X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=blobdiff_plain;f=runner%2Fcompbio%2Fpipeline%2F_jpred%2FJackHmmerHitParser.java;fp=runner%2Fcompbio%2Fpipeline%2F_jpred%2FJackHmmerHitParser.java;h=0000000000000000000000000000000000000000;hp=771f3f46f42eeef3ae6c07b0c5f8d36c33a3135d;hb=b19d5c38c97cf895fc3379a918b5dcf1f3f2031e;hpb=b7a076f21e11b8cfa99f9e52759dcff702b957fd

diff --git a/runner/compbio/pipeline/_jpred/JackHmmerHitParser.java b/runner/compbio/pipeline/_jpred/JackHmmerHitParser.java
deleted file mode 100644
index 771f3f4..0000000
--- a/runner/compbio/pipeline/_jpred/JackHmmerHitParser.java
+++ /dev/null
@@ -1,97 +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.BufferedReader;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Scanner;
-import java.util.Set;
-
-/**
- * Parser for the following files:
- * 
- * @author pvtroshin
- * 
- */
-public class JackHmmerHitParser {
-    //#                                                                      --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
-    //# target name          accession  query name                accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
-    //#  ------------------- ----------      -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
-    //tr|Q6TVU2|Q6TVU2_ORFV  -          gi_74230740_gb_ABA00545.1 -           4.5e-271  910.4   0.0  5.1e-271  910.2   0.0   1.0   1   0   0   1   1   1   1 Putative uncharacterized protein OS=Orf virus PE=4 SV=1
-
-    Set<Hit> hits;
-
-    public JackHmmerHitParser(String file) throws IOException {
-
-	BufferedReader bfr = new BufferedReader(new InputStreamReader(
-		new FileInputStream(file), "ISO-8859-1"), 64000);
-	// throw away first three lines; 
-	this.hits = new HashSet<Hit>();
-	String line = bfr.readLine();
-	bfr.readLine();
-	bfr.readLine();
-	int hitc = 0;
-	while ((line = bfr.readLine()) != null) {
-	    hitc++;
-	    Scanner scan = new Scanner(line);
-	    scan.useDelimiter("\\s+");
-	    extractData(scan, hitc);
-	}
-	List<Hit> lhits = new ArrayList<Hit>(hits);
-	Collections.sort(lhits, new Hit.NumberComporator());
-    }
-
-    void extractData(Scanner scan, int hitcounter) {
-	Hit pseq = new Hit();
-
-	String tname = scan.next();
-	pseq.name = tname;
-	//System.out.println(tname);
-
-	String tacc = scan.next();
-	pseq.accession = tacc;
-	//System.out.println(tacc);
-	String qname = scan.next();
-	//System.out.println(qname);
-	String qacc = scan.next();
-	//System.out.println(qacc);
-
-	Double evalue = scan.nextDouble();
-	//System.out.println(evalue);
-	pseq.evalue = evalue.toString();
-
-	Double score = scan.nextDouble();
-	//System.out.println(score);
-	pseq.evalue = evalue.toString();
-	pseq.number = new Integer(hitcounter).toString();
-	boolean unique = hits.add(pseq);
-	assert unique : "Unique hits are expected!";
-    }
-
-    public static void main(String[] args) throws IOException {
-	assert args[0] != null;
-	JackHmmerHitParser parser = new JackHmmerHitParser(args[0]);
-	BlastParser.printHits(parser.hits);
-    }
-}