Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 0ad4841..7e41f77 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -20,16 +20,14 @@
  */
 package jalview.controller;
 
-import java.awt.Color;
-import java.util.BitSet;
-import java.util.List;
-
+import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
@@ -37,6 +35,11 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
+
 public class AlignViewController implements AlignViewControllerI
 {
   AlignViewportI viewport = null;
@@ -76,14 +79,26 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public boolean makeGroupsFromSelection()
   {
-
-    if (viewport.getSelectionGroup() != null)
+    SequenceGroup sg = viewport.getSelectionGroup();
+    ColumnSelection cs = viewport.getColumnSelection();
+    SequenceGroup[] gps = null;
+    if (sg != null
+            && (cs == null || cs.getSelected() == null || cs.size() == 0))
     {
-      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+      gps = jalview.analysis.Grouping.makeGroupsFrom(
               viewport.getSequenceSelection(),
               viewport.getAlignmentView(true).getSequenceStrings(
                       viewport.getGapCharacter()), viewport.getAlignment()
                       .getGroups());
+    } else {
+      if (cs!=null) {
+        gps = jalview.analysis.Grouping.makeGroupsFromCols(
+                (sg == null) ? viewport.getAlignment().getSequencesArray()
+                        : sg.getSequences().toArray(new SequenceI[0]), cs,
+                viewport.getAlignment().getGroups());
+      }
+    }
+    if (gps!=null) {
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
@@ -97,7 +112,9 @@ public class AlignViewController implements AlignViewControllerI
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
         for (SequenceI sq : gps[g].getSequences(null))
+        {
           viewport.setSequenceColour(sq, col);
+        }
       }
       return true;
     }
@@ -296,4 +313,76 @@ public class AlignViewController implements AlignViewControllerI
       return false;
     }
   }
+
+
+
+  @Override
+  public void sortAlignmentByFeatureDensity(String[] typ)
+  {
+    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+  }
+
+  protected void sortBy(String[] typ, String methodText, final String method)
+  {
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
+    if (typ == null)
+    {
+      typ = fr==null ? null : fr.getDisplayedFeatureTypes();
+    }
+    String gps[] = null;
+    gps = fr==null ? null : fr.getDisplayedFeatureGroups();
+    if (typ != null)
+    {
+      ArrayList types = new ArrayList();
+      for (int i = 0; i < typ.length; i++)
+      {
+        if (typ[i] != null)
+        {
+          types.add(typ[i]);
+        }
+        typ = new String[types.size()];
+        types.toArray(typ);
+      }
+    }
+    if (gps != null)
+    {
+      ArrayList grps = new ArrayList();
+
+      for (int i = 0; i < gps.length; i++)
+      {
+        if (gps[i] != null)
+        {
+          grps.add(gps[i]);
+        }
+      }
+      gps = new String[grps.size()];
+      grps.toArray(gps);
+    }
+    AlignmentI al = viewport.getAlignment();
+
+    int start, stop;
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg != null)
+    {
+      start = sg.getStartRes();
+      stop = sg.getEndRes();
+    }
+    else
+    {
+      start = 0;
+      stop = al.getWidth();
+    }
+    SequenceI[] oldOrder = al.getSequencesArray();
+    AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+    avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
+            .getAlignment()));
+    alignPanel.paintAlignment(true);
+
+  }
+
+  @Override
+  public void sortAlignmentByFeatureScore(String[] typ)
+  {
+    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+  }
 }