todo for sortbyPID operating on current selection rather than all alignment

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index cde4b4f..a3493f7 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -25,7 +25,12 @@ import jalview.util.*;
 
 /** 
  * Routines for manipulating the order of a multiple sequence alignment
- * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization. 
+ * TODO: this class retains some global states concerning sort-order which should be made attributes for the caller's alignment visualization.
+ * TODO: refactor to allow a subset of selected sequences to be sorted within the context of a whole alignment.
+ * Sort method template is: SequenceI[] tobesorted, [ input data mapping to each tobesorted element to use ], Alignment context of tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie seuqence to be sorted w.r.t.])
+ * sortinplace implies that the sorted vector resulting from applying the operation to tobesorted should be mapped back to the original positions in alignment.
+ * Otherwise, normal behaviour is to re order alignment so that tobesorted is sorted and grouped together starting from the first tobesorted position in the alignment.
+ * e.g. (a,tb2,b,tb1,c,tb3 becomes a,tb1,tb2,tb3,b,c)
  */
 public class AlignmentSorter
 {
@@ -39,12 +44,13 @@ public class AlignmentSorter
   private static String lastSortByScore;
 
   /**
-   * Sort by Percentage Identity
+   * Sort by Percentage Identity w.r.t. s
    *
    * @param align AlignmentI
    * @param s SequenceI
+   * @param tosort sequences from align that are to be sorted.
    */
-  public static void sortByPID(AlignmentI align, SequenceI s)
+  public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort)
   {
     int nSeq = align.getHeight();
 

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5b6a8a5..5620a3e 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2106,7 +2106,7 @@ public class AlignFrame
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
-                              viewport.getAlignment().getSequenceAt(0));
+                              viewport.getAlignment().getSequenceAt(0), null);
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
                                     viewport.alignment));
     alignPanel.paintAlignment(true);

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 289ffbc..1c488fe 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2866,7 +2866,7 @@ public class AlignFrame
   {
     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
-                              viewport.getAlignment().getSequenceAt(0));
+                              viewport.getAlignment().getSequenceAt(0), null);
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
                                     viewport.alignment));
     alignPanel.paintAlignment(true);
@@ -3129,7 +3129,7 @@ public class AlignFrame
       public void actionPerformed(ActionEvent e)
       {
         SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
-        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
+        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup());
         addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
         alignPanel.paintAlignment(true);
       }