X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentGenerator.java;fp=test%2Fjalview%2Fanalysis%2FAlignmentGenerator.java;h=9d3877c6d3eb3b676673b37c724b653ef60ea4df;hb=0efc6021e63ff62bb2e275501586c1900561b303;hp=3187fd964fc7d863e39cbe2bb2c319e53e98149a;hpb=771d1758a42abc6e3e330dd6c5117734acf0067f;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentGenerator.java b/test/jalview/analysis/AlignmentGenerator.java
index 3187fd9..9d3877c 100644
--- a/test/jalview/analysis/AlignmentGenerator.java
+++ b/test/jalview/analysis/AlignmentGenerator.java
@@ -27,39 +27,25 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 import jalview.io.FastaFile;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
 import java.util.Arrays;
 import java.util.Random;
 
 import org.testng.annotations.BeforeClass;
 
 /**
- * Generates, and outputs in Fasta format, a random DNA alignment for given
+ * Generates, and outputs in Fasta format, a random peptide or nucleotide 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).
  * Not guaranteed to reproduce the same results between versions, as the rules
  * may get tweaked to produce more 'realistic' results.
  * 
- * Arguments:
- * <ul>
- * <li>length (number of bases in each sequence)</li>
- * <li>height (number of sequences)</li>
- * <li>a whole number random seed</li>
- * <li>percentage of gaps to include (0-100)</li>
- * <li>percentage chance of variation of each position (0-100)</li>
- * </ul>
- * 
  * @author gmcarstairs
- *
  */
 public class AlignmentGenerator
 {
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
   private static final char GAP = '-';
 
   private static final char ZERO = '0';
@@ -72,51 +58,76 @@ public class AlignmentGenerator
 
   private Random random;
 
+  private PrintStream ps;
 
   /**
-   * Outputs a DNA 'alignment' where each position is a random choice from
-   * 'GTCA-'.
+   * Outputs a pseudo-randomly generated nucleotide or peptide alignment
+   * Arguments:
+   * <ul>
+   * <li>n (for nucleotide) or p (for peptide)</li>
+   * <li>length (number of bases in each sequence)</li>
+   * <li>height (number of sequences)</li>
+   * <li>a whole number random seed</li>
+   * <li>percentage of gaps to include (0-100)</li>
+   * <li>percentage chance of variation of each position (0-100)</li>
+   * <li>(optional) path to a file to write the alignment to</li>
+   * </ul>
+   * 
    * 
    * @param args
+   * @throws FileNotFoundException
    */
-  public static void main(String[] args)
+  public static void main(String[] args) throws FileNotFoundException
   {
-    if (args.length != 6)
+    if (args.length != 6 && args.length != 7)
     {
       usage();
       return;
     }
+
+    PrintStream ps = System.out;
+    if (args.length == 7)
+    {
+      ps = new PrintStream(new File(args[6]));
+    }
+
     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(nucleotide).generate(width,
-            height,
-            randomSeed, gapPercentage, changePercentage);
 
-    System.out.println("; " + height + " sequences of " + width
+    ps.println("; " + height + " sequences of " + width
             + " bases with " + gapPercentage + "% gaps and "
             + changePercentage + "% mutations (random seed = " + randomSeed
             + ")");
-    System.out.println(new FastaFile().print(al.getSequencesArray(), true));
+
+    new AlignmentGenerator(nucleotide, ps).generate(width, height,
+            randomSeed, gapPercentage, changePercentage);
+
+    if (ps != System.out)
+    {
+      ps.close();
+    }
   }
 
   /**
-   * Print parameter help.
+   * Prints parameter help
    */
   private static void usage()
   {
     System.out.println("Usage:");
     System.out.println("arg0: n (for nucleotide) or p (for peptide)");
     System.out.println("arg1: number of (non-gap) bases per sequence");
-    System.out.println("arg2: number sequences");
+    System.out.println("arg2: number of sequences");
     System.out
             .println("arg3: an integer as random seed (same seed = same results)");
     System.out.println("arg4: percentage of gaps to (randomly) generate");
     System.out
             .println("arg5: percentage of 'mutations' to (randomly) generate");
+    System.out
+            .println("arg6: (optional) path to output file (default is sysout)");
     System.out.println("Example: AlignmentGenerator n 12 15 387 10 5");
     System.out
             .println("- 15 nucleotide sequences of 12 bases each, approx 10% gaps and 5% mutations, random seed = 387");
@@ -124,16 +135,28 @@ public class AlignmentGenerator
   }
 
   /**
-   * Constructor that sets nucleotide or peptide symbol set
+   * Constructor that sets nucleotide or peptide symbol set, and also writes the
+   * generated alignment to sysout
    */
   public AlignmentGenerator(boolean nuc)
   {
-    BASES = nuc ? NUCS : PEPS;
+    this(nuc, System.out);
+  }
+
+  /**
+   * Constructor that sets nucleotide or peptide symbol set, and also writes the
+   * generated alignment to the specified output stream (if not null). This can
+   * be used to write the alignment to a file or sysout.
+   */
+  public AlignmentGenerator(boolean nucleotide, PrintStream printStream)
+  {
+    BASES = nucleotide ? NUCS : PEPS;
+    ps = printStream;
   }
 
   /**
-   * Outputs a DNA 'alignment' of given width and height, where each position is
-   * a random choice from 'GTCA-'.
+   * Outputs an 'alignment' of given width and height, where each position is a
+   * random choice from the symbol alphabet, or - for gap
    * 
    * @param width
    * @param height
@@ -153,6 +176,12 @@ public class AlignmentGenerator
               seqno + 1, width, changePercentage);
     }
     AlignmentI al = new Alignment(seqs);
+
+    if (ps != null)
+    {
+      ps.println(new FastaFile().print(al.getSequencesArray(), true));
+    }
+
     return al;
   }