Merge branch 'JABAWS_Release_2_0'

[jabaws.git] / runner / compbio / pipeline / _jpred / JackHmmerHitParser.java

diff --git a/runner/compbio/pipeline/_jpred/JackHmmerHitParser.java b/runner/compbio/pipeline/_jpred/JackHmmerHitParser.java
deleted file mode 100644 (file)
index 771f3f4..0000000
--- a/runner/compbio/pipeline/_jpred/JackHmmerHitParser.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/* Copyright (c) 2011 Peter Troshin\r
- *  \r
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \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
-package compbio.pipeline._jpred;\r
-\r
-import java.io.BufferedReader;\r
-import java.io.FileInputStream;\r
-import java.io.IOException;\r
-import java.io.InputStreamReader;\r
-import java.util.ArrayList;\r
-import java.util.Collections;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-import java.util.Scanner;\r
-import java.util.Set;\r
-\r
-/**\r
- * Parser for the following files:\r
- * \r
- * @author pvtroshin\r
- * \r
- */\r
-public class JackHmmerHitParser {\r
-    //#                                                                      --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----\r
-    //# 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\r
-    //#  ------------------- ----------      -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------\r
-    //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\r
-\r
-    Set<Hit> hits;\r
-\r
-    public JackHmmerHitParser(String file) throws IOException {\r
-\r
-       BufferedReader bfr = new BufferedReader(new InputStreamReader(\r
-               new FileInputStream(file), "ISO-8859-1"), 64000);\r
-       // throw away first three lines; \r
-       this.hits = new HashSet<Hit>();\r
-       String line = bfr.readLine();\r
-       bfr.readLine();\r
-       bfr.readLine();\r
-       int hitc = 0;\r
-       while ((line = bfr.readLine()) != null) {\r
-           hitc++;\r
-           Scanner scan = new Scanner(line);\r
-           scan.useDelimiter("\\s+");\r
-           extractData(scan, hitc);\r
-       }\r
-       List<Hit> lhits = new ArrayList<Hit>(hits);\r
-       Collections.sort(lhits, new Hit.NumberComporator());\r
-    }\r
-\r
-    void extractData(Scanner scan, int hitcounter) {\r
-       Hit pseq = new Hit();\r
-\r
-       String tname = scan.next();\r
-       pseq.name = tname;\r
-       //System.out.println(tname);\r
-\r
-       String tacc = scan.next();\r
-       pseq.accession = tacc;\r
-       //System.out.println(tacc);\r
-       String qname = scan.next();\r
-       //System.out.println(qname);\r
-       String qacc = scan.next();\r
-       //System.out.println(qacc);\r
-\r
-       Double evalue = scan.nextDouble();\r
-       //System.out.println(evalue);\r
-       pseq.evalue = evalue.toString();\r
-\r
-       Double score = scan.nextDouble();\r
-       //System.out.println(score);\r
-       pseq.evalue = evalue.toString();\r
-       pseq.number = new Integer(hitcounter).toString();\r
-       boolean unique = hits.add(pseq);\r
-       assert unique : "Unique hits are expected!";\r
-    }\r
-\r
-    public static void main(String[] args) throws IOException {\r
-       assert args[0] != null;\r
-       JackHmmerHitParser parser = new JackHmmerHitParser(args[0]);\r
-       BlastParser.printHits(parser.hits);\r
-    }\r
-}\r