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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
workers
/
ConsensusThread.java
diff --git
a/src/jalview/workers/ConsensusThread.java
b/src/jalview/workers/ConsensusThread.java
index
284f1a1
..
8882b53
100644
(file)
--- a/
src/jalview/workers/ConsensusThread.java
+++ b/
src/jalview/workers/ConsensusThread.java
@@
-46,7
+46,7
@@
public class ConsensusThread extends AlignCalcWorker
return;
}
calcMan.notifyStart(this);
return;
}
calcMan.notifyStart(this);
- long started = System.currentTimeMillis();
+ // long started = System.currentTimeMillis();
try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
@@
-58,12
+58,13
@@
public class ConsensusThread extends AlignCalcWorker
}
while (!calcMan.notifyWorking(this))
{
}
while (!calcMan.notifyWorking(this))
{
- // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
+ // jalview.bin.Console.errPrintln("Thread
+ // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
try
{
if (ap != null)
{
try
{
if (ap != null)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
Thread.sleep(200);
} catch (Exception ex)
}
Thread.sleep(200);
} catch (Exception ex)
@@
-92,7
+93,7
@@
public class ConsensusThread extends AlignCalcWorker
if (ap != null)
{
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
} catch (OutOfMemoryError error)
{
}
} catch (OutOfMemoryError error)
{
@@
-117,7
+118,10
@@
public class ConsensusThread extends AlignCalcWorker
protected void eraseConsensus(int aWidth)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
protected void eraseConsensus(int aWidth)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- consensus.annotations = new Annotation[aWidth];
+ if (consensus != null)
+ {
+ consensus.annotations = new Annotation[aWidth];
+ }
AlignmentAnnotation gap = getGapAnnotation();
if (gap != null)
{
AlignmentAnnotation gap = getGapAnnotation();
if (gap != null)
{