X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Fpipeline%2F_jpred%2FPairwise.java;fp=runner%2Fcompbio%2Fpipeline%2F_jpred%2FPairwise.java;h=0000000000000000000000000000000000000000;hb=a6f4c70ca7af2302c60217480a534a9ac2320acb;hp=517f361d679855c0c4887d5f2d431c342d58ccae;hpb=bea86782341eb4d30559dea2857dace7f9f3a313;p=jabaws.git

diff --git a/runner/compbio/pipeline/_jpred/Pairwise.java b/runner/compbio/pipeline/_jpred/Pairwise.java
deleted file mode 100644
index 517f361..0000000
--- a/runner/compbio/pipeline/_jpred/Pairwise.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/* Copyright (c) 2011 Peter Troshin
- *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
- * 
- *  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.pipeline._jpred;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.SequenceUtil;
-
-public class Pairwise {
-
-	private final List<FastaSequence> sequences; 
-	final Set<PScore> pscores; 
-	
-	public Pairwise(List<FastaSequence> sequences) {
-		this.sequences = sequences;
-		pscores = new HashSet<PScore>(); 
-	}
-
-	void compare() {
-		for (int i = 0; i < sequences.size(); i++) {
-			FastaSequence seq1 = sequences.get(i); 
-			System.out.println(seq1.getId());
-			for (int j = i+1; j < sequences.size(); j++) {
-				FastaSequence seq2 = sequences.get(j);
-				PScore pscore = new PScore();
-				pscore.name = seq1.getId();
-				pscore.otherName = seq2.getId();
-				pscores.add(pscore);
-				compare(pscore, seq1.getSequence(), seq2.getSequence());
-			}
-		}
-	}
-
-	void compare(PScore pscore, String seq1, String seq2) { 
-		char[] chars1 = seq1.trim().toUpperCase().toCharArray(); 
-		char[] chars2 = seq2.trim().toUpperCase().toCharArray();
-		if(chars1.length != chars2.length) { 
-			throw new IllegalArgumentException("Different lenght sequence are provided but same expected! \n Sequence 1: \n" + pscore.name+ 
-					"\n Length:"+chars1.length +"\n "+ 
-					"Sequence 2: \n " + pscore.otherName + 
-					" \n Lenght: " + chars2.length ); 
-		}
-		compare(pscore, chars1, chars2); 
-	}
-	
-	void compare(PScore pscore, char[] seq1, char[] seq2) { 
-		int sameResedue = 0; 
-		for (int i = 0; i < seq1.length; i++) {
-			if(seq1[i]==seq2[i]) { 
-				sameResedue++;
-			}
-		}
-		pscore.score = (double)sameResedue /seq1.length;
-		System.out.println(pscore.score*100);
-	}
-	
-	public static final void main(String[]  args) throws FileNotFoundException, IOException {
-		File in = new File(args[0]);
-		List<FastaSequence> fslist = SequenceUtil.readFasta(new BufferedInputStream(new FileInputStream(in)));
-		Pairwise pair = new Pairwise(fslist);
-		pair.compare(); 
-		System.out.println(pair.pscores);
-	}
-}