From: jprocter Date: Sat, 9 Jul 2011 11:15:28 +0000 (+0100) Subject: menu item and constructor to open a bunch of structures associated X-Git-Tag: Release_2_7~138 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ad07946b57c7e3d85d6d2e6dc060fc5af5536cd1;p=jalview.git menu item and constructor to open a bunch of structures associated with the current selection and align them in new Jmol window (JAL-860) --- diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index c292af3..a269860 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -26,6 +26,7 @@ import java.awt.event.*; import java.io.*; import jalview.jbgui.GStructureViewer; +import jalview.api.AlignmentViewPanel; import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; import jalview.datamodel.*; @@ -227,6 +228,13 @@ 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 + * @param ap + */ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, AlignmentPanel ap) { @@ -306,27 +314,41 @@ public class AppJmol extends GStructureViewer implements Runnable, } } // ///////////////////////////////// - - jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }, null, null); + openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); + } + private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { + boolean promptUser=pdbentrys.length==1; + progressBar = ap.alignFrame; + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length>1) + { + alignAddedStructures=true; + useAlignmentPanelForSuperposition(ap); + } jmb.setColourBySequence(true); setSize(400, 400); // probably should be a configurable/dynamic default here initMenus(); - - if (pdbentry.getFile() != null) - { - initJmol("load \"" + pdbentry.getFile() + "\""); - } - else + worker=null; + String filelist=""; +// for (PDBEntry pe: pdbentrys) +// { +// if (pe.getFile()==null) + { + addingStructures = false; + worker = new Thread(this); + worker.start(); +// break; + } +// filelist+=" \""+pe.getFile()+"\""; + +/* } + if (worker==null) { - addingStructures = false; - worker = new Thread(this); - worker.start(); + initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist); } - +*/ this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) @@ -338,6 +360,17 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** + * create a new Jmol containing several structures superimposed using the given alignPanel. + * @param ap + * @param pe + * @param seqs + */ + public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs) + { + openNewJmol(ap, pe, seqs); + } + + /** * list of sequenceSet ids associated with the view */ ArrayList _aps = new ArrayList(); @@ -747,6 +780,7 @@ public class AppJmol extends GStructureViewer implements Runnable, "Couldn't load file", JOptionPane.ERROR_MESSAGE); } + long lastnotify = jmb.getLoadNotifiesHandled(); if (files.length() > 0) { if (!addingStructures) @@ -772,7 +806,8 @@ public class AppJmol extends GStructureViewer implements Runnable, cmd.append("\nloadingJalviewdata=null"); final String command = cmd.toString(); cmd = null; - long lastnotify = jmb.getLoadNotifiesHandled(); + lastnotify = jmb.getLoadNotifiesHandled(); + try { jmb.evalStateCommand(command); @@ -786,37 +821,40 @@ 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 (lastnotify >= jmb.getLoadNotifiesHandled()) - ; + } + + // need to wait around until script has finished + while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() + : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length)) + { + try { - try - { - Thread.sleep(35); - } catch (Exception e) - { - } - } - // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) + Cache.log.debug("Waiting around for jmb notify."); + Thread.sleep(35); + } catch (Exception e) { - jmb.updateColours(ap); } - // do superposition if asked to - if (alignAddedStructures) + } + // refresh the sequence colours for the new structure(s) + for (AlignmentPanel ap : _colourwith) + { + jmb.updateColours(ap); + } + // do superposition if asked to + if (alignAddedStructures) + { + javax.swing.SwingUtilities.invokeLater(new Runnable() { - javax.swing.SwingUtilities.invokeLater(new Runnable() + public void run() { - public void run() - { - alignStructs_withAllAlignPanels(); - // jmb.superposeStructures(ap.av.getAlignment(), -1, null); - } - }); - alignAddedStructures = false; - } - addingStructures = false; + alignStructs_withAllAlignPanels(); + // jmb.superposeStructures(ap.av.getAlignment(), -1, null); + } + }); + alignAddedStructures = false; } + addingStructures = false; + } _started = false; worker = null; diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d44ecdf..30feec2 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -21,6 +21,7 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import MCview.*; @@ -228,33 +229,11 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - Vector seqs = new Vector(); - for (int i = 0; i < ap.av.alignment.getHeight(); i++) - { - Vector pdbs = ap.av.alignment.getSequenceAt(i) - .getDatasetSequence().getPDBId(); - if (pdbs == null) - continue; - - for (int p = 0; p < pdbs.size(); p++) - { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) - { - if (!seqs.contains(ap.av.alignment.getSequenceAt(i))) - seqs.addElement(ap.av.alignment.getSequenceAt(i)); - - continue; - } - } - } - - SequenceI[] seqs2 = new SequenceI[seqs.size()]; - seqs.toArray(seqs2); - - new AppJmol(pdb, seqs2, null, ap); + // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence + new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); } + }); viewStructureMenu.add(menuItem); @@ -406,6 +385,33 @@ public class PopupMenu extends JPopupMenu { buildGroupURLMenu(sg, groupLinks); } + // Add a 'show all structures' for the current selection + Hashtable pdbe=new Hashtable(); + for (SequenceI sq: ap.av.getSequenceSelection()) + { + Vector pes = (Vector) sq.getDatasetSequence().getPDBId(); + if (pes!=null) { + for (PDBEntry pe: pes) + { + pdbe.put(pe.getId(), pe); + } + } + } + if (pdbe.size()>0) + { + final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); + final JMenuItem gpdbview; + structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures.")); + gpdbview.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new AppJmol(ap, pe, ap.av.collateForPDB(pe)); + } + }); + } } else {