JAL-1712 fixes/tests for Castor binding of EMBL XML / show flanking

region

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 98c78fc..36ffdf3 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -131,7 +131,7 @@ public class PDBEntry
   }
   public void setType(PDBEntry.Type type)
   {
-    this.type = type.toString();
+    this.type = type == null ? null : type.toString();
   }
 
   public String getType()

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index b2f8b2b..5d8a297 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -20,6 +20,13 @@
  */
 package jalview.io;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -28,13 +35,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 /**
  * DOCUMENT ME!
  * 
@@ -188,7 +188,7 @@ public abstract class AlignFile extends FileParse
 
     for (int i = 0; i < seqs.size(); i++)
     {
-      s[i] = (SequenceI) seqs.elementAt(i);
+      s[i] = seqs.elementAt(i);
     }
 
     return s;
@@ -212,7 +212,7 @@ public abstract class AlignFile extends FileParse
        * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
        * Rna.HelixMap(pairArray);
        */
-      AlignmentAnnotation an = (AlignmentAnnotation) annotations
+      AlignmentAnnotation an = annotations
               .elementAt(i);
       an.validateRangeAndDisplay();
       al.addAnnotation(an);
@@ -287,8 +287,8 @@ public abstract class AlignFile extends FileParse
    */
   protected void initData()
   {
-    seqs = new Vector();
-    annotations = new Vector();
+    seqs = new Vector<SequenceI>();
+    annotations = new Vector<AlignmentAnnotation>();
     seqGroups = new ArrayList<SequenceGroup>();
     parseCalled=false;
   }
@@ -301,7 +301,7 @@ public abstract class AlignFile extends FileParse
    */
   protected void setSeqs(SequenceI[] s)
   {
-    seqs = new Vector();
+    seqs = new Vector<SequenceI>();
 
     for (int i = 0; i < s.length; i++)
     {
@@ -361,13 +361,13 @@ public abstract class AlignFile extends FileParse
   /**
    * vector of String[] treeName, newickString pairs
    */
-  Vector newickStrings = null;
+  Vector<String[]> newickStrings = null;
 
   protected void addNewickTree(String treeName, String newickString)
   {
     if (newickStrings == null)
     {
-      newickStrings = new Vector();
+      newickStrings = new Vector<String[]>();
     }
     newickStrings.addElement(new String[]
     { treeName, newickString });
@@ -375,11 +375,7 @@ public abstract class AlignFile extends FileParse
 
   protected int getTreeCount()
   {
-    if (newickStrings == null)
-    {
-      return 0;
-    }
-    return newickStrings.size();
+    return newickStrings == null ? 0 : newickStrings.size();
   }
 
 }

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 6c06955..02955f1 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -195,9 +195,7 @@ public class AlignmentUtilsTests
      * Expand the subsequence to the full sequence abcDEFghi
      */
     AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
-    // FIXME expandContext adds an unnecessary gap; need tests to cover all
-    // cases for which 'maxOffset' is computed
-    assertEquals("-abcDEFghi", expanded.getSequenceAt(0)
+    assertEquals("abcDEFghi", expanded.getSequenceAt(0)
             .getSequenceAsString());
 
     /*
@@ -215,13 +213,12 @@ public class AlignmentUtilsTests
     assertNull(ann.annotations[0]);
     assertNull(ann.annotations[1]);
     assertNull(ann.annotations[2]);
-    assertNull(ann.annotations[3]);
-    assertEquals(4, ann.annotations[4].value, 0.001);
-    assertEquals(5, ann.annotations[5].value, 0.001);
-    assertEquals(6, ann.annotations[6].value, 0.001);
+    assertEquals(4, ann.annotations[3].value, 0.001);
+    assertEquals(5, ann.annotations[4].value, 0.001);
+    assertEquals(6, ann.annotations[5].value, 0.001);
+    assertNull(ann.annotations[6]);
     assertNull(ann.annotations[7]);
     assertNull(ann.annotations[8]);
-    assertNull(ann.annotations[9]);
 
     /*
      * sequence position mappings should be unchanged

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 29d5549..6a61d2c 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -4,6 +4,14 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -14,14 +22,6 @@ import jalview.gui.Desktop;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
-import java.io.File;
-import java.util.Vector;
-
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
 public class AnnotatedPDBFileInputTest
 {
 
@@ -38,8 +38,8 @@ public class AnnotatedPDBFileInputTest
     AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
             FormatAdapter.FILE);
     al = af.getViewport().getAlignment();
-    pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
-            .get(0)).getId();
+    pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId()
+            .get(0).getId();
   }
 
   @Test
@@ -194,7 +194,7 @@ public class AnnotatedPDBFileInputTest
       }
       assertNotNull(sq.getPDBId());
       assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
-      for (PDBEntry pdbentry : (Vector<PDBEntry>) sq.getPDBId())
+      for (PDBEntry pdbentry : sq.getPDBId())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "
                 + pdbentry.getFile());