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NCBI C++ Toolkit Cross ReferenceC++/src/algo/ms/omssa/omssacl.cpp |
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1 /* $Id: omssacl.cpp 127992 2008-05-19 16:21:50Z lewisg $
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 authors in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Authors: Lewis Y. Geer, Douglas J. Slotta
27 *
28 * File Description:
29 * command line OMSSA search
30 *
31 *
32 * ===========================================================================
33 */
34
35 #include <ncbi_pch.hpp>
36 #include <corelib/ncbiargs.hpp>
37 #include <corelib/ncbiapp.hpp>
38 #include <corelib/ncbienv.hpp>
39 #include <corelib/ncbistre.hpp>
40 #include <corelib/ncbi_system.hpp>
41 #include <serial/serial.hpp>
42 #include <serial/objistrasn.hpp>
43 #include <serial/objistrasnb.hpp>
44 #include <serial/objostrasn.hpp>
45 #include <serial/objostrasnb.hpp>
46 #include <serial/iterator.hpp>
47 #include <objects/omssa/omssa__.hpp>
48 #include <serial/objostrxml.hpp>
49 #include <corelib/ncbifile.hpp>
50
51 #include <fstream>
52 #include <string>
53 #include <list>
54 #include <stdio.h>
55
56 #include "omssa.hpp"
57 #include "SpectrumSet.hpp"
58 #include "Mod.hpp"
59 #include "omssaapp.hpp"
60
61
62 USING_NCBI_SCOPE;
63 USING_SCOPE(objects);
64 USING_SCOPE(omssa);
65
66 /////////////////////////////////////////////////////////////////////////////
67 //
68 // COMSSA
69 //
70 // Main application
71 //
72
73
74 class COMSSA : public COMSSABase {
75 public:
76 virtual int Run();
77 virtual void AppInit(CArgDescriptions *argDesc);
78 };
79
80
81 void COMSSA::AppInit(CArgDescriptions *argDesc)
82 {
83 if(!argDesc) return;
84 argDesc->AddFlag("ns", "depreciated flag"); // to be deprecated
85 argDesc->AddFlag("os", "use omssa 1.0 scoring"); // to be deprecated
86 argDesc->SetUsageContext(GetArguments().GetProgramBasename(),
87 "Search engine for identifying MS/MS peptide spectra");
88 }
89
90
91 int main(int argc, const char* argv[])
92 {
93 COMSSA theTestApp;
94 return theTestApp.AppMain(argc, argv, 0, eDS_Default, 0);
95 }
96
97
98 /** progress callback */
99 static void OMSSACallback(int TotalSeq, int Completed, void* Anything)
100 {
101 ERR_POST(Info << "Sequence=" << Completed << " Percent=" << (double)Completed/TotalSeq*100.0 <<
102 "%");
103 }
104
105 int COMSSA::Run()
106 {
107
108 try {
109
110 CArgs args = GetArgs();
111 CRef <CMSModSpecSet> Modset(new CMSModSpecSet);
112
113 // turn off informational messages if requested
114 if(args["ni"])
115 SetDiagPostLevel(eDiag_Warning);
116
117 // read in modifications
118 if(CSearchHelper::ReadModFiles(args["mx"].AsString(), args["mux"].AsString(),
119 GetProgramExecutablePath(), Modset))
120 return 1;
121 Modset->CreateArrays();
122
123 // print out the modification list
124 if(args["ml"]) {
125 PrintMods(Modset);
126 return 0;
127 }
128
129 // print out the enzymes list
130 if(args["el"]) {
131 PrintEnzymes();
132 return 0;
133 }
134
135 // print out the ions list
136 if(args["il"]) {
137 PrintIons();
138 return 0;
139 }
140
141 CMSSearch MySearch;
142
143 // which search settings to use
144 CRef <CMSSearchSettings> SearchSettings;
145
146 // if search settings to be loaded from param file, create and load
147 if(args["pm"].AsString().size() != 0) {
148 SearchSettings.Reset(new CMSSearchSettings);
149 CSearchHelper::CreateSearchSettings(args["pm"].AsString(),
150 SearchSettings);
151 }
152 else if (args["fxml"].AsString().size() != 0) {
153 // load in MSRequest
154 CSearchHelper::ReadSearchRequest(args["fxml"].AsString(),
155 eSerial_Xml,
156 MySearch);
157 // todo: SearchSettings needs to be set or will be overwritten!
