JAL-3010 double-click selects columns for term and sub-terms in Summary View

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index a7ec69e..f7575c3 100644 (file)
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -62,11 +62,11 @@ public interface AlignViewControllerI
    * @param toggle
    *          - rather than explicitly set, toggle selection state
    * @param featureType
-   *          - feature type string
+   *          - one or more feature types to match
    * @return true if operation affected state
    */
   boolean markColumnsContainingFeatures(boolean invert,
-          boolean extendCurrent, boolean toggle, String featureType);
+          boolean extendCurrent, boolean toggle, String... featureType);
 
   /**
    * sort the alignment or current selection by average score over the given set

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index d992e4e..cacde84 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -157,7 +157,7 @@ public class AlignViewController implements AlignViewControllerI
 
   @Override
   public boolean markColumnsContainingFeatures(boolean invert,
-          boolean extendCurrent, boolean toggle, String featureType)
+          boolean extendCurrent, boolean toggle, String... featureType)
   {
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
@@ -166,7 +166,7 @@ public class AlignViewController implements AlignViewControllerI
             || extendCurrent) ? viewport.getAlignment()
                     : viewport.getSelectionGroup();
 
-    int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+    int nseq = findColumnsWithFeature(sqcol, bs, featureType);
 
     ColumnSelection cs = viewport.getColumnSelection();
     if (cs == null)
@@ -174,6 +174,9 @@ public class AlignViewController implements AlignViewControllerI
       cs = new ColumnSelection();
     }
 
+    String featureTypeString = featureType.length == 1 ? featureType[0]
+            : featureType.toString();
+
     if (bs.cardinality() > 0 || invert)
     {
       boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
@@ -194,7 +197,7 @@ public class AlignViewController implements AlignViewControllerI
                     invert ? MessageManager
                             .getString("label.not_containing")
                             : MessageManager.getString("label.containing"),
-                    featureType, Integer.valueOf(nseq).toString() }));
+                    featureTypeString, Integer.valueOf(nseq).toString() }));
         return true;
       }
     }
@@ -202,7 +205,7 @@ public class AlignViewController implements AlignViewControllerI
     {
       avcg.setStatus(MessageManager
               .formatMessage("label.no_feature_of_type_found", new String[]
-              { featureType }));
+              { featureTypeString }));
       if (!extendCurrent)
       {
         cs.clear();
@@ -214,17 +217,18 @@ public class AlignViewController implements AlignViewControllerI
 
   /**
    * Sets a bit in the BitSet for each column (base 0) in the sequence
-   * collection which includes a visible feature of the specified feature type.
-   * Returns the number of sequences which have the feature visible in the
-   * selected range.
+   * collection which includes a visible feature of the specified feature
+   * type(s). Returns the number of sequences which have the feature(s) visible
+   * in the selected range.
    * 
-   * @param featureType
    * @param sqcol
    * @param bs
+   * @param featureType
+   * 
    * @return
    */
-  int findColumnsWithFeature(String featureType,
-          SequenceCollectionI sqcol, BitSet bs)
+  int findColumnsWithFeature(SequenceCollectionI sqcol,
+          BitSet bs, String... featureType)
   {
     FeatureRenderer fr = alignPanel == null ? null : alignPanel
             .getFeatureRenderer();

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 0c90646..48b623f 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -362,8 +362,9 @@ public class FeatureSettings extends JPanel
           boolean invertSelection = evt.isAltDown();
           boolean toggleSelection = Platform.isControlDown(evt);
           boolean extendSelection = evt.isShiftDown();
+          String[] terms = getTermsInScope(type);
           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
-                  invertSelection, extendSelection, toggleSelection, type);
+                  invertSelection, extendSelection, toggleSelection, terms);
         }
       }
 
@@ -392,6 +393,37 @@ public class FeatureSettings extends JPanel
     });
   }
 
+  /**
+   * Answers an array consisting of the given type, and also (if 'Summary View'
+   * is selected), any child terms in the sequence ontology
+   * 
+   * @param type
+   * @return
+   */
+  protected String[] getTermsInScope(String type)
+  {
+    if (!summaryView.isSelected())
+    {
+      return new String[] { type };
+    }
+
+    List<String> terms = new ArrayList<>();
+    terms.add(type);
+
+    OntologyI so = SequenceOntologyFactory.getInstance();
+
+    Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+    for (Object[] row : data)
+    {
+      String type2 = (String) row[TYPE_COLUMN];
+      if (!type2.equals(type) && so.isA(type2, type))
+      {
+        terms.add(type2);
+      }
+    }
+    return terms.toArray(new String[terms.size()]);
+  }
+
   protected void popupMenu(final int rowSelected, final String type,
           final Object typeCol, int x, int y)
   {

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 335529c..78c6da2 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -118,7 +118,10 @@ public class ConsensusThread extends AlignCalcWorker
   protected void eraseConsensus(int aWidth)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    consensus.annotations = new Annotation[aWidth];
+    if (consensus != null)
+    {
+      consensus.annotations = new Annotation[aWidth];
+    }
     AlignmentAnnotation gap = getGapAnnotation();
     if (gap != null)
     {

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index efee93b..469481d 100644 (file)
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -102,7 +102,7 @@ public class AlignViewControllerTest
             af.alignPanel);
 
     BitSet bs = new BitSet();
-    int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+    int seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
     assertTrue(bs.get(3)); // base 0
@@ -113,7 +113,7 @@ public class AlignViewControllerTest
      */
     sg.setEndRes(6);
     bs.clear();
-    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+    seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
     assertEquals(2, seqCount);
     assertEquals(4, bs.cardinality());
     assertTrue(bs.get(3));
@@ -127,7 +127,7 @@ public class AlignViewControllerTest
     sg.setStartRes(13);
     sg.setEndRes(13);
     bs.clear();
-    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+    seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
     assertEquals(1, seqCount);
     assertEquals(1, bs.cardinality());
     assertTrue(bs.get(13));
@@ -138,7 +138,7 @@ public class AlignViewControllerTest
     sg.setStartRes(17);
     sg.setEndRes(19);
     bs.clear();
-    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+    seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
     assertEquals(0, seqCount);
     assertEquals(0, bs.cardinality());
 
@@ -154,7 +154,7 @@ public class AlignViewControllerTest
     sg.setStartRes(0);
     sg.setEndRes(6);
     bs.clear();
-    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+    seqCount = avc.findColumnsWithFeature(sg, bs, "Metal");
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
     assertTrue(bs.get(5));
@@ -166,7 +166,7 @@ public class AlignViewControllerTest
     sg.setStartRes(10);
     sg.setEndRes(12);
     bs.clear();
-    seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
+    seqCount = avc.findColumnsWithFeature(sg, bs, "disulfide bond");
     assertEquals(0, seqCount);
     assertEquals(0, bs.cardinality());
 
@@ -176,7 +176,7 @@ public class AlignViewControllerTest
     sg.setStartRes(5);
     sg.setEndRes(17);
     bs.clear();
-    seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
+    seqCount = avc.findColumnsWithFeature(sg, bs, "disulfide bond");
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
     assertTrue(bs.get(8));
@@ -188,7 +188,7 @@ public class AlignViewControllerTest
     sg.setStartRes(0);
     sg.setEndRes(19);
     bs.clear();
-    seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
+    seqCount = avc.findColumnsWithFeature(sg, bs, "Pfam");
     assertEquals(0, seqCount);
     assertEquals(0, bs.cardinality());
   }