JAL-2110 fixes to dbref resolution and mappings, use same dataset for

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 2fc5325..9600fdc 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -995,23 +995,22 @@ public class AlignmentUtilsTests
     AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
     dna.setDataset(null);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     MapList map = new MapList(new int[] { 4, 6, 10, 12 },
             new int[] { 1, 2 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
     map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
             3, 1);
     acf = new AlignedCodonFrame();
     acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
 
     /*
      * execute method under test:
      */
     AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
-        dna1, dna2 }, mappings, dna);
+        dna1, dna2 }, dna);
 
     assertEquals(2, cds.getSequences().size());
     assertEquals("GGGTTT", cds.getSequenceAt(0)
@@ -1125,40 +1124,38 @@ public class AlignmentUtilsTests
             new DBRefEntry("EMBLCDS", "4", "A12347"));
 
     /*
+     * Create the CDS alignment
+     */
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
+    dna.setDataset(null);
+
+    /*
      * Make the mappings from dna to protein
      */
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     // map ...GGG...TTT to GF
     MapList map = new MapList(new int[] { 4, 6, 10, 12 },
             new int[] { 1, 2 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
 
     // map aaa...ccc to KP
     map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
     acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
 
     // map aaa......TTT to KF
     map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
     acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
-    mappings.add(acf);
-
-    /*
-     * Create the CDS alignment; also augments the dna-to-protein mappings with
-     * exon-to-protein and exon-to-dna mappings
-     */
-    AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
-    dna.setDataset(null);
+    dna.addCodonFrame(acf);
 
     /*
      * execute method under test
      */
     AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
-            new SequenceI[] { dna1 }, mappings, dna);
+            new SequenceI[] { dna1 }, dna);
 
     /*
      * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
@@ -1509,24 +1506,24 @@ public class AlignmentUtilsTests
             null));
     dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 16, 18, 0f,
             null));
+
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+    dna.setDataset(null);
   
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     MapList map = new MapList(new int[] { 4, 12, 16, 18 },
             new int[] { 1, 4 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
     map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
             new int[] { 1, 3 },
             3, 1);
     acf = new AlignedCodonFrame();
     acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
-    mappings.add(acf);
+    dna.addCodonFrame(acf);
   
-    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
-    dna.setDataset(null);
     AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
-        dna1, dna2, dna3 }, mappings, dna);
+        dna1, dna2, dna3 }, dna);
     List<SequenceI> cdsSeqs = cds.getSequences();
     assertEquals(2, cdsSeqs.size());
     assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());