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Commit MetaInfo

Revision619a409b044a2c2ae424dbe348e077d5c94f21c7 (tree)
Time2015-06-07 21:52:12
AuthorMasaki Murase
CommiterMasaki Murase

Log Message

added MascotPMFForLCMS Plug-in

Change Summary

Incremental Difference

diff -r c58797fa5711 -r 619a409b044a build/msvs/solutions/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSPlugin.vcxproj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/build/msvs/solutions/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSPlugin.vcxproj Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,180 @@
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175+ <ClCompile Include="..\..\..\..\..\src\common-plugin-analyze\MascotPMFForLCMSPlugin\MascotPmfManager.cpp" />
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diff -r c58797fa5711 -r 619a409b044a build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln
--- a/build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln Sat Jun 06 01:35:56 2015 +0900
+++ b/build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln Sun Jun 07 21:52:12 2015 +0900
@@ -65,6 +65,8 @@
6565 EndProject
6666 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MsbackadjBaselineDetectionPlugin", "MsbackadjBaselineDetectionPlugin\MsbackadjBaselineDetectionPlugin.vcxproj", "{CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}"
6767 EndProject
68+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MascotPMFForLCMSPlugin", "MascotPMFForLCMSPlugin\MascotPMFForLCMSPlugin.vcxproj", "{84090F00-9281-4844-A1A8-B46C907F3684}"
69+EndProject
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diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSFunctions.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSFunctions.cpp Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,60 @@
1+/**
2+ * @file MascotPMFForLCMSFunctions.cpp
3+ * @brief implementation of plug-in functions
4+ *
5+ * @author s.Tanaka
6+ * @date 2012.10.26
7+ *
8+ * Copyright(C) 2006-2014 Shimadzu Corporation All rights reserved.
9+ */
10+
11+
12+#include "stdafx.h"
13+#include "MascotPMFForLCMSFunctions.h"
14+#include "MascotPmfManager.h"
15+
16+
17+using namespace kome::mascot;
18+
19+
20+#include <crtdbg.h>
21+#ifdef _DEBUG
22+ #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
23+ #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
24+#endif // _DEBUG
25+
26+
27+
28+// get PMF search engine
29+kome::objects::Variant getPmfSearchEngine( kome::objects::Parameters* params ) {
30+ // manager
31+ MascotPmfManager& mgr = MascotPmfManager::getInstance();
32+
33+ // return value
34+ kome::objects::Variant ret;
35+ ret.prim.pt = mgr.getPmfEngine();
36+ ret.type = kome::objects::Variant::OTHER;
37+
38+ return ret;
39+}
40+
41+// check modifications
42+kome::objects::Variant checkModifications( kome::objects::Parameters* params ) {
43+ // return value
44+ kome::objects::Variant ret;
45+ ret.type = kome::objects::Variant::STRING;
46+ ret.setString( "" );
47+
48+ // settings
49+ kome::objects::SettingParameterValues* settings = kome::plugin::PluginCallTool::getSettingValues( params );
50+ if( settings == NULL ) {
51+ ret.setString( "Failed to get the parameters." );
52+ return ret;
53+ }
54+
55+ // modifications
56+ std::string msg = MascotSearchEngineBase::checkMods( settings );
57+ ret.setString( msg.c_str() );
58+
59+ return ret;
60+}
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSFunctions.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSFunctions.h Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,35 @@
1+/**
2+ * @file MascotPMFForLCMSFunctions.h
3+ * @brief interfaces of plug-in functions
4+ *
5+ * @author S.Tanaka
6+ * @date 2012.10.26
7+ *
8+ * Copyright(C) 2006-2014 Shimadzu Corporation All rights reserved.
