X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=74e4940b43ffefa5e53dadbaf03d9ca3f6369399;hb=239d28bd8c08790bbc513a09b2b869fff862f63f;hp=2beacfee7509cff25808b9ec3970850f419cfe26;hpb=52288466dd1e71946a06fd1e6ea15fa8e652c693;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 2beacfe..74e4940 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -281,7 +281,7 @@ public class AlignmentUtilsTests
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testMapProteinToCdna_noXrefs() throws IOException
+  public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
     protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
@@ -298,7 +298,7 @@ public class AlignmentUtilsTests
     AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
     cdna.setDataset(null);
 
-    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+    assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
 
     // 3 mappings made, each from 1 to 1 sequence
     assertEquals(3, protein.getCodonFrames().size());
@@ -617,7 +617,7 @@ public class AlignmentUtilsTests
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testMapProteinToCdna_withStartAndStopCodons()
+  public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
           throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@ -638,7 +638,7 @@ public class AlignmentUtilsTests
     AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
     cdna.setDataset(null);
 
-    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+    assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
 
     // 3 mappings made, each from 1 to 1 sequence
     assertEquals(3, protein.getCodonFrames().size());
@@ -710,7 +710,7 @@ public class AlignmentUtilsTests
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testMapProteinToCdna_withXrefs() throws IOException
+  public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
     protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
@@ -739,7 +739,7 @@ public class AlignmentUtilsTests
     // A11111 should be mapped to V12347
     // A55555 is spare and has no xref so is not mapped
 
-    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+    assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
 
     // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
     assertEquals(3, protein.getCodonFrames().size());
@@ -786,7 +786,8 @@ public class AlignmentUtilsTests
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testMapProteinToCdna_prioritiseXrefs() throws IOException
+  public void testMapProteinAlignmentToCdna_prioritiseXrefs()
+          throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
     protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
@@ -806,7 +807,7 @@ public class AlignmentUtilsTests
     // A11111 should then be mapped to the unmapped V12346
     dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
 
-    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
+    assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
 
     // 2 protein mappings made
     assertEquals(2, protein.getCodonFrames().size());
@@ -987,7 +988,7 @@ public class AlignmentUtilsTests
     assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
 
     // now the other way round
-    seq1.setDBRef(null);
+    seq1.setDBRefs(null);
     seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
     assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
     assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
@@ -1123,8 +1124,8 @@ public class AlignmentUtilsTests
 
     assertEquals("GGGTTT", exon.getSequenceAsString());
     assertEquals("dna1|A12345", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    DBRefEntry cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    DBRefEntry cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("2", cdsRef.getVersion());
     assertEquals("A12345", cdsRef.getAccessionId());
@@ -1194,8 +1195,8 @@ public class AlignmentUtilsTests
     SequenceI exon = exons.get(0);
     assertEquals("GGGTTT", exon.getSequenceAsString());
     assertEquals("dna1|A12345", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    DBRefEntry cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    DBRefEntry cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("2", cdsRef.getVersion());
     assertEquals("A12345", cdsRef.getAccessionId());
@@ -1203,8 +1204,8 @@ public class AlignmentUtilsTests
     exon = exons.get(1);
     assertEquals("aaaccc", exon.getSequenceAsString());
     assertEquals("dna1|A12346", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("3", cdsRef.getVersion());
     assertEquals("A12346", cdsRef.getAccessionId());
@@ -1212,8 +1213,8 @@ public class AlignmentUtilsTests
     exon = exons.get(2);
     assertEquals("aaaTTT", exon.getSequenceAsString());
     assertEquals("dna1|A12347", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("4", cdsRef.getVersion());
     assertEquals("A12347", cdsRef.getAccessionId());
@@ -1279,4 +1280,27 @@ public class AlignmentUtilsTests
     assertTrue(AlignmentUtils.isMappable(al1, al2));
     assertTrue(AlignmentUtils.isMappable(al2, al1));
   }
+
+  /**
+   * Test creating a mapping when the sequences involved do not start at residue
+   * 1
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testMapProteinSequenceToCdna_forSubsequence()
+          throws IOException
+  {
+    SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
+    prot.createDatasetSequence();
+
+    SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
+    dna.createDatasetSequence();
+
+    MapList map = AlignmentUtils.mapProteinSequenceToCdna(prot, dna);
+    assertEquals(10, map.getToLowest());
+    assertEquals(12, map.getToHighest());
+    assertEquals(40, map.getFromLowest());
+    assertEquals(48, map.getFromHighest());
+  }
 }