Merge develop to Release_2_8_3_Branch

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index c546310..bd4cc22 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -804,19 +804,23 @@ public class AlignSeq
   }
 
   /**
-   * DOCUMENT ME!
+   * Returns the given sequence with all of the given gap characters removed.
    * 
-   * @param gapChar
-   *          DOCUMENT ME!
+   * @param gapChars
+   *          a string of characters to be treated as gaps
    * @param seq
-   *          DOCUMENT ME!
+   *          the input sequence
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
-  public static String extractGaps(String gapChar, String seq)
+  public static String extractGaps(String gapChars, String seq)
   {
-    StringTokenizer str = new StringTokenizer(seq, gapChar);
-    StringBuffer newString = new StringBuffer();
+    if (gapChars == null || seq == null)
+    {
+      return null;
+    }
+    StringTokenizer str = new StringTokenizer(seq, gapChars);
+    StringBuilder newString = new StringBuilder(seq.length());
 
     while (str.hasMoreTokens())
     {
@@ -1020,22 +1024,29 @@ 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;
@@ -1146,9 +1157,10 @@ public class AlignSeq
               ap++;
             }
           }
-          if (sq.getAnnotation() != null)
+          if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
           {
-            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+            annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+                    Arrays.asList(sq.getAnnotation()));
           }
         }
       }