import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.jws1.Discoverer;
AlignViewport viewport;
+ ViewportRanges vpRanges;
+
public AlignViewControllerI avc;
List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ vpRanges = viewport.getRanges();
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
- alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+ .getStartRes();
+ alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+ .getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
break;
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ alignPanel.setScrollValues(vpRanges.getStartRes(),
+ 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
}
break;
case KeyEvent.VK_PAGE_DOWN:
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ alignPanel.setScrollValues(vpRanges.getStartRes(),
+ vpRanges.getEndSeq());
}
break;
}
{
// propagate alignment changed.
- viewport.setEndSeq(alignment.getHeight());
+ vpRanges.setEndSeq(alignment.getHeight());
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
- viewport.setStartRes(0);
+ vpRanges.setStartRes(0);
}
else
{
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(vpRanges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ vpRanges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(vpRanges.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ vpRanges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
*/
newap.av.replaceMappings(viewport.getAlignment());
+ /*
+ * start up cDNA consensus (if applicable) now mappings are in place
+ */
+ if (newap.av.initComplementConsensus())
+ {
+ newap.refresh(true); // adjust layout of annotations
+ }
+
newap.av.viewName = getNewViewName(viewTitle);
addAlignmentPanel(newap, true);
*/
if (ResidueColourScheme.USER_DEFINED.equals(name))
{
- new UserDefinedColours(alignPanel, null);
+ new UserDefinedColours(alignPanel);
return;
}
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
- if (cs != null)
- {
- ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
- }
+ ColourMenuHelper.setColourSelected(colourMenu, cs);
viewport.setGlobalColourScheme(cs);
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
+ PDBEntry pe = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq((String) fm[0],
(DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
colourMenu.add(annotationColour);
ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
- String schemeName = colourScheme == null ? null : colourScheme
- .getSchemeName();
-
- ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+ ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
}
}