X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=ca2ae6d552f7cef5bca66cfc13d24270eaf4946b;hb=08c587d9947f357382199bdb6900c263efc62739;hp=dbc3524e4a509d2c3e177d64a4fe5ff4a9e04a54;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index dbc3524..ca2ae6d 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,23 +20,26 @@
  */
 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.io.FeaturesFile;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
 public class AlignViewController implements AlignViewControllerI
 {
   AlignViewportI viewport = null;
@@ -76,14 +79,28 @@ 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.isEmpty()))
+    {
+      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)
     {
-      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
-              viewport.getSequenceSelection(),
-              viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()), viewport.getAlignment()
-                      .getGroups());
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
@@ -97,7 +114,9 @@ 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;
     }
@@ -162,13 +181,7 @@ public class AlignViewController implements AlignViewControllerI
       int tfeat = 0;
       if (sq != null)
       {
-        SequenceI dsq = sq.getDatasetSequence();
-        while (dsq.getDatasetSequence() != null)
-        {
-          dsq = dsq.getDatasetSequence();
-        }
-        ;
-        SequenceFeature[] sf = dsq.getSequenceFeatures();
+        SequenceFeature[] sf = sq.getSequenceFeatures();
         if (sf != null)
         {
           int ist = sq.findIndex(sq.getStart());
@@ -277,17 +290,22 @@ public class AlignViewController implements AlignViewControllerI
       }
       viewport.setColumnSelection(cs);
       alignPanel.paintAlignment(true);
-      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()
-      		 	}));
+      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(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
+      avcg.setStatus(MessageManager.formatMessage(
+              "label.no_feature_of_type_found",
+              new String[] { featureType }));
       if (!extendCurrent && cs != null)
       {
         cs.clear();
@@ -296,4 +314,85 @@ public class AlignViewController implements AlignViewControllerI
       return false;
     }
   }
+
+  @Override
+  public void sortAlignmentByFeatureDensity(List<String> typ)
+  {
+    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+  }
+
+  protected void sortBy(List<String> typ, String methodText,
+          final String method)
+  {
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
+    if (typ == null && fr != null)
+    {
+      typ = fr.getDisplayedFeatureTypes();
+    }
+    List<String> gps = null;
+    if (fr != null)
+    {
+      gps = fr.getDisplayedFeatureGroups();
+    }
+    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(List<String> typ)
+  {
+    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+  }
+
+  @Override
+  public boolean parseFeaturesFile(String file, String protocol,
+          boolean relaxedIdMatching)
+  {
+    boolean featuresFile = false;
+    try
+    {
+      featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
+              .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+              .getFeatureColours(), false, relaxedIdMatching);
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    if (featuresFile)
+    {
+      avcg.refreshFeatureUI(true);
+      if (alignPanel.getFeatureRenderer() != null)
+      {
+        // update the min/max ranges where necessary
+        alignPanel.getFeatureRenderer().findAllFeatures(true);
+      }
+      if (avcg.getFeatureSettingsUI() != null)
+      {
+        avcg.getFeatureSettingsUI().discoverAllFeatureData();
+      }
+      alignPanel.paintAlignment(true);
+    }
+
+    return featuresFile;
+
+  }
 }