import jalview.schemes.ColourSchemes;
import jalview.structure.StructureMapping;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.structures.models.AAStructureBindingModel.ColourBy;
import jalview.util.MessageManager;
import java.awt.Color;
}
/**
+ * @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 true if this Jmol instance is linked with the given alignPanel
return _aps.contains(ap2.av.getSequenceSetId());
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ public boolean isUsedForAligment(AlignmentPanel ap2)
{
return (_alignwith != null) && _alignwith.contains(ap2);
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ public boolean isUsedForColourBy(Object o)
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ return (_colourwith != null) && _colourwith.contains(o);
}
/**
boolean enableColourBySeq)
{
useAlignmentPanelForColourbyseq(nap);
- getBinding().setColourBySequence(enableColourBySeq);
seqColour.setSelected(enableColourBySeq);
viewerColour.setSelected(!enableColourBySeq);
+
+ getBinding().setColourBy(enableColourBySeq ? ColourBy.Sequence : ColourBy.Viewer);
}
public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
*/
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;
{ 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);
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
- */
@Override
- public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+ public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
String[] chains, final AlignmentViewPanel apanel, String pdbId)
{
/*
* JAL-1742 exclude view with this structure already mapped (don't offer
- * to align chain B to chain A of the same structure)
+ * to align chain B to chain A of the same structure); code may defend
+ * against this possibility before we reach here
*/
if (hasPdbId(pdbId))
{
- return false;
+ return;
}
- AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this
+ AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this
// cast fails
- useAlignmentPanelForSuperposition(ap);
- addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return true;
+ useAlignmentPanelForSuperposition(alignPanel);
+ addStructure(pdbentry, seq, chains, alignPanel.alignFrame);
}
/**
}
}
- /**
- * 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
- */
@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)
+ if (alreadyMapped == null)
{
- /*
- * the PDB file is already loaded
- */
- addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
- finished = true;
+ return false;
}
- return finished;
+
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ return true;
}
void setChainMenuItems(List<String> chainNames)
AlignmentI al = getAlignmentPanel().av.getAlignment();
ColourSchemeI cs = ColourSchemes.getInstance()
.getColourScheme(colourSchemeName, al, null);
- getBinding().setJalviewColourScheme(cs);
+ getBinding().setJalviewColourScheme(cs, getAlignmentPanel());
}
/**
colourMenu.removeAll();
AlignmentI al = getAlignmentPanel().av.getAlignment();
+ colourMenu.addSeparator();
+
/*
* add colour by sequence, by chain, by charge and cysteine
*/
colourMenu.add(chargeColour);
chargeColour.setEnabled(!al.isNucleotide());
- /*
- * add all 'simple' (per-residue) colour schemes registered to Jalview
- */
+ /*
+ * add all colour schemes registered to Jalview
+ */
ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
- al, true);
+ al);
/*
* add 'colour by viewer' (menu item text is set in subclasses)
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
int[] alm = new int[_alignwith.size()];
int a = 0;
- for (AlignmentPanel ap : _alignwith)
+ for (AlignmentPanel alignPanel : _alignwith)
{
- als[a] = ap.av.getAlignment();
+ als[a] = alignPanel.av.getAlignment();
alm[a] = -1;
- alc[a++] = ap.av.getAlignment().getHiddenColumns();
+ alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
}
reply = getBinding().superposeStructures(als, alm, alc);
if (reply != null)
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
+ for (AlignmentPanel alignPanel : _alignwith)
{
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
}
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
if (viewerColour.isSelected())
{
// disable automatic sequence colouring.
- getBinding().setColourBySequence(false);
+ getBinding().setColourBy(ColourBy.Viewer);
}
}
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
AAStructureBindingModel binding = getBinding();
- binding.setColourBySequence(seqColour.isSelected());
+ boolean colourBySequence = seqColour.isSelected();
if (_colourwith == null)
{
_colourwith = new Vector<>();
}
- if (binding.isColourBySequence())
+ if (colourBySequence)
{
if (!binding.isLoadingFromArchive())
{
}
}
// Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
+ for (AlignmentPanel alignPanel : _colourwith)
{
- binding.colourBySequence(ap);
+ binding.colourBySequence(alignPanel);
}
seqColoursApplied = true;
}
/**
* Configures the title and menu items of the viewer panel.
*/
+ @Override
public void updateTitleAndMenus()
{
AAStructureBindingModel binding = getBinding();
}
@Override
+ public String toString()
+ {
+ return getTitle();
+ }
+
+ @Override
public boolean hasMapping()
{
if (worker != null && (addingStructures || _started))
return seqColoursApplied;
}
+ @Override
+ public void raiseViewer()
+ {
+ toFront();
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff