}
} catch (Exception e)
{
- logger.error("REST call " + command + " failed: " + e.getMessage());
+ logger.error("REST call '" + command + "' failed: " + e.getMessage());
} finally
{
if (response != null)
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
- /*
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
boolean allChainsSelected = false;
/*
return null;
}
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
/**
*
*/
*/
private boolean loadingFinished = true;
- /*
- * state flag used to check if the Chimera viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
public String fileLoadingError;
/*
return true;
}
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
/**
* Returns a list of chains mapped in this viewer. Note this list is not
* currently scoped per structure.
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;
/**
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;
return ViewerType.JMOL;
}
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
+
}
*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+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.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+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 javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-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.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
-
/**
* GUI elements for handling an external chimera display
*
private boolean allChainsSelected = false;
- private boolean alignAddedStructures = false;
-
- /*
- * state flag for PDB retrieval thread
- */
- private boolean _started = false;
-
- private boolean addingStructures = false;
-
private IProgressIndicator progressBar = null;
/*
- * pdb retrieval thread.
- */
- private Thread worker = null;
-
- /*
* Path to Chimera session file. This is set when an open Jalview/Chimera
* session is saved, or on restore from a Jalview project (if it holds the
* filename of any saved Chimera sessions).
String[] chains, final AlignmentPanel ap)
{
super();
-
- /*
- * is the pdb file already loaded?
- */
String pdbId = pdbentry.getId();
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbId);
-
- if (alreadyMapped != null)
- {
- int option = chooseAddSequencesToViewer(pdbId);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- addSequenceMappingsToStructure(seq, chains, ap, alreadyMapped);
- return;
- }
- }
/*
- * Check if there are other Chimera views involving this alignment and give
- * user the option to add and align this molecule to one of them
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
*/
- List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
- for (ChimeraViewFrame view : existingViews)
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- // TODO: highlight view somehow
- /*
- * JAL-1742 exclude view with this structure already mapped (don't offer
- * to align chain B to chain A of the same structure)
- */
- if (view.hasPdbId(pdbId))
- {
- continue;
- }
- int option = chooseAlignStructureToViewer(pdbId, view);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- view.useAlignmentPanelForSuperposition(ap);
- view.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
+ return;
}
/*
- * If the options above are declined or do not apply, open a new viewer
- */
- openNewChimera(ap, new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq });
- }
-
- /**
- * Presents a dialog with the option to add an align a structure to an
- * existing Chimera view
- *
- * @param pdbId
- * @param view
- * @return YES, NO or CANCEL JOptionPane code
- */
- protected int chooseAlignStructureToViewer(String pdbId,
- ChimeraViewFrame view)
- {
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[]
- { pdbId, view.getTitle() }), MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
- return option;
- }
-
- /**
- * Presents a dialog with the option to add sequences to a viewer which
- * already has their structure open
- *
- * @param pdbId
- * @return YES, NO or CANCEL JOptionPane code
- */
- protected int chooseAddSequencesToViewer(String pdbId)
- {
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbId }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new Object[]
- { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
- return option;
- }
-
- /**
- * Adds mappings for the given sequences to an already opened PDB structure,
- * and updates any viewers that have the PDB file
- *
- * @param seq
- * @param chains
- * @param ap
- * @param pdbFilename
- */
- protected void addSequenceMappingsToStructure(SequenceI[] seq,
- String[] chains, final AlignmentPanel ap, String pdbFilename)
- {
- // TODO : Fix multiple seq to one chain issue here.
- /*
- * create the mappings
- */
- ap.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
- AppletFormatAdapter.FILE);
-
- /*
- * alert the FeatureRenderer to show new (PDB RESNUM) features
+ * Check if there are other Chimera views involving this alignment and give
+ * user the option to add and align this molecule to one of them (or cancel)
*/
- if (ap.getSeqPanel().seqCanvas.fr != null)
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
{
- ap.getSeqPanel().seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
+ return;
}
/*
- * add the sequences to any other Chimera viewers for this pdb file
+ * If the options above are declined or do not apply, show the structure in
+ * a new viewer
*/
- // JBPNOTE: this looks like a binding routine, rather than a gui routine
- for (JInternalFrame frame : Desktop.instance.getAllFrames())
- {
- if (frame instanceof ChimeraViewFrame)
- {
- ChimeraViewFrame chimeraView = ((ChimeraViewFrame) frame);
- for (int pe = 0; pe < chimeraView.jmb.getPdbCount(); pe++)
- {
- if (chimeraView.jmb.getPdbEntry(pe).getFile().equals(pdbFilename))
- {
- chimeraView.jmb.addSequence(pe, seq);
- chimeraView.addAlignmentPanel(ap);
- /*
- * add it to the set of alignments used for colouring structure by
- * sequence
- */
- chimeraView.useAlignmentPanelForColourbyseq(ap);
- chimeraView.buildActionMenu();
- ap.getStructureSelectionManager().sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
+ openNewChimera(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);
}
/**
- * 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
+ * Returns a list of any Chimera viewers in the desktop. The list is
+ * restricted to those linked to the given alignment panel if it is not null.
