Merge branch 'JABAWS_Release_2_0'

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

diff --git a/runner/compbio/pipeline/_jpred/BlastHmmerComparator.java b/runner/compbio/pipeline/_jpred/BlastHmmerComparator.java
deleted file mode 100644 (file)
index 28c64d4..0000000
--- a/runner/compbio/pipeline/_jpred/BlastHmmerComparator.java
+++ /dev/null
@@ -1,60 +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.IOException;\r
-import java.util.HashSet;\r
-import java.util.Set;\r
-\r
-import javax.xml.stream.XMLStreamException;\r
-\r
-public class BlastHmmerComparator {\r
-\r
-    /**\r
-     * args[0] is assumed to be the name of a Blast output file\r
-     * \r
-     * @throws XMLStreamException\r
-     * @throws IOException\r
-     */\r
-    public static void main(String[] args) throws XMLStreamException,\r
-           IOException {\r
-       BlastParser res1 = new BlastParser(args[0]);\r
-       JackHmmerHitParser res2 = new JackHmmerHitParser(args[1]);\r
-       Set<Hit> list = res1.iters.get(3);\r
-       Set<Hit> otherList = res2.hits;\r
-       System.out.print("Iter " + 3 + " arg0: " + list.size());\r
-       System.out.println(" arg1: " + otherList.size());\r
-       BlastParser.printNames(getDiff(list, otherList));\r
-       BlastParser.printNames(getDiff(otherList, list));\r
-       // System.out.println("Diffs: " + getDiff(list, otherList));\r
-       // System.out.println("Diffs: " + getDiff(otherList, list));\r
-\r
-    }\r
-\r
-    static Set<Hit> getDiff(Set<Hit> list, Set<Hit> otherList) {\r
-       Set diff = new HashSet<Hit>();\r
-       for (Hit pseq : list) {\r
-           if (otherList.contains(pseq)) {\r
-               continue;\r
-           }\r
-           diff.add(pseq);\r
-       }\r
-       return diff;\r
-    }\r
-\r
-}\r