1 /** 2 * UGENE - Integrated Bioinformatics Tools. 3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru> 4 * http://ugene.net 5 * 6 * This program is free software; you can redistribute it and/or 7 * modify it under the terms of the GNU General Public License 8 * as published by the Free Software Foundation; either version 2 9 * of the License, or (at your option) any later version. 10 * 11 * This program is distributed in the hope that it will be useful, 12 * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 * GNU General Public License for more details. 15 * 16 * You should have received a copy of the GNU General Public License 17 * along with this program; if not, write to the Free Software 18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, 19 * MA 02110-1301, USA. 20 */ 21 22 #ifndef _REMOTE_QUERY_CONSTS_ 23 #define _REMOTE_QUERY_CONSTS_ 24 25 #include <QStringList> 26 27 namespace U2 { 28 29 #define MAX_BLAST_SEQ_LEN 3000 30 31 #define CDD_DESCRIPTION "CDD (Conserved Domain Database) is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins." 32 #define BLAST_DESCRIPTION "Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold." 33 34 #define EXPECTED_ATTR "expected_results" 35 #define SIMPLE_ATTR "simple" 36 #define MIN_LEN_ATTR "min_length" 37 #define MAX_LEN_ATTR "max_length" 38 #define TRANSL_ATTR "transl" 39 #define DATABASE_ATTR "db" 40 #define EVALUE_ATTR "e-value" 41 #define INDEX_ATTR "index" 42 #define SEQUENCE_ATTR "seq" 43 #define SHORTSEQ_ATTR "short_seq" 44 #define HITS_ATTR "hits" 45 #define ALG_ATTR "alg" 46 #define FILTERS_ATTR "filters" 47 #define GAP_ATTR "gap_costs" 48 #define MATCHSCORE_ATTR "match_scores" 49 #define MATRIX_ATTR "matrix" 50 #define MEGABLAST_ATTR "megablast" 51 #define WORD_SIZE_ATTR "word_size" 52 #define ALPH_ATTR "alph" 53 #define SERVICE_ATTR "service" 54 #define PATTERN_ATTR "phi-pattern" 55 #define ENTREZ_QUERY_ATTR "entrez_query" 56 57 class ParametersLists { 58 public: 59 static const QStringList blastn_wordSize; 60 static const QStringList blastp_wordSize; 61 static const QStringList megablast_wordSize; 62 63 static const QStringList blastn_gapCost; 64 static const QStringList blastp_gapCost; 65 66 static const QStringList blastn_scores; 67 68 static const QStringList blastn_dataBase; 69 static const QStringList blastp_dataBase; 70 static const QStringList cdd_dataBase; 71 72 static const QStringList blastp_matrix; 73 }; 74 75 class ReqParams { 76 public: 77 static const QString program; 78 static const QString expect; 79 static const QString wordSize; 80 static const QString hits; 81 static const QString database; 82 static const QString gapCost; 83 static const QString matchScore; 84 static const QString mismatchScore; 85 static const QString matrix; 86 static const QString filter; 87 static const QString megablast; 88 static const QString lowCaseMask; 89 static const QString sequence; 90 static const QString service; 91 static const QString phiPattern; 92 static const QString entrezQuery; 93 94 static const QString cdd_eValue; 95 static const QString cdd_hits; 96 static const QString cdd_sequence; 97 static const QString cdd_db; 98 }; 99 100 void addParametr(QString &str, const QString ¶mName, const QString ¶m); 101 void addParametr(QString &str, const QString ¶mName, const double param); 102 void addParametr(QString &str, const QString ¶mName, const int param); 103 104 } // namespace U2 105 106 #endif 107