Merge branch 'develop' into spike/JAL-1950_hmmer3client

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

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 1ed846a..6a31b31 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -136,7 +136,8 @@ public class DnaTest
             FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     assertNotNull("Couldn't do a full width translation of test data.",
@@ -166,7 +167,7 @@ public class DnaTest
       }
       cs.hideColumns(ipos + vwidth, alf.getWidth());
       Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
-              alf.getWidth());
+              alf.getWidth(), false);
       AlignViewportI av = new AlignViewport(alf, cs);
       Dna dna = new Dna(av, vcontigs);
       AlignmentI transAlf = dna.translateCdna();
@@ -193,7 +194,8 @@ public class DnaTest
             DataSourceType.PASTE, FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     String aa = translated.getSequenceAt(0).getSequenceAsString();
@@ -217,7 +219,8 @@ public class DnaTest
     cs.hideColumns(24, 35); // hide codons 9-12
     cs.hideColumns(177, 191); // hide codons 60-64
     AlignViewportI av = new AlignViewport(alf, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     String aa = translated.getSequenceAt(0).getSequenceAsString();
@@ -303,7 +306,8 @@ public class DnaTest
             .generate(12, 8, 97, 5, 5);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(cdna, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
 
@@ -319,7 +323,7 @@ public class DnaTest
     }
     AlignmentI cdnaReordered = new Alignment(sorted);
     av = new AlignViewport(cdnaReordered, cs);
-    contigs = cs.getVisContigsIterator(0, cdna.getWidth());
+    contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
     dna = new Dna(av, contigs);
     AlignmentI translated2 = dna.translateCdna();
 
@@ -551,7 +555,8 @@ public class DnaTest
 
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(al, cs);
-    Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth());
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+            false);
     Dna testee = new Dna(av, contigs);
     AlignmentI reversed = testee.reverseCdna(false);
     assertEquals(1, reversed.getHeight());