JAL-3253-applet JAL-3423 Windows TestNG

[jalview.git] / test / jalview / datamodel / AlignmentTest.java

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 8aed114..cdcc219 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -243,7 +243,24 @@ 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)
                   {
@@ -1173,14 +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" })
@@ -1532,4 +1549,34 @@ public class AlignmentTest
     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());
+  }
 }