JAL-2050 hide introns also when fetching Ensembl xrefs for Uniprot

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 62c813a..be5f040 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1027,7 +1027,7 @@ error.implementation_error_need_to_have_httpresponse = Implementation Error: nee
 error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
 error.implementation_error_dbinstance_must_implement_interface = Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given{0})
 error.implementation_error_must_init_dbsources =Implementation error. Must initialise dbSources
-label.view_controller_toggled_marked = {0} {1} columns {2} containing features of type {3}  across {4} sequence(s)
+label.view_controller_toggled_marked = {0} {1} columns containing features of type {2}  across {3} sequence(s)
 label.toggled = Toggled
 label.marked = Marked
 label.not = not

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 3535f4b..8943860 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -962,7 +962,7 @@ error.implementation_error_need_to_have_httpresponse = Error de implementaci
 error.dbrefsource_implementation_exception = Excepción de implementación DBRefSource
 error.implementation_error_dbinstance_must_implement_interface = Error de Implementación- getDbInstances debe recibir una clase que implemente jalview.ws.seqfetcher.DbSourceProxy (recibió {0})
 error.implementation_error_must_init_dbsources =Error de implementación. Debe inicializar dbSources
-label.view_controller_toggled_marked = {0} {1} columnas {2} conteniendo características del tipo  {3} en {4} secuencia(s)
+label.view_controller_toggled_marked = {0} {1} columnas conteniendo características del tipo {2} en {3} secuencia(s)
 label.toggled = Invertida
 label.marked = Marcada
 label.not = no

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 17a1563..26966ba 100644 (file)
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -64,7 +64,7 @@ public interface AlignViewControllerI
    * @return true if operation affected state
    */
   boolean markColumnsContainingFeatures(boolean invert,
-          boolean extendCurrent, boolean clearColumns, 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 ca2ae6d..24439ca 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -238,6 +238,7 @@ public class AlignViewController implements AlignViewControllerI
     ColumnSelection cs = viewport.getColumnSelection();
     if (bs.cardinality() > 0 || invert)
     {
+      boolean changed = false;
       if (cs == null)
       {
         cs = new ColumnSelection();
@@ -246,6 +247,7 @@ public class AlignViewController implements AlignViewControllerI
       {
         if (!extendCurrent)
         {
+          changed = !cs.isEmpty();
           cs.clear();
         }
       }
@@ -257,6 +259,7 @@ public class AlignViewController implements AlignViewControllerI
         {
           if (ibs < 0 || i < ibs)
           {
+            changed = true;
             if (toggle && cs.contains(i))
             {
               cs.removeElement(i++);
@@ -278,6 +281,7 @@ public class AlignViewController implements AlignViewControllerI
         for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
                 .nextSetBit(i + 1))
         {
+          changed = true;
           if (toggle && cs.contains(i))
           {
             cs.removeElement(i);
@@ -288,18 +292,21 @@ 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() }));
-      return true;
+      if (changed)
+      {
+        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() }));
+        return true;
+      }
     }
     else
     {
@@ -311,8 +318,8 @@ public class AlignViewController implements AlignViewControllerI
         cs.clear();
         alignPanel.paintAlignment(true);
       }
-      return false;
     }
+    return false;
   }
 
   @Override

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8ec5366..7e7bdd3 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -74,6 +74,7 @@ import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.gff.SequenceOntologyI;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -4713,6 +4714,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
                     DEFAULT_HEIGHT);
+            if (Cache.getDefault("HIDE_INTRONS", true))
+            {
+              newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+            }
             String newtitle = String.format("%s %s %s",
                     MessageManager.getString(dna ? "label.proteins"
                             : "label.nucleotides"), MessageManager
@@ -6142,6 +6147,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       System.err.println("Can't run Groovy script as console not found");
     }
   }
+
+  /**
+   * Hides columns containing (or not containing) a specified feature, provided
+   * that would not leave all columns hidden
+   * 
+   * @param featureType
+   * @param columnsContaining
+   * @return
+   */
+  public boolean hideFeatureColumns(String featureType,
+          boolean columnsContaining)
+  {
+    boolean notForHiding = avc.markColumnsContainingFeatures(
+            columnsContaining, false, false, featureType);
+    if (notForHiding)
+    {
+      if (avc.markColumnsContainingFeatures(!columnsContaining, false,
+              false, featureType))
+      {
+        getViewport().hideSelectedColumns();
+        return true;
+      }
+    }
+    return false;
+  }
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index d5a04a9..e567d20 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -919,7 +919,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
-          hideIntronsIfPresent(af);
+          af.hideFeatureColumns(SequenceOntologyI.EXON, false);
         }
 
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
@@ -944,25 +944,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     return al;
   }
 
-  /**
-   * Hide columns not containing 'exon' features, provided there are exon
-   * features on the alignment
-   * 
-   * @param af
-   */
-  public void hideIntronsIfPresent(AlignFrame af)
-  {
-    boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
-            false,
-            SequenceOntologyI.EXON);
-    if (hasExons)
-    {
-      af.avc.markColumnsContainingFeatures(true, false, true,
-              SequenceOntologyI.EXON);
-      af.getViewport().hideSelectedColumns();
-    }
-  }
-
   void showErrorMessage(final String error)
   {
     resetDialog();

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
new file mode 100644 (file)
index 0000000..80e3d5a
--- /dev/null
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -0,0 +1,71 @@
+package jalview.gui;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class AlignFrameTest
+{
+
+  @Test
+  public void testHideFeatureColumns()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
+    SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
+    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
+            Float.NaN, null));
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
+            Float.NaN, null));
+    seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
+            Float.NaN, null));
+    seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
+            Float.NaN, null));
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignFrame af = new AlignFrame(al, al.getWidth(), al.getHeight());
+
+    /*
+     * hiding a feature not present does nothing
+     */
+    assertFalse(af.hideFeatureColumns("exon", true));
+    assertTrue(af.getViewport().getColumnSelection().isEmpty());
+    assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+            .isEmpty());
+    assertFalse(af.hideFeatureColumns("exon", false));
+    assertTrue(af.getViewport().getColumnSelection().isEmpty());
+    assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+            .isEmpty());
+
+    /*
+     * hiding a feature in all columns does nothing
+     */
+    assertFalse(af.hideFeatureColumns("Metal", true));
+    assertTrue(af.getViewport().getColumnSelection().isEmpty());
+    List<int[]> hidden = af.getViewport().getColumnSelection()
+            .getHiddenColumns();
+    assertTrue(hidden.isEmpty());
+
+    /*
+     * hide a feature present in some columns
+     * sequence positions [2-4], [7-9] are column positions
+     * [1-3], [6-8] base zero
+     */
+    assertTrue(af.hideFeatureColumns("Turn", true));
+    hidden = af.getViewport().getColumnSelection()
+            .getHiddenColumns();
+    assertEquals(2, hidden.size());
+    assertEquals(1, hidden.get(0)[0]);
+    assertEquals(3, hidden.get(0)[1]);
+    assertEquals(6, hidden.get(1)[0]);
+    assertEquals(8, hidden.get(1)[1]);
+  }
+}