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 13dae11..27ae8cd 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -28,19 +28,30 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 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;
 
 public class DnaTest
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // @formatter:off
   // AA encoding codons as ordered on the Jalview help page Amino Acid Table
   private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
@@ -123,10 +134,13 @@ public class DnaTest
     AlignmentI alf = new FormatAdapter().readFile(
             JAL_1312_example_align_fasta, DataSourceType.PASTE,
             FileFormat.Fasta);
-    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
-    AlignmentI translated = dna.translateCdna();
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     assertNotNull("Couldn't do a full width translation of test data.",
             translated);
   }
@@ -147,16 +161,18 @@ public class DnaTest
     int vwidth = 15;
     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
     {
-      ColumnSelection cs = new ColumnSelection();
+      HiddenColumns cs = new HiddenColumns();
       if (ipos > 0)
       {
         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();
+      AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+              .getStandardCodeTable());
 
       assertTrue("Translation failed (ipos=" + ipos
               + ") No alignment data.", transAlf != null);
@@ -178,10 +194,13 @@ public class DnaTest
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
             DataSourceType.PASTE, FileFormat.Fasta);
-    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
-    AlignmentI translated = dna.translateCdna();
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals(
             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
@@ -198,13 +217,16 @@ public class DnaTest
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
             DataSourceType.PASTE, FileFormat.Fasta);
-    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns cs = new HiddenColumns();
     cs.hideColumns(6, 14); // hide codons 3/4/5
     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 });
-    AlignmentI translated = dna.translateCdna();
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
   }
@@ -284,11 +306,15 @@ public class DnaTest
     /*
      * Generate cDNA - 8 sequences of 12 bases each.
      */
-    AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5);
-    ColumnSelection cs = new ColumnSelection();
+    AlignmentI cdna = new AlignmentGenerator(true)
+            .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 });
-    AlignmentI translated = dna.translateCdna();
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
+    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
 
     /*
      * Jumble the cDNA sequences and translate.
@@ -302,8 +328,10 @@ public class DnaTest
     }
     AlignmentI cdnaReordered = new Alignment(sorted);
     av = new AlignViewport(cdnaReordered, cs);
-    dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
-    AlignmentI translated2 = dna.translateCdna();
+    contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
+    dna = new Dna(av, contigs);
+    AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+            .getStandardCodeTable());
 
     /*
      * Check translated sequences are the same in both alignments.
@@ -500,17 +528,46 @@ public class DnaTest
   @Test(groups = "Functional")
   public void testReverseSequence()
   {
-    String seq = "AcGtUrYkMbVdHNX";
+    String seq = "-Ac-GtU--rYkMbVdHNX-";
+    String seqRev = new StringBuilder(seq).reverse().toString();
 
     // reverse:
     SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
-    assertEquals(new StringBuilder(seq).reverse()
-            .toString(), reversed.getSequenceAsString());
+    assertEquals(1, reversed.getStart());
+    assertEquals(15, reversed.getEnd());
+    assertEquals(20, reversed.getLength());
+    assertEquals(seqRev, reversed.getSequenceAsString());
     assertEquals("Seq1|rev", reversed.getName());
 
     // reverse complement:
     SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
-    assertEquals("XNDhBvKmRyAaCgT", revcomp.getSequenceAsString());
+    assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
     assertEquals("Seq1|revcomp", revcomp.getName());
   }
+
+  @Test(groups = "Functional")
+  public void testReverseCdna()
+  {
+    String seq = "-Ac-GtU--rYkMbVdHNX-";
+    String seqRev = new StringBuilder(seq).reverse().toString();
+    String seqDs = seq.replaceAll("-", "");
+    String seqDsRev = new StringBuilder(seqDs).reverse().toString();
+
+    SequenceI dna = new Sequence("Seq1", seq);
+    Alignment al = new Alignment(new SequenceI[] { dna });
+    al.createDatasetAlignment();
+    assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
+            .getSequenceAsString());
+
+    HiddenColumns cs = new HiddenColumns();
+    AlignViewportI av = new AlignViewport(al, cs);
+    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());
+    assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
+            .getSequenceAsString());
+  }
 }