/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.schemes.BuriedColourScheme;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
RenderPanel renderPanel;
- private boolean addingStructures = false;
-
ViewSelectionMenu seqColourBy;
/**
_alignwith = new Vector<AlignmentPanel>();
}
- seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
+ seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
+ JMenu alpanels = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new String[]
- { new Integer(_alignwith.size()).toString() }));
+ new String[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
final AlignmentPanel ap)
{
progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ String pdbId = pdbentry.getId();
- if (alreadyMapped != null)
+ /*
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
+ */
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new String[]
- { pdbentry.getId() }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new String[]
- { pdbentry.getId() }),
- JOptionPane.YES_NO_CANCEL_OPTION);
-
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- // TODO : Fix multiple seq to one chain issue here.
- ap.getStructureSelectionManager().setMapping(seq, chains,
- alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.getSeqPanel().seqCanvas.fr != null)
- {
- ap.getSeqPanel().seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
-
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AppJmol)
- {
- final AppJmol topJmol = ((AppJmol) frames[i]);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topJmol.jmb.getPdbCount(); pe++)
- {
- if (topJmol.jmb.getPdbEntry(pe).getFile()
- .equals(alreadyMapped))
- {
- topJmol.jmb.addSequence(pe, seq);
- topJmol.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topJmol.useAlignmentPanelForColourbyseq(ap);
- topJmol.buildActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
-
- return;
- }
+ return;
}
/*
* Check if there are other Jmol views involving this alignment and prompt
* user about adding this molecule to one of them
*/
- for (AppJmol topJmol : getJmolsFor(ap))
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
{
- // TODO: highlight topJmol in view somehow
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new String[]
- { pdbentry.getId(), topJmol.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
+ return;
}
- // /////////////////////////////////
- openNewJmol(ap, new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq });
+
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ }
+
+ /**
+ * Answers true if this viewer already involves the given PDB ID
+ */
+ @Override
+ protected boolean hasPdbId(String pdbId)
+ {
+ return jmb.hasPdbId(pdbId);
}
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
}
/**
- * pdb retrieval thread.
+ * Returns a list of any Jmol viewers. The list is restricted to those linked
+ * to the given alignment panel if it is not null.
*/
- private Thread worker = null;
-
- /**
- * add a new structure (with associated sequences and chains) to this viewer,
- * retrieving it if necessary first.
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param alignFrame
- * @param align
- * if true, new structure(s) will be align using associated alignment
- */
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b,
- final IProgressIndicator alignFrame)
- {
- if (pdbentry.getFile() == null)
- {
- if (worker != null && worker.isAlive())
- {
- // a retrieval is in progress, wait around and add ourselves to the
- // queue.
- new Thread(new Runnable()
- {
- public void run()
- {
- while (worker != null && worker.isAlive() && _started)
- {
- try
- {
- Thread.sleep(100 + ((int) Math.random() * 100));
-
- } catch (Exception e)
- {
- }
-
- }
- // and call ourselves again.
- addStructure(pdbentry, seq, chains, b, alignFrame);
- }
- }).start();
- return;
- }
- }
- // otherwise, start adding the structure.
- jmb.addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- addingStructures = true;
- _started = false;
- alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
- (worker = new Thread(this)).start();
- return;
- }
-
- private Vector<AppJmol> getJmolsFor(AlignmentPanel apanel)
+ @Override
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
{
- Vector<AppJmol> result = new Vector<AppJmol>();
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof AppJmol)
{
- if (((AppJmol) frame).isLinkedWith(apanel))
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
{
- result.addElement((AppJmol) frame);
+ result.add((StructureViewerBase) frame);
}
}
}
boolean allChainsSelected = false;
- private boolean alignAddedStructures = false;
-
void centerViewer()
{
Vector<String> toshow = new Vector<String>();
public void closeViewer(boolean closeExternalViewer)
{
- // JMol does not use an external viewer
- jmb.closeViewer();
+ // Jmol does not use an external viewer
+ if (jmb != null)
+ {
+ jmb.closeViewer();
+ }
setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
jmb = null;
}
- /**
- * state flag for PDB retrieval thread
- */
- private boolean _started = false;
-
public void run()
{
_started = true;
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
}
try
{
}
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
// just transfer the file name from the first sequence's first
// PDBEntry
- file = new File(pdbseq.getSequenceAt(0).getPDBId()
+ file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
.elementAt(0).getFile()).getAbsolutePath();
jmb.getPdbEntry(pi).setFile(file);
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new String[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
jmb.updateColours(ap);
}
// do superposition if asked to
- if (alignAddedStructures)
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
- alignStructs_withAllAlignPanels();
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ if (jmb.viewer.isScriptExecuting())
+ {
+ javax.swing.SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ return;
+ }
+ else
+ {
+ alignStructs_withAllAlignPanels();
+ }
}
});
alignAddedStructures = false;
try
{
// TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(
- jmb.getPdbFile()[0]));
+ in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG,
- "Make PNG image from view", width, height, null, null);
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null);
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS,
- "Make EPS file from view", width, height, null,
- this.getTitle());
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle());
}
else
{
@Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
- java.awt.Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"), null);
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
return ViewerType.JMOL;
}
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff