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1110493
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JAL-1373 pass size of sequence set to consensus rendering routines so appropriate...
author
Jim Procter
<jprocter@compbio.dundee.ac.uk>
Mon, 2 Sep 2013 17:07:42 +0000
(18:07 +0100)
committer
Jim Procter
<jprocter@compbio.dundee.ac.uk>
Mon, 2 Sep 2013 17:07:42 +0000
(18:07 +0100)
src/jalview/analysis/AAFrequency.java
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src/jalview/analysis/StructureFrequency.java
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src/jalview/datamodel/SequenceGroup.java
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src/jalview/workers/ConsensusThread.java
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src/jalview/workers/StrucConsensusThread.java
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diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
50b1b4b
..
33660b5
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-194,14
+194,15
@@
public class AAFrequency
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
* @param width
* @param ignoreGapsInConsensusCalculation
* @param includeAllConsSymbols
+ * @param nseq
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols)
+ boolean includeAllConsSymbols, long nseq)
{
completeConsensus(consensus, hconsensus, iStart, width,
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
// char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
// char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
@@
-209,7
+210,7
@@
public class AAFrequency
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols, char[] alphabet)
+ boolean includeAllConsSymbols, char[] alphabet, long nseq)
{
float tval, value;
if (consensus == null || consensus.annotations == null
{
float tval, value;
if (consensus == null || consensus.annotations == null
diff --git
a/src/jalview/analysis/StructureFrequency.java
b/src/jalview/analysis/StructureFrequency.java
index
08bb3fd
..
fe022c0
100644
(file)
--- a/
src/jalview/analysis/StructureFrequency.java
+++ b/
src/jalview/analysis/StructureFrequency.java
@@
-299,7
+299,7
@@
public class StructureFrequency
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols)
+ boolean includeAllConsSymbols, long nseq)
{
float tval, value;
if (consensus == null || consensus.annotations == null
{
float tval, value;
if (consensus == null || consensus.annotations == null
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
65dc13f
..
5fcd2bf
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-493,7
+493,7
@@
public class SequenceGroup implements AnnotatedCollectionI
endRes + 1, showSequenceLogo);
if (consensus != null)
{
endRes + 1, showSequenceLogo);
if (consensus != null)
{
- _updateConsensusRow(cnsns);
+ _updateConsensusRow(cnsns, sequences.size());
}
if (cs != null)
{
}
if (cs != null)
{
@@
-552,7
+552,7
@@
public class SequenceGroup implements AnnotatedCollectionI
public Hashtable[] consensusData = null;
public Hashtable[] consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns)
+ private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
{
if (consensus == null)
{
{
if (consensus == null)
{
@@
-569,7
+569,7
@@
public class SequenceGroup implements AnnotatedCollectionI
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
- ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
// for
// ignoreGapsInConsensusCalculation);
}
// for
// ignoreGapsInConsensusCalculation);
}
diff --git
a/src/jalview/workers/ConsensusThread.java
b/src/jalview/workers/ConsensusThread.java
index
343e64d
..
c2b4d66
100644
(file)
--- a/
src/jalview/workers/ConsensusThread.java
+++ b/
src/jalview/workers/ConsensusThread.java
@@
-24,6
+24,7
@@
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import java.util.Hashtable;
import jalview.schemes.ColourSchemeI;
import java.util.Hashtable;
@@
-31,6
+32,8
@@
import java.util.Hashtable;
public class ConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
public class ConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
+ private long nseq=-1;
+
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
@@
-94,7
+97,9
@@
public class ConsensusThread extends AlignCalcWorker implements
hconsensus = new Hashtable[aWidth];
try
{
hconsensus = new Hashtable[aWidth];
try
{
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ SequenceI aseqs[] = alignment.getSequencesArray();
+ nseq = aseqs.length;
+ AAFrequency.calculate(aseqs, 0,
alignment.getWidth(), hconsensus, true);
} catch (ArrayIndexOutOfBoundsException x)
{
alignment.getWidth(), hconsensus, true);
} catch (ArrayIndexOutOfBoundsException x)
{
@@
-150,7
+155,7
@@
public class ConsensusThread extends AlignCalcWorker implements
{
AAFrequency.completeConsensus(consensus, hconsensus, 0,
hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
{
AAFrequency.completeConsensus(consensus, hconsensus, 0,
hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ alignViewport.isShowSequenceLogo(), nseq);
}
}
}
}
}
}
diff --git
a/src/jalview/workers/StrucConsensusThread.java
b/src/jalview/workers/StrucConsensusThread.java
index
86c3336
..
25e5cde
100644
(file)
--- a/
src/jalview/workers/StrucConsensusThread.java
+++ b/
src/jalview/workers/StrucConsensusThread.java
@@
-26,6
+26,7
@@
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
@@
-40,6
+41,8
@@
public class StrucConsensusThread extends AlignCalcWorker implements
Hashtable[] hStrucConsensus;
Hashtable[] hStrucConsensus;
+ private long nseq=-1;
+
@Override
public void run()
{
@Override
public void run()
{
@@
-107,8
+110,10
@@
public class StrucConsensusThread extends AlignCalcWorker implements
try
{
try
{
- jalview.analysis.StructureFrequency.calculate(
- alignment.getSequencesArray(), 0, alignment.getWidth(),
+ final SequenceI[] arr=
+ alignment.getSequencesArray();
+ nseq = arr.length;
+ jalview.analysis.StructureFrequency.calculate(arr, 0, alignment.getWidth(),
hStrucConsensus, true, rnaStruc);
} catch (ArrayIndexOutOfBoundsException x)
{
hStrucConsensus, true, rnaStruc);
} catch (ArrayIndexOutOfBoundsException x)
{
@@
-159,7
+164,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
alignViewport.getIgnoreGapsConsensus(),
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ alignViewport.isShowSequenceLogo(), nseq);
}
}
}
}