/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.
*
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;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
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.JInternalFrame;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
*/
public class ChimeraViewFrame extends StructureViewerBase
{
- private JalviewChimeraBinding jmb;
+ JalviewChimeraBinding jmb;
private boolean allChainsSelected = false;
*/
private void initMenus()
{
- viewerActionMenu.setText(MessageManager.getString("label.chimera"));
+ String chimera = MessageManager.getString("label.chimera");
+ viewerActionMenu.setText(chimera);
viewerColour.setText(MessageManager
.getString("label.colour_with_chimera"));
viewerColour.setToolTipText(MessageManager
viewerActionMenu.add(alpanels);
viewerActionMenu.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
}
});
+
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_viewer_attributes"));
+ writeFeatures.setToolTipText(MessageManager.formatMessage(
+ "label.create_viewer_attributes_tip", chimera));
+ writeFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sendFeaturesToViewer();
+ }
+ });
+ viewerActionMenu.add(writeFeatures);
+
+ final JMenu fetchAttributes = new JMenu(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes", chimera));
+ fetchAttributes.setToolTipText(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes_tip", chimera));
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
+ }
+
+ /**
+ * Asks Chimera for residues with the given attribute name, and set as
+ * features on the corresponding sequence positions (if any)
+ *
+ * @param attName
+ */
+ @Override
+ protected void getResidueAttributes(String attName)
+ {
+ jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
+ }
+
+ /**
+ * Send a command to Chimera to create residue attributes for Jalview features
+ * <p>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * <p>
+ * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ */
+ @Override
+ protected void sendFeaturesToViewer()
+ {
+ jmb.sendFeaturesToViewer(getAlignmentPanel());
}
/**
public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
String[] chains, final AlignmentPanel ap)
{
- super();
+ this();
String pdbId = pdbentry.getId();
/*
SequenceI[][] seqs)
{
createProgressBar();
- 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)
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
/**
- * 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<PDBEntry> 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
* file
*
SequenceI[][] seqsArray, boolean colourByChimera,
boolean colourBySequence, String newViewId)
{
- super();
+ this();
setViewId(newViewId);
this.chimeraSessionFile = chimeraSessionFile;
openNewChimera(alignPanel, pdbArray, seqsArray);
public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
AlignmentPanel ap)
{
- super();
+ this();
openNewChimera(ap, pe, seqs);
}
- public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> 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<PDBEntry> 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<SequenceI> seqsForPdb = toView.get(pdbs[i]);
- seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
- }
-
- openNewChimera(alignPanel, pdbs, seqsForPdbs);
+ setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
}
/**
*/
void initChimera()
{
- jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this,
- jmb.getViewerTitle("Chimera", true), getBounds().width,
- getBounds().height);
+ Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
+ getBounds().width, getBounds().height);
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;
}
+ chimeraSessionFile);
}
}
- jmb.setFinishedInit(true);
jmb.startChimeraListener();
}
*
* @param chainNames
*/
+ @Override
void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
menuItem = new JCheckBoxMenuItem(chainName, true);
menuItem.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
/**
* Show only the selected chain(s) in the viewer
*/
+ @Override
void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
* @param closeChimera
* if true, close any linked Chimera process; if false, prompt first
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
if (jmb != null && jmb.isChimeraRunning())
"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);
}
// 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;
List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
List<Integer> filePDBpos = new ArrayList<Integer>();
PDBEntry thePdbEntry = null;
+ StructureFile pdb = null;
try
{
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
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)
{
+ jmb.setFinishedInit(false);
if (!addingStructures)
{
try
{
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)
{
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(
}
}
}
+
+ jmb.refreshGUI();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
alignStructs_withAllAlignPanels();
* @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;
setChainMenuItems(jmb.getChainNames());
this.setTitle(jmb.getViewerTitle("Chimera", true));
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
+ // if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
+ // {
viewerActionMenu.setVisible(true);
- }
+ // }
if (!jmb.isLoadingFromArchive())
{
seqColour_actionPerformed(null);
}
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
{
return jmb;
}
+
+ @Override
+ protected List<String> getResidueAttributeNames()
+ {
+ return jmb.getResidueAttributes();
+ }
}
git://source.jalview.org / jalview.git / blobdiff