*/
package jalview.gui;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.DataSourceType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemes;
-import jalview.structure.StructureMapping;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
+import java.util.Random;
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.DataSourceType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
+
/**
* Base class with common functionality for JMol, Chimera or other structure
* viewers.
public abstract class StructureViewerBase extends GStructureViewer
implements Runnable, ViewSetProvider
{
+ private static final String UNMAPPED = "(unmapped)";
+
/*
* names for colour options (additional to Jalview colour schemes)
*/
*/
protected volatile boolean seqColoursApplied = false;
+ private IProgressIndicator progressBar = null;
+
+ private Random random = new Random();
+
/**
* Default constructor
*/
return _aps.contains(ap2.av.getSequenceSetId());
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ public boolean isUsedforaligment(AlignmentViewPanel ap2)
{
return (_alignwith != null) && _alignwith.contains(ap2);
}
@Override
- public boolean isUsedforcolourby(AlignmentViewPanel avp)
+ public boolean isUsedForColourBy(AlignmentViewPanel avp)
{
return (_colourwith != null) && _colourwith.contains(avp);
}
this.viewId = viewId;
}
- public abstract String getStateInfo();
-
protected void buildActionMenu()
{
if (_alignwith == null)
}
}
+ @Override
public AlignmentPanel getAlignmentPanel()
{
return ap;
*
* @param nap
*/
- public void removeAlignmentPanel(AlignmentPanel nap)
+ @Override
+ public void removeAlignmentPanel(AlignmentViewPanel nap)
{
try
{
public abstract ViewerType getViewerType();
- protected abstract IProgressIndicator getIProgressIndicator();
-
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
- pdbFilename, DataSourceType.FILE, getIProgressIndicator());
+ pdbFilename, DataSourceType.FILE, getProgressIndicator());
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
{
return;
}
+
+ /*
+ * add the 'All' menu item
+ */
JMenuItem menuItem = new JMenuItem(
MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
allChainsSelected = false;
}
});
-
chainMenu.add(menuItem);
+ /*
+ * add a menu item for each structure and chain
+ */
+ Collections.sort(chainNames);
for (String chain : chainNames)
{
- menuItem = new JCheckBoxMenuItem(chain, true);
+ String seqName = getSequenceNameForChain(chain);
+ if (seqName == null)
+ {
+ seqName = UNMAPPED;
+ }
+ int nameLength = seqName.length();
+ if (nameLength > 16)
+ {
+ seqName = seqName.substring(0, 8) + "..."
+ + seqName.substring(nameLength - 8, nameLength);
+ }
+ String text = chain + " " + seqName;
+ menuItem = new JCheckBoxMenuItem(text, true);
menuItem.addItemListener(new ItemListener()
{
@Override
}
}
- abstract void showSelectedChains();
+ /**
+ * Answers the name of the sequence mapped to the given chain (formatted as
+ * pdbId:chainId, e.g. 1A70:A). Answers null if no mapped sequence is found. If
+ * more than one sequence is matched, just answers the name of the first one
+ * found.
+ *
+ * @param chain
+ * @return
+ */
+ private String getSequenceNameForChain(String chain)
+ {
+ String[] tokens = chain.split(":");
+ String pdbId = tokens[0];
+ String chainId = tokens[1];
+ List<StructureMapping> mappings = getBinding().getSsm()
+ .getMappingForChain(pdbId, chainId);
+ return mappings.isEmpty() ? null
+ : mappings.get(0).getSequence().getName();
+ }
/**
* Action on selecting one of Jalview's registered colour schemes
ColourSchemeI cs = ColourSchemes.getInstance()
.getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
null);
- getBinding().setJalviewColourScheme(cs);
+ getBinding().colourByJalviewColourScheme(cs);
}
/**
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- viewerColour_actionPerformed(actionEvent);
+ viewerColour_actionPerformed();
}
});
colourMenu.add(viewerColour);
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- background_actionPerformed(actionEvent);
+ background_actionPerformed();
}
});
colourMenu.add(backGround);
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- seqColour_actionPerformed(actionEvent);
+ seqColour_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- chainColour_actionPerformed(actionEvent);
+ chainColour_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- chargeColour_actionPerformed(actionEvent);
+ chargeColour_actionPerformed();
}
});
viewerColour = new JRadioButtonMenuItem();
- // text is set in overrides of this method
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_viewer"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_viewer_manage_structure_colours"));
viewerColour.setName(ViewerColour.ByViewer.name());
viewerColour.setSelected(!binding.isColourBySequence());
}
else
{
- // update the Chimera display now.
