*/
package jalview.gui;
+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.structure.StructureSelectionManager;
+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.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+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.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+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;
/**
* Base class with common functionality for JMol, Chimera or other structure
public abstract class StructureViewerBase extends GStructureViewer
implements Runnable, ViewSetProvider
{
+ /*
+ * names for colour options (additional to Jalview colour schemes)
+ */
+ enum ViewerColour
+ {
+ BySequence, ByChain, ChargeCysteine, ByViewer
+ }
/**
* 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 boolean allChainsSelected = false;
+ 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
{
if (_alignwith == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ _alignwith = new Vector<>();
}
if (_alignwith.size() == 0 && ap != null)
{
public abstract ViewerType getViewerType();
- protected abstract AAStructureBindingModel getBindingModel();
+ protected abstract IProgressIndicator getIProgressIndicator();
/**
* add a new structure (with associated sequences and chains) to this viewer,
*/
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.
- getBindingModel().addSequenceAndChain(new PDBEntry[] { pdbentry },
- new SequenceI[][] { seqs }, new String[][] { chains });
+ getBinding().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 JvOptionPane code
- */
- protected int chooseAlignStructureToViewer(String pdbId,
- StructureViewerBase view)
+ protected boolean hasPdbId(String pdbId)
{
- 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;
+ return getBinding().hasPdbId(pdbId);
}
- protected abstract boolean hasPdbId(String pdbId);
-
/**
- * Returns a list of any structure viewers of the same type. The list is
+ * 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){
-
- List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (JInternalFrame frame : frames)
- {
- if (this.getClass().isAssignableFrom(frame.getClass()))
- {
- if (alp == null
- || ((StructureViewerBase) frame).isLinkedWith(alp))
- {
- result.add((StructureViewerBase) frame);
- }
- }
- }
- return result;
-
+ 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
- * 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)
+ @Override
+ public void 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); 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);
}
/*
// JBPNOTE: this looks like a binding routine, rather than a gui routine
for (StructureViewerBase viewer : getViewersFor(null))
{
- AAStructureBindingModel bindingModel = viewer.getBindingModel();
+ AAStructureBindingModel bindingModel = viewer.getBinding();
for (int pe = 0; pe < bindingModel.getPdbCount(); pe++)
{
if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename))
*/
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)
- {
- boolean finished = false;
- StructureSelectionManager ssm = apanel.getStructureSelectionManager();
- String alreadyMapped = ssm.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;
- }
+ @Override
+ public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ final AlignmentViewPanel apanel, String pdbId)
+ {
+ String alreadyMapped = apanel.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbId);
+
+ if (alreadyMapped == null)
+ {
+ return false;
}
- return finished;
+
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ return true;
}
void setChainMenuItems(List<String> chainNames)
abstract void showSelectedChains();
+ /**
+ * Action on selecting one of Jalview's registered colour schemes
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+ ColourSchemeI cs = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+ null);
+ getBinding().setJalviewColourScheme(cs);
+ }
+
+ /**
+ * Builds the colour menu
+ */
+ protected void buildColourMenu()
+ {
+ colourMenu.removeAll();
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+
+ /*
+ * add colour by sequence, by chain, by charge and cysteine
+ */
+ colourMenu.add(seqColour);
+ colourMenu.add(chainColour);
+ colourMenu.add(chargeColour);
+ chargeColour.setEnabled(!al.isNucleotide());
+
+ /*
+ * add all 'simple' (per-residue) colour schemes registered to Jalview
+ */
+ ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
+ al, true);
+
+ /*
+ * add 'colour by viewer' (menu item text is set in subclasses)
+ */
+ viewerColour.setSelected(false);
+ viewerColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ viewerColour_actionPerformed(actionEvent);
+ }
+ });
+ colourMenu.add(viewerColour);
+
+ /*
+ * add 'set background colour'
+ */
+ JMenuItem backGround = new JMenuItem();
+ backGround
+ .setText(MessageManager.getString("action.background_colour"));
