X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=4d734c7b179cce6d778760ba1e7b70b18d46c3e6;hb=0155cd99a3b96570ad67dbc992c731ba2ce74bb9;hp=077f9cd7aaccd3f039f04946abccb321625bd510;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 077f9cd..4d734c7 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -20,21 +20,25 @@
  */
 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;
 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
 {
@@ -96,7 +100,9 @@ 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;
     }
@@ -276,16 +282,17 @@ public class AlignViewController implements AlignViewControllerI
       }
       viewport.setColumnSelection(cs);
       alignPanel.paintAlignment(true);
-      avcg.setStatus((toggle ? "Toggled " : "Marked ")
-              + (invert ? (alw - alStart) - bs.cardinality() : bs
-                      .cardinality()) + " columns "
-              + (invert ? "not " : "") + "containing features of type "
-              + featureType + " across " + nseq + " sequence(s)");
+      avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
+    		  new String[]{
+    	  			(toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
+    	  			(invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
+    	  			featureType, Integer.valueOf(nseq).toString()
+      		 	}));
       return true;
     }
     else
     {
-      avcg.setStatus("No features of type " + featureType + " found.");
+      avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
       if (!extendCurrent && cs != null)
       {
         cs.clear();
@@ -294,4 +301,76 @@ 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);
+  }
 }