From f92f257fedde23c96bef9efc48c9df85f3b9f9d9 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 20 Jan 2015 09:11:43 +0000
Subject: [PATCH] JAL-1619 tweaked for better reusability

---
 test/jalview/analysis/DnaAlignmentGenerator.java |   49 ++++++++++++++++++----
 1 file changed, 40 insertions(+), 9 deletions(-)

diff --git a/test/jalview/analysis/DnaAlignmentGenerator.java b/test/jalview/analysis/DnaAlignmentGenerator.java
index 59a08be..4215df7 100644
--- a/test/jalview/analysis/DnaAlignmentGenerator.java
+++ b/test/jalview/analysis/DnaAlignmentGenerator.java
@@ -1,10 +1,25 @@
 package jalview.analysis;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+
 import java.util.Random;
 
 /**
- * Generates a random Fasta format DNA alignment for given sequence length and
- * count.
+ * Generates, and outputs in Fasta format, a random DNA alignment for given
+ * sequence length and count. Will regenerate the same alignment each time if
+ * the same random seed is used (so may be used for reproducible unit tests).
+ * The alignment is not padded with gaps.
+ * 
+ * Arguments:
+ * <ul>
+ * <li>length (number of bases in each sequence)</li>
+ * <li>height (number of sequences)</li>
+ * <li>a whole number random seed</li>
+ * </ul>
  * 
  * @author gmcarstairs
  *
@@ -31,7 +46,17 @@ public class DnaAlignmentGenerator
     int width = Integer.parseInt(args[0]);
     int height = Integer.parseInt(args[1]);
     long randomSeed = Long.valueOf(args[2]);
-    new DnaAlignmentGenerator().generate(width, height, randomSeed);
+    AlignmentI al = new DnaAlignmentGenerator().generate(width, height,
+            randomSeed);
+    System.out.println(new FastaFile().print(al.getSequencesArray()));
+  }
+
+  /**
+   * Default constructor
+   */
+  public DnaAlignmentGenerator()
+  {
+
   }
 
   /**
@@ -42,13 +67,16 @@ public class DnaAlignmentGenerator
    * @param height
    * @param randomSeed
    */
-  private void generate(int width, int height, long randomSeed)
+  public AlignmentI generate(int width, int height, long randomSeed)
   {
+    SequenceI[] seqs = new SequenceI[height];
     random = new Random(randomSeed);
     for (int seqno = 0; seqno < height; seqno++)
     {
-      generateSequence(seqno + 1, width);
+      seqs[seqno] = generateSequence(seqno + 1, width);
     }
+    AlignmentI al = new Alignment(seqs);
+    return al;
   }
 
   /**
@@ -57,13 +85,12 @@ public class DnaAlignmentGenerator
    * @param seqno
    * @param length
    */
-  private void generateSequence(int seqno, int length)
+  private SequenceI generateSequence(int seqno, int length)
   {
-    System.out.println(">SEQ" + seqno);
     StringBuilder seq = new StringBuilder(length);
 
     /*
-     * Loop till we've output 'length' real bases (excluding gaps)
+     * Loop till we've added 'length' bases (excluding gaps)
      */
     for (int count = 0 ; count < length ; ) {
       char c = BASES[random.nextInt(Integer.MAX_VALUE) % 5];
@@ -73,6 +100,10 @@ public class DnaAlignmentGenerator
         count++;
       }
     }
-    System.out.println(seq.toString());
+    final String seqName = ">SEQ" + seqno;
+    final String seqString = seq.toString();
+    SequenceI sq = new Sequence(seqName, seqString);
+    sq.createDatasetSequence();
+    return sq;
   }
 }
-- 
1.7.10.2