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JAL-1925 update source version in license
[jalview.git]
/
src
/
jalview
/
workers
/
StrucConsensusThread.java
diff --git
a/src/jalview/workers/StrucConsensusThread.java
b/src/jalview/workers/StrucConsensusThread.java
index
6449a2b
..
9694b37
100644
(file)
--- a/
src/jalview/workers/StrucConsensusThread.java
+++ b/
src/jalview/workers/StrucConsensusThread.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-98,7
+98,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
// select rna struct to use for calculation
for (int i = 0; i < aa.length; i++)
{
// select rna struct to use for calculation
for (int i = 0; i < aa.length; i++)
{
- if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+ if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
{
rnaStruc = aa[i];
break;
{
rnaStruc = aa[i];
break;
@@
-126,11
+126,6
@@
public class StrucConsensusThread extends AlignCalcWorker implements
alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
// TODO AlignmentAnnotation rnaStruc!!!
updateResultAnnotation(true);
alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
// TODO AlignmentAnnotation rnaStruc!!!
updateResultAnnotation(true);
- if (alignViewport.getGlobalColourScheme() != null)
- {
- alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
- }
-
} catch (OutOfMemoryError error)
{
calcMan.workerCannotRun(this);
} catch (OutOfMemoryError error)
{
calcMan.workerCannotRun(this);
@@
-166,7
+161,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
+ alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);
}
}
alignViewport.isShowSequenceLogo(), nseq);
}
}