JAL-4062 avc operation and model method for copying SearchResultsI.getMatchingSubSequ...

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index f45afa5..4434331 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -20,6 +20,10 @@
  */
 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;
@@ -29,19 +33,17 @@ 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;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
 import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
-import java.awt.Color;
-import java.util.BitSet;
-import java.util.List;
-
 public class AlignViewController implements AlignViewControllerI
 {
   AlignViewportI viewport = null;
@@ -168,8 +170,9 @@ public class AlignViewController implements AlignViewControllerI
     BitSet bs = new BitSet();
     boolean searchSelection = viewport.getSelectionGroup() != null
             && !extendCurrent;
-    SequenceCollectionI sqcol = searchSelection ? viewport
-            .getSelectionGroup() : viewport.getAlignment();
+    SequenceCollectionI sqcol = searchSelection
+            ? viewport.getSelectionGroup()
+            : viewport.getAlignment();
 
     int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
@@ -207,8 +210,9 @@ public class AlignViewController implements AlignViewControllerI
     {
       String key = searchSelection ? "label.no_feature_found_selection"
               : "label.no_feature_of_type_found";
-      avcg.setStatus(MessageManager.formatMessage(key,
-              new String[] { featureType }));
+      avcg.setStatus(
+              MessageManager.formatMessage(key, new String[]
+              { featureType }));
       if (!extendCurrent)
       {
         cs.clear();
@@ -229,11 +233,11 @@ public class AlignViewController implements AlignViewControllerI
    * @param bs
    * @return
    */
-  int findColumnsWithFeature(String featureType,
-          SequenceCollectionI sqcol, BitSet bs)
+  int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol,
+          BitSet bs)
   {
-    FeatureRenderer fr = alignPanel == null ? null : alignPanel
-            .getFeatureRenderer();
+    FeatureRenderer fr = alignPanel == null ? null
+            : alignPanel.getFeatureRenderer();
 
     final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
     final int endColumn = sqcol.getEndRes() + 1;
@@ -244,8 +248,8 @@ public class AlignViewController implements AlignViewControllerI
       if (sq != null)
       {
         // int ist = sq.findPosition(sqcol.getStartRes());
-        List<SequenceFeature> sfs = sq.findFeatures(startColumn,
-                endColumn, featureType);
+        List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn,
+                featureType);
 
         boolean found = false;
         for (SequenceFeature sf : sfs)
@@ -310,16 +314,33 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureDensity(List<String> typ)
   {
-    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+    String methodText = MessageManager.getString("label.sort_by_density");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
   }
 
-  protected void sortBy(List<String> typ, String methodText,
+  /**
+   * Sorts the alignment (or current selection) by either average score or
+   * density of the specified feature types, and adds to the command history. If
+   * {@code types} is null, all visible feature types are used for the sort. If
+   * no feature types apply, does nothing.
+   * 
+   * @param types
+   * @param methodText
+   *          - text shown in Undo/Redo command
+   * @param method
+   *          - passed to jalview.analysis.AlignmentSorter.sortByFeatures()
+   */
+  protected void sortByFeatures(List<String> types, String methodText,
           final String method)
   {
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
-    if (typ == null && fr != null)
+    if (types == null && fr != null)
+    {
+      types = fr.getDisplayedFeatureTypes();
+    }
+    if (types.isEmpty())
     {
-      typ = fr.getDisplayedFeatureTypes();
+      return; // nothing to do
     }
     List<String> gps = null;
     if (fr != null)
@@ -341,7 +362,7 @@ public class AlignViewController implements AlignViewControllerI
       stop = al.getWidth();
     }
     SequenceI[] oldOrder = al.getSequencesArray();
-    AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+    AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
     avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
             viewport.getAlignment()));
     alignPanel.paintAlignment(true, false);
@@ -351,11 +372,12 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureScore(List<String> typ)
   {
-    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+    String methodText = MessageManager.getString("label.sort_by_score");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+  public boolean parseFeaturesFile(Object file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
     boolean featuresAdded = false;
@@ -441,7 +463,7 @@ public class AlignViewController implements AlignViewControllerI
     else
     {
       avcg.setStatus(MessageManager
-              .formatMessage("No highlighted regions marked"));
+              .getString("label.no_highlighted_regions_marked"));
       if (!extendCurrent)
       {
         cs.clear();
@@ -451,4 +473,31 @@ public class AlignViewController implements AlignViewControllerI
     return false;
   }
 
+  @Override
+  public boolean copyHighlightedRegionsToClipboard()
+  {
+    if (!viewport.hasSearchResults())
+    {
+      // do nothing if no selection exists
+      return false;
+    }
+
+    SearchResultsI searchResults = viewport.getSearchResults();
+    if (searchResults.isEmpty())
+    {
+      return false; // shouldn't happen
+    }
+    List<SequenceI> seqs = searchResults.getMatchingSubSequences();
+
+    // TODO: pass in hiddenColumns according to intersection of searchResults
+    // and visible columns. Currently this isn't done, since each contig becomes
+    // a single subsequence
+    Desktop.jalviewClipboard = new Object[] {
+        seqs.toArray(new SequenceI[0]),
+        alignPanel.getAlignment().getDataset(), null };
+    avcg.setStatus(MessageManager.formatMessage(
+            "label.copied_sequences_to_clipboard", seqs.size()));
+    // Technically we should return false, since view has not changed
+    return false;
+  }
 }