JAL-2110 copy alcodonframes only if copy constructor called on dataset alignmentI...

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index bd445c4..08a9441 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -32,6 +32,7 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
@@ -397,6 +398,8 @@ public class AlignmentTest
     // TODO should the copy constructor copy the dataset?
     // or make a new one referring to the same dataset sequences??
     assertNull(copy.getDataset());
+    // TODO test metadata is copied when AlignmentI is a dataset
+
     // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
     // .getDataset().getSequencesArray());
   }
@@ -435,8 +438,7 @@ public class AlignmentTest
     // TODO promote this method to AlignmentI
     ((Alignment) protein).createDatasetAlignment();
 
-    // TODO this method should return AlignmentI not Alignment !!
-    Alignment ds = protein.getDataset();
+    AlignmentI ds = protein.getDataset();
 
     // side-effect: dataset created on second sequence
     assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
@@ -474,4 +476,33 @@ public class AlignmentTest
     align.addCodonFrame(acf2);
     assertTrue(align.getDataset().getCodonFrames().contains(acf));
   }
+
+  @Test(groups = "Functional")
+  public void getVisibleStartAndEndIndexTest()
+  {
+    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    AlignmentI align = new Alignment(new SequenceI[] { seq });
+    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
+
+    int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    assertEquals(0, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hiddenCols.add(new int[] { 0, 0 });
+    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hiddenCols.add(new int[] { 6, 9 });
+    hiddenCols.add(new int[] { 11, 12 });
+    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hiddenCols.add(new int[] { 24, 25 });
+    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
+    System.out.println(startEnd[0] + " : " + startEnd[1]);
+    assertEquals(1, startEnd[0]);
+    assertEquals(23, startEnd[1]);
+  }
 }