JAL-2505 correct handling of change of feature type

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 435e78d..8721ff4 100644 (file)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -413,7 +413,8 @@ public class FeatureRenderer extends
         if (!colourPanel.isGcol)
         {
           // update colour - otherwise its already done.
-          setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
+          setColour(enteredType,
+                  new FeatureColour(colourPanel.getBackground()));
         }
         int newBegin = sf.begin;
         int newEnd = sf.end;
@@ -431,14 +432,14 @@ public class FeatureRenderer extends
          * (to ensure integrity of SequenceFeatures data store)
          */
         sequences.get(0).deleteFeature(sf);
-        SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd,
-                enteredGroup, sf.getScore());
+        SequenceFeature newSf = new SequenceFeature(sf, enteredType,
+                newBegin, newEnd, enteredGroup, sf.getScore());
         newSf.setDescription(enteredDesc);
         ffile.parseDescriptionHTML(newSf, false);
         // amend features dialog only updates one sequence at a time
         sequences.get(0).addSequenceFeature(newSf);
-        boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
-                .equals(sf.featureGroup));
+        boolean typeOrGroupChanged = (!featureType.equals(newSf.getType()) || !featureGroup
+                .equals(newSf.getFeatureGroup()));
 
         ffile.parseDescriptionHTML(sf, false);
         if (typeOrGroupChanged)

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 9a6cf2b..ba7412c 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -143,15 +143,16 @@ public class SequenceFeature implements FeatureLocationI
    * A copy constructor that allows the value of final fields to be 'modified'
    * 
    * @param sf
+   * @param newType
    * @param newBegin
    * @param newEnd
    * @param newGroup
    * @param newScore
    */
-  public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
-          String newGroup, float newScore)
+  public SequenceFeature(SequenceFeature sf, String newType, int newBegin,
+          int newEnd, String newGroup, float newScore)
   {
-    this(sf.getType(), sf.getDescription(), newBegin, newEnd, newScore,
+    this(newType, sf.getDescription(), newBegin, newEnd, newScore,
             newGroup);
 
     if (sf.otherDetails != null)
@@ -173,6 +174,21 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
+   * A copy constructor that allows the value of final fields to be 'modified'
+   * 
+   * @param sf
+   * @param newBegin
+   * @param newEnd
+   * @param newGroup
+   * @param newScore
+   */
+  public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
+          String newGroup, float newScore)
+  {
+    this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore);
+  }
+
+  /**
    * Two features are considered equal if they have the same type, group,
    * description, start, end, phase, strand, and (if present) 'Name', ID' and
    * 'Parent' attributes.

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index ac56590..5c7bd4e 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -448,8 +448,8 @@ public class FeatureRenderer extends
          * (to ensure integrity of SequenceFeatures data store)
          */
         sequences.get(0).deleteFeature(sf);
-        SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd,
-                enteredGroup, sf.getScore());
+        SequenceFeature newSf = new SequenceFeature(sf, enteredType,
+                newBegin, newEnd, enteredGroup, sf.getScore());
         sf.setDescription(enteredDescription);
         ffile.parseDescriptionHTML(newSf, false);
         // amend features dialog only updates one sequence at a time

diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index d105cc5..fbeb365 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -42,7 +42,7 @@ public class SequenceFeatureTest
   }
 
   @Test(groups = { "Functional" })
-  public void testCopyConstructor()
+  public void testCopyConstructors()
   {
     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
             12.5f, "group");
@@ -56,10 +56,41 @@ public class SequenceFeatureTest
     assertEquals("desc", sf2.getDescription());
     assertEquals(22, sf2.getBegin());
     assertEquals(33, sf2.getEnd());
+    assertEquals(12.5f, sf2.getScore());
     assertEquals("+", sf2.getValue("STRAND"));
     assertEquals("Testing", sf2.getValue("Note"));
     // shallow clone of otherDetails map - contains the same object values!
     assertSame(count, sf2.getValue("Count"));
+
+    /*
+     * copy constructor modifying begin/end/group/score
+     */
+    SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f);
+    assertEquals("type", sf3.getType());
+    assertEquals("desc", sf3.getDescription());
+    assertEquals(11, sf3.getBegin());
+    assertEquals(14, sf3.getEnd());
+    assertEquals(17.4f, sf3.getScore());
+    assertEquals("+", sf3.getValue("STRAND"));
+    assertEquals("Testing", sf3.getValue("Note"));
+    // shallow clone of otherDetails map - contains the same object values!
+    assertSame(count, sf3.getValue("Count"));
+
+    /*
+     * copy constructor modifying type/begin/end/group/score
+     */
+    SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12,
+            15, "group3", -9.1f);
+    assertEquals("Disulfide bond", sf4.getType());
+    assertTrue(sf4.isContactFeature());
+    assertEquals("desc", sf4.getDescription());
+    assertEquals(12, sf4.getBegin());
+    assertEquals(15, sf4.getEnd());
+    assertEquals(-9.1f, sf4.getScore());
+    assertEquals("+", sf4.getValue("STRAND"));
+    assertEquals("Testing", sf4.getValue("Note"));
+    // shallow clone of otherDetails map - contains the same object values!
+    assertSame(count, sf4.getValue("Count"));
   }
 
   /**