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JAL-3201 restore group colours correctly from project
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
01ec8b1
..
0ea31d7
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-662,7
+662,8
@@
public abstract class AlignmentViewport
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(cs);
+ sg.setColourScheme(
+ cs == null ? null : cs.getInstance(sg, hiddenRepSequences));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
@@
-1636,6
+1637,7
@@
public abstract class AlignmentViewport
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+ isColSelChanged(true);
}
@Override
}
@Override
@@
-2786,7
+2788,7
@@
public abstract class AlignmentViewport
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
for (int seqNo = ranges
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))
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))