9+ */
10+
11+
12+
13+#ifndef __KOME_MASCOT_PMF_FOR_LCMS_FUNCTIONS_H__
14+#define __KOME_MASCOT_PMF_FOR_LCMS_FUNCTIONS_H__
15+
16+
17+/**
18+ * @fn kome::objects::Variant getPmfSearchEngine( kome::objects::Parameters* params )
19+ * @brief gets the PMF search engine
20+ * @params[in] params parameters
21+ * @return PMF search engine
22+ */
23+kome::objects::Variant getPmfSearchEngine( kome::objects::Parameters* params );
24+
25+
26+/**
27+ * @fn kome::objects::Variant checkModifications( kome::objects::Parameters* params )
28+ * @brief check modifications
29+ * @param[in] params parameters
30+ * @return error message (string)
31+*/
32+kome::objects::Variant checkModifications( kome::objects::Parameters* params );
33+
34+
35+#endif __KOME_MASCOT_PMF_FOR_LCMS_FUNCTIONS_H__
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSPlugin.def
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPMFForLCMSPlugin.def Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,3 @@
1+EXPORTS
2+ getPmfSearchEngine
3+ checkModifications
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfForLCMSSearchEngine.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfForLCMSSearchEngine.cpp Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,350 @@
1+/**
2+ * @file MascotPmfForLCMSSearchEngine.cpp
3+ * @brief implements of MascotPmfForLCMSSearchEngine class
4+ *
5+ * @author S.Tanaka
6+ * @date 2012.08.09
7+ *
8+ * Copyright(C) 2006-2014 Shimadzu Corporation. All rights reserved.
9+ */
10+
11+
12+#include "stdafx.h"
13+#include "MascotPmfForLCMSSearchEngine.h"
14+#include "MascotManager.h"
15+
16+
17+using namespace kome::mascot;
18+
19+
20+#include <crtdbg.h>
21+#ifdef _DEBUG
22+ #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
23+ #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
24+#endif // _DEBUG
25+
26+
27+
28+// constructor
29+MascotPmfForLCMSSearchEngine::MascotPmfForLCMSSearchEngine() : MascotSearchEngineBase( "Mascot PMF (for LC)", "PMF", false ) {
30+ m_peakTol = 0.25;
31+ m_peakNum = 999;
32+ m_peakTolUnit = TOL_DA;
33+ m_protein = NULL;
34+}
35+
36+// destructor
37+MascotPmfForLCMSSearchEngine::~MascotPmfForLCMSSearchEngine() {
38+}
39+
40+// on hit
41+void MascotPmfForLCMSSearchEngine::onHit( kome::ident::Hit* hit ) {
42+ // check the parameterr
43+ if( hit == NULL ) {
44+ return;
45+ }
46+
47+ // protein
48+ kome::ident::Substance* peptide = hit->getSubstance();
49+ if( peptide == NULL ) {
50+ return;
51+ }
52+
53+ kome::ident::Substance* protein = peptide->getParentSubstance();
54+ if( protein == NULL ) {
55+ return;
56+ }
57+
58+ // spectra
59+ if( m_protein != protein ) {
60+ m_spectra.clear();
61+
62+ // excluded peaks
63+ std::string unmatched = hit->getValueInfo( "Unmatched" )->value;
64+ std::vector< std::string > tokens;
65+ stringtoken( unmatched.c_str(), " ,\t\r\n:", tokens );
66+ std::vector< double > unmatchedPeaks;
67+ for( unsigned int i = 0; i < tokens.size(); i++ ) {
68+ double peakPos = -1.0;
69+ if( isdouble( tokens[ i ].c_str(), &peakPos ) ) {
70+ if( peakPos >= 0.0 ) {
71+ unmatchedPeaks.push_back( peakPos );
72+ }
73+ }
74+ }
75+
76+ std::set< PeakInfo* > excluded;
77+ int startIdx = 0;
78+ for( unsigned int i = 0; i < unmatchedPeaks.size(); i++ ) {
