import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import java.util.Deque;
import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
public abstract class AlignmentViewport
implements AlignViewportI, CommandListener, VamsasSource
{
- final protected ViewportRanges ranges;
+ protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(cs);
+ sg.setColourScheme(cs.getInstance(sg, hiddenRepSequences));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
groupConsensus = null;
groupConservation = null;
hconsensus = null;
+ hconservation = null;
hcomplementConsensus = null;
- // colour scheme may hold reference to consensus
- residueShading = null;
- // TODO remove listeners from changeSupport?
+ gapcounts = null;
+ calculator = null;
+ residueShading = null; // may hold a reference to Consensus
changeSupport = null;
+ ranges = null;
+ currentTree = null;
+ selectionGroup = null;
setAlignment(null);
}
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
- changeSupport.removePropertyChangeListener(listener);
+ if (changeSupport != null)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
}
/**
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
{
{
if (start == 0)
{
- start = hidden.adjustForHiddenColumns(start);
+ 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.adjustForHiddenColumns(end);
- start = hidden.getHiddenBoundaryLeft(start) + 1;
+ start = hidden.visibleToAbsoluteColumn(end);
+ 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);
}
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))
*/
private SearchResultsI searchResults = null;
+ protected TreeModel currentTree = null;
+
@Override
public boolean hasSearchResults()
{
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
+
+ @Override
+ public void setCurrentTree(TreeModel tree)
+ {
+ currentTree = tree;
+ }
+
+ @Override
+ public TreeModel getCurrentTree()
+ {
+ return currentTree;
+ }
}