Merge branch 'releases/Release_2_10_4_Branch_merged_JAL-2759' into releases/Release_2...

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

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 1851517..6a31b31 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -28,18 +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"
@@ -120,11 +132,13 @@ public class DnaTest
           throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
-            "FASTA");
-    ColumnSelection cs = new ColumnSelection();
+            JAL_1312_example_align_fasta, 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();
     assertNotNull("Couldn't do a full width translation of test data.",
             translated);
@@ -141,18 +155,19 @@ public class DnaTest
           throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
-            "FASTA");
+            JAL_1312_example_align_fasta, DataSourceType.PASTE,
+            FileFormat.Fasta);
     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();
@@ -176,10 +191,12 @@ public class DnaTest
   public void testTranslateCdna_simple() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
-            FormatAdapter.PASTE, "FASTA");
-    ColumnSelection cs = new ColumnSelection();
+            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(
@@ -196,13 +213,15 @@ public class DnaTest
   public void testTranslateCdna_hiddenColumns() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
-            FormatAdapter.PASTE, "FASTA");
-    ColumnSelection cs = new jalview.datamodel.ColumnSelection();
+            DataSourceType.PASTE, FileFormat.Fasta);
+    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 });
+    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);
@@ -283,10 +302,13 @@ 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 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
 
     /*
@@ -301,7 +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();
 
     /*
@@ -530,9 +553,11 @@ public class DnaTest
     assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
             .getSequenceAsString());
 
-    ColumnSelection cs = new ColumnSelection();
+    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());