79+ double diff = FLT_MAX;
80+ PeakInfo* currentPeak = NULL;
81+ bool loop = true;
82+ for( int j = startIdx; j < (int)m_pmfPeaks.size() && loop; j++ ) {
83+ const double tmpDiff = fabs( m_pmfPeaks[ j ].x - unmatchedPeaks[ i ] );
84+ if( tmpDiff < diff ) {
85+ diff = tmpDiff;
86+ currentPeak = &( m_pmfPeaks[ j ] );
87+ startIdx = j;
88+ }
89+ else {
90+ loop = false;
91+ }
92+ }
93+
94+ excluded.insert( currentPeak );
95+ }
96+
97+ // spectra
98+ std::set< kome::ident::SpecInfo* > specSet;
99+ for( unsigned int i = 0; i < m_pmfPeaks.size(); i++ ) {
100+ PeakInfo* pk = &( m_pmfPeaks[ i ] );
101+
102+ if( excluded.find( pk ) == excluded.end() ) {
103+ kome::ident::SpecInfo* spec = pk->spec;
104+
105+ if( specSet.find( spec ) == specSet.end() ) {
106+ specSet.insert( spec );
107+ m_spectra.push_back( spec );
108+ }
109+ }
110+ }
111+ }
112+
113+ for( unsigned int i = 0; i < m_spectra.size(); i++ ) {
114+ hit->addSpectrum( m_spectra[ i ] );
115+ }
116+}
117+
118+// judges the specified spectrum is valied or not
119+bool MascotPmfForLCMSSearchEngine::isValidSpectrum( kome::objects::Spectrum* spec ) {
120+ if( spec == NULL ) {
121+ return false;
122+ }
123+
124+ return ( spec->getMsStage() == 1 );
125+}
126+
127+// on spectrum peaks
128+void MascotPmfForLCMSSearchEngine::onSpectrumPeaks(
129+ kome::objects::Spectrum* spec,
130+ kome::ident::SpecInfo* specInfo,
131+ kome::objects::Peaks* peaks,
132+ int* peakIds,
133+ const unsigned int peakIdsSize
134+) {
135+ // manager
136+ kome::ident::MgfManager& mgfMgr = kome::ident::MgfManager::getInstance();
137+
138+ // check the peak
139+ if( peaks == NULL || peaks->getLength() == 0 ) {
140+ return;
141+ }
142+
143+ // add peaks
144+ for( unsigned int i = 0; i < peaks->getLength(); i++ ) {
145+ PeakInfo peak;
146+ peak.x = peaks->getX( i );
147+ peak.y = peaks->getY( i );
148+ peak.maxY = peak.y;
149+ peak.spec = specInfo;
150+
151+ m_pmfPeaks.push_back( peak );
152+ }
153+}
154+
155+// on finish peak detection
156+bool MascotPmfForLCMSSearchEngine::onFinishPeakDetection() {
157+ // check the peak
158+ if( m_pmfPeaks.size() == 0 ) {
159+ LOG_ERROR( FMT( "PMF Error: No peaks are detected." ) );
160+ return false;
161+ }
162+
163+ // copy
164+ std::vector< PeakInfo > peaks;
165+ for( unsigned int i = 0; i < m_pmfPeaks.size(); i++ ) {
166+ peaks.push_back( m_pmfPeaks[ i ] );
167+ }
168+
169+ // sort
170+ std::sort( peaks.begin(), peaks.end(), lessPeakX );
171+
172+ // merge
173+ m_pmfPeaks.clear();
174+ for( unsigned int i = 0; i < peaks.size(); i++ ) {
175+ // peak
176+ PeakInfo& tmp = peaks[ i ];
177+
178+ // merge
179+ bool flg = true;
180+ if( m_pmfPeaks.size() > 0 ) {
181+ PeakInfo& peak = m_pmfPeaks.back();
182+
183+ double tol = m_peakTol;
184+ if( m_peakTolUnit == TOL_PPM ) {
185+ tol = peak.x * tol / 1000000.0;
186+ }
187+
188+ if( tmp.x <= peak.x + tol ) {
189+ flg = false;
190+
191+ if( peak.maxY > tmp.maxY ) {
192+ peak.maxY = tmp.maxY;
193+ peak.spec = tmp.spec;
194+ }
195+
196+ double y = peak.y + tmp.y;
197+ double x = peak.x * peak.y + tmp.x * tmp.y;
198+ if( y > 0.0 ) {
199+ peak.x = x / y;
200+ peak.y = y;
201+ }
202+ }
203+ }
204+
205+ // add
206+ if( flg ) {
207+ m_pmfPeaks.push_back( tmp );
208+ }
209+ }
210+
211+ // remove
212+ if( m_peakNum > 0 ) {
213+ std::sort( m_pmfPeaks.begin(), m_pmfPeaks.end(), lessPeakY );
214+ while( m_pmfPeaks.size() > (unsigned int)m_peakNum ) {
215+ m_pmfPeaks.pop_back();
216+ }
217+
218+ std::sort( m_pmfPeaks.begin(), m_pmfPeaks.end(), lessPeakX );
219+ }
220+
221+ return true;
222+}
223+
224+// on search
225+std::string MascotPmfForLCMSSearchEngine::onSearch(
226+ const char* title,
227+ const char* comment,
228+ kome::ident::SpecInfo** spectra,
229+ const unsigned int specNum,
230+ kome::objects::SettingParameterValues* settings,
231+ kome::core::Progress& progress
232+) {
233+ // return value
234+ std::string ret;
235+
236+ // manager
237+ MascotManager& mgr = MascotManager::getInstance();
238+
239+ // progress
240+ if( specNum == 0 ) {
241+ LOG_WARN( FMT( "There are no spectra." ) );
242+ return ret;
243+ }
244+
245+ if( m_pmfPeaks.size() == 0 ) {
246+ LOG_WARN( FMT( "There are no peaks" ) );
247+ return ret;
248+ }
249+ progress.createSubProgresses( 3 );
250+
251+ // export peaks
252+ progress.setStatus( "Exporting Peaks..." );
253+ kome::core::Progress* prgs = progress.getSubProgress( 0 );
254+
255+ std::string peaksPath = getpath( m_peaksDir.c_str(), "peaks.pmf" );
256+ FILE* fp = fileopen( peaksPath.c_str(), "w" );
257+ if( fp == NULL ) {
258+ return ret;
259+ }
260+
261+ for( unsigned int i = 0; i < m_pmfPeaks.size(); i++ ) {
262+ fprintf( fp, "%f %f\n", m_pmfPeaks[ i ].x, m_pmfPeaks[ i ].y );
263+ }
264+
265+ fflush( fp );
266+ fclose( fp );
267+
268+ if( prgs->isStopped() ) {
269+ return ret;
270+ }
271+ prgs->fill();
272+
273+ // search
274+ progress.setStatus( "Identifying with PMF Search..." );
275+ prgs = progress.getSubProgress( 1 );
276+
277+ std::vector< std::string > peakFiles;
278+ peakFiles.push_back( peaksPath );
279+
280+ ret = performSearch( peakFiles, title, settings, *prgs );
281+
282+ if( prgs->isStopped() ) {
283+ return ret;
284+ }
285+ progress.fill();
286+
287+ return ret;
288+}
289+
290+// prepares peak detection
291+bool MascotPmfForLCMSSearchEngine::onPreparePeakDetection(
292+ kome::objects::SettingParameterValues* searchSettings,
293+ const char* peakDetector,
294+ kome::objects::SettingParameterValues* peakSettings,
295+ const char* chargeDetector,
296+ kome::objects::SettingParameterValues* chargeSettings,
297+ const char* peakFilter
298+) {
299+ // manager
300+ kome::core::MsppManager& msppMgr = kome::core::MsppManager::getInstance();
301+
302+ // clear peaks
303+ m_pmfPeaks.clear();
304+
305+ // temporary directory
306+ std::string tmpDir = msppMgr.getTmpDir();
307+ std::string mascotDir = getpath( tmpDir.c_str(), "mascot" );
308+ if( !fileexists( mascotDir.c_str() ) ) {
309+ makedirectory( mascotDir.c_str() );
310+ }
311+ std::string pmfDir = getpath( mascotDir.c_str(), "pmf" );
312+ if( !fileexists( pmfDir.c_str() ) ) {
313+ makedirectory( pmfDir.c_str() );
314+ }
315+
316+ std::string peaksDir = getpath( pmfDir.c_str(), FMT( "%lld", getcurrenttime() ).c_str() );
317+ if( !fileexists( peaksDir.c_str() ) ) {
318+ makedirectory( peaksDir.c_str() );
319+ }
320+
321+ m_peaksDir = peaksDir;
322+
323+ // get parameters
324+ m_peakTol = searchSettings->getDoubleValue( "peak_tol", 0.25 );
325+ m_peakNum = searchSettings->getIntValue( "peak_num", 999 );
326+ m_peakTolUnit = TOL_DA;
327+
328+ std::string u = tolowercase( searchSettings->getParameterValue( "peak_tol_unit" ) );
329+ if( u.compare( "ppm" ) == 0 ) {
330+ m_peakTolUnit = TOL_PPM;
331+ }
332+
333+ return true;
334+}
335+
336+// on end search
337+void MascotPmfForLCMSSearchEngine::onEndSearch() {
338+ m_pmfPeaks.clear();
339+ m_peaksDir.clear();
340+}
341+
342+// comapre peaks by x
343+bool MascotPmfForLCMSSearchEngine::lessPeakX( PeakInfo& peak0, PeakInfo& peak1 ) {
344+ return ( peak0.x < peak1.x );
345+}
346+
347+// compare peaks by y
348+bool MascotPmfForLCMSSearchEngine::lessPeakY( PeakInfo& peak0, PeakInfo& peak1 ) {
349+ return ( peak0.y > peak1.y );
350+}
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfForLCMSSearchEngine.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfForLCMSSearchEngine.h Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,215 @@
1+/**
2+ * @file MascotPmfForLCMSSearchEngine.h
3+ * @brief interfaces of MascotPmfForLCMSSearchEngine class
4+ *
5+ * @author S.Tanaka
6+ * @date 2012.08.09
7+ *
8+ * Copyright(C) 2006-2014 Shimadzu Corporation. All rights reserved.
9+ */
10+
11+
12+#ifndef __KOME_MASCOT_PMF_FOR_LCMS_SEARCH_ENGINE_H__
13+#define __KOME_MASCOT_PMF_FOR_LCMS_SEARCH_ENGINE_H__
14+
15+
16+#include "MascotSearchEngineBase.h"
17+
18+
19+namespace kome {
20+ namespace mascot {
21+
22+ /**
23+ * @fn MascotPmfForLCMSSearchEngine
24+ * @brief mascot PMF search engine class
25+ */
26+ class MascotPmfForLCMSSearchEngine : public MascotSearchEngineBase {
27+ public:
28+ /**
29+ * @fn MascotPmfForLCMSSearchEngine()
30+ * @brief constructor
31+ */
32+ MascotPmfForLCMSSearchEngine();
33+
34+ /**
35+ * @fn virtual ~MascotPmfForLCMSSearchEngine()
36+ * @brief destructor
37+ */
38+ virtual ~MascotPmfForLCMSSearchEngine();
39+
40+ protected:
41+ /**
42+ * @struct PeakInfo
43+ * @brief peak information
44+ */
45+ struct PeakInfo {
46+ double x;
47+ double y;
48+ double maxY;
49+ kome::ident::SpecInfo* spec;
50+ };
51+
52+ /**
53+ * @typedef Tolerance Unit
54+ * @brief tolerance unit
55+ */
56+ typedef enum {
57+ TOL_DA,
58+ TOL_PPM
59+ } ToleranceUnit;
60+
61+ protected:
62+ /** peaks folder */
63+ std::string m_peaksDir;
64+
65+ /** peak tolerance */
66+ double m_peakTol;
67+
68+ /** tolerance unit */
69+ ToleranceUnit m_peakTolUnit;
70+
71+ /** peaks */
72+ std::vector< PeakInfo > m_pmfPeaks;
73+
74+ /** number of peaks */
75+ int m_peakNum;
76+
77+ /** spectra */
78+ std::vector< kome::ident::SpecInfo* > m_spectra;
79+
80+ /** protein */
81+ kome::ident::Substance* m_protein;
82+
83+ protected:
84+ /**
85+ * @fn virtual void onHit( kome::ident::Hit* hit )
86+ * @brief on hit
87+ * @param[in] hit hit (override method)
88+ */
89+ virtual void onHit( kome::ident::Hit* hit );
90+
91+ public:
92+ /**
93+ * @fn virtual bool isValidSpectrum( kome::objects::Spectrum* spec )
94+ * @brief judges the specified spectrum is valid to this search engine. (override method)
95+ * @param[in] spec spectrum to be judged
96+ * @return If true, the specified spectrum is valid to this search engine.
97+ */
98+ virtual bool isValidSpectrum( kome::objects::Spectrum* spec );
99+
100+ /**
101+ * @fn virtual void onSpectrumPeaks(
102+ kome::objects::Spectrum* spec,
103+ kome::ident::SpecInfo* specInfo,
104+ kome::objects::Peaks* peaks,
105+ int* peakIds,
106+ const unsigned int peakIdsSize
107+ )
108+ * @brief This method is called when peaks of a spectrum are detected. (override method)
109+ * @param[in] spec spectrum
110+ * @param[in] specInfo spectrum information
111+ * @param[in] peaks detected peaks
112+ * @param[in] peakIds the array of peak IDs of peak matrix.
113+ * @param[in] peakIdsSize the array size of peakIds
114+ */
115+ virtual void onSpectrumPeaks(
116+ kome::objects::Spectrum* spec,
117+ kome::ident::SpecInfo* specInfo,
118+ kome::objects::Peaks* peaks,
119+ int* peakIds,
120+ const unsigned int peakIdsSize
121+ );
122+
123+ /**
124+ * @fn virtual bool onFinishPeakDetection()
125+ * @brief on finished peak detection (override method)
126+ */
127+ virtual bool onFinishPeakDetection();
128+
129+ protected:
130+ /**
131+ * @fn virtual std::string onSearch(
132+ const char* title,
133+ const char* comment,
134+ kome::ident::SpecInfo** spectra,
135+ const unsigned int specNum,
136+ kome::objects::SettingParameterValues* settings,
137+ kome::core::Progress& progress
138+ )
139+ * @brief This method is called from search method. (override method)
140+ * @param[in] title title
141+ * @param[in] comment commetn
142+ * @param[in] spectra the array of spectra
143+ * @param[in] specNum the array size of spectra
144+ * @param[in] settings settings of search
145+ * @param[in,out] progress the object to show the progress
146+ * @return identifier of search
147+ */
148+ virtual std::string onSearch(
149+ const char* title,
150+ const char* comment,
151+ kome::ident::SpecInfo** spectra,
152+ const unsigned int specNum,
153+ kome::objects::SettingParameterValues* settings,
154+ kome::core::Progress& progress
155+ );
156+
157+ /**
158+ * @fn virtual bool onPreparePeakDetection(
159+ kome::objects::SettingParameterValues* searchSettings,
160+ const char* peakDetector,
161+ kome::objects::SettingParameterValues* peakSettings,
162+ const char* chargeDetector,
163+ kome::objects::SettingParameterValues* chargeSettings,
164+ const char* peakFilter
165+ )
166+ * @brief This method is called by preparePeakDetection method. (override method)
167+ * @param[in] settings search parameters
168+ * @param[in] settings search parameters
169+ * @param[in] peakDetector peak detector algorithm
170+ * @param[in] peakSettings peak detection settings
171+ * @param[in] chargeDetector charge calculation algorithm
172+ * @param[in] chargeSettings charge calculation settings
173+ * @param[in] peakFilter peak filter
174+ * @return If true, preparation of peak detection is finished successfully.
