Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104

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

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index d2fa99a..6a31b31 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -38,6 +38,7 @@ import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.IOException;
+import java.util.Iterator;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -135,7 +136,9 @@ public class DnaTest
             FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+    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.",
             translated);
@@ -163,7 +166,8 @@ public class DnaTest
         cs.hideColumns(0, ipos - 1);
       }
       cs.hideColumns(ipos + vwidth, alf.getWidth());
-      int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
+      Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
+              alf.getWidth(), false);
       AlignViewportI av = new AlignViewport(alf, cs);
       Dna dna = new Dna(av, vcontigs);
       AlignmentI transAlf = dna.translateCdna();
@@ -190,7 +194,9 @@ public class DnaTest
             DataSourceType.PASTE, FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+    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();
     assertEquals(
@@ -213,7 +219,9 @@ 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);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+    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();
     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
@@ -298,7 +306,9 @@ public class DnaTest
             .generate(12, 8, 97, 5, 5);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(cdna, cs);
-    Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
 
     /*
@@ -313,7 +323,8 @@ public class DnaTest
     }
     AlignmentI cdnaReordered = new Alignment(sorted);
     av = new AlignViewport(cdnaReordered, cs);
-    dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+    contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
+    dna = new Dna(av, contigs);
     AlignmentI translated2 = dna.translateCdna();
 
     /*
@@ -544,7 +555,9 @@ public class DnaTest
 
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(al, cs);
-    Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+            false);
+    Dna testee = new Dna(av, contigs);
     AlignmentI reversed = testee.reverseCdna(false);
     assertEquals(1, reversed.getHeight());
     assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());