Merge branch 'JABAWS_Release_2_0'

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

diff --git a/runner/compbio/pipeline/_jpred/BlastParser.java b/runner/compbio/pipeline/_jpred/BlastParser.java
deleted file mode 100644 (file)
index 45f0244..0000000
--- a/runner/compbio/pipeline/_jpred/BlastParser.java
+++ /dev/null
@@ -1,134 +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.BufferedInputStream;\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.util.Collection;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
-import java.util.Map;\r
-import java.util.Set;\r
-\r
-import javax.xml.stream.XMLInputFactory;\r
-import javax.xml.stream.XMLStreamException;\r
-import javax.xml.stream.XMLStreamReader;\r
-\r
-public class BlastParser {\r
-\r
-    Map<Integer, Set<Hit>> iters;\r
-\r
-    public BlastParser(String file) throws FileNotFoundException,\r
-           XMLStreamException {\r
-       XMLInputFactory f = XMLInputFactory.newInstance();\r
-       XMLStreamReader r = f.createXMLStreamReader(new BufferedInputStream(\r
-               new FileInputStream(new File(file))));\r
-       Set<Hit> pl = new HashSet<Hit>();\r
-       Hit psi = null;\r
-       this.iters = new HashMap<Integer, Set<Hit>>();\r
-       Integer iternum = null;\r
-       while (r.hasNext()) {\r
-           int idx = r.next();\r
-           if (r.isStartElement()) {\r
-               String name = r.getLocalName();\r
-               if (name.equals("Iteration_iter-num")) {\r
-                   iternum = Integer.parseInt(r.getElementText().trim());\r
-                   System.out.println("Iter " + iternum);\r
-               }\r
-               if (name.equals("Hit")) {\r
-                   psi = new Hit();\r
-               }\r
-               if (name.equals("Hit_num")) {\r
-                   psi.number = r.getElementText();\r
-               }\r
-               if (name.equals("Hit_accession")) {\r
-                   psi.accession = r.getElementText();\r
-                   // System.out.println(psi.id);\r
-               }\r
-               if (name.equals("Hit_def")) {\r
-                   // System.out.println(r.getElementText());\r
-                   psi.name = r.getElementText().split("\\s+")[0].trim();\r
-                   // System.out.println(psi.id);\r
-               }\r
-               if (name.equals("Hsp_hseq")) {\r
-                   psi.seq = r.getElementText();\r
-                   // System.out.println(psi.seq);\r
-               }\r
-               if (name.equals("Hsp_evalue")) {\r
-                   psi.evalue = r.getElementText();\r
-                   // System.out.println(psi.seq);\r
-               }\r
-\r
-           }\r
-\r
-           if (r.isEndElement()) {\r
-               String name = r.getLocalName();\r
-               if (name.equals("Hit")) {\r
-                   boolean replaced = pl.add(psi);\r
-                   assert replaced : "Expect unique elements only!";\r
-                   psi = null;\r
-               }\r
-               if (name.equals("Iteration")) {\r
-                   iters.put(iternum, pl);\r
-                   pl = new HashSet<Hit>();\r
-               }\r
-           }\r
-       }\r
-\r
-    }\r
-\r
-    /**\r
-     * args[0] is assumed to be the name of a Blast output file\r
-     * \r
-     * @throws XMLStreamException\r
-     * @throws FileNotFoundException\r
-     */\r
-    public static void main(String[] args) throws FileNotFoundException,\r
-           XMLStreamException {\r
-       BlastParser parser = new BlastParser(args[0]);\r
-       printHits(parser.iters);\r
-    }\r
-\r
-    static final void printHits(Map<Integer, Set<Hit>> iterNumPsiSeqs) {\r
-       for (Integer iterNum : iterNumPsiSeqs.keySet()) {\r
-           System.out.println("Iteration " + iterNum);\r
-           printHits(iterNumPsiSeqs.get(iterNum));\r
-       }\r
-    }\r
-\r
-    static final void printHits(Collection<Hit> psiseqs) {\r
-       assert psiseqs != null;\r
-       System.out.println("Total hits: " + psiseqs.size());\r
-       for (Hit pseq : psiseqs) {\r
-           System.out.println("Hit: " + pseq.number + " Accession: "\r
-                   + pseq.accession + " name " + pseq.name);\r
-       }\r
-    }\r
-\r
-    static final void printNames(Collection<Hit> psiseqs) {\r
-       assert psiseqs != null;\r
-       System.out.println("Total hits: " + psiseqs.size());\r
-       for (Hit pseq : psiseqs) {\r
-           System.out.print(pseq.number + "     ");\r
-           System.out.println(pseq.name);\r
-       }\r
-    }\r
-\r
-}\r