From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 2 Sep 2013 17:07:42 +0000 (+0100)
Subject: JAL-1373 pass size of sequence set to consensus rendering routines so appropriate... 
X-Git-Tag: Jalview_2_9~222^2~2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=abeb1ce92e146611f2e7b57ff3e0f8169a216991

JAL-1373 pass size of sequence set to consensus rendering routines so appropriate precision can be chosen
---

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 50b1b4b..33660b5 100755
--- 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 nseq 
    */
   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,
-            ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
+            ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
                                                                             // 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,
-          boolean includeAllConsSymbols, char[] alphabet)
+          boolean includeAllConsSymbols, char[] alphabet, long nseq)
   {
     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
--- 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,
-          boolean includeAllConsSymbols)
+          boolean includeAllConsSymbols, long nseq)
   {
     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
--- 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)
       {
-        _updateConsensusRow(cnsns);
+        _updateConsensusRow(cnsns, sequences.size());
       }
       if (cs != null)
       {
@@ -552,7 +552,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public Hashtable[] consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns)
+  private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
   {
     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,
-            ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+            ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
                                                       // for
                                                       // ignoreGapsInConsensusCalculation);
   }
diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 343e64d..c2b4d66 100644
--- 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.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
 import java.util.Hashtable;
@@ -31,6 +32,8 @@ import java.util.Hashtable;
 public class ConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
+  private long nseq=-1;
+
   public ConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
@@ -94,7 +97,9 @@ public class ConsensusThread extends AlignCalcWorker implements
       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)
       {
@@ -150,7 +155,7 @@ public class ConsensusThread extends AlignCalcWorker implements
     {
       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
--- 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.SequenceI;
 
 public class StrucConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
@@ -40,6 +41,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
   Hashtable[] hStrucConsensus;
 
+  private long nseq=-1;
+
   @Override
   public void run()
   {
@@ -107,8 +110,10 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
       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)
       {
@@ -159,7 +164,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
               alignViewport.getIgnoreGapsConsensus(),
-              alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }