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NCBI C++ Toolkit Cross ReferenceC++/src/algo/ms/omssa/omssamerge.cpp |
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1 /*
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 * Author: Lewis Y. Geer
27 *
28 * File Description:
29 * program for splitting omssa files
30 *
31 *
32 * ===========================================================================
33 */
34
35 #include <ncbi_pch.hpp>
36 #include <corelib/ncbistl.hpp>
37 #include <corelib/ncbiargs.hpp>
38 #include <corelib/ncbiapp.hpp>
39 #include <corelib/ncbienv.hpp>
40 #include <corelib/ncbistre.hpp>
41 #include <corelib/ncbifile.hpp>
42 #include <connect/ncbi_memory_connector.h>
43 #include <connect/ncbi_conn_stream.hpp>
44 #include <serial/serial.hpp>
45 #include <serial/objistrasn.hpp>
46 #include <serial/objistrasnb.hpp>
47 #include <serial/objostrasn.hpp>
48 #include <serial/objostrasnb.hpp>
49 #include <serial/iterator.hpp>
50 #include <serial/objostrxml.hpp>
51 #include <objects/omssa/omssa__.hpp>
52 #include <util/compress/bzip2.hpp>
53
54 #include "omssa.hpp"
55 #include "msmerge.hpp"
56
57 #include <fstream>
58 #include <string>
59 #include <list>
60
61
62 USING_NCBI_SCOPE;
63 USING_SCOPE(objects);
64 USING_SCOPE(omssa);
65
66 /////////////////////////////////////////////////////////////////////////////
67 //
68 // COMSSAMerge
69 //
70 // Main application
71 //
72
73 class COMSSAMerge : public CNcbiApplication {
74 public:
75 COMSSAMerge();
76 private:
77 virtual int Run();
78 virtual void Init();
79
80 };
81
82 COMSSAMerge::COMSSAMerge()
83 {
84 SetVersion(CVersionInfo(2, 1, 4));
85 }
86
87
88
89
90
91 void COMSSAMerge::Init()
92 {
93
94 auto_ptr<CArgDescriptions> argDesc(new CArgDescriptions);
95
96 argDesc->AddDefaultKey("i", "infiles",
97 "file containing list of input files on separate lines",
98 CArgDescriptions::eString,
99 "");
100
101 argDesc->AddFlag("sw", "output search results without spectra");
102
103 argDesc->AddFlag("it", "input as text asn.1 formatted search results");
104 argDesc->AddFlag("ib", "input as binary asn.1 formatted search results");
105 argDesc->AddFlag("ix", "input as xml formatted search results");
106 argDesc->AddFlag("ibz2", "input as xml formatted search results compressed by bzip2");
107
108 argDesc->AddPositional("o", "output file name", CArgDescriptions::eString);
109
110
111 argDesc->AddFlag("ot", "output as text asn.1 formatted search results");
112 argDesc->AddFlag("ob", "output as binary asn.1 formatted search results");
113 argDesc->AddFlag("ox", "output as xml formatted search results");
114 argDesc->AddFlag("obz2", "output as xml formatted search results compressed by bzip2");
115
116 argDesc->AddExtra(0,10000, "input file names", CArgDescriptions::eString);
117
118
119 SetupArgDescriptions(argDesc.release());
120
121 // allow info posts to be seen
122 SetDiagPostLevel(eDiag_Info);
123 }
124
125 int main(int argc, const char* argv[])
126 {
127 COMSSAMerge theTestApp;
128 return theTestApp.AppMain(argc, argv, 0, eDS_Default, 0);
129 }
130
131
132
133
134 int COMSSAMerge::Run()
135 {
136
137 try {
138
139 CArgs args = GetArgs();
140
141
142 CRef <COMSSASearch> MySearch(new COMSSASearch);
143
144 ESerialDataFormat InFileType(eSerial_Xml), OutFileType(eSerial_Xml);
145
146 bool obz2(false); // output bzip2 compressed?
147 bool ibz2(false); // input bzip2 compressed?
