X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=2e89b0ecd6d95dc5a8e0c24c8fd2204b570e1e3b;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=7ac1452354a519a59ca6ffcefc4c761bd4ce0d9f;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index 7ac1452..2e89b0e 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -33,8 +33,8 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 
 import java.util.Arrays;
 import java.util.BitSet;
@@ -55,10 +55,10 @@ public class AlignViewControllerTest
   @Test(groups = "Functional")
   public void testFindColumnsWithFeature()
   {
-    SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
-    SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
-    SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
-    SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+    SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
+    SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
+    SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
+    SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
 
     /*
      * features start/end are base 1
@@ -71,13 +71,16 @@ public class AlignViewControllerTest
             null));
     seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
             0f, null));
+    // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
+    seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
+            0f, null));
 
     /*
-     * select the first three columns --> Metal in seq1 2-3
+     * select the first five columns --> Metal in seq1 cols 4-5
      */
     SequenceGroup sg = new SequenceGroup();
     sg.setStartRes(0); // base 0
-    sg.setEndRes(2);
+    sg.setEndRes(4);
     sg.addSequence(seq1, false);
     sg.addSequence(seq2, false);
     sg.addSequence(seq3, false);
@@ -88,36 +91,37 @@ public class AlignViewControllerTest
             bs);
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
-    assertTrue(bs.get(1));
-    assertTrue(bs.get(2));
+    assertTrue(bs.get(3)); // base 0
+    assertTrue(bs.get(4));
 
     /*
-     * select the first four columns: Metal in seq1 2:4, seq2 4:4
+     * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7 
      */
-    sg.setEndRes(3);
+    sg.setEndRes(6);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(2, seqCount);
-    assertEquals(3, bs.cardinality());
-    assertTrue(bs.get(1));
-    assertTrue(bs.get(2));
+    assertEquals(4, bs.cardinality());
     assertTrue(bs.get(3));
+    assertTrue(bs.get(4));
+    assertTrue(bs.get(5));
+    assertTrue(bs.get(6));
 
     /*
-     * select column 11: Metal in seq3 only
+     * select column 14: Metal in seq3 only
      */
-    sg.setStartRes(10);
-    sg.setEndRes(10);
+    sg.setStartRes(13);
+    sg.setEndRes(13);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(1, seqCount);
     assertEquals(1, bs.cardinality());
-    assertTrue(bs.get(10));
+    assertTrue(bs.get(13));
 
     /*
-     * select columns 16-20: no Metal feature
+     * select columns 18-20: no Metal feature
      */
-    sg.setStartRes(15);
+    sg.setStartRes(17);
     sg.setEndRes(19);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
@@ -125,6 +129,30 @@ public class AlignViewControllerTest
     assertEquals(0, bs.cardinality());
 
     /*
+     * columns 11-13 should not match disulfide bond at 8/12
+     */
+    sg.setStartRes(10);
+    sg.setEndRes(12);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+            sg, bs);
+    assertEquals(0, seqCount);
+    assertEquals(0, bs.cardinality());
+
+    /*
+     * columns 6-18 should match disulfide bond at columns 9, 14
+     */
+    sg.setStartRes(5);
+    sg.setEndRes(17);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+            sg, bs);
+    assertEquals(1, seqCount);
+    assertEquals(2, bs.cardinality());
+    assertTrue(bs.get(8));
+    assertTrue(bs.get(13));
+
+    /*
      * look for a feature that isn't there
      */
     sg.setStartRes(0);
@@ -145,7 +173,7 @@ public class AlignViewControllerTest
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
                     + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
-                    + "seq4 aaaaaaaaaaaaaaaaaaaa\n", FormatAdapter.PASTE);
+                    + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
 
     SearchResultsI sr = new SearchResults();
     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();