*/
package jalview.gui;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
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;
/**
* list of sequenceSet ids associated with the view
*/
- protected List<String> _aps = new ArrayList<String>();
+ protected List<String> _aps = new ArrayList<>();
/**
* list of alignment panels to use for superposition
*/
- protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+ protected Vector<AlignmentPanel> _alignwith = new Vector<>();
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
- protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+ protected Vector<AlignmentPanel> _colourwith = new Vector<>();
private String viewId = null;
protected boolean alignAddedStructures = false;
- protected boolean _started = false;
+ protected volatile boolean _started = false;
- protected boolean addingStructures = false;
+ protected volatile boolean addingStructures = false;
protected Thread worker = null;
protected JMenu viewSelectionMenu;
/**
+ * set after sequence colouring has been applied for this structure viewer.
+ * used to determine if the final sequence/structure mapping has been
+ * determined
+ */
+ protected volatile boolean seqColoursApplied = false;
+
+ /**
* Default constructor
*/
public StructureViewerBase()
{
super();
}
+
/**
*
* @param ap2
{
if (_alignwith == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ _alignwith = new Vector<>();
}
if (_alignwith.size() == 0 && ap != null)
{
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.
}
// otherwise, start adding the structure.
getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
- new SequenceI[][] { seqs }, new String[][] { chains });
+ new SequenceI[][]
+ { seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
alignAddedStructures = align;
{
int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[] { pdbId, view.getTitle() }),
+ new Object[]
+ { pdbId, view.getTitle() }),
MessageManager
.getString("label.align_to_existing_structure_view"),
JvOptionPane.YES_NO_CANCEL_OPTION);
return getBinding().hasPdbId(pdbId);
}
- protected abstract List<StructureViewerBase> getViewersFor(
- AlignmentPanel alp);
+ /**
+ * Returns a list of any viewer of the instantiated type. The list is
+ * restricted to those linked to the given alignment panel if it is not null.
+ */
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
+ {
+ return Desktop.instance.getStructureViewers(alp, this.getClass());
+ }
+
/**
* Check for any existing views involving this alignment and give user the
* @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)
+ @Override
+ public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentViewPanel 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 == JvOptionPane.CANCEL_OPTION)
- {
- return true;
- }
- else if (option == JvOptionPane.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
+ * JAL-1742 exclude view with this structure already mapped (don't offer
+ * to align chain B to chain A of the same structure)
*/
- return false;
+ if (hasPdbId(pdbId))
+ {
+ return false;
+ }
+ AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this
+ // cast fails
+ useAlignmentPanelForSuperposition(ap);
+ addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return true;
}
/**
* @param apanel
* @param pdbFilename
*/
- protected void addSequenceMappingsToStructure(SequenceI[] seq,
- String[] chains, final AlignmentPanel apanel, String pdbFilename)
+ public void addSequenceMappingsToStructure(SequenceI[] seq,
+ String[] chains, final AlignmentViewPanel alpanel,
+ String pdbFilename)
{
+ AlignmentPanel apanel = (AlignmentPanel) alpanel;
+
// TODO : Fix multiple seq to one chain issue here.
/*
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
- pdbFilename, DataSourceType.FILE);
+ pdbFilename, DataSourceType.FILE, getIProgressIndicator());
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
if (apanel.getSeqPanel().seqCanvas.fr != null)
{
apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
- apanel.paintAlignment(true);
+ // note - we don't do a refresh for structure here because we do it
+ // explicitly for all panels later on
+ apanel.paintAlignment(true, false);
}
/*
*/
viewer.useAlignmentPanelForColourbyseq(apanel);
viewer.buildActionMenu();
- apanel.getStructureSelectionManager().sequenceColoursChanged(
- apanel);
+ apanel.getStructureSelectionManager()
+ .sequenceColoursChanged(apanel);
break;
}
}
* @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)
+ @Override
+ public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ final AlignmentViewPanel apanel, String pdbId)
{
boolean finished = false;
String alreadyMapped = apanel.getStructureSelectionManager()
/*
* the PDB file is already loaded
*/
- int option = JvOptionPane.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 }),
- JvOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JvOptionPane.CANCEL_OPTION)
- {
- finished = true;
- }
- else if (option == JvOptionPane.YES_OPTION)
- {
- addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
- finished = true;
- }
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ finished = true;
}
return finished;
}
public void changeColour_actionPerformed(String colourSchemeName)
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
- ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
- colourSchemeName, al, null);
+ ColourSchemeI cs = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, al, null);
getBinding().setJalviewColourScheme(cs);
}
if (_colourwith == null)
{
- _colourwith = new Vector<AlignmentPanel>();
+ _colourwith = new Vector<>();
}
if (_alignwith == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ _alignwith = new Vector<>();
}
ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
alignStructs.setEnabled(!_alignwith.isEmpty());
alignStructs.setToolTipText(MessageManager.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new String[] { String.valueOf(_alignwith.size()) }));
+ _alignwith.size()));
}
};
viewSelectionMenu = new ViewSelectionMenu(
MessageManager.getString("label.superpose_with"), this,
_alignwith, handler);
handler.itemStateChanged(null);
- viewerActionMenu.add(viewSelectionMenu);
+ viewerActionMenu.add(viewSelectionMenu, 0);
viewerActionMenu.addMenuListener(new MenuListener()
{
@Override
}
@Override
- public void setJalviewColourScheme(ColourSchemeI cs) {
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
getBinding().setJalviewColourScheme(cs);
}
+
+ /**
+ * Sends commands to the structure viewer to superimpose structures based on
+ * currently associated alignments. May optionally return an error message for
+ * the operation.