158 SearchSettings.Reset(&((*(MySearch.SetRequest().begin()))->SetSettings()));
159 }
160 else {
161 // use command line to set up search settings if no param file
162 SearchSettings.Reset(new CMSSearchSettings);
163 SetSearchSettings(args, SearchSettings);
164 }
165
166 CSearchHelper::ValidateSearchSettings(SearchSettings);
167
168 SetThreadCount(args["nt"].AsInteger());
169
170 CRef <CSearch> SearchEngine (new CSearch(0));
171 SetsearchThreads().push_back(SearchEngine);
172
173 //CSearch* SearchEngine = new CSearch();
174
175 // set up rank scoring
176 if(args["os"]) SearchEngine->SetRankScore() = false;
177 else SearchEngine->SetRankScore() = true;
178
179 int FileRetVal(1);
180
181 if(args["fxml"].AsString().size() == 0) {
182 // load in files only if infile specified and not a loaded MSRequest
183 if(SearchSettings->GetInfiles().size() == 1) {
184 FileRetVal =
185 CSearchHelper::LoadAnyFile(MySearch,
186 *(SearchSettings->GetInfiles().begin()),
187 &(SearchEngine->SetIterative()));
188 if(FileRetVal == -1) {
189 ERR_POST(Fatal << "omssacl: too many spectra in input file");
190 return 1;
191 }
192 else if(FileRetVal == 1) {
193 ERR_POST(Fatal << "omssacl: unable to read spectrum file -- incorrect file type?");
194 return 1;
195 }
196 }
197 else {
198 ERR_POST(Fatal << "omssacl: input file not given or too many input files given.");
199 return 1;
200 }
201
202 // place search settings in search object
203 MySearch.SetUpSearchSettings(SearchSettings,
204 SearchEngine->GetIterative());
205 }
206
207 try {
208 SearchEngine->InitBlast(SearchSettings->GetDb().c_str(),
209 args["umm"]);
210 }
211 catch (const NCBI_NS_STD::exception &e) {
212 ERR_POST(Fatal << "Unable to open blast library " << SearchSettings->GetDb() << " with error:" <<
213 e.what());
214 }
215 catch (...) {
216 ERR_POST(Fatal << "Unable to open blast library " << SearchSettings->GetDb());
217 }
218
219 // set up the response object
220 if(MySearch.SetResponse().empty()) {
221 CRef <CMSResponse> Response (new CMSResponse);
222 MySearch.SetResponse().push_back(Response);
223 }
224
225 // Used to be a call to SearchEngine.Search(...)
226 SearchEngine->SetupSearch(*MySearch.SetRequest().begin(),
227 *MySearch.SetResponse().begin(),
228 Modset,
229 SearchSettings,
230 &OMSSACallback);
231
232 RunSearch(SearchEngine);
233 _TRACE("omssa: search end");
234
235
236 #if _DEBUG
237 // read out hits
238 CMSResponse::THitsets::const_iterator iHits;
239 iHits = (*MySearch.SetResponse().begin())->GetHitsets().begin();
240 for(; iHits != (*MySearch.SetResponse().begin())->GetHitsets().end(); iHits++) {
241 CRef< CMSHitSet > HitSet = *iHits;
242 ERR_POST(Info << "Hitset: " << HitSet->GetNumber());
243 if( HitSet-> CanGetError() && HitSet->GetError() ==
244 eMSHitError_notenuffpeaks) {
245 ERR_POST(Info << "Hitset Empty");
246 continue;
247 }
248 CRef< CMSHits > Hit;
249 CMSHitSet::THits::const_iterator iHit;
250 CMSHits::TPephits::const_iterator iPephit;
251 for(iHit = HitSet->GetHits().begin();
252 iHit != HitSet->GetHits().end(); iHit++) {
253 ERR_POST(Info << (*iHit)->GetPepstring() << ": " << "P = " <<
254 (*iHit)->GetPvalue() << " E = " <<
255 (*iHit)->GetEvalue());
256 for(iPephit = (*iHit)->GetPephits().begin();
257 iPephit != (*iHit)->GetPephits().end();
258 iPephit++) {
259 ERR_POST(Info << ((*iPephit)->CanGetGi()?(*iPephit)->GetGi():0) <<
260 ": " << (*iPephit)->GetStart() << "-" << (*iPephit)->GetStop() <<
261 ":" << (*iPephit)->GetDefline());
262 }
263
264 }
265 }
266 #endif
267
268 // Check to see if there is a hitset
269
270 if(!(*MySearch.SetResponse().begin())->CanGetHitsets()) {
271 ERR_POST(Fatal << "No results found");
272 }
273
274 CSearchHelper::SaveAnyFile(MySearch,
275 SearchSettings->GetOutfiles(),
276 Modset);
277
278 } catch (NCBI_NS_STD::exception& e) {
279 ERR_POST(Fatal << "Exception in COMSSA::Run: " << e.what());
280 }
281
282 return 0;
283 }
284
285
286
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