X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=ab23e62b67bfea8c089f62c72aac6ee908584002;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=967d93fc1f8138f8eb8be0d659b703c7dc65f0c4;hpb=6fbc6ba37a390e3cbac8f7577146ef45772c12ec;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 967d93f..ab23e62 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -28,9 +28,10 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.JalviewChimeraBinding; import jalview.gui.StructureViewer.ViewerType; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; +import jalview.io.StructureFile; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; @@ -46,7 +47,6 @@ import jalview.util.Platform; import jalview.ws.dbsources.Pdb; import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.io.BufferedReader; @@ -59,16 +59,13 @@ import java.io.InputStream; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; -import java.util.Map; import java.util.Random; -import java.util.Set; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; -import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; @@ -156,8 +153,8 @@ public class ChimeraViewFrame extends StructureViewerBase alignStructs.setToolTipText(MessageManager .formatMessage( "label.align_structures_using_linked_alignment_views", - new Object[] - { new Integer(_alignwith.size()).toString() })); + new Object[] { new Integer(_alignwith + .size()).toString() })); } }); handler.itemStateChanged(null); @@ -196,7 +193,7 @@ public class ChimeraViewFrame extends StructureViewerBase public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq, String[] chains, final AlignmentPanel ap) { - super(); + this(); String pdbId = pdbentry.getId(); /* @@ -249,10 +246,9 @@ public class ChimeraViewFrame extends StructureViewerBase SequenceI[][] seqs) { createProgressBar(); - String[][] chains = extractChains(seqs); + // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs jmb = new JalviewChimeraBindingModel(this, - ap.getStructureSelectionManager(), pdbentrys, seqs, chains, - null); + ap.getStructureSelectionManager(), pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); if (pdbentrys.length > 1) @@ -270,6 +266,7 @@ public class ChimeraViewFrame extends StructureViewerBase this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { closeViewer(false); @@ -278,37 +275,7 @@ public class ChimeraViewFrame extends StructureViewerBase } - /** - * Retrieve chains for sequences by inspecting their PDB refs. The hope is - * that the first will be to the sequence's own chain. Really need a more - * managed way of doing this. - * - * @param seqs - * @return - */ - protected String[][] extractChains(SequenceI[][] seqs) - { - String[][] chains = new String[seqs.length][]; - for (int i = 0; i < seqs.length; i++) - { - chains[i] = new String[seqs[i].length]; - int seqno = 0; - for (SequenceI seq : seqs[i]) - { - String chain = null; - if (seq.getDatasetSequence() != null) - { - Vector pdbrefs = seq.getDatasetSequence().getAllPDBEntries(); - if (pdbrefs != null && pdbrefs.size() > 0) - { - chain = pdbrefs.get(0).getChainCode(); - } - } - chains[i][seqno++] = chain; - } - } - return chains; - } + /** * Create a new viewer from saved session state data including Chimera session @@ -323,12 +290,11 @@ public class ChimeraViewFrame extends StructureViewerBase * @param newViewId */ public ChimeraViewFrame(String chimeraSessionFile, - AlignmentPanel alignPanel, - PDBEntry[] pdbArray, + AlignmentPanel alignPanel, PDBEntry[] pdbArray, SequenceI[][] seqsArray, boolean colourByChimera, boolean colourBySequence, String newViewId) { - super(); + this(); setViewId(newViewId); this.chimeraSessionFile = chimeraSessionFile; openNewChimera(alignPanel, pdbArray, seqsArray); @@ -357,31 +323,22 @@ public class ChimeraViewFrame extends StructureViewerBase public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs, AlignmentPanel ap) { - super(); + this(); openNewChimera(ap, pe, seqs); } - public ChimeraViewFrame(Map> toView, - AlignmentPanel alignPanel) + /** + * Default constructor + */ + public ChimeraViewFrame() { super(); /* - * Convert the map of sequences per pdb entry into the tied arrays expected - * by openNewChimera - * - * TODO pass the Map down to openNewChimera and its callees instead + * closeViewer will decide whether or not to close this frame + * depending on whether user chooses to Cancel or not */ - final Set pdbEntries = toView.keySet(); - PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]); - SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][]; - for (int i = 0; i < pdbs.length; i++) - { - final List seqsForPdb = toView.get(pdbs[i]); - seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]); - } - - openNewChimera(alignPanel, pdbs, seqsForPdbs); + setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE); } /** @@ -414,14 +371,13 @@ public class ChimeraViewFrame extends StructureViewerBase void initChimera() { jmb.setFinishedInit(false); - jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true), - getBounds().width, getBounds().height); + jalview.gui.Desktop.addInternalFrame(this, + jmb.getViewerTitle("Chimera", true), getBounds().width, + getBounds().height); if (!jmb.launchChimera()) { - JOptionPane - .showMessageDialog( - Desktop.desktop, + JOptionPane.showMessageDialog(Desktop.desktop, MessageManager.getString("label.chimera_failed"), MessageManager.getString("label.error_loading_file"), JOptionPane.ERROR_MESSAGE); @@ -444,61 +400,11 @@ public class ChimeraViewFrame extends StructureViewerBase jmb.startChimeraListener(); } - /** - * If the list is not empty, add menu items for 'All' and each individual - * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed. - * - * @param chainNames - */ - void setChainMenuItems(List chainNames) - { - chainMenu.removeAll(); - if (chainNames == null || chainNames.isEmpty()) - { - return; - } - JMenuItem menuItem = new JMenuItem( - MessageManager.getString("label.all")); - menuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - allChainsSelected = true; - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - { - ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); - } - } - showSelectedChains(); - allChainsSelected = false; - } - }); - - chainMenu.add(menuItem); - - for (String chainName : chainNames) - { - menuItem = new JCheckBoxMenuItem(chainName, true); - menuItem.