Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

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

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 96ac0c3..27ae8cd 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -38,8 +38,7 @@ import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.Iterator;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -137,11 +136,11 @@ public class DnaTest
             FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    int[] contig = new int[] { 0, alf.getWidth() - 1 };
-    List<int[]> contigs = new ArrayList<>();
-    contigs.add(contig);
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     assertNotNull("Couldn't do a full width translation of test data.",
             translated);
   }
@@ -168,10 +167,12 @@ public class DnaTest
         cs.hideColumns(0, ipos - 1);
       }
       cs.hideColumns(ipos + vwidth, alf.getWidth());
-      List<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();
+      AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+              .getStandardCodeTable());
 
       assertTrue("Translation failed (ipos=" + ipos
               + ") No alignment data.", transAlf != null);
@@ -195,11 +196,11 @@ public class DnaTest
             DataSourceType.PASTE, FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    int[] contig = new int[] { 0, alf.getWidth() - 1 };
-    List<int[]> contigs = new ArrayList<>();
-    contigs.add(contig);
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals(
             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
@@ -221,11 +222,11 @@ 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);
-    int[] contig = new int[] { 0, alf.getWidth() - 1 };
-    List<int[]> contigs = new ArrayList<>();
-    contigs.add(contig);
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
   }
@@ -309,11 +310,11 @@ public class DnaTest
             .generate(12, 8, 97, 5, 5);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(cdna, cs);
-    int[] contig = new int[] { 0, cdna.getWidth() - 1 };
-    List<int[]> contigs = new ArrayList<>();
-    contigs.add(contig);
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+            false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna();
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
 
     /*
      * Jumble the cDNA sequences and translate.
@@ -327,11 +328,10 @@ public class DnaTest
     }
     AlignmentI cdnaReordered = new Alignment(sorted);
     av = new AlignViewport(cdnaReordered, cs);
-    contig = new int[] { 0, cdna.getWidth() - 1 };
-    contigs = new ArrayList<>();
-    contigs.add(contig);
+    contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
     dna = new Dna(av, contigs);
-    AlignmentI translated2 = dna.translateCdna();
+    AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
 
     /*
      * Check translated sequences are the same in both alignments.
@@ -561,9 +561,8 @@ public class DnaTest
 
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(al, cs);
-    int[] contig = new int[] { 0, al.getWidth() - 1 };
-    List<int[]> contigs = new ArrayList<>();
-    contigs.add(contig);
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+            false);
     Dna testee = new Dna(av, contigs);
     AlignmentI reversed = testee.reverseCdna(false);
     assertEquals(1, reversed.getHeight());