1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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18 package compbio.pipeline._jpred;
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20 import java.util.List;
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22 import compbio.data.sequence.FastaSequence;
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26 * jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
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27 * <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
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29 * jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
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30 * want to predict OR
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32 * [--alignment <clustalW alignment>] The alignment which to use for prediction
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34 * [--profile=<path to HMM profile>]
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36 * [--db <database>] Database to use for PSI-BLAST querying. Default: uniref90 (
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37 * /homes/www-jpred/databases/uniref90.filt) Please note that database must be
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40 * [--pred-nohits] Toggle allowing Jpred to make predictions even when there are
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41 * no PSI-BLAST hits.
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43 * [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help]
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49 public class Jpred4 {
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51 List<FastaSequence> readFastaSequence() {
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55 public void runPsiBlast() {
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