JAL-1270 tweaks to AlignmentGenerator / client class

diff --git a/test/jalview/analysis/AlignmentGenerator.java b/test/jalview/analysis/AlignmentGenerator.java
index 0e3bbbb..3187fd9 100644 (file)
--- a/test/jalview/analysis/AlignmentGenerator.java
+++ b/test/jalview/analysis/AlignmentGenerator.java
@@ -53,7 +53,6 @@ import org.testng.annotations.BeforeClass;
  */
 public class AlignmentGenerator
 {
-
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -87,13 +86,14 @@ public class AlignmentGenerator
       usage();
       return;
     }
-    BASES = args[0].toLowerCase().startsWith("n") ? NUCS : PEPS;
+    boolean nucleotide = args[0].toLowerCase().startsWith("n");
     int width = Integer.parseInt(args[1]);
     int height = Integer.parseInt(args[2]);
     long randomSeed = Long.valueOf(args[3]);
     int gapPercentage = Integer.valueOf(args[4]);
     int changePercentage = Integer.valueOf(args[5]);
-    AlignmentI al = new AlignmentGenerator().generate(width, height,
+    AlignmentI al = new AlignmentGenerator(nucleotide).generate(width,
+            height,
             randomSeed, gapPercentage, changePercentage);
 
     System.out.println("; " + height + " sequences of " + width
@@ -124,11 +124,11 @@ public class AlignmentGenerator
   }
 
   /**
-   * Default constructor
+   * Constructor that sets nucleotide or peptide symbol set
    */
-  public AlignmentGenerator()
+  public AlignmentGenerator(boolean nuc)
   {
-
+    BASES = nuc ? NUCS : PEPS;
   }
 
   /**

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index cd5d3ca..2e21d9c 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -294,7 +294,8 @@ public class DnaTest
     /*
      * Generate cDNA - 8 sequences of 12 bases each.
      */
-    AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5);
+    AlignmentI cdna = new AlignmentGenerator(true)
+            .generate(12, 8, 97, 5, 5);
     ColumnSelection cs = new ColumnSelection();
     AlignViewportI av = new AlignViewport(cdna, cs);
     Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });