X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=b45547ea1022f481603d292cf013fad0b4ea8f40;hb=48e68905336d8ee17ee6b3903d80b36bac8c56cf;hp=128bc5c8e994369b950840d62d35f0cb093546f0;hpb=9b85e1552fa57f02cf6cd312cfbd7efdfd079ea3;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 128bc5c..b45547e 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -27,7 +27,16 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentUtils.DnaVariant;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -41,7 +50,6 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
@@ -52,17 +60,6 @@ import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class AlignmentUtilsTests
 {
   private static Sequence ts = new Sequence("short",
@@ -974,7 +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));
@@ -1052,11 +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:
@@ -1084,8 +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());
@@ -1101,8 +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());
@@ -1113,14 +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);
@@ -1129,14 +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);