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent evt) - { - if (!allChainsSelected) - { - showSelectedChains(); - } - } - }); - - chainMenu.add(menuItem); - } - } /** * Show only the selected chain(s) in the viewer */ + @Override void showSelectedChains() { List toshow = new ArrayList(); @@ -524,6 +430,7 @@ public class ChimeraViewFrame extends StructureViewerBase * @param closeChimera * if true, close any linked Chimera process; if false, prompt first */ + @Override public void closeViewer(boolean closeChimera) { if (jmb != null && jmb.isChimeraRunning()) @@ -531,12 +438,20 @@ public class ChimeraViewFrame extends StructureViewerBase if (!closeChimera) { String prompt = MessageManager.formatMessage( - "label.confirm_close_chimera", new Object[] - { jmb.getViewerTitle("Chimera", false) }); + "label.confirm_close_chimera", + new Object[] { jmb.getViewerTitle("Chimera", false) }); prompt = JvSwingUtils.wrapTooltip(true, prompt); int confirm = JOptionPane.showConfirmDialog(this, prompt, MessageManager.getString("label.close_viewer"), - JOptionPane.YES_NO_OPTION); + JOptionPane.YES_NO_CANCEL_OPTION); + /* + * abort closure if user hits escape or Cancel + */ + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } closeChimera = confirm == JOptionPane.YES_OPTION; } jmb.closeViewer(closeChimera); @@ -548,12 +463,14 @@ public class ChimeraViewFrame extends StructureViewerBase // TODO: check for memory leaks where instance isn't finalised because jmb // holds a reference to the window jmb = null; + dispose(); } /** * Open any newly added PDB structures in Chimera, having first fetched data * from PDB (if not already saved). */ + @Override public void run() { _started = true; @@ -563,6 +480,7 @@ public class ChimeraViewFrame extends StructureViewerBase List filePDB = new ArrayList(); List filePDBpos = new ArrayList(); PDBEntry thePdbEntry = null; + StructureFile pdb = null; try { String[] curfiles = jmb.getPdbFile(); // files currently in viewer @@ -625,9 +543,8 @@ public class ChimeraViewFrame extends StructureViewerBase JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new Object[] - { errormsgs.toString() }), MessageManager - .getString("label.couldnt_load_file"), + new Object[] { errormsgs.toString() }), + MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE); } @@ -653,16 +570,17 @@ public class ChimeraViewFrame extends StructureViewerBase { int pos = filePDBpos.get(num).intValue(); long startTime = startProgressBar("Chimera " - + MessageManager.getString("status.opening_file")); + + MessageManager.getString("status.opening_file_for") + + " " + pe.getId()); jmb.openFile(pe); jmb.addSequence(pos, jmb.getSequence()[pos]); File fl = new File(pe.getFile()); - String protocol = AppletFormatAdapter.URL; + DataSourceType protocol = DataSourceType.URL; try { if (fl.exists()) { - protocol = AppletFormatAdapter.FILE; + protocol = DataSourceType.FILE; } } catch (Throwable e) { @@ -671,10 +589,9 @@ public class ChimeraViewFrame extends StructureViewerBase stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; - jmb.getSsm().setMapping(jmb.getSequence()[pos], - jmb.getChains()[pos], - pe.getFile(), - protocol); + pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], + jmb.getChains()[pos], pe.getFile(), protocol); + stashFoundChains(pdb, pe.getFile()); } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -690,6 +607,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } } + jmb.refreshGUI(); jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); @@ -703,6 +621,7 @@ public class ChimeraViewFrame extends StructureViewerBase { new Thread(new Runnable() { + @Override public void run() { alignStructs_withAllAlignPanels(); @@ -724,8 +643,20 @@ public class ChimeraViewFrame extends StructureViewerBase * @return * @throws Exception */ + + private void stashFoundChains(StructureFile pdb, String file) + { + for (int i = 0; i < pdb.getChains().size(); i++) + { + String chid = new String(pdb.getId() + ":" + + pdb.getChains().elementAt(i).id); + jmb.getChainNames().add(chid); + jmb.getChainFile().put(chid, file); + } + } private String fetchPdbFile(PDBEntry processingEntry) throws Exception { + // FIXME: this is duplicated code with Jmol frame ? String filePath = null; Pdb pdbclient = new Pdb(); AlignmentI pdbseq = null; @@ -737,8 +668,7 @@ public class ChimeraViewFrame extends StructureViewerBase * Write 'fetching PDB' progress on AlignFrame as we are not yet visible */ String msg = MessageManager.formatMessage("status.fetching_pdb", - new Object[] - { pdbid }); + new Object[] { pdbid }); getAlignmentPanel().alignFrame.setProgressBar(msg, handle); // long hdl = startProgressBar(MessageManager.formatMessage( // "status.fetching_pdb", new Object[] @@ -751,8 +681,7 @@ public class ChimeraViewFrame extends StructureViewerBase new OOMWarning("Retrieving PDB id " + pdbid, oomerror); } finally { - msg = pdbid + " " - + MessageManager.getString("label.state_completed"); + msg = pdbid + " " + MessageManager.getString("label.state_completed"); getAlignmentPanel().alignFrame.setProgressBar(msg, handle); // stopProgressBar(msg, hdl); } @@ -1097,6 +1026,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } + @Override public void setJalviewColourScheme(ColourSchemeI ucs) { jmb.setJalviewColourScheme(ucs);