JAL-1483 cut and paste from SW score model to allow scores based on sequences to...

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 693291f..5d0841e 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
@@ -493,7 +494,7 @@ public class SequenceGroup implements AnnotatedCollectionI
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
-        _updateConsensusRow(cnsns);
+        _updateConsensusRow(cnsns, sequences.size());
       }
       if (cs != null)
       {
@@ -552,7 +553,7 @@ 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 +570,7 @@ 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);
   }
@@ -612,9 +613,9 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * 
+   * @return the first column selected by this group. Runs from 0<=i<N_cols
    */
   public int getStartRes()
   {
@@ -622,9 +623,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return the groups last selected column. Runs from 0<=i<N_cols
    */
   public int getEndRes()
   {
@@ -1034,12 +1034,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
               100f, AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
+      consensus.groupRef = this;
+      consensus.label = "Consensus for " + getName();
+      consensus.description = "Percent Identity";
     }
-    consensus.hasText = true;
-    consensus.autoCalculated = true;
-    consensus.groupRef = this;
-    consensus.label = "Consensus for " + getName();
-    consensus.description = "Percent Identity";
     return consensus;
   }