- seqColour_actionPerformed(null);
+ // update the viewer display now.
+ seqColour_actionPerformed();
}
}
});
}
});
viewMenu.add(hideHiddenRegions);
+ viewMenu.add(fitToWindow);
final ItemListener handler = new ItemListener()
{
@Override
public void itemStateChanged(ItemEvent e)
{
- alignStructs.setEnabled(!_alignwith.isEmpty());
- alignStructs.setToolTipText(MessageManager.formatMessage(
- "label.align_structures_using_linked_alignment_views",
- _alignwith.size()));
+ if (_alignwith.isEmpty())
+ {
+ alignStructs.setEnabled(false);
+ alignStructs.setToolTipText(null);
+ }
+ else
+ {
+ alignStructs.setEnabled(true);
+ alignStructs.setToolTipText(MessageManager.formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ _alignwith.size()));
+ }
}
};
viewSelectionMenu = new ViewSelectionMenu(
}
});
+ viewerActionMenu.setText(getViewerName());
+ helpItem.setText(MessageManager.formatMessage("label.viewer_help",
+ getViewerName()));
+
buildColourMenu();
}
* the operation.
*/
@Override
- protected String alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- return alignStructs_withAllAlignPanels();
- }
-
- protected String alignStructs_withAllAlignPanels()
+ protected String alignStructsWithAllAlignPanels()
{
if (getAlignmentPanel() == null)
{
String reply = null;
try
{
- AlignmentI[] als = new Alignment[_alignwith.size()];
- HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentViewPanel alignPanel : _alignwith)
- {
- AlignViewportI av = alignPanel.getAlignViewport();
- als[a] = av.getAlignment();
- alm[a] = -1;
- alc[a++] = av.getAlignment().getHiddenColumns();
- }
- reply = getBinding().superposeStructures(als, alm, alc);
- if (reply != null)
+ reply = getBinding().superposeStructures(_alignwith);
+ if (reply != null && !reply.isEmpty())
{
String text = MessageManager
.formatMessage("error.superposition_failed", reply);
}
} catch (Exception e)
{
- StringBuffer sp = new StringBuffer();
- for (AlignmentViewPanel avp : _alignwith)
+ StringBuilder sb = new StringBuilder();
+ for (AlignmentViewPanel alignPanel : _alignwith)
{
- sp.append(
- "'" + ((AlignmentPanel) avp).alignFrame.getTitle() + "' ");
+ sb.append("'").append(alignPanel.getViewName()).append("' ");
}
- Cache.log.info("Couldn't align structures with the " + sp.toString()
+ Cache.log.info("Couldn't align structures with the " + sb.toString()
+ "associated alignment panels.", e);
}
return reply;
}
+ /**
+ * Opens a colour chooser dialog, and applies the chosen colour to the
+ * background of the structure viewer
+ */
@Override
- public void background_actionPerformed(ActionEvent actionEvent)
+ public void background_actionPerformed()
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_background_colour"),
- null);
- if (col != null)
+ String ttl = MessageManager.getString("label.select_background_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- getBinding().setBackgroundColour(col);
- }
+ @Override
+ public void colourSelected(Color c)
+ {
+ getBinding().setBackgroundColour(c);
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, null, listener);
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
+ public void viewerColour_actionPerformed()
{
if (viewerColour.isSelected())
{
}
@Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
+ public void chainColour_actionPerformed()
{
chainColour.setSelected(true);
getBinding().colourByChain();
}
@Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ public void chargeColour_actionPerformed()
{
chargeColour.setSelected(true);
getBinding().colourByCharge();
}
@Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
+ public void seqColour_actionPerformed()
{
AAStructureBindingModel binding = getBinding();
binding.setColourBySequence(seqColour.isSelected());
// Set the colour using the current view for the associated alignframe
for (AlignmentViewPanel avp : _colourwith)
{
- binding.colourBySequence(avp);
+ binding.updateStructureColours(avp);
}
seqColoursApplied = true;
}
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ public void pdbFile_actionPerformed()
{
+ // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
}
@Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ public void viewMapping_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
* enable 'Superpose with' if more than one mapped structure
*/
viewSelectionMenu.setEnabled(false);
- if (getBinding().getStructureFiles().length > 1
+ if (getBinding().getMappedStructureCount() > 1
&& getBinding().getSequence().length > 1)
{
viewSelectionMenu.setEnabled(true);
if (!binding.isLoadingFromArchive())
{
- seqColour_actionPerformed(null);
+ seqColour_actionPerformed();
}
}
toFront();
}
+ @Override
+ public abstract AAStructureBindingModel getBinding();
+
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ protected void showSelectedChains()
+ {
+ setChainsToHide();
+
+ /*
+ * refresh display without resizing - easier to see what changed
+ */
+ getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+ false);
+ }
+
+ @Override
+ public long startProgressBar(String msg)
+ {
+ // TODO would rather have startProgress/stopProgress as the
+ // IProgressIndicator interface
+ long tm = random.nextLong();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, tm);
+ }
+ return tm;
+ }
+
+ @Override
+ public void stopProgressBar(String msg, long handle)
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, handle);
+ }
+ }
+
+ protected IProgressIndicator getProgressIndicator()
+ {
+ return progressBar;
+ }
+
+ protected void setProgressIndicator(IProgressIndicator pi)
+ {
+ progressBar = pi;
+ }
+
+ protected void setProgressMessage(String message, long id)
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(message, id);
+ }
+ }
+
+ @Override
+ public void showConsole(boolean show)
+ {
+ // default does nothing
+ }
+
+ /**
+ * Tries to fetch a PDB file and save to a temporary local file. Returns the
+ * saved file path if successful, or null if not.
+ *
+ * @param processingEntry
+ * @return
+ */
+ protected String fetchPdbFile(PDBEntry processingEntry)
+ {
+ String filePath = null;
+ Pdb pdbclient = new Pdb();
+ AlignmentI pdbseq = null;
+ String pdbid = processingEntry.getId();
+ long handle = System.currentTimeMillis()
+ + Thread.currentThread().hashCode();
+
+ /*
+ * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
+ */
+ String msg = MessageManager.formatMessage("status.fetching_pdb",
+ new Object[]
+ { pdbid });
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // long hdl = startProgressBar(MessageManager.formatMessage(
+ // "status.fetching_pdb", new Object[]
+ // { pdbid }));
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
+ } finally
+ {
+ msg = pdbid + " " + MessageManager.getString("label.state_completed");
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // stopProgressBar(msg, hdl);
+ }
+ /*
+ * If PDB data were saved and are not invalid (empty alignment), return the
+ * file path.
+ */
+ if (pdbseq != null && pdbseq.getHeight() > 0)
+ {
+ // just use the file name from the first sequence's first PDBEntry
+ filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ processingEntry.setFile(filePath);
+ }
+ return filePath;
+ }
+
+ /**
+ * If supported, saves the state of the structure viewer to a temporary file
+ * and returns the file, else returns null
+ *
+ * @return
+ */
+ public File saveSession()
+ {
+ // TODO: a wait loop to ensure the file is written fully before returning?
+ return getBinding() == null ? null : getBinding().saveSession();
+ }
+
+ /**
+ * Close down this instance of Jalview's Chimera viewer, giving the user the
+ * option to close the associated Chimera window (process). They may wish to
+ * keep it open until they have had an opportunity to save any work.
+ *
+ * @param forceClose
+ * if true, close any linked Chimera process; if false, prompt first
+ */
+ @Override
+ public void closeViewer(boolean forceClose)
+ {
+ AAStructureBindingModel binding = getBinding();
+ if (binding != null && binding.isViewerRunning())
+ {
+ if (!forceClose)
+ {
+ String viewerName = getViewerName();
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_viewer", new Object[]
+ { binding.getViewerTitle(viewerName, false), viewerName });
+ prompt = JvSwingUtils.wrapTooltip(true, prompt);
+ int confirm = JvOptionPane.showConfirmDialog(this, prompt,
+ MessageManager.getString("label.close_viewer"),
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+ /*
+ * abort closure if user hits escape or Cancel
+ */
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
+ forceClose = confirm == JvOptionPane.YES_OPTION;
+ }
+ binding.closeViewer(forceClose);
+ }
+ setAlignmentPanel(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;
+ dispose();
+ }
+
+ @Override
+ public void showHelp_actionPerformed()
+ {
+ try
+ {
+ String url = getBinding().getHelpURL();
+ if (url != null)
+ {
+ BrowserLauncher.openURL(url);
+ }
+ } catch (IOException ex)
+ {
+ System.err
+ .println("Show " + getViewerName() + " failed with: "
+ + ex.getMessage());
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff