JAL-1620 version bump and release notes

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index dd29d73..eacceb0 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,13 +20,24 @@
  */
 package jalview.analysis;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
+import jalview.util.Comparison;
+import jalview.util.Format;
+import jalview.util.MapList;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
 
 /**
  * 
@@ -1009,22 +1020,29 @@ public class AlignSeq
 
       if (allowmismatch || c1 == c2)
       {
-        lastmatch = true;
-        // extend mapping interval.
+        // extend mapping interval
         if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
         {
           as1.add(Integer.valueOf(alignpos));
           as2.add(Integer.valueOf(pdbpos));
         }
+        lastmatch = true;
         lp1 = alignpos;
         lp2 = pdbpos;
       }
       else
       {
+        // extend mapping interval
+        if (lastmatch)
+        {
+          as1.add(Integer.valueOf(lp1));
+          as2.add(Integer.valueOf(lp2));
+        }
         lastmatch = false;
       }
     }
     // construct range pairs
+
     int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
             .size() + (lastmatch ? 1 : 0)];
     int i = 0;
@@ -1058,11 +1076,19 @@ public class AlignSeq
    * @param ochains
    * @param al
    * @param dnaOrProtein
-   * @param removeOldAnnots when true, old annotation is cleared before new annotation transferred
+   * @param removeOldAnnots
+   *          when true, old annotation is cleared before new annotation
+   *          transferred
+   * @return List<List<SequenceI> originals, List<SequenceI> replacement,
+   *         List<AlignSeq> alignment between each>
    */
-  public static void replaceMatchingSeqsWith(List<SequenceI> seqs, List<AlignmentAnnotation> annotations, List<SequenceI> ochains,
+  public static List<List<? extends Object>> replaceMatchingSeqsWith(
+          List<SequenceI> seqs, List<AlignmentAnnotation> annotations,
+          List<SequenceI> ochains,
           AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
   {
+    List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
+    List<AlignSeq> aligs = new ArrayList<AlignSeq>();
     if (al != null && al.getHeight() > 0)
     {
       ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
@@ -1097,10 +1123,13 @@ public class AlignSeq
         if ((q = ochains.indexOf(sp)) > -1)
         {
           seqs.set(p, sq = matches.get(q));
+          orig.add(sp);
+          repl.add(sq);
           sq.setName(sp.getName());
           sq.setDescription(sp.getDescription());
           Mapping sp2sq;
           sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+          aligs.add(aligns.get(q));
           int inspos = -1;
           for (int ap = 0; ap < annotations.size();)
           {
@@ -1113,9 +1142,10 @@ public class AlignSeq
               if (removeOldAnnots) {
                 annotations.remove(ap);
               } else {
-                AlignmentAnnotation alan = annotations.get(ap);
+                AlignmentAnnotation alan = annotations.remove(ap);
                 alan.liftOver(sq, sp2sq);
                 alan.setSequenceRef(sq);
+                sq.addAlignmentAnnotation(alan);
               }
             }
             else
@@ -1123,13 +1153,14 @@ public class AlignSeq
               ap++;
             }
           }
-          if (sq.getAnnotation() != null)
+          if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
           {
             annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
           }
         }
       }
     }
+    return Arrays.asList(orig, repl, aligs);
   }
 
   /**