JAL-1620 version bump and release notes

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 2feeb91..64d5cd0 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.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.
@@ -20,12 +20,13 @@
  */
 package jalview.analysis;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.AlignmentI;
-
 /**
  * grab bag of useful alignment manipulation operations Expect these to be
  * refactored elsewhere at some point.
@@ -121,7 +122,41 @@ public class AlignmentUtils
     }
     AlignmentI newAl = new jalview.datamodel.Alignment(
             sq.toArray(new SequenceI[0]));
+    for (SequenceI s : sq)
+    {
+      if (s.getAnnotation() != null)
+      {
+        for (AlignmentAnnotation aa : s.getAnnotation())
+        {
+          newAl.addAnnotation(aa);
+        }
+      }
+    }
     newAl.setDataset(core.getDataset());
     return newAl;
   }
+
+  /**
+   * Returns the index (zero-based position) of a sequence in an alignment, or
+   * -1 if not found.
+   * 
+   * @param al
+   * @param seq
+   * @return
+   */
+  public static int getSequenceIndex(AlignmentI al, SequenceI seq)
+  {
+    int result = -1;
+    int pos = 0;
+    for (SequenceI alSeq : al.getSequences())
+    {
+      if (alSeq == seq)
+      {
+        result = pos;
+        break;
+      }
+      pos++;
+    }
+    return result;
+  }
 }