X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Fdata%2Fsequence%2FFastaSequenceGenerator.java;fp=testsrc%2Fcompbio%2Fdata%2Fsequence%2FFastaSequenceGenerator.java;h=0000000000000000000000000000000000000000;hb=0965a336a3bc311c2527d7aacfa733e38fcfc4be;hp=c1aeb4e56f032b01b1a2e1845759f3f978851d24;hpb=2858c357fe831fda3f1114671732540dd55ad43a;p=proteocache.git

diff --git a/testsrc/compbio/data/sequence/FastaSequenceGenerator.java b/testsrc/compbio/data/sequence/FastaSequenceGenerator.java
deleted file mode 100644
index c1aeb4e..0000000
--- a/testsrc/compbio/data/sequence/FastaSequenceGenerator.java
+++ /dev/null
@@ -1,151 +0,0 @@
-/* Copyright (c) 2009 Peter Troshin
- *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     
- * 
- *  This library is free software; you can redistribute it and/or modify it under the terms of the
- *  Apache License version 2 as published by the Apache Software Foundation
- * 
- *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
- *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
- *  License for more details.
- * 
- *  A copy of the license is in apache_license.txt. It is also available here:
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
- * 
- * Any republication or derived work distributed in source code form
- * must include this copyright and license notice.
- */
-
-package compbio.data.sequence;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Random;
-
-public class FastaSequenceGenerator {
-
-	enum SeqType {
-		DNA, PROTEIN
-	}
-
-	enum ProteinAlphabet {
-		A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, V
-	};
-
-	enum DNAAlphabet {
-		C, T, G, A, U
-	};
-
-	enum Letters {
-		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
-	};
-
-	final SeqType seqtype;
-	final int seqNumber;
-	final Random rand;
-
-	/**
-	 * 
-	 * @param type
-	 *            of the sequence to be generated one of DNA or PROTEIN
-	 * @param seqNumber
-	 *            number of sequences to be generated
-	 */
-	public FastaSequenceGenerator(SeqType type, int seqNumber) {
-		this.seqtype = type;
-		this.seqNumber = seqNumber;
-		this.rand = new Random();
-	}
-
-	/**
-	 * Generate a list of Fasta formatted sequences with sequence length between
-	 * 0.5 to 1 of maxLenght. Name of the sequence as well as the sequence is
-	 * generated randomly
-	 * 
-	 * @param maxSeqLength
-	 *            maximum length of generated sequence
-	 * @return
-	 */
-	public List<FastaSequence> generateFasta(int maxSeqLength) {
-		List<FastaSequence> fastal = new ArrayList<FastaSequence>();
-		FastaSequence seq = null;
-		for (int i = 0; i < seqNumber; i++) {
-			switch (this.seqtype) {
-			case DNA:
-				seq = new FastaSequence(generateName(), generateDna(
-						maxSeqLength, getRandomNumber(0.5, 0.99)));
-				break;
-			case PROTEIN:
-				seq = new FastaSequence(generateName(), generateProtein(
-						maxSeqLength, getRandomNumber(0.5, 0.99)));
-				break;
-			default:
-				throw new AssertionError("Cannot recognise a type!");
-			}
-			fastal.add(seq);
-		}
-		return fastal;
-	}
-
-	private String generateName() {
-		Letters[] letters = Letters.values();
-		int max = letters.length - 1;
-		StringBuilder sb = new StringBuilder();
-		for (int i = 0; i < 10; i++) {
-			sb.append(letters[getRandomNumber(0, max)]);
-		}
-		return sb.toString();
-	}
-
-	private String generateProtein(int length, double variability) {
-		ProteinAlphabet[] proteinA = ProteinAlphabet.values();
-		int max = proteinA.length - 1;
-		StringBuilder sb = new StringBuilder();
-		for (int i = 0; i < length * variability; i++) {
-			sb.append(proteinA[getRandomNumber(max)]);
-		}
-		return sb.toString();
-	}
-
-	private String generateDna(int length, double variability) {
-		if (variability == 0) {
-			variability = 1;
-		}
-		DNAAlphabet[] dnaA = DNAAlphabet.values();
-		int max = dnaA.length - 1;
-		StringBuilder sb = new StringBuilder();
-		for (int i = 0; i < length * variability; i++) {
-			sb.append(dnaA[getRandomNumber(max)]);
-		}
-		return sb.toString();
-	}
-
-	/*
-	 * Returns random integers in range from 0 to max
-	 * 
-	 * @param max
-	 * 
-	 * @return
-	 */
-	private int getRandomNumber(int max) {
-		return rand.nextInt(max);
-	}
-
-	/*
-	 * Returns random integers with value in range from min to max
-	 * 
-	 * @param min
-	 * 
-	 * @param max
-	 * 
-	 * @return
-	 */
-	private int getRandomNumber(int min, int max) {
-		return new Long(Math.round((max - min) * rand.nextDouble() + min))
-				.intValue();
-	}
-
-	private double getRandomNumber(double min, double max) {
-		return (max - min) * rand.nextDouble() + min;
-	}
-}