1 /* $Id: cuCdUpdateParameters.cpp 607023 2020-04-29 18:39:50Z lanczyck $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government have not placed any restriction on its use or reproduction.
13 *
14 * Although all reasonable efforts have been taken to ensure the accuracy
15 * and reliability of the software and data, the NLM and the U.S.
16 * Government do not and cannot warrant the performance or results that
17 * may be obtained by using this software or data. The NLM and the U.S.
18 * Government disclaim all warranties, express or implied, including
19 * warranties of performance, merchantability or fitness for any particular
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Author: Charlie Liu
27 *
28 * File Description:
29 *
30 *
31 * ===========================================================================
32 */
33
34 #include <ncbi_pch.hpp>
35 #include <algo/structure/cd_utils/cuCdUpdateParameters.hpp>
36 #include <stdio.h>
37
38 BEGIN_NCBI_SCOPE
39 BEGIN_SCOPE(cd_utils)
40
41 string BlastTypeNames[] = {
42 "blast",
43 "psi-blast"
44 };
45
46 string BlastDatabaseNames[] = {
47 "nr",
48 "swissprot",
49 "pdb",
50 "pat",
51 "Yeast",
52 "ecoli",
53 "Drosophila genome",
54 "month",
55 "SMARTBLAST/landmark",
56 "CDSEARCH_TEST/nr_v4",
57 "CDSEARCH_TEST/pdb_v5",
58 "CDSEARCH/CDDupdate"
59 };
60
61 string OrganismNames[] = {
62 "All organisms",
63 "Cellular organisms",
64 "Viruses",
65 "Archaea",
66 "Bacteria",
67 "Eukaryota",
68 "Viridiplantae",
69 "Fungi",
70 "Metazoa",
71 "Arthropoda",
72 "Vertebrata",
73 "Mammalia",
74 "Rodentia",
75 "Primates"
76 };
77
78 string EnvironmentalTaxNames[] = {
79 "unclassified",
80 "environmental samples",
81 "environmental sequence"
82 };
83
84
CdUpdateParameters()85 CdUpdateParameters::CdUpdateParameters()
86 : blastType(ePSI_BLAST),
87 database(eNR),
88 organism(eAll_organisms),
89 entrezQuery(),
90 numHits(0),
91 evalue(0.01),
92 timeToCheck(100000),
93 missingResidueThreshold(1),
94 excludingTaxNodes(true),
95 nonRedundify(false),
96 refresh(false),
97 useNRPrefs(false),
98 noFilter(false),
99 replaceOldAcc(true),
100 identityThreshold(-1),
101 allowedOverlapWithCDRow(0)
102 {
103 }
104
105
~CdUpdateParameters()106 CdUpdateParameters::~CdUpdateParameters()
107 {
108 }
109
toString()110 string CdUpdateParameters::toString()
111 {
112 string result("CD-Updating parameters:");
113 result += getBlastTypeName(blastType);
114 result += ',';
115 result += getBlastDatabaseName(database);
116 result += ',';
117 result += getOrganismName(organism);
118 result += ',';
119 result += entrezQuery;
120 result += ',';
121
122 char evalueStr[100];
123 sprintf(evalueStr,"e-value:%.2e", evalue);
124 result += evalueStr;
125 return result;
126 }
127
getBlastTypeName(enum BlastType bt)128 string CdUpdateParameters::getBlastTypeName(enum BlastType bt)
129 {
130 if (bt >= eBlastTypeEnd)
131 return "";
132 else
133 return BlastTypeNames[bt];
134 }
135
getBlastDatabaseName(BlastDatabase db)136 string CdUpdateParameters::getBlastDatabaseName(BlastDatabase db)
137 {
138 if (db >= eBlastDatabaseEnd)
139 return "";
140 else
141 return BlastDatabaseNames[db];
142 }
143
getOrganismName(Organism org)144 string CdUpdateParameters::getOrganismName(Organism org)
145 {
146 if (org >= eOrganismEnd)
147 return "";
148 else
149 return OrganismNames[org];
150 }
151
getEnvironmentalTaxName(EnvironmentalTax et)152 string CdUpdateParameters::getEnvironmentalTaxName(EnvironmentalTax et)
153 {
154 if (et >= eEnvironmentalTaxEnd)
155 return "";
156 else
157 return EnvironmentalTaxNames[et];
158 }
159
160 END_SCOPE(cd_utils)
161 END_NCBI_SCOPE
162