+ backGround.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ background_actionPerformed(actionEvent);
+ }
+ });
+ colourMenu.add(backGround);
+
+ /*
+ * add colour buttons to a group so their selection is
+ * mutually exclusive (background colour is a separate option)
+ */
+ itemGroup.add(seqColour);
+ itemGroup.add(chainColour);
+ itemGroup.add(chargeColour);
+ itemGroup.add(viewerColour);
+ }
+
+ /**
+ * Construct menu items
+ */
+ protected void initMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+
+ seqColour = new JRadioButtonMenuItem();
+ seqColour.setText(MessageManager.getString("action.by_sequence"));
+ seqColour.setName(ViewerColour.BySequence.name());
+ seqColour.setSelected(binding.isColourBySequence());
+ seqColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ seqColour_actionPerformed(actionEvent);
+ }
+ });
+
+ chainColour = new JRadioButtonMenuItem();
+ chainColour.setText(MessageManager.getString("action.by_chain"));
+ chainColour.setName(ViewerColour.ByChain.name());
+ chainColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour_actionPerformed(actionEvent);
+ }
+ });
+
+ chargeColour = new JRadioButtonMenuItem();
+ chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
+ chargeColour.setName(ViewerColour.ChargeCysteine.name());
+ chargeColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour_actionPerformed(actionEvent);
+ }
+ });
+
+ viewerColour = new JRadioButtonMenuItem();
+ // text is set in overrides of this method
+ viewerColour.setName(ViewerColour.ByViewer.name());
+ viewerColour.setSelected(!binding.isColourBySequence());
+
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<>();
+ }
+
+ ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
+ new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the Chimera display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+
+ 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()));
+ }
+ };
+ viewSelectionMenu = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
+ _alignwith, handler);
+ handler.itemStateChanged(null);
+ viewerActionMenu.add(viewSelectionMenu, 0);
+ viewerActionMenu.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+
+ 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)
+ {
+ return alignStructs_withAllAlignPanels();
+ }
+
+ protected String alignStructs_withAllAlignPanels()
+ {
+ if (getAlignmentPanel() == null)
+ {
+ return null;
+ }
+
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(getAlignmentPanel());
+ }
+
+ 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 (AlignmentPanel alignPanel : _alignwith)
+ {
+ als[a] = alignPanel.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
+ }
+ reply = getBinding().superposeStructures(als, alm, alc);
+ if (reply != null)
+ {
+ String text = MessageManager
+ .formatMessage("error.superposition_failed", reply);
+ statusBar.setText(text);
+ }
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel alignPanel : _alignwith)
+ {
+ sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+ }
+ return reply;
+ }
+
+ @Override
+ public void background_actionPerformed(ActionEvent actionEvent)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_background_colour"),
+ null);
+ if (col != null)
+ {
+ getBinding().setBackgroundColour(col);
+ }
+ }
+
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (viewerColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ 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)
+ {
+ AAStructureBindingModel binding = getBinding();
+ binding.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<>();
+ }
+ if (binding.isColourBySequence())
+ {
+ if (!binding.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel alignPanel : _colourwith)
+ {
+ binding.colourBySequence(alignPanel);
+ }
+ 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;
+ try
+ {
+ // TODO: cope with multiple PDB files in view
+ in = new BufferedReader(
+ new FileReader(getBinding().getStructureFiles()[0]));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+ }
+
+ @Override
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.appendText(getBinding().printMappings());
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ }
+
+ protected abstract String getViewerName();
+
+ /**
+ * Configures the title and menu items of the viewer panel.
+ */
+ @Override
+ public void updateTitleAndMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+ if (binding.hasFileLoadingError())
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(binding.getChainNames());
+
+ this.setTitle(binding.getViewerTitle(getViewerName(), true));
+
+ /*
+ * enable 'Superpose with' if more than one mapped structure
+ */
+ viewSelectionMenu.setEnabled(false);
+ if (getBinding().getStructureFiles().length > 1
+ && getBinding().getSequence().length > 1)
+ {
+ 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 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();
+ }
+
}