Add testing dirs

[proteocache.git] / testsrc / compbio / data / sequence / FastaGeneratorManager.java

diff --git a/testsrc/compbio/data/sequence/FastaGeneratorManager.java b/testsrc/compbio/data/sequence/FastaGeneratorManager.java
new file mode 100644 (file)
index 0000000..9305d8b
--- /dev/null
+++ b/testsrc/compbio/data/sequence/FastaGeneratorManager.java
@@ -0,0 +1,61 @@
+/* Copyright (c) 2009 Peter Troshin\r
+ *  \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
+ * \r
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ *  Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ *  License for more details.\r
+ * \r
+ *  A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.data.sequence;\r
+\r
+import java.io.IOException;\r
+import java.util.List;\r
+\r
+import compbio.util.FileUtil;\r
+\r
+public class FastaGeneratorManager {\r
+\r
+       public static void main(String[] args) throws IOException {\r
+               FastaSequenceGenerator fgen = new FastaSequenceGenerator(\r
+                               FastaSequenceGenerator.SeqType.PROTEIN, 50);\r
+\r
+               List<FastaSequence> fslist = fgen.generateFasta(400);\r
+               writeToFile(fslist, "SmallProtein.fasta");\r
+\r
+               fgen = new FastaSequenceGenerator(\r
+                               FastaSequenceGenerator.SeqType.PROTEIN, 200);\r
+\r
+               fslist = fgen.generateFasta(500);\r
+               writeToFile(fslist, "200x500Protein.fasta");\r
+\r
+               fgen = new FastaSequenceGenerator(FastaSequenceGenerator.SeqType.DNA,\r
+                               1000);\r
+               fslist = fgen.generateFasta(3000);\r
+               writeToFile(fslist, "1000x3000Dna.fasta");\r
+\r
+               fgen = new FastaSequenceGenerator(FastaSequenceGenerator.SeqType.DNA,\r
+                               50000);\r
+               fslist = fgen.generateFasta(300);\r
+               writeToFile(fslist, "50000x300Dna.fasta");\r
+               System.out.println("Done");\r
+       }\r
+\r
+       static void writeToFile(List<FastaSequence> fastalist, String filepath)\r
+                       throws IOException {\r
+               StringBuilder sb = new StringBuilder();\r
+               for (FastaSequence fs : fastalist) {\r
+                       sb.append(fs.getOnelineFasta() + "\n");\r
+               }\r
+               FileUtil.writeToFile(sb.toString(), filepath);\r
+       }\r
+}\r