*/
- 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 List<ChimeraViewFrame> getChimeraWindowsFor(AlignmentPanel apanel)
+ @Override
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
{
- List<ChimeraViewFrame> result = new ArrayList<ChimeraViewFrame>();
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof ChimeraViewFrame)
{
- if (((StructureViewerBase) frame).isLinkedWith(apanel))
+ if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
{
- result.add((ChimeraViewFrame) frame);
+ result.add((StructureViewerBase) frame);
}
}
}
*/
public void closeViewer(boolean closeChimera)
{
- if (jmb.isChimeraRunning())
+ if (jmb != null && jmb.isChimeraRunning())
{
if (!closeChimera)
{
{
return ViewerType.CHIMERA;
}
+
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
}
package jalview.gui;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AppletFormatAdapter;
+import jalview.jbgui.GStructureViewer;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+
import java.awt.Component;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import javax.swing.JMenuItem;
-
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.jbgui.GStructureViewer;
+import javax.swing.JOptionPane;
/**
* Base class with common functionality for JMol, Chimera or other structure
protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
private String viewId = null;
private AlignmentPanel ap;
+ protected boolean alignAddedStructures = false;
+ protected boolean _started = false;
+ protected boolean addingStructures = false;
+ protected Thread worker = null;
/**
*
}
public abstract ViewerType getViewerType();
+
+ protected abstract AAStructureBindingModel getBindingModel();
+
+ /**
+ * add a new structure (with associated sequences and chains) to this viewer,
+ * retrieving it if necessary first.
+ *
+ * @param pdbentry
+ * @param seqs
+ * @param chains
+ * @param align
+ * if true, new structure(s) will be aligned using associated
+ * alignment
+ * @param alignFrame
+ */
+ protected void addStructure(final PDBEntry pdbentry, final SequenceI[] seqs, final String[] chains,
+ final boolean align, 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, seqs, chains, align, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ getBindingModel().addSequenceAndChain(new PDBEntry[] { pdbentry },
+ new SequenceI[][] { seqs }, new String[][] { chains });
+ addingStructures = true;
+ _started = false;
+ alignAddedStructures = align;
+ worker = new Thread(this);
+ worker.start();
+ return;
+ }
+
+ /**
+ * Presents a dialog with the option to add an align a structure to an
+ * existing structure view
+ *
+ * @param pdbId
+ * @param view
+ * @return YES, NO or CANCEL JOptionPane code
+ */
+ protected int chooseAlignStructureToViewer(String pdbId, StructureViewerBase view)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view",
+ new Object[]
+ { pdbId, view.getTitle() }), MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ return option;
+ }
+
+ protected abstract boolean hasPdbId(String pdbId);
+
+ protected abstract List<StructureViewerBase> getViewersFor(
+ AlignmentPanel alp);
+
+ /**
+ * Check for any existing views involving this alignment and give user the
+ * option to add and align this molecule to one of them
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param apanel
+ * @param pdbId
+ * @return true if user adds to a view, or cancels entirely, else false
+ */
+ protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentPanel apanel, String pdbId)
+ {
+ for (StructureViewerBase view : getViewersFor(apanel))
+ {
+ // TODO: highlight the view somehow
+ /*
+ * JAL-1742 exclude view with this structure already mapped (don't offer
+ * to align chain B to chain A of the same structure)
+ */
+ if (view.hasPdbId(pdbId))
+ {
+ continue;
+ }
+ int option = chooseAlignStructureToViewer(pdbId, view);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return true;
+ }
+ else if (option == JOptionPane.YES_OPTION)
+ {
+ view.useAlignmentPanelForSuperposition(apanel);
+ view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
+ return true;
+ }
+ else
+ {
+ // NO_OPTION - offer the next viewer if any
+ }
+ }
+
+ /*
+ * nothing offered and selected
+ */
+ return false;
+ }
+
+ /**
+ * Adds mappings for the given sequences to an already opened PDB structure,
+ * and updates any viewers that have the PDB file
+ *
+ * @param seq
+ * @param chains
+ * @param apanel
+ * @param pdbFilename
+ */
+ protected void addSequenceMappingsToStructure(SequenceI[] seq,
+ String[] chains, final AlignmentPanel apanel, String pdbFilename)
+ {
+ // TODO : Fix multiple seq to one chain issue here.
