(MenuEvent e) + { + // TODO Auto-generated method stub + + } + }); + + } IProgressIndicator progressBar = null; public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, @@ -182,6 +260,8 @@ public class AppJmol extends GStructureViewer implements Runnable, if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) { topJmol.jmb.addSequence(pe, seq); + topJmol.addAlignmentPanel(ap); + topJmol.buildJmolActionMenu(); break; } } @@ -209,6 +289,7 @@ public class AppJmol extends GStructureViewer implements Runnable, JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { + topJmol.useAlignmentPanelForSuperposition(ap); topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); return; } @@ -219,9 +300,10 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb = new AppJmolBinding(this, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }, null, null); - this.ap = ap; + addAlignmentPanel(ap); setSize(400, 400); // probably should be a configurable/dynamic default here - + initMenus(); + if (pdbentry.getFile() != null) { initJmol("load \"" + pdbentry.getFile() + "\""); @@ -244,6 +326,124 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** + * list of sequenceSet ids associated with the view + */ + ArrayList _aps = new ArrayList(); + + 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; + } + + /** + * list of alignment panels to use for superposition + */ + ArrayList _alignwith = new ArrayList(); + + /** + * list of alignment panels that are used for colouring structures by aligned + * sequences + */ + ArrayList _colourwith = new ArrayList(); + + /** + * 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) + { + addAlignmentPanel(nap); + if (!_colourwith.contains(nap)) + { + _colourwith.add(nap); + } + } + + public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) + { + if (_colourwith.contains(nap)) + { + _colourwith.remove(nap); + } + } + + /** * pdb retrieval thread. */ private Thread worker = null; @@ -316,7 +516,7 @@ public class AppJmol extends GStructureViewer implements Runnable, if (frames[i] instanceof AppJmol) { AppJmol topJmol = ((AppJmol) frames[i]); - if (topJmol.ap == ap2) + if (topJmol.isLinkedWith(ap2)) { otherJmols.addElement(topJmol); } @@ -417,7 +617,10 @@ public class AppJmol extends GStructureViewer implements Runnable, void closeViewer() { jmb.closeViewer(); - + ap = null; + _aps.clear(); + _alignwith.clear(); + _colourwith.clear(); // TODO: check for memory leaks where instance isn't finalised because jmb // holds a reference to the window jmb = null; @@ -572,7 +775,10 @@ public class AppJmol extends GStructureViewer implements Runnable, } } // refresh the sequence colours for the new structure(s) - jmb.updateColours(ap); + for (AlignmentPanel ap : _colourwith) + { + jmb.updateColours(ap); + } // do superposition if asked to if (alignAddedStructures) { @@ -580,7 +786,8 @@ public class AppJmol extends GStructureViewer implements Runnable, { public void run() { - jmb.superposeStructures(ap.av.getAlignment(), -1, null); + alignStructs_withAllAlignPanels(); + // jmb.superposeStructures(ap.av.getAlignment(), -1, null); } }); alignAddedStructures = false; @@ -705,9 +912,14 @@ public class AppJmol extends GStructureViewer implements Runnable, public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); + if (_colourwith==null) { _colourwith=new ArrayList();}; + if (_colourwith.size()==0){ _colourwith.add(ap); }; + // Set the colour using the current view for the associated alignframe - jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures, - ap.alignFrame.viewport.alignment); + for (AlignmentPanel ap : _colourwith) + { + jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + } } public void chainColour_actionPerformed(ActionEvent actionEvent) @@ -894,13 +1106,29 @@ public class AppJmol extends GStructureViewer implements Runnable, return; } setChainMenuItems(jmb.chainNames); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); this.setTitle(jmb.getViewerTitle()); if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) { jmolActionMenu.setVisible(true); } + if (!jmb.isLoadingFromArchive()) { + seqColour_actionPerformed(null); + } + } + + protected void buildJmolActionMenu() + { + if (_alignwith==null) { _alignwith=new ArrayList();} + if (_alignwith.size()==0 && ap!