175+ */
176+ virtual bool onPreparePeakDetection(
177+ kome::objects::SettingParameterValues* searchSettings,
178+ const char* peakDetector,
179+ kome::objects::SettingParameterValues* peakSettings,
180+ const char* chargeDetector,
181+ kome::objects::SettingParameterValues* chargeSettings,
182+ const char* peakFilter
183+ );
184+
185+
186+ /**
187+ * @fn virtual void onEndSearch()
188+ * @brief This method is called when identification is finished. (override method)
189+ */
190+ virtual void onEndSearch();
191+
192+ protected:
193+ /**
194+ * @fn static bool lessPeakX( PeakInfo& peak0, PeakInfo& peak1 )
195+ * @brief compares peaks by x coordinate
196+ * @param[in] peak0 peak to compare
197+ * @param[in] peak1 peak to be compared
198+ * @return If true, peak0 sorts before peak1.
199+ */
200+ static bool lessPeakX( PeakInfo& peak0, PeakInfo& peak1 );
201+
202+ /**
203+ * @fn static bool lessPeakY( PeakInfo& peak0, PeakInfo& peak1 )
204+ * @brief compares peaks by y coordinate
205+ * @param[in] peak0 peak to compare
206+ * @param[in] peak1 peak to be compared
207+ * @return If true, peak0 sorts before peak1.
208+ */
209+ static bool lessPeakY( PeakInfo& peak0, PeakInfo& peak1 );
210+ };
211+ }
212+}
213+
214+
215+#endif // __KOME_MASCOT_PMF_FOR_LCMS_SEARCH_ENGINE_H__
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfManager.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfManager.cpp Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,46 @@
1+/**
2+ * @file MascotPmfManager.cpp
3+ * @brief implements of MascotPmfManager class
4+ *
5+ * @author S.Tanaka
6+ * @date 2012.10.26
7+ *
8+ * Copyright(C) 2006-2014 Eisai Co., Ltd. All rights reserved.
9+ */
10+
11+
12+#include "stdafx.h"
13+#include "MascotPmfManager.h"
14+
15+
16+using namespace kome::mascot;
17+
18+
19+#include <crtdbg.h>
20+#ifdef _DEBUG
21+ #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
22+ #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
23+#endif // _DEBUG
24+
25+
26+
27+// constructor
28+MascotPmfManager::MascotPmfManager() {
29+}
30+
31+// destructor
32+MascotPmfManager::~MascotPmfManager() {
33+}
34+
35+// get PMF search engine
36+MascotSearchEngineBase* MascotPmfManager::getPmfEngine() {
37+ return &m_pmfEngine;
38+}
39+
40+// get instance
41+MascotPmfManager& MascotPmfManager::getInstance() {
42+ // create the object
43+ static MascotPmfManager mgr;
44+
45+ return mgr;
46+}
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfManager.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/MascotPmfManager.h Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,63 @@
1+/**
2+ * @file MascotPmfManager.h
3+ * @brief interfaces of MascotPmfManager class
4+ *
5+ * @author S.Tanaka
6+ * @date 2012.10.26
7+ *
8+ * Copyright(C) 2006-2014 Eisai Co., Ltd. All rights reserved.
9+ */
10+
11+
12+#ifndef __KOME_MASCOT_MASCOT_PMF_MANAGER_H__
13+#define __KOME_MASCOT_MASCOT_PMF_MANAGER_H__
14+
15+
16+#include "MascotPmfForLCMSSearchEngine.h"
17+
18+
19+namespace kome {
20+ namespace mascot {
21+
22+ /**
23+ * @class MascotPmfManager
24+ * @brief mascot search management class
25+ */
26+ class MascotPmfManager {
27+ protected:
28+ /**
29+ * @fn MascotPmfManager()
30+ * @brief constructor
31+ */
32+ MascotPmfManager();
33+
34+ /**
35+ * @fn virtual ~MascotPmfManager()
36+ * @brief destructor
37+ */
38+ virtual ~MascotPmfManager();
39+
40+ protected:
41+ /** PMF engine */
42+ MascotPmfForLCMSSearchEngine m_pmfEngine;
43+
44+ public:
45+ /**
46+ * @fn MascotSearchEngineBase* getPmfEngine()
47+ * @brief gets the PMF search engine
48+ * @return PMF search engine
49+ */
50+ MascotSearchEngineBase* getPmfEngine();
51+
52+ public:
53+ /**
54+ * @fn static MascotPmfManager& getInstance()
55+ * @brief gets object
56+ * @return MascotPmfManager object. (This is the only object.)
