*/
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.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.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import java.util.Vector;
/**
* 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<AlignmentViewPanel> _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<AlignmentViewPanel> _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();
}
+
+ /**
+ * @return true if added structures should be aligned to existing one(s)
+ */
+ @Override
+ public boolean isAlignAddedStructures()
+ {
+ return alignAddedStructures;
+ }
+
+ /**
+ *
+ * @param true
+ * if added structures should be aligned to existing one(s)
+ */
+ @Override
+ public void setAlignAddedStructures(boolean alignAdded)
+ {
+ alignAddedStructures = alignAdded;
+ }
+
/**
*
* @param ap2
return (_alignwith != null) && _alignwith.contains(ap2);
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ @Override
+ public boolean isUsedforcolourby(AlignmentViewPanel avp)
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ return (_colourwith != null) && _colourwith.contains(avp);
}
/**
{
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.
*/
protected void addStructure(final PDBEntry pdbentry,
final SequenceI[] seqs, final String[] chains,
- final boolean align, final IProgressIndicator alignFrame)
+ final IProgressIndicator alignFrame)
{
if (pdbentry.getFile() == null)
{
}
}
// and call ourselves again.
- addStructure(pdbentry, seqs, chains, align, alignFrame);
+ addStructure(pdbentry, seqs, chains, alignFrame);
}
}).start();
return;
}
// 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;
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 JvOptionPane code
- */
- protected int chooseAlignStructureToViewer(String pdbId,
- StructureViewerBase view)
- {
- int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[] { pdbId, view.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JvOptionPane.YES_NO_CANCEL_OPTION);
- return option;
- }
-
protected boolean hasPdbId(String pdbId)
{
return getBinding().hasPdbId(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
+ * 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 boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, final AlignmentPanel apanel, String pdbId)
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
{
- 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
- }
- }
+ return Desktop.instance.getStructureViewers(alp, this.getClass());
+ }
+ @Override
+ public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentViewPanel apanel, String pdbId)
+ {
/*
- * 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); code may defend
+ * against this possibility before we reach here
*/
- return false;
+ if (hasPdbId(pdbId))
+ {
+ return;
+ }
+ AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this
+ // cast fails
+ useAlignmentPanelForSuperposition(alignPanel);
+ addStructure(pdbentry, seq, chains, alignPanel.alignFrame);
}
/**
* @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;
}
}
}
}
- /**
- * 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)
+ @Override
+ public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ final AlignmentViewPanel apanel, String pdbId)
{
- boolean finished = false;
String alreadyMapped = apanel.getStructureSelectionManager()
.alreadyMappedToFile(pdbId);
- if (alreadyMapped != null)
- {
- /*
- * 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;
- }
+ if (alreadyMapped == null)
+ {
+ return false;
}
- return finished;
+
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ return true;
}
void setChainMenuItems(List<String> chainNames)
{
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);
+ String lastSeqName = "";
for (String chain : chainNames)
{
- menuItem = new JCheckBoxMenuItem(chain, true);
+ String seqName = getSequenceNameForChain(chain);
+ int nameLength = seqName.length();
+ if (nameLength > 16)
+ {
+ seqName = seqName.substring(0, 8) + "..."
+ + seqName.substring(nameLength - 8, nameLength);
+ }
+ String text = chain;
+ if (!lastSeqName.equals(seqName))
+ {
+ text = text + " " + seqName;
+ }
+ lastSeqName = 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
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, getAlignmentPanel().av, 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(
});
viewMenu.add(seqColourBy);
+ showAlignmentOnly = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_alignment_only"));
+ showAlignmentOnly.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideHiddenRegions.setEnabled(showAlignmentOnly.isSelected());
+ getBinding().setShowAlignmentOnly(showAlignmentOnly.isSelected());
+ getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+ true);
+ }
+ });
+ viewMenu.add(showAlignmentOnly);
+
+ hideHiddenRegions = new JCheckBoxMenuItem(
+ MessageManager.getString("label.hide_hidden_regions"));
+ hideHiddenRegions.setEnabled(false);
+ hideHiddenRegions.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getBinding().setHideHiddenRegions(hideHiddenRegions.isSelected());
+ getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+ false);
+ }
+ });
+ viewMenu.add(hideHiddenRegions);
+
final ItemListener handler = new ItemListener()
{
@Override
buildColourMenu();
}
- @Override
- 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 String alignStructs_actionPerformed(
- ActionEvent actionEvent)
+ protected String alignStructs_actionPerformed(ActionEvent actionEvent)
{
return alignStructs_withAllAlignPanels();
}
{
return null;
}
-
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
-
+
String reply = null;
try
{
HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
int[] alm = new int[_alignwith.size()];
int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
+
+ for (AlignmentViewPanel alignPanel : _alignwith)
{
- als[a] = ap.av.getAlignment();
+ AlignViewportI av = alignPanel.getAlignViewport();
+ als[a] = av.getAlignment();
alm[a] = -1;
- alc[a++] = ap.av.getAlignment().getHiddenColumns();
+ alc[a++] = av.getAlignment().getHiddenColumns();
}
reply = getBinding().superposeStructures(als, alm, alc);
if (reply != null)
{
- String text = MessageManager.formatMessage(
- "error.superposition_failed", reply);
+ String text = MessageManager
+ .formatMessage("error.superposition_failed", reply);
statusBar.setText(text);
}
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
+ for (AlignmentViewPanel avp : _alignwith)
{
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ sp.append(
+ "'" + ((AlignmentPanel) avp).alignFrame.getTitle() + "' ");
}
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
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())
{
}
}
// Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
+ for (AlignmentViewPanel avp : _colourwith)
{
- binding.colourBySequence(ap);
+ binding.updateStructureColours(avp);
}
+ 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)
{
/**
* 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));
/*
* enable 'Superpose with' if more than one mapped structure
*/
viewSelectionMenu.setEnabled(false);
- if (getBinding().getPdbFile().length > 1
+ if (getBinding().getStructureFiles().length > 1
&& getBinding().getSequence().length > 1)
{
viewSelectionMenu.setEnabled(true);
seqColour_actionPerformed(null);
}
}
+
+ @Override
+ public String toString()
+ {
+ return getTitle();
+ }
+
+ @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;
+ }
+
+ @Override
+ public void raiseViewer()
+ {
+ toFront();
+ }
+
+ @Override
+ public abstract AAStructureBindingModel getBinding();
+
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ protected void showSelectedChains()
+ {
+ setSelectedChains();
+
+ /*
+ * refresh display without resizing - easier to see what changed
+ */
+ getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+ false);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff