X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2FAlignmentGenerator.java;h=9d3877c6d3eb3b676673b37c724b653ef60ea4df;hb=f624bc5b0ddc40d2f03d5e55e11a132239dae046;hp=3187fd964fc7d863e39cbe2bb2c319e53e98149a;hpb=fe28b89504fd1b76cc9d9631184aa6e065d7e243;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:
- *
- * - length (number of bases in each sequence)
- * - height (number of sequences)
- * - a whole number random seed
- * - percentage of gaps to include (0-100)
- * - percentage chance of variation of each position (0-100)
- *
- *
* @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:
+ *
+ * - n (for nucleotide) or p (for peptide)
+ * - length (number of bases in each sequence)
+ * - height (number of sequences)
+ * - a whole number random seed
+ * - percentage of gaps to include (0-100)
+ * - percentage chance of variation of each position (0-100)
+ * - (optional) path to a file to write the alignment to
+ *
+ *
*
* @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;
}