git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
(JAL-1052) basic consensus line parsing to rna structure lines
[jalview.git]
/
src
/
jalview
/
workers
/
StrucConsensusThread.java
diff --git
a/src/jalview/workers/StrucConsensusThread.java
b/src/jalview/workers/StrucConsensusThread.java
index
9143ad7
..
69236d8
100644
(file)
--- a/
src/jalview/workers/StrucConsensusThread.java
+++ b/
src/jalview/workers/StrucConsensusThread.java
@@
-18,6
+18,9
@@
public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
{
super(alignViewport, alignPanel);
}
{
super(alignViewport, alignPanel);
}
+ AlignmentAnnotation strucConsensus;
+ Hashtable[] hStrucConsensus;
+
public void run()
{
try
public void run()
{
try
@@
-51,8
+54,8
@@
public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
calcMan.workerComplete(this);
return;
}
calcMan.workerComplete(this);
return;
}
- AlignmentAnnotation strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
- Hashtable[] hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
+ strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
+ hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
strucConsensus.annotations = null;
strucConsensus.annotations = new Annotation[aWidth];
strucConsensus.annotations = null;
strucConsensus.annotations = new Annotation[aWidth];
@@
-64,7
+67,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
// 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)
+ if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
{
rnaStruc = aa[i];
break;
{
rnaStruc = aa[i];
break;
@@
-115,9
+118,6
@@
public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
public void updateResultAnnotation(boolean immediate)
{
public void updateResultAnnotation(boolean immediate)
{
- AlignmentAnnotation strucConsensus = alignViewport
- .getAlignmentStrucConsensusAnnotation();
- Hashtable[] hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
{
StructureFrequency.completeConsensus(strucConsensus,
if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
{
StructureFrequency.completeConsensus(strucConsensus,