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JAL-653 AlignedCodonFrame collections changed from Set to List
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignViewport.java
diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
fdc6a0c
..
7ef2d59
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-20,8
+20,6
@@
*/
package jalview.appletgui;
*/
package jalview.appletgui;
-import java.awt.Font;
-
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.JalviewLite;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.JalviewLite;
@@
-40,8
+38,10
@@
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Font;
+
public class AlignViewport extends AlignmentViewport implements
public class AlignViewport extends AlignmentViewport implements
- AlignViewportI, SelectionSource, VamsasSource, CommandListener
+ SelectionSource, VamsasSource, CommandListener
{
boolean cursorMode = false;
{
boolean cursorMode = false;
@@
-187,8
+187,13
@@
public class AlignViewport extends AlignmentViewport implements
if (applet != null)
{
if (applet != null)
{
- String colour = applet.getParameter("defaultColour");
-
+ String colour = al.isNucleotide() ? applet
+ .getParameter("defaultColourNuc") : applet
+ .getParameter("defaultColourProt");
+ if (colour == null)
+ {
+ colour = applet.getParameter("defaultColour");
+ }
if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
@@
-287,7
+292,6
@@
public class AlignViewport extends AlignmentViewport implements
return font;
}
return font;
}
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
@@
-303,7
+307,6
@@
public class AlignViewport extends AlignmentViewport implements
return currentTree;
}
return currentTree;
}
-
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
@@
-325,8
+328,8
@@
public class AlignViewport extends AlignmentViewport implements
public void sendSelection()
{
getStructureSelectionManager().sendSelection(
public void sendSelection()
{
getStructureSelectionManager().sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
/**
}
/**