From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 13 Nov 2017 14:11:08 +0000 (+0000)
Subject: JAL-2176 removed unused Sequence.index
X-Git-Tag: Release_2_10_3b1~43
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2353023a8b9d78c2da77f1d17b2ffc41bcec55c7;hp=4c06e8c6f75364866922a4e5a26b2433d237d850

JAL-2176 removed unused Sequence.index
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 96b0757..d254a17 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -77,11 +77,6 @@ public class Sequence extends ASequence implements SequenceI
    */
   Vector<AlignmentAnnotation> annotation;
 
-  /**
-   * The index of the sequence in a MSA
-   */
-  int index = -1;
-
   private SequenceFeaturesI sequenceFeatureStore;
 
   /*
@@ -1682,30 +1677,6 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-  /**
-   * @return The index (zero-based) on this sequence in the MSA. It returns
-   *         {@code -1} if this information is not available.
-   */
-  @Override
-  public int getIndex()
-  {
-    return index;
-  }
-
-  /**
-   * Defines the position of this sequence in the MSA. Use the value {@code -1}
-   * if this information is undefined.
-   * 
-   * @param The
-   *          position for this sequence. This value is zero-based (zero for
-   *          this first sequence)
-   */
-  @Override
-  public void setIndex(int value)
-  {
-    index = value;
-  }
-
   @Override
   public void setRNA(RNA r)
   {
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6e6d1aa..9ad0a61 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -449,17 +449,6 @@ public interface SequenceI extends ASequenceI
   public void transferAnnotation(SequenceI entry, Mapping mp);
 
   /**
-   * @param index
-   *          The sequence index in the MSA
-   */
-  public void setIndex(int index);
-
-  /**
-   * @return The index of the sequence in the alignment
-   */
-  public int getIndex();
-
-  /**
    * @return The RNA of the sequence in the alignment
    */
 
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a603cca..2340283 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -174,11 +174,6 @@ public abstract class AlignFile extends FileParse
     }
     parseCalled = true;
     parse();
-    // sets the index of each sequence in the alignment
-    for (int i = 0, c = seqs.size(); i < c; i++)
-    {
-      seqs.get(i).setIndex(i);
-    }
   }
 
   /**