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Merge branch 'develop' into patch/JAL-4110_stdout_for_tests
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
a8c93cf
..
42768a6
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-934,7
+934,7
@@
public abstract class AlignmentViewport
}
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
}
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
- // System.err.println("grey out ("+alignmentAnnotation.label+")");
+ // jalview.bin.Console.errPrintln("grey out ("+alignmentAnnotation.label+")");
return true;
}
return false;
return true;
}
return false;
@@
-1207,7
+1207,7
@@
public abstract class AlignmentViewport
{
if (sequenceSetID != null)
{
{
if (sequenceSetID != null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning - overwriting a sequenceSetId for a viewport!");
}
sequenceSetID = new String(newid);
"Warning - overwriting a sequenceSetId for a viewport!");
}
sequenceSetID = new String(newid);
@@
-2100,7
+2100,7
@@
public abstract class AlignmentViewport
{
if (aa == null)
{
{
if (aa == null)
{
- System.err.println("Null annotation row: ignoring.");
+ jalview.bin.Console.errPrintln("Null annotation row: ignoring.");
continue;
}
if (!aa.visible)
continue;
}
if (!aa.visible)
@@
-2132,7
+2132,7
@@
public abstract class AlignmentViewport
if (aa.graph > 0)
{
if (aa.graph > 0)
{
- aa.height += aa.graphHeight;
+ aa.height += aa.graphHeight+20;
}
if (aa.height == 0)
}
if (aa.height == 0)
@@
-2293,7
+2293,7
@@
public abstract class AlignmentViewport
{
if (this == av)
{
{
if (this == av)
{
- System.err.println("Ignoring recursive setCodingComplement request");
+ jalview.bin.Console.errPrintln("Ignoring recursive setCodingComplement request");
}
else
{
}
else
{