From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 12 Jun 2012 11:48:03 +0000 (+0100)
Subject: JAL-1115 refactor reordering code operating directly on Sequence collection as Alignm... 
X-Git-Tag: Jalview_2_9~481
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6357db6c20614a666b7b446aeb3260c5379637eb;p=jalview.git

JAL-1115 refactor reordering code operating directly on Sequence collection as AlignmentI method
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 9e5c4fb..5a199bb 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1457,48 +1457,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     {
       return;
     }
-
-    if (up)
-    {
-      for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
-      }
-    }
-    else
-    {
-      for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-        if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
-        if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
-      }
-    }
-
+    viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }
 
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f9de115..5a49540 100755
--- 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);
+        }
+      }
+
+    }
+  }
+
 }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 1f6390e..3d61037 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -444,4 +444,15 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
           SequenceI seqRef, SequenceGroup groupRef);
+
+  /**
+   * move the given group up or down in the alignment by the given number of rows.
+   * Implementor assumes given group is already present on alignment - no recalculations are triggered.
+   * @param sg
+   * @param map
+   * @param up
+   * @param i
+   */
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up);
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f597a60..d8157c0 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1508,52 +1508,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-
-    if (up)
-    {
-      for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
-
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
-      }
-    }
-    else
-    {
-      for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
-
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.getAlignment().getSequences().setElementAt(temp, i);
-        viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
-      }
-    }
-
+    viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }