X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=90ad51dafbbd5ce57287c6605ae857cc202c7866;hb=fee1b781ca14aadea5d112fc554fe14879c787c5;hp=ad638d3650aae12b4b31218b777eb1e5dfabb0d3;hpb=3ab582bfeeab1563bedf60e97994e63e672d2e31;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index ad638d3..90ad51d 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 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. * @@ -31,6 +31,7 @@ import jalview.gui.StructureViewer.ViewerType; import jalview.io.AppletFormatAdapter; 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; @@ -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(); /* @@ -250,10 +247,8 @@ public class ChimeraViewFrame extends StructureViewerBase { createProgressBar(); // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs - String[][] chains = extractChains(seqs); jmb = new JalviewChimeraBindingModel(this, - ap.getStructureSelectionManager(), pdbentrys, seqs, chains, - null); + ap.getStructureSelectionManager(), pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); if (pdbentrys.length > 1) @@ -280,41 +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) - { - // FIXME: SequenceI.PDBEntry[0] chain mapping used for - // ChimeraViewFrame. Is this even used ??? - chain = pdbrefs.get(0).getChainCode(); - } - } - chains[i][seqno++] = chain; - } - } - return chains; - } /** * Create a new viewer from saved session state data including Chimera session @@ -333,7 +294,7 @@ public class ChimeraViewFrame extends StructureViewerBase SequenceI[][] seqsArray, boolean colourByChimera, boolean colourBySequence, String newViewId) { - super(); + this(); setViewId(newViewId); this.chimeraSessionFile = chimeraSessionFile; openNewChimera(alignPanel, pdbArray, seqsArray); @@ -362,31 +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); } /** @@ -425,10 +377,10 @@ public class ChimeraViewFrame extends StructureViewerBase if (!jmb.launchChimera()) { - JOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager.getString("label.chimera_failed"), MessageManager.getString("label.error_loading_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); this.dispose(); return; } @@ -448,63 +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() - { - @Override - 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() - { - @Override - 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(); @@ -541,10 +441,18 @@ public class ChimeraViewFrame extends StructureViewerBase "label.confirm_close_chimera", new Object[] { jmb.getViewerTitle("Chimera", false) }); prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JOptionPane.showConfirmDialog(this, prompt, + int confirm = JvOptionPane.showConfirmDialog(this, prompt, MessageManager.getString("label.close_viewer"), - JOptionPane.YES_NO_OPTION); - closeChimera = confirm == JOptionPane.YES_OPTION; + JvOptionPane.YES_NO_CANCEL_OPTION); + /* + * abort closure if user hits escape or Cancel + */ + if (confirm == JvOptionPane.CANCEL_OPTION + || confirm == JvOptionPane.CLOSED_OPTION) + { + return; + } + closeChimera = confirm == JvOptionPane.YES_OPTION; } jmb.closeViewer(closeChimera); } @@ -555,6 +463,7 @@ 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(); } /** @@ -571,6 +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 @@ -631,11 +541,11 @@ public class ChimeraViewFrame extends StructureViewerBase if (errormsgs.length() > 0) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", new Object[] { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } if (files.length() > 0) @@ -679,8 +589,9 @@ public class ChimeraViewFrame extends StructureViewerBase stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; - jmb.getSsm().setMapping(jmb.getSequence()[pos], + pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos], jmb.getChains()[pos], pe.getFile(), protocol); + stashFoundChains(pdb, pe.getFile()); } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -696,6 +607,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } } + jmb.refreshGUI(); jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); @@ -731,6 +643,17 @@ 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 ?