JAL-2054 Renamed getStartEnd in AlignFrame to getVisibleStartAndEndIndex, and refacto...

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index bd445c4..5a45176 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;
@@ -474,4 +475,33 @@ 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]);
+  }
 }