Merge branch 'JABAWS_Release_2_0'

[jabaws.git] / runner / compbio / pipeline / _jpred / Jpred4.java

diff --git a/runner/compbio/pipeline/_jpred/Jpred4.java b/runner/compbio/pipeline/_jpred/Jpred4.java
deleted file mode 100644 (file)
index ebb5f09..0000000
--- a/runner/compbio/pipeline/_jpred/Jpred4.java
+++ /dev/null
@@ -1,58 +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.util.List;\r
-\r
-import compbio.data.sequence.FastaSequence;\r
-\r
-/**\r
- * \r
- * jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db\r
- * <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]\r
- * \r
- * jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you\r
- * want to predict OR\r
- * \r
- * [--alignment <clustalW alignment>] The alignment which to use for prediction\r
- * \r
- * [--profile=<path to HMM profile>]\r
- * \r
- * [--db <database>] Database to use for PSI-BLAST querying. Default: uniref90 (\r
- * /homes/www-jpred/databases/uniref90.filt) Please note that database must be\r
- * psi-blast indexed\r
- * \r
- * [--pred-nohits] Toggle allowing Jpred to make predictions even when there are\r
- * no PSI-BLAST hits.\r
- * \r
- * [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help]\r
- * \r
- * \r
- * @author pvtroshin\r
- * \r
- */\r
-public class Jpred4 {\r
-\r
-       List<FastaSequence> readFastaSequence() {\r
-               return null;\r
-       }\r
-\r
-       public void runPsiBlast() {\r
-       };\r
-\r
-}\r