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Merge branch 'develop' into bug/JAL-2399textColour
[jalview.git]
/
src
/
jalview
/
appletgui
/
OverviewPanel.java
diff --git
a/src/jalview/appletgui/OverviewPanel.java
b/src/jalview/appletgui/OverviewPanel.java
index
e2d986e
..
3ef2936
100755
(executable)
--- a/
src/jalview/appletgui/OverviewPanel.java
+++ b/
src/jalview/appletgui/OverviewPanel.java
@@
-21,6
+21,7
@@
package jalview.appletgui;
import jalview.datamodel.SequenceI;
package jalview.appletgui;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
@@
-76,7
+77,8
@@
public class OverviewPanel extends Panel implements Runnable,
sr.forOverview = true;
fr = new FeatureRenderer(av);
sr.forOverview = true;
fr = new FeatureRenderer(av);
- od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
+ od = new OverviewDimensions(av.getRanges(),
+ (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
setSize(new Dimension(od.getWidth(), od.getHeight()));
addComponentListener(new ComponentAdapter()
setSize(new Dimension(od.getWidth(), od.getHeight()));
addComponentListener(new ComponentAdapter()
@@
-208,7
+210,9
@@
public class OverviewPanel extends Panel implements Runnable,
buildImage(sampleRow, sampleCol, mg);
buildImage(sampleRow, sampleCol, mg);
- if (av.isShowAnnotation())
+ // check for conservation annotation to make sure overview works for DNA too
+ if (av.isShowAnnotation()
+ && (av.getAlignmentConservationAnnotation() != null))
{
for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
{
{
for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
{
@@
-248,6
+252,7
@@
public class OverviewPanel extends Panel implements Runnable,
int sameCol = 0;
SequenceI seq = null;
int sameCol = 0;
SequenceI seq = null;
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
final boolean hasHiddenCols = av.hasHiddenColumns();
boolean hiddenRow = false;
final boolean hasHiddenCols = av.hasHiddenColumns();
boolean hiddenRow = false;
@@
-277,7
+282,7
@@
public class OverviewPanel extends Panel implements Runnable,
lastcol = (int) (col * sampleCol);
color = getColumnColourFromSequence(seq, hiddenRow,
lastcol = (int) (col * sampleCol);
color = getColumnColourFromSequence(seq, hiddenRow,
- hasHiddenCols, lastcol);
+ hasHiddenCols, lastcol, finder);
mg.setColor(color);
if (sameCol == 1 && sameRow == 1)
mg.setColor(color);
if (sameCol == 1 && sameRow == 1)
@@
-305,21
+310,12
@@
public class OverviewPanel extends Panel implements Runnable,
*/
private Color getColumnColourFromSequence(
jalview.datamodel.SequenceI seq, boolean hiddenRow,
*/
private Color getColumnColourFromSequence(
jalview.datamodel.SequenceI seq, boolean hiddenRow,
- boolean hasHiddenCols, int lastcol)
+ boolean hasHiddenCols, int lastcol, FeatureColourFinder finder)
{
{
- Color color;
+ Color color = Color.white;
if (seq.getLength() > lastcol)
{
if (seq.getLength() > lastcol)
{
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white;
+ color = sr.getResidueColour(seq, lastcol, finder);
}
if (hiddenRow
}
if (hiddenRow