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JAL-3285 small code changes to ConsensusThread not included in merge
author
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 12:38:44 +0000
(13:38 +0100)
committer
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 12:38:44 +0000
(13:38 +0100)
src/jalview/workers/ConsensusThread.java
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diff --git
a/src/jalview/workers/ConsensusThread.java
b/src/jalview/workers/ConsensusThread.java
index
2c4cbde
..
f5cad71
100644
(file)
--- a/
src/jalview/workers/ConsensusThread.java
+++ b/
src/jalview/workers/ConsensusThread.java
@@
-50,7
+50,7
@@
public class ConsensusThread extends AlignCalcWorker
try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- AlignmentAnnotation gap = getOccupancyAnnotation();
+ AlignmentAnnotation gap = getGapAnnotation();
if ((consensus == null && gap == null) || calcMan.isPending(this))
{
calcMan.workerComplete(this);
if ((consensus == null && gap == null) || calcMan.isPending(this))
{
calcMan.workerComplete(this);
@@
-140,7
+140,7
@@
public class ConsensusThread extends AlignCalcWorker
ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
true);
ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
true);
- alignViewport.setConsensusProfiles(hconsensus);
+ alignViewport.setSequenceConsensusHash(hconsensus);
setColourSchemeConsensus(hconsensus);
}
setColourSchemeConsensus(hconsensus);
}
@@
-179,9
+179,9
@@
public class ConsensusThread extends AlignCalcWorker
*
* @return
*/
*
* @return
*/
- protected AlignmentAnnotation getOccupancyAnnotation()
+ protected AlignmentAnnotation getGapAnnotation()
{
{
- return alignViewport.getOccupancyAnnotation();
+ return alignViewport.getAlignmentGapAnnotation();
}
/**
}
/**
@@
-202,10
+202,10
@@
public class ConsensusThread extends AlignCalcWorker
&& hconsensus != null)
{
deriveConsensus(consensus, hconsensus);
&& hconsensus != null)
{
deriveConsensus(consensus, hconsensus);
- AlignmentAnnotation occupancy = getOccupancyAnnotation();
- if (occupancy != null)
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
{
{
- deriveOccupancy(occupancy, hconsensus);
+ deriveOccupancy(gap, hconsensus);
}
}
}
}
}
}
@@
-237,11
+237,11
@@
public class ConsensusThread extends AlignCalcWorker
* @param hconsensus
* the computed consensus data
*/
* @param hconsensus
* the computed consensus data
*/
- protected void deriveOccupancy(AlignmentAnnotation gapAnnotation,
+ protected void deriveGap(AlignmentAnnotation gapAnnotation,
ProfilesI hconsensus)
{
long nseq = getSequences().length;
ProfilesI hconsensus)
{
long nseq = getSequences().length;
- AAFrequency.completeOccupancyAnnot(gapAnnotation, hconsensus,
+ AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
nseq);
}
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
nseq);
}
@@
-254,6
+254,6
@@
public class ConsensusThread extends AlignCalcWorker
protected Object getViewportConsensus()
{
// TODO convert ComplementConsensusThread to use Profile
protected Object getViewportConsensus()
{
// TODO convert ComplementConsensusThread to use Profile
- return alignViewport.getConsensusProfiles();
+ return alignViewport.getSequenceConsensusHash();
}
}
}
}