JAL-1115 refactor reordering code operating directly on Sequence collection as Alignm...

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f9de115..5a49540 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1375,4 +1375,55 @@ public class Alignment implements AlignmentI
     return aa;
   }
 
+  @Override
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up)
+  {
+    synchronized (sequences)
+    {
+      if (up)
+      {
+
+        for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i - 1);
+          if (sg.getSequences(null).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i - 1, seq);
+        }
+      }
+      else
+      {
+        for (int i = sequences.size() - 2; i > -1; i--)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i + 1);
+          if (sg.getSequences(map).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i + 1, seq);
+        }
+      }
+
+    }
+  }
+
 }