JAL-2110 remove hardwired detection of search context from the dataset ‘isNucleotide...

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

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index ecfedb1..eab8d5d 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -103,7 +103,7 @@ public class CrossRefTest
      * first with no dbrefs to search
      */
     sources = new CrossRef(new SequenceI[] { seq }, al)
-            .findXrefSourcesForSequences();
+            .findXrefSourcesForSequences(false);
     assertTrue(sources.isEmpty());
 
     /*
@@ -120,7 +120,7 @@ public class CrossRefTest
     seq.addDBRef(new DBRefEntry("ENSEMBL", "0", "E2349"));
     seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
     sources = new CrossRef(new SequenceI[] { seq }, al)
-            .findXrefSourcesForSequences();
+            .findXrefSourcesForSequences(false);
     assertEquals(4, sources.size());
     assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]",
             sources.toString());
@@ -140,7 +140,7 @@ public class CrossRefTest
     // TODO include ENSEMBLGENOMES in DBRefSource.DNACODINGDBS ?
     al.addSequence(seq2);
     sources = new CrossRef(new SequenceI[] { seq }, al)
-            .findXrefSourcesForSequences();
+            .findXrefSourcesForSequences(false);
     assertEquals(3, sources.size());
     assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString());
   }
@@ -171,7 +171,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
     Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertEquals(1, xrefs.getHeight());
     assertSame(uniprotSeq, xrefs.getSequenceAt(0));
   }
@@ -206,7 +206,8 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
     Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq },
-            al).findXrefSequences("EMBL");
+ al)
+            .findXrefSequences("EMBL", true);
     assertEquals(1, xrefs.getHeight());
     assertSame(emblSeq, xrefs.getSequenceAt(0));
   }
@@ -233,7 +234,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 });
     Alignment xrefs = new CrossRef(new SequenceI[] { dna2 }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertNull(xrefs);
   }
 
@@ -262,7 +263,8 @@ public class CrossRefTest
      */
     DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "P30419");
     CrossRef testee = new CrossRef(al.getSequencesArray(), al);
-    boolean found = testee.searchDataset(dna1, dbref, result, null, true);
+    boolean found = testee.searchDataset(true, dna1, dbref, result, null,
+            true);
     assertFalse(found);
     assertTrue(result.isEmpty());
 
@@ -273,7 +275,7 @@ public class CrossRefTest
      * search for a protein sequence with dbref UNIPROT:Q9ZTS2
      */
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
-    found = testee.searchDataset(dna1, dbref, result, null, true);
+    found = testee.searchDataset(true, dna1, dbref, result, null, true);
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(pep1, result.get(0));
@@ -283,7 +285,7 @@ public class CrossRefTest
      */
     result.clear();
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
-    found = testee.searchDataset(pep1, dbref, result, null, false);
+    found = testee.searchDataset(false, pep1, dbref, result, null, false);
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(dna1, result.get(0));
@@ -332,7 +334,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { dna1 });
     Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertEquals(2, xrefs.getHeight());
 
     /*
@@ -418,7 +420,7 @@ public class CrossRefTest
      */
     AlignmentI al = new Alignment(new SequenceI[] { dna1 });
     Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
-            .findXrefSequences("UNIPROT");
+            .findXrefSequences("UNIPROT", true);
     assertEquals(2, xrefs.getHeight());
     assertSame(pep1, xrefs.getSequenceAt(0));
     assertSame(pep2, xrefs.getSequenceAt(1));
@@ -500,7 +502,8 @@ public class CrossRefTest
     SequenceI[] seqs = new SequenceI[] { gene, braf001, braf002 };
     AlignmentI al = new Alignment(seqs);
     Alignment xrefs = new CrossRef(seqs, al)
-            .findXrefSequences("UNIPROT");
+.findXrefSequences("UNIPROT",
+            true);
     assertEquals(2, xrefs.getHeight());
     assertSame(pep1, xrefs.getSequenceAt(0));
     assertSame(pep2, xrefs.getSequenceAt(1));
@@ -652,8 +655,8 @@ public class CrossRefTest
      */
     SequenceI[] seqs = new SequenceI[] { p0ce19, p0ce20 };
     AlignmentI al = new Alignment(seqs);
-    Alignment xrefs = new CrossRef(seqs, al)
-            .findXrefSequences("EMBL");
+    Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("EMBL",
+            false);
 
     /*
      * verify retrieved sequences