Add testing dirs

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

diff --git a/testsrc/compbio/data/sequence/FastaSequenceGenerator.java b/testsrc/compbio/data/sequence/FastaSequenceGenerator.java
new file mode 100644 (file)
index 0000000..c1aeb4e
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+++ b/testsrc/compbio/data/sequence/FastaSequenceGenerator.java
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+/* 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.util.ArrayList;\r
+import java.util.List;\r
+import java.util.Random;\r
+\r
+public class FastaSequenceGenerator {\r
+\r
+       enum SeqType {\r
+               DNA, PROTEIN\r
+       }\r
+\r
+       enum ProteinAlphabet {\r
+               A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, V\r
+       };\r
+\r
+       enum DNAAlphabet {\r
+               C, T, G, A, U\r
+       };\r
+\r
+       enum Letters {\r
+               q, w, e, r, t, y, u, i, o, p, a, s, d, f, g, h, j, k, l, z, x, c, v, b, n, m\r
+       };\r
+\r
+       final SeqType seqtype;\r
+       final int seqNumber;\r
+       final Random rand;\r
+\r
+       /**\r
+        * \r
+        * @param type\r
+        *            of the sequence to be generated one of DNA or PROTEIN\r
+        * @param seqNumber\r
+        *            number of sequences to be generated\r
+        */\r
+       public FastaSequenceGenerator(SeqType type, int seqNumber) {\r
+               this.seqtype = type;\r
+               this.seqNumber = seqNumber;\r
+               this.rand = new Random();\r
+       }\r
+\r
+       /**\r
+        * Generate a list of Fasta formatted sequences with sequence length between\r
+        * 0.5 to 1 of maxLenght. Name of the sequence as well as the sequence is\r
+        * generated randomly\r
+        * \r
+        * @param maxSeqLength\r
+        *            maximum length of generated sequence\r
+        * @return\r
+        */\r
+       public List<FastaSequence> generateFasta(int maxSeqLength) {\r
+               List<FastaSequence> fastal = new ArrayList<FastaSequence>();\r
+               FastaSequence seq = null;\r
+               for (int i = 0; i < seqNumber; i++) {\r
+                       switch (this.seqtype) {\r
+                       case DNA:\r
+                               seq = new FastaSequence(generateName(), generateDna(\r
+                                               maxSeqLength, getRandomNumber(0.5, 0.99)));\r
+                               break;\r
+                       case PROTEIN:\r
+                               seq = new FastaSequence(generateName(), generateProtein(\r
+                                               maxSeqLength, getRandomNumber(0.5, 0.99)));\r
+                               break;\r
+                       default:\r
+                               throw new AssertionError("Cannot recognise a type!");\r
+                       }\r
+                       fastal.add(seq);\r
+               }\r
+               return fastal;\r
+       }\r
+\r
+       private String generateName() {\r
+               Letters[] letters = Letters.values();\r
+               int max = letters.length - 1;\r
+               StringBuilder sb = new StringBuilder();\r
+               for (int i = 0; i < 10; i++) {\r
+                       sb.append(letters[getRandomNumber(0, max)]);\r
+               }\r
+               return sb.toString();\r
+       }\r
+\r
+       private String generateProtein(int length, double variability) {\r
+               ProteinAlphabet[] proteinA = ProteinAlphabet.values();\r
+               int max = proteinA.length - 1;\r
+               StringBuilder sb = new StringBuilder();\r
+               for (int i = 0; i < length * variability; i++) {\r
+                       sb.append(proteinA[getRandomNumber(max)]);\r
+               }\r
+               return sb.toString();\r
+       }\r
+\r
+       private String generateDna(int length, double variability) {\r
+               if (variability == 0) {\r
+                       variability = 1;\r
+               }\r
+               DNAAlphabet[] dnaA = DNAAlphabet.values();\r
+               int max = dnaA.length - 1;\r
+               StringBuilder sb = new StringBuilder();\r
+               for (int i = 0; i < length * variability; i++) {\r
+                       sb.append(dnaA[getRandomNumber(max)]);\r
+               }\r
+               return sb.toString();\r
+       }\r
+\r
+       /*\r
+        * Returns random integers in range from 0 to max\r
+        * \r
+        * @param max\r
+        * \r
+        * @return\r
+        */\r
+       private int getRandomNumber(int max) {\r
+               return rand.nextInt(max);\r
+       }\r
+\r
+       /*\r
+        * Returns random integers with value in range from min to max\r
+        * \r
+        * @param min\r
+        * \r
+        * @param max\r
+        * \r
+        * @return\r
+        */\r
+       private int getRandomNumber(int min, int max) {\r
+               return new Long(Math.round((max - min) * rand.nextDouble() + min))\r
+                               .intValue();\r
+       }\r
+\r
+       private double getRandomNumber(double min, double max) {\r
+               return (max - min) * rand.nextDouble() + min;\r
+       }\r
+}\r