X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=cdcc219777eb12cfdbfc8660a3201892e5e850ea;hb=6babd7c2387996384a49042ed4290095c13d5ed9;hp=2fed815eaac736fbf895a6c06dacc9cd70d8c65a;hpb=cfed9d8a9e10be992877d6097260758ee5563630;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 2fed815..cdcc219 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -243,12 +243,31 @@ public class AlignmentTest
                   return false;
 
                 }
-                if (alignment.findIndex(dbr.getMap().getTo()) == -1)
+
+                SequenceI x = dbr.getMap().getTo();
+//                System.out.println(alignment.toString());
+//                System.out.println(dbr);
+//                System.out.println("map " + dbr.getMap());
+//                System.out.println("to " + dbr.getMap().getTo());
+//                if (x.toString().indexOf("ENSP00000395337") >= 0)
+//                {
+//                  // The TO name here is "ENSP00000395337"
+//                  // But the name in the table is "LDAH_HUMAN"
+//                  System.out.println(x.getSequenceAsString());
+//                  SequenceI y = alignment.getSequenceAt(0);
+//                  System.out.println(y.getSequenceAsString());
+//                  System.out.println(x.getSequenceAsString()
+//                          .equals(y.getSequenceAsString()));
+//
+//                }
+                if (alignment.findIndex(x) == -1)
                 {
                   if (raiseAssert)
                   {
                     Assert.fail(message
-                            + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                            + " DBRefEntry " + dbr + " for sequence "
+                            + seqds
+                            + " in alignment has map to sequence not in dataset");
                   }
                   return false;
                 }
@@ -669,6 +688,17 @@ public class AlignmentTest
     // third found.. so
     assertFalse(iter.hasNext());
 
+    // search for annotation on one sequence with a particular label - expect
+    // one
+    SequenceI sqfound;
+    anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+            "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    // expect reference to sequence 1 in the alignment
+    assertTrue(sqfound == iter.next().sequenceRef);
+    assertFalse(iter.hasNext());
+
     // null on all parameters == find all annotations
     anns = al.findAnnotations(null, null, null);
     iter = anns.iterator();
@@ -1160,14 +1190,14 @@ public class AlignmentTest
     /*
      * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset
      */
-    DBRefEntry[] dbRefs = pep.getDBRefs();
-    assertEquals(2, dbRefs.length);
-    assertSame(dna, dbRefs[0].map.to);
-    assertSame(cds, dbRefs[1].map.to);
-    assertEquals(1, dna.getDBRefs().length);
-    assertSame(pep.getDatasetSequence(), dna.getDBRefs()[0].map.to);
-    assertEquals(1, cds.getDBRefs().length);
-    assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
+    List<DBRefEntry> dbRefs = pep.getDBRefs();
+    assertEquals(2, dbRefs.size());
+    assertSame(dna, dbRefs.get(0).map.to);
+    assertSame(cds, dbRefs.get(1).map.to);
+    assertEquals(1, dna.getDBRefs().size());
+    assertSame(pep.getDatasetSequence(), dna.getDBRefs().get(0).map.to);
+    assertEquals(1, cds.getDBRefs().size());
+    assertSame(pep.getDatasetSequence(), cds.getDBRefs().get(0).map.to);
   }
 
   @Test(groups = { "Functional" })
@@ -1323,6 +1353,24 @@ public class AlignmentTest
     // hidden sequences, properties
   }
 
+  /**
+   * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+   * an annotation with a null calcId
+   * 
+   */
+  @Test(groups = "Functional")
+  public void testFindOrCreateForNullCalcId()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+    AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+            "Temperature Factor", null, false, seq, null);
+    assertNotNull(ala);
+    assertEquals(seq, ala.sequenceRef);
+    assertEquals("", ala.calcId);
+  }
+
   @Test(groups = "Functional")
   public void testPropagateInsertions()
   {
@@ -1437,4 +1485,98 @@ public class AlignmentTest
     assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
     assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
   }
+
+  @Test(groups = { "Functional" })
+  public void testPadGaps()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    a.setGapCharacter('.'); // this replaces existing gaps
+    assertEquals("ABCDEF..", seq1.getSequenceAsString());
+    a.padGaps();
+    // trailing gaps are pruned, short sequences padded with gap character
+    assertEquals("ABCDEF.", seq1.getSequenceAsString());
+    assertEquals(".JKLMNO", seq2.getSequenceAsString());
+    assertEquals(".PQR...", seq3.getSequenceAsString());
+  }
+
+  /**
+   * Test for setHiddenColumns, to check it returns true if the hidden columns
+   * have changed, else false
+   */
+  @Test(groups = { "Functional" })
+  public void testSetHiddenColumns()
+  {
+    AlignmentI al = new Alignment(new SequenceI[] {});
+    assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+    HiddenColumns hc = new HiddenColumns();
+    assertFalse(al.setHiddenColumns(hc)); // no change
+    assertSame(hc, al.getHiddenColumns());
+
+    hc.hideColumns(2, 4);
+    assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+    /*
+     * set a different object but with the same columns hidden
+     */
+    HiddenColumns hc2 = new HiddenColumns();
+    hc2.hideColumns(2, 4);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+    assertSame(hc2, al.getHiddenColumns());
+
+    assertTrue(al.setHiddenColumns(null));
+    assertNull(al.getHiddenColumns());
+    assertTrue(al.setHiddenColumns(hc));
+    assertSame(hc, al.getHiddenColumns());
+
+    al.getHiddenColumns().hideColumns(10, 12);
+    hc2.hideColumns(10, 12);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+
+    /*
+     * hide columns 15-16 then 17-18 in hc
+     * hide columns 15-18 in hc2
+     * these are not now 'equal' objects even though they
+     * represent the same set of columns
+     */
+    assertSame(hc2, al.getHiddenColumns());
+    hc.hideColumns(15, 16);
+    hc.hideColumns(17, 18);
+    hc2.hideColumns(15, 18);
+    assertFalse(hc.equals(hc2));
+    assertTrue(al.setHiddenColumns(hc)); // 'changed'
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getWidth());
+
+    // width includes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(9, a.getWidth());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getVisibleWidth());
+
+    // width excludes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(5, a.getVisibleWidth());
+  }
 }