+ /*
+ * create the mappings
+ */
+ apanel.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
+ AppletFormatAdapter.FILE);
+
+ /*
+ * alert the FeatureRenderer to show new (PDB RESNUM) features
+ */
+ if (apanel.getSeqPanel().seqCanvas.fr != null)
+ {
+ apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
+ apanel.paintAlignment(true);
+ }
+
+ /*
+ * add the sequences to any other viewers (of the same type) for this pdb
+ * file
+ */
+ // JBPNOTE: this looks like a binding routine, rather than a gui routine
+ for (StructureViewerBase viewer : getViewersFor(null))
+ {
+ AAStructureBindingModel bindingModel = viewer.getBindingModel();
+ for (int pe = 0; pe < bindingModel.getPdbCount(); pe++)
+ {
+ if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename))
+ {
+ bindingModel.addSequence(pe, seq);
+ viewer.addAlignmentPanel(apanel);
+ /*
+ * add it to the set of alignments used for colouring structure by
+ * sequence
+ */
+ viewer.useAlignmentPanelForColourbyseq(apanel);
+ viewer.buildActionMenu();
+ apanel.getStructureSelectionManager().sequenceColoursChanged(apanel);
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * Check if the PDB file is already loaded, if so offer to add it to the
+ * existing viewer
+ *
+ * @param seq
+ * @param chains
+ * @param apanel
+ * @param pdbId
+ * @return true if the user chooses to add to a viewer, or to cancel entirely
+ */
+ protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ final AlignmentPanel apanel, String pdbId)
+ {
+ boolean finished = false;
+ String alreadyMapped = apanel.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbId);
+
+ if (alreadyMapped != null)
+ {
+ /*
+ * the PDB file is already loaded
+ */
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new Object[]
+ { pdbId }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ finished = true;
+ }
+ else if (option == JOptionPane.YES_OPTION)
+ {
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ finished = true;
+ }
+ }
+ return finished;
+ }
}
private boolean nucleotide;
+ private boolean finishedInit = false;
+
/**
* Data bean class to simplify parameterisation in superposeStructures
*/
}
return false;
}
+
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean fi)
+ {
+ this.finishedInit = fi;
+ }
}
\ No newline at end of file
package jalview.ext.rbvi.chimera;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Preferences;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.FormatAdapter;
@AfterClass
public static void tearDownAfterClass() throws Exception
{
- try
- {
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
- } catch (Exception e)
- {
- // ignore NullPointerException thrown by JMol
- }
-
}
@Test(groups ={ "Functional" })
public void testSingleSeqViewJMol()
{
+ Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
String inFile = "examples/1gaq.txt";
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
inFile, FormatAdapter.FILE);
new SequenceI[]
{ sq }, af.getCurrentView().getAlignPanel());
/*
- * Wait for viewer thread to start
+ * Wait for viewer load thread to complete
*/
try
{
- Thread.sleep(1000);
+ while (!jmolViewer.getBinding().isFinishedInit())
+ {
+ Thread.sleep(500);
+ }
} catch (InterruptedException e)
{
}
@Test(groups ={ "Functional" })
public void testSingleSeqViewChimera()
{
+ Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+ ViewerType.CHIMERA.name());
String inFile = "examples/1gaq.txt";
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
inFile, FormatAdapter.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
for (SequenceI sq : af.getViewport().getAlignment().getSequences())
{
+ System.out.println("** sq=" + sq.getName());
SequenceI dsq = sq.getDatasetSequence();
while (dsq.getDatasetSequence() != null)
{
new SequenceI[]
{ sq }, af.getCurrentView().getAlignPanel());
/*
- * Wait for viewer thread to start
+ * Wait for viewer load thread to complete
*/
- try
- {
- Thread.sleep(1000);
- } catch (InterruptedException e)
+ while (!chimeraViewer.getBinding().isFinishedInit())
{
+ try
+ {
+ Thread.sleep(500);
+ } catch (InterruptedException e)
+ {
+ }
}
+ assertEquals(1, chimeraViewer.getBinding().getPdbCount());
chimeraViewer.closeViewer(true);
// todo: break here means only once through this loop?
break;
}
/**
- * Verify that the method determines that columns 2, 5 and 6 of the aligment
+ * Verify that the method determines that columns 2, 5 and 6 of the alignment
* are alignable in structure
*/
@Test(groups ={ "Functional" })
git://source.jalview.org / jalview.git / commitdiff