import java.util.Deque;
import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(cs);
+ sg.setColourScheme(
+ cs == null ? null : cs.getInstance(this, sg));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
ranges = null;
currentTree = null;
selectionGroup = null;
+ colSel = null;
setAlignment(null);
}
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+ isColSelChanged(true);
}
@Override
if (alignment.getHiddenColumns() != null
&& alignment.getHiddenColumns().hasHiddenColumns())
{
- selection = alignment.getHiddenColumns()
- .getVisibleSequenceStrings(start, end, seqs);
+ for (i = 0; i < iSize; i++)
+ {
+ Iterator<int[]> blocks = alignment.getHiddenColumns()
+ .getVisContigsIterator(start, end + 1, false);
+ selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+ }
}
else
{
start = hidden.visibleToAbsoluteColumn(start);
}
- end = hidden.getHiddenBoundaryRight(start);
+ end = hidden.getNextHiddenBoundary(false, start);
if (start == end)
{
end = max;
if (hidden != null && hidden.hasHiddenColumns())
{
start = hidden.visibleToAbsoluteColumn(end);
- start = hidden.getHiddenBoundaryLeft(start) + 1;
+ start = hidden.getNextHiddenBoundary(true, start) + 1;
}
} while (end < max);
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
- alignment.getHiddenColumns().makeVisibleAnnotation(
+ clone.makeVisibleAnnotation(
selectionGroup.getStartRes(), selectionGroup.getEndRes(),
- clone);
+ alignment.getHiddenColumns());
}
else
{
- alignment.getHiddenColumns().makeVisibleAnnotation(clone);
+ clone.makeVisibleAnnotation(alignment.getHiddenColumns());
}
ala.add(clone);
}
viewStyle.setProteinFontAsCdna(b);
}
+ @Override
+ public void setShowComplementFeatures(boolean b)
+ {
+ viewStyle.setShowComplementFeatures(b);
+ }
+
+ @Override
+ public boolean isShowComplementFeatures()
+ {
+ return viewStyle.isShowComplementFeatures();
+ }
+
+ @Override
+ public void setShowComplementFeaturesOnTop(boolean b)
+ {
+ viewStyle.setShowComplementFeaturesOnTop(b);
+ }
+
+ @Override
+ public boolean isShowComplementFeaturesOnTop()
+ {
+ return viewStyle.isShowComplementFeaturesOnTop();
+ }
+
/**
* @return true if view should scroll to show the highlighted region of a
* sequence
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
for (int seqNo = ranges
- .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
{
return currentTree;
}
+
+ /**
+ * flag set to indicate if structure views might be out of sync with sequences
+ * in the alignment
+ */
+
+ private boolean needToUpdateStructureViews = false;
+
+ @Override
+ public boolean isUpdateStructures()
+ {
+ return needToUpdateStructureViews;
+ }
+
+ @Override
+ public void setUpdateStructures(boolean update)
+ {
+ needToUpdateStructureViews = update;
+ }
+
+ @Override
+ public boolean needToUpdateStructureViews()
+ {
+ boolean update = needToUpdateStructureViews;
+ needToUpdateStructureViews = false;
+ return update;
+ }
+
+ @Override
+ public void addSequenceGroup(SequenceGroup sequenceGroup)
+ {
+ alignment.addGroup(sequenceGroup);
+
+ Color col = sequenceGroup.idColour;
+ if (col != null)
+ {
+ col = col.brighter();
+
+ for (SequenceI sq : sequenceGroup.getSequences())
+ {
+ setSequenceColour(sq, col);
+ }
+ }
+
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils
+ .mapSequenceGroup(sequenceGroup, this, codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+
+ if (col != null)
+ {
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, col);
+ }
+ }
+ }
+ // propagate the structure view update flag according to our own setting
+ codingComplement.setUpdateStructures(needToUpdateStructureViews);
+ }
+ }
+
+ @Override
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
+ }
}