=null) { _alignwith.add(ap);}; + for (Component c : jmolActionMenu.getMenuComponents()) + { + if (c != alignStructs) + { + jmolActionMenu.remove((JMenuItem) c); + } + } + final ItemListener handler; } /* @@ -913,17 +1141,39 @@ public class AppJmol extends GStructureViewer implements Runnable, @Override protected void alignStructs_actionPerformed(ActionEvent actionEvent) { + alignStructs_withAllAlignPanels(); + } + private void alignStructs_withAllAlignPanels() + { + if (ap==null) { return; }; + if (_alignwith.size()==0) { _alignwith.add(ap);}; try { - jmb.superposeStructures(ap.av.getAlignment(), -1, - ap.av.getColumnSelection()); + AlignmentI[] als = new Alignment[_alignwith.size()]; + ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; + int[] alm = new int[_alignwith.size()]; + int a = 0; + + for (AlignmentPanel ap : _alignwith) + { + als[a] = ap.av.getAlignment(); + alm[a] = -1; + alc[a++] = ap.av.getColumnSelection(); + } + jmb.superposeStructures(als, alm, alc); } catch (Exception e) { - Cache.log.info("Couldn't align structures in alignframe " - + ap.alignFrame.getTitle(), e); + StringBuffer sp = new StringBuffer(); + for (AlignmentPanel ap : _alignwith) + { + sp.append("'" + ap.alignFrame.getTitle() + "' "); + } + Cache.log.info("Couldn't align structures with the " + sp.toString() + + "associated alignment panels.", e); } + } public void setJalviewColourScheme(ColourSchemeI ucs) @@ -932,4 +1182,43 @@ public class AppJmol extends GStructureViewer implements Runnable, } + /** + * + * @param alignment + * @return first alignment panel displaying given alignment, or the default + * alignment panel + */ + public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) + { + for (AlignmentPanel ap : getAllAlignmentPanels()) + { + if (ap.av.getAlignment() == alignment) + { + return ap; + } + } + return ap; + } + + /** + * + * @param ap2 + * @return true if this Jmol instance is linked with the given alignPanel + */ + public boolean isLinkedWith(AlignmentPanel ap2) + { + return _aps.contains(ap2.av.getSequenceSetId()); + } + + public boolean isUsedforaligment(AlignmentPanel ap2) + { + + return (_alignwith != null) && _alignwith.contains(ap2); + } + + public boolean isUsedforcolourby(AlignmentPanel ap2) + { + return (_colourwith != null) && _colourwith.contains(ap2); + } + } diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java index ed56ebb..c8d9ae3 100644 --- a/src/jalview/gui/AppJmolBinding.java +++ b/src/jalview/gui/AppJmolBinding.java @@ -26,7 +26,9 @@ import java.util.BitSet; import javax.swing.JPanel; +import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; @@ -53,26 +55,27 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding FeatureRenderer fr = null; @Override - public jalview.api.FeatureRenderer getFeatureRenderer() + public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) { - if (appJmolWindow.ap.av.showSequenceFeatures) + AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment; + if (ap.av.showSequenceFeatures) { if (fr == null) { - fr = new FeatureRenderer(appJmolWindow.ap); + fr = new FeatureRenderer((AlignmentPanel)alignment); } - fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas - .getFeatureRenderer()); + fr.transferSettings(((AlignmentPanel)alignment). + seqPanel.seqCanvas.getFeatureRenderer()); } return fr; } @Override - public jalview.api.SequenceRenderer getSequenceRenderer() + public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) { - return new SequenceRenderer(appJmolWindow.ap.av); + return new SequenceRenderer(((AlignmentPanel)alignment).av); } public void sendConsoleEcho(String strEcho) @@ -122,11 +125,13 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding public void updateColours(Object source) { - AlignmentPanel ap = (AlignmentPanel) source; - if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av) + AlignmentPanel ap = (AlignmentPanel) source,topap; + // ignore events from unrelated or non-user interactive frames + if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || appJmolWindow.isUsedforcolourby(ap)) return; - - colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); + if (!isLoadingFromArchive()) { + colourBySequence(ap.av.getShowSequenceFeatures(), ap); + } } public void notifyScriptTermination(String strStatus, int msWalltime) @@ -212,4 +217,13 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding } } + + @Override + public void releaseReferences(Object svl) + { + if (svl instanceof SeqPanel) { + appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap); + + }; + } } -- 1.7.10.2