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

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 58a58e9..3e689d1 100644 (file)
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -20,10 +20,10 @@
  */
 package jalview.api;
 
-import jalview.io.DataSourceType;
-
 import java.util.List;
 
+import jalview.io.DataSourceType;
+
 /**
  * prototype abstract controller for a Jalview alignment view
  * 
@@ -111,4 +111,12 @@ public interface AlignViewControllerI
   boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
           boolean toggle);
 
+  /**
+   * copies each distinct highlighted region on the current view as a new
+   * sequence on the clipboard
+   * 
+   * @return
+   */
+  boolean copyHighlightedRegionsToClipboard();
+
 }

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 2fb9cdd..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;
@@ -471,4 +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;
+  }
 }

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 880f970..909a0fe 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -370,4 +370,27 @@ public class SearchResults implements SearchResultsI
   {
     matches.addAll(toAdd.getResults());
   }
+
+  @Override
+  public List<SequenceI> getMatchingSubSequences()
+  {
+    List<SequenceI> seqs = new ArrayList<>();
+
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    for (SearchResultMatchI match : matches)
+    {
+      SequenceI seq = match.getSequence();
+      while (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
+      // getSubSequence is index-base0, findIndex returns index-base1
+      seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()) - 1,
+              seq.findIndex(match.getEnd())));
+    }
+    return seqs;
+  }
 }

diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index c89f363..7946824 100644 (file)
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -118,4 +118,12 @@ public interface SearchResultsI
    * @return number of bits set
    */
   int markColumns(SequenceCollectionI sqcol, BitSet bs);
+
+  /**
+   * Return sub-sequences corresponding to distinct contiguous ranges in the
+   * matching set
+   * 
+   * @return list of sequence objects
+   */
+  List<SequenceI> getMatchingSubSequences();
 }
\ No newline at end of file

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 6dacbd8..6527cdc 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -260,28 +260,8 @@ public class Finder extends GFinder
     {
       return; // shouldn't happen
     }
-    List<SequenceI> seqs = new ArrayList<>();
-
-    String searchString = searchBox.getUserInput();
-    String desc = "Search Results";
-
-    /*
-     * assemble dataset sequences, and template new sequence features,
-     * for the amend features dialog
-     */
-    for (SearchResultMatchI match : searchResults.getResults())
-    {
-      SequenceI seq = match.getSequence();
-      while (seq.getDatasetSequence() != null)
-      {
-        seq = seq.getDatasetSequence();
-      }
-      seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()),
-              seq.findIndex(match.getEnd()) + 1));
-    }
-    Desktop.jalviewClipboard = new Object[] {
-        seqs.toArray(new SequenceI[0]), ap.av.getAlignment().getDataset(),
-        ap.av.getAlignment().getHiddenColumns() };
+    // assume viewport controller has same searchResults as we do...
+    ap.alignFrame.avc.copyHighlightedRegionsToClipboard();
   }
 
   /**

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index 5d2b8a4..b1bb43c 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import java.util.BitSet;
+import java.util.List;
 
 import org.junit.Assert;
 import org.testng.annotations.BeforeClass;
@@ -369,4 +370,44 @@ public class SearchResultsTest
     sr.addResult(cds2, 7, 9); // start-end overlap
     assertTrue(sr.involvesSequence(cds2));
   }
+
+  /**
+   * Test extraction of Sequence objects for matched ranges on a sequence
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSequences()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "nopqrstuvwxyz");
+    seq2.setStart(23);
+    seq2.setEnd(35);
+    List<SequenceI> seqres = null;
+
+    SearchResultsI sr = new SearchResults();
+    seqres = sr.getMatchingSubSequences();
+    assertEquals(0, seqres.size());
+
+    sr.addResult(seq1, 3, 5);
+    seqres = sr.getMatchingSubSequences();
+
+    assertEquals(1, seqres.size());
+    assertEquals("cde", seqres.get(0).getSequenceAsString());
+    assertEquals(3, seqres.get(0).getStart());
+    assertEquals(seq1, seqres.get(0).getDatasetSequence());
+
+    sr.addResult(seq1, 3, 6);
+    seqres = sr.getMatchingSubSequences();
+
+    assertEquals(2, seqres.size());
+    assertEquals("cdef", seqres.get(1).getSequenceAsString());
+    assertEquals(3, seqres.get(1).getStart());
+
+    // this is a quirk - match on 26-29 yields subsequence 27-30
+    sr.addResult(seq2, 26, 29);
+    seqres = sr.getMatchingSubSequences();
+    assertEquals(3, seqres.size());
+    assertEquals("qrst", seqres.get(2).getSequenceAsString());
+    assertEquals(26, seqres.get(2).getStart());
+  }
+
 }