X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=cfd0938173cdc525b33dab24f8de477b955a2fee;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=a28efdf75df002a5f6e5e1b75db416e4b18a19c2;hpb=3609d4b908fa64cab35f2348401baab3347188fc;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index a28efdf..cfd0938 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -971,7 +971,7 @@ public class AlignmentUtilsTests
     assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
 
     // now the other way round
-    seq1.setDBRefs(null);
+	seq1.setDBRefs(null);
     seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
     assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
     assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
@@ -1049,11 +1049,11 @@ public class AlignmentUtilsTests
     DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
             new Mapping(mapfordna1));
     dna1.addDBRef(dna1xref);
-    assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
+    assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
     DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
             new Mapping(mapfordna2));
     dna2.addDBRef(dna2xref);
-    assertEquals(2, dna2.getDBRefs().length); // to self and to pep2
+    assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
 
     /*
      * execute method under test:
@@ -1081,8 +1081,8 @@ public class AlignmentUtilsTests
      * verify CDS has a dbref with mapping to peptide
      */
     assertNotNull(cds1Dss.getDBRefs());
-    assertEquals(2, cds1Dss.getDBRefs().length);
-    dbref = cds1Dss.getDBRefs()[0];
+    assertEquals(2, cds1Dss.getDBRefs().size());
+    dbref = cds1Dss.getDBRefs().get(0);
     assertEquals(dna1xref.getSource(), dbref.getSource());
     // version is via ensembl's primary ref
     assertEquals(dna1xref.getVersion(), dbref.getVersion());
@@ -1098,8 +1098,8 @@ public class AlignmentUtilsTests
      */
     assertNotNull(pep1.getDBRefs());
     // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
-    assertEquals(2, pep1.getDBRefs().length);
-    dbref = pep1.getDBRefs()[1];
+    assertEquals(2, pep1.getDBRefs().size());
+    dbref = pep1.getDBRefs().get(1);
     assertEquals("ENSEMBL", dbref.getSource());
     assertEquals("0", dbref.getVersion());
     assertEquals("CDS|dna1", dbref.getAccessionId());
@@ -1110,14 +1110,14 @@ public class AlignmentUtilsTests
     /*
      * verify cDNA has added a dbref with mapping to CDS
      */
-    assertEquals(3, dna1.getDBRefs().length);
-    DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
+    assertEquals(3, dna1.getDBRefs().size());
+    DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
     assertSame(cds1Dss, dbRefEntry.getMap().getTo());
     MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
             new int[] { 1, 6 }, 1, 1);
     assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
-    assertEquals(3, dna2.getDBRefs().length);
-    dbRefEntry = dna2.getDBRefs()[2];
+    assertEquals(3, dna2.getDBRefs().size());
+    dbRefEntry = dna2.getDBRefs().get(2);
     assertSame(cds2Dss, dbRefEntry.getMap().getTo());
     dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
             new int[] { 1, 9 }, 1, 1);
@@ -1126,14 +1126,14 @@ public class AlignmentUtilsTests
     /*
      * verify CDS has added a dbref with mapping to cDNA
      */
-    assertEquals(2, cds1Dss.getDBRefs().length);
-    dbRefEntry = cds1Dss.getDBRefs()[1];
+    assertEquals(2, cds1Dss.getDBRefs().size());
+    dbRefEntry = cds1Dss.getDBRefs().get(1);
     assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
     MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
         4, 6, 10, 12 }, 1, 1);
     assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
-    assertEquals(2, cds2Dss.getDBRefs().length);
-    dbRefEntry = cds2Dss.getDBRefs()[1];
+    assertEquals(2, cds2Dss.getDBRefs().size());
+    dbRefEntry = cds2Dss.getDBRefs().get(1);
     assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
     cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
         9, 13, 15 }, 1, 1);