JAL-345 also include any sequences that have highlighted regions

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 5662d0c..e9205f6 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -29,6 +29,7 @@ import jalview.api.FeatureRenderer;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -38,6 +39,7 @@ import jalview.io.FeaturesFile;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
+import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.List;
 
@@ -352,25 +354,25 @@ public class AlignViewController implements AlignViewControllerI
   public boolean parseFeaturesFile(String file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
-    boolean featuresFile = false;
+    boolean featuresAdded = false;
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(
-              viewport.getAlignment().getDataset(),
-              alignPanel.getFeatureRenderer().getFeatureColours(), false,
-              relaxedIdMatching);
+      featuresAdded = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+              fr.getFeatureFilters(), false, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if (featuresFile)
+    if (featuresAdded)
     {
       avcg.refreshFeatureUI(true);
-      if (alignPanel.getFeatureRenderer() != null)
+      if (fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.getFeatureRenderer().findAllFeatures(true);
+        fr.findAllFeatures(true);
       }
       if (avcg.getFeatureSettingsUI() != null)
       {
@@ -379,8 +381,108 @@ public class AlignViewController implements AlignViewControllerI
       alignPanel.paintAlignment(true, true);
     }
 
-    return featuresFile;
+    return featuresAdded;
+
+  }
+
+  /**
+   * 
+   * Add highlighted sequences to selected rows. Exclude highlighted sequences
+   * from selected rows. toggle inclusion or exclusion of highlighted sequences.
+   * or add/exclude/toggle for sequences not highlighted.
+   * 
+   * @param invert
+   *          - when true, sequences that are not highlighted are used to modify
+   *          selection
+   * @param extendCurrent
+   *          - normally true , the current selected group is modified.
+   * @param toggle
+   *          - if a select
+   * @return
+   */
+  public boolean selectHighlightedSequences(boolean invert,
+          boolean extendCurrent, boolean toggle)
+  {
+    List<SequenceI> results = alignPanel.getAlignViewport()
+            .getHighlightedSeqs();
+
+    SequenceGroup sq = (extendCurrent
+            && viewport.getSelectionGroup() != null)
+                    ? viewport.getSelectionGroup()
+                    : new SequenceGroup();
+
+    SearchResultsI searchResults = viewport.getSearchResults();
+    if (invert)
+    {
+      List<SequenceI> nothighlighted = new ArrayList();
+      for (SequenceI seq : alignPanel.getAlignViewport().getAlignment()
+              .getSequences())
+      {
+        if (!results.contains(seq) && (searchResults == null
+                || !searchResults.involvesSequence(seq)))
+        {
+          nothighlighted.add(seq);
+        }
+      }
+      results = nothighlighted;
+    }
+    else
+    {
+      // copy list and add in search results
+      results = new ArrayList(results);
+      if (searchResults != null)
+      {
+        for (SequenceI seq : alignPanel.getAlignViewport().getAlignment()
+                .getSequences())
+        {
+          if (searchResults.involvesSequence(seq))
+          {
+            results.add(seq);
+          }
+        }
+      }
+    }
+
+    if (results == null || results.size() == 0)
+    {
+      // do nothing if no selection exists
+      // unless toggle ??
+      return false;
+    }
+
+    boolean changed = false;
+
+    for (SequenceI seq : results)
+    {
+      int size = sq.getSize();
+      if (toggle)
+      {
+        sq.addOrRemove(seq, false);
+      }
+      else
+      {
+        sq.addSequence(seq, false);
+      }
+      changed |= size != sq.getSize();
+    }
+
+    if (sq.getSize() == 0)
+    {
+      viewport.setSelectionGroup(null);
+    }
+    else
+    {
+      if (sq != viewport.getSelectionGroup())
+    {
+      sq.setStartRes(0);
+      sq.setEndRes(viewport.getRanges().getAbsoluteAlignmentWidth());
+    }
+      viewport.setSelectionGroup(sq);
+    }
+
+    alignPanel.paintAlignment(false, false);
 
+    return changed;
   }
 
   @Override