+ */
@Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ protected String alignStructs_actionPerformed(ActionEvent actionEvent)
{
- alignStructs_withAllAlignPanels();
+ return alignStructs_withAllAlignPanels();
}
- protected void alignStructs_withAllAlignPanels()
+
+ protected String alignStructs_withAllAlignPanels()
{
if (getAlignmentPanel() == null)
{
- return;
+ return null;
}
-
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
-
+
+ String reply = null;
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
int[] alm = new int[_alignwith.size()];
int a = 0;
-
+
for (AlignmentPanel ap : _alignwith)
{
als[a] = ap.av.getAlignment();
alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
+ alc[a++] = ap.av.getAlignment().getHiddenColumns();
+ }
+ reply = getBinding().superposeStructures(als, alm, alc);
+ if (reply != null)
+ {
+ String text = MessageManager
+ .formatMessage("error.superposition_failed", reply);
+ statusBar.setText(text);
}
- getBinding().superposeStructures(als, alm, alc);
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
+ return reply;
}
+
@Override
public void background_actionPerformed(ActionEvent actionEvent)
{
getBinding().setBackgroundColour(col);
}
}
+
@Override
public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
getBinding().setColourBySequence(false);
}
}
+
@Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
getBinding().colourByChain();
}
+
@Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
getBinding().colourByCharge();
}
+
@Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
binding.setColourBySequence(seqColour.isSelected());
if (_colourwith == null)
{
- _colourwith = new Vector<AlignmentPanel>();
+ _colourwith = new Vector<>();
}
if (binding.isColourBySequence())
{
{
binding.colourBySequence(ap);
}
+ seqColoursApplied = true;
}
}
+
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
-
+
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
+
int value = chooser.showSaveDialog(this);
-
+
if (value == JalviewFileChooser.APPROVE_OPTION)
{
BufferedReader in = null;
{
// TODO: cope with multiple PDB files in view
in = new BufferedReader(
- new FileReader(getBinding().getPdbFile()[0]));
+ new FileReader(getBinding().getStructureFiles()[0]));
File outFile = chooser.getSelectedFile();
-
+
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
while ((data = in.readLine()) != null)
}
}
}
+
@Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
}
protected abstract String getViewerName();
+
+ /**
+ * Configures the title and menu items of the viewer panel.
+ */
+ @Override
public void updateTitleAndMenus()
{
AAStructureBindingModel binding = getBinding();
return;
}
setChainMenuItems(binding.getChainNames());
-
+
this.setTitle(binding.getViewerTitle(getViewerName(), true));
- if (binding.getPdbFile().length > 1 && binding.getSequence().length > 1)
+
+ /*
+ * enable 'Superpose with' if more than one mapped structure
+ */
+ viewSelectionMenu.setEnabled(false);
+ if (getBinding().getStructureFiles().length > 1
+ && getBinding().getSequence().length > 1)
{
- viewerActionMenu.setVisible(true);
+ viewSelectionMenu.setEnabled(true);
}
+
+ /*
+ * Show action menu if it has any enabled items
+ */
+ viewerActionMenu.setVisible(false);
+ for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
+ {
+ if (viewerActionMenu.getItem(i).isEnabled())
+ {
+ viewerActionMenu.setVisible(true);
+ break;
+ }
+ }
+
if (!binding.isLoadingFromArchive())
{
seqColour_actionPerformed(null);
}
}
+
+ @Override
+ public boolean hasMapping()
+ {
+ if (worker != null && (addingStructures || _started))
+ {
+ return false;
+ }
+ if (getBinding() == null)
+ {
+ if (_aps == null || _aps.size() == 0)
+ {
+ // viewer has been closed, but we did at some point run.
+ return true;
+ }
+ return false;
+ }
+ String[] pdbids = getBinding().getStructureFiles();
+ if (pdbids == null)
+ {
+ return false;
+ }
+ int p=0;
+ for (String pdbid:pdbids) {
+ StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
+ if (sm!=null && sm.length>0 && sm[0]!=null) {
+ p++;
+ }
+ }
+ // only return true if there is a mapping for every structure file we have loaded
+ if (p == 0 || p != pdbids.length)
+ {
+ return false;
+ }
+ // and that coloring has been applied
+ return seqColoursApplied;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff