001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on 2012-02-11
021 *
022 */
023
024package org.biojava.nbio.ws.alignment.qblast;
025
026/**
027 * Alignment request parameters accepted by QBlast service.<br/>
028 * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
029 * <p/>
030 * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
031 *
032 * @author Gediminas Rimsa
033 */
034public enum BlastAlignmentParameterEnum {
035
036        CMD,
037        TOOL,
038        EMAIL,
039
040        ALIGNMENTS,
041        BLAST_PROGRAM,
042        CDD_SEARCH,
043        COMPOSITION_BASED_STATISTICS,
044        DATABASE_PREFIX,
045        DATABASE,
046        DB_GENETIC_CODE,
047        DESCRIPTIONS,
048        ENTREZ_QUERY,
049        EXPECT,
050        FILTER,
051        FIRST_QUERY_NUM,
052        GAPCOSTS,
053        GENETIC_CODE,
054        HITLIST_SIZE,
055        I_THRESH,
056        LCASE_MASK,
057        MATCH_SCORES,
058        MATRIX_NAME,
059        MAX_NUM_SEQ,
060        MEGABLAST,
061        NUM_OVERVIEW,
062        OTHER_ADVANCED,
063        PERC_IDENT,
064        PHI_PATTERN,
065        PROGRAM,
066        PSSM,
067        QUERY,
068        QUERY_BELIEVE_DEFLINE,
069        QUERY_FROM,
070        QUERY_TO,
071        REPEATS,
072        SHORT_QUERY_ADJUST,
073        SEARCHSP_EFF,
074        TEMPLATE_LENTH,
075        TEMPLATE_TYPE,
076        THRESHOLD,
077        TWO_HITS,
078        WORD_SIZE,
079        WWW_BLAST_TYPE
080
081}