148
149 if(args["ox"]) OutFileType = eSerial_Xml;
150 else if(args["ob"]) OutFileType = eSerial_AsnBinary;
151 else if(args["ot"]) OutFileType = eSerial_AsnText;
152 else if(args["obz2"]) {
153 OutFileType = eSerial_Xml;
154 obz2 = true;
155 }
156 else ERR_POST(Fatal << "output file type not given");
157
158 if(args["ix"]) InFileType = eSerial_Xml;
159 else if(args["ib"]) InFileType = eSerial_AsnBinary;
160 else if(args["it"]) InFileType = eSerial_AsnText;
161 else if(args["ibz2"]) {
162 InFileType = eSerial_Xml;
163 ibz2 = true;
164 }
165 else ERR_POST(Fatal << "input file type not given");
166
167
168 // loop thru input files
169 if ( args["i"].AsString() != "") {
170 ifstream is(args["i"].AsString().c_str());
171 bool Begin(true);
172 if(!is)
173 ERR_POST(Fatal << "unable to open input file list " << args["i"].AsString());
174 while(!is.eof()) {
175 string iFileName;
176 NcbiGetline(is, iFileName, "\x0d\x0a");
177 if(iFileName == "" || is.eof()) continue;
178 try {
179 CRef <COMSSASearch> InSearch(new COMSSASearch);
180 CSearchHelper::ReadCompleteSearch(iFileName, InFileType, ibz2, *InSearch);
181 // InSearch->ReadCompleteSearch(iFileName, InFileType, ibz2);
182 if(Begin) {
183 Begin = false;
184 MySearch->CopyCMSSearch(InSearch);
185 }
186 else {
187 // add
188 MySearch->AppendSearch(InSearch);
189 }
190 }
191 catch(CException& e) {
192 ERR_POST(Fatal << "exception: " << e.what());
193 return 1;
194 }
195 }
196 }
197 else if ( args.GetNExtra() ) {
198 for (size_t extra = 1; extra <= args.GetNExtra(); extra++) {
199 CRef <COMSSASearch> InSearch(new COMSSASearch);
200 CSearchHelper::ReadCompleteSearch(args[extra].AsString(), InFileType, ibz2, *InSearch);
201 //InSearch->ReadCompleteSearch(args[extra].AsString(), InFileType, ibz2);
202 try {
203 if(extra == 1) {
204 // copy
205 MySearch->CopyCMSSearch(InSearch);
206 }
207 else {
208 // add
209 MySearch->AppendSearch(InSearch);
210 }
211 }
212 catch(CException& e) {
213 ERR_POST(Fatal << "exception: " << e.what());
214 return 1;
215 }
216 }
217 }
218
219 // write out the new search
220
221 auto_ptr <CNcbiOfstream> raw_out;
222 auto_ptr <CCompressionOStream> compress_out;
223 auto_ptr <CObjectOStream> txt_out;
224
225 if( obz2 ) {
226 raw_out.reset(new CNcbiOfstream(args["o"].AsString().c_str()));
227 compress_out.reset( new CCompressionOStream (*raw_out,
228 new CBZip2StreamCompressor(),
229 CCompressionStream::fOwnProcessor));
230 txt_out.reset(CObjectOStream::Open(OutFileType, *compress_out));
231 }
232 else {
233 txt_out.reset(CObjectOStream::Open(args["o"].AsString().c_str(), OutFileType));
234 }
235
236
237 // auto_ptr <CObjectOStream> txt_out(
238 // CObjectOStream::Open(args["o"].AsString(), OutFileType));
239
240 if(txt_out.get()) {
241 SetUpOutputFile(txt_out.get(), OutFileType);
242 if (args["sw"]) {
243 txt_out->Write(ObjectInfo(*(*MySearch->SetResponse().begin())));
244 }
245 else {
246 txt_out->Write(ObjectInfo(*MySearch));
247 }
248 txt_out->Flush();
249 txt_out->Close();
250 }
251
252
253 } catch (NCBI_NS_STD::exception& e) {
254 ERR_POST(Fatal << "Exception in COMSSAMerge::Run: " << e.what());
255 }
256
257 return 0;
258 }
259
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