57+ */
58+ static MascotPmfManager& getInstance();
59+ };
60+ }
61+}
62+
63+#endif // __KOME_MASCOT_MASCOT_PMF_MANAGER_H__
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/plugin.xml Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,67 @@
1+<?xml version="1.0"?>
2+
3+<plugin
4+ xmlns="http://xml.first-ms3d.jp/masspp/plugin"
5+ xsi:schemaLocation="http://xml.first-ms3d.jp/masspp/plugin http://first-ms3d.jp/development/masspp-plugin110.xsd"
6+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
7+ <name>LCMS Mascot Search</name>
8+ <version>1.00</version>
9+ <provider>Shimadzu Corporation</provider>
10+ <link>MascotPMFForLCMSPlugin</link>
11+ <function>
12+ <call type="identification">
13+ <call-name>pmf</call-name>
14+ <call-function>getPmfSearchEngine</call-function>
15+ <params>
16+ <param>
17+ <param-name>long name</param-name>
18+ <param-value>Mascot (PMF) for LC/MS</param-value>
19+ </param>
20+ <param>
21+ <param-name>short name</param-name>
22+ <param-value>mascot-pmf-lcms</param-value>
23+ </param>
24+ <param>
25+ <param-name>page</param-name>
26+ <param-value>pmf</param-value>
27+ </param>
28+ </params>
29+ <call-description>Mascot Peptide Mass Fingerprint</call-description>
30+ </call>
31+ <call type="check_params">
32+ <call-name>check_mods</call-name>
33+ <call-function>checkModifications</call-function>
34+ <params>
35+ <param>
36+ <param-name>long name</param-name>
37+ <param-value>LC/MS PMF Modifications</param-value>
38+ </param>
39+ <param>
40+ <param-name>short name</param-name>
41+ <param-value>pmf_lcms_mods</param-value>
42+ </param>
43+ </params>
44+ </call>
45+ </function>
46+ <components>
47+ <component>
48+ <component-name>pmf</component-name>
49+ <component-desc>Mascot PMF Search for LC/MS Data</component-desc>
50+ <component-calls>
51+ <component-call>pmf</component-call>
52+ <component-call>check_mods</component-call>
53+ </component-calls>
54+ </component>
55+ </components>
56+ <packages>
57+ <package>
58+ <package-name>Identification</package-name>
59+ <package-components>
60+ <package-component>pmf</package-component>
61+ </package-components>
62+ </package>
63+ </packages>
64+ <parameters>
65+ <parameters-file>settings.xml</parameters-file>
66+ </parameters>
67+</plugin>
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/settings.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/settings.xml Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,434 @@
1+<?xml version="1.0"?>
2+
3+<settings
4+ xmlns="http://xml.first-ms3d.jp/masspp/settings"
5+ xsi:schemaLocation="http://xml.first-ms3d.jp/masspp/settings http://first-ms3d.jp/development/masspp-settings110.xsd"
6+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
7+ <values>
8+ <value id="0" type="string" default="" required="true" />
9+ <value id="1" type="email" default="" required="true" />
10+ <value id="2" type="string" default="1" required="true">
11+ <enum>
12+ <enum-name>1</enum-name>
13+ <enum-value>1</enum-value>
14+ </enum>
15+ <enum>
16+ <enum-name>2</enum-name>
17+ <enum-value>2</enum-value>
18+ </enum>
19+ <enum>
20+ <enum-name>3</enum-name>
21+ <enum-value>3</enum-value>
22+ </enum>
23+ <enum>
24+ <enum-name>4</enum-name>
25+ <enum-value>4</enum-value>
26+ </enum>
27+ <enum>
28+ <enum-name>5</enum-name>
29+ <enum-value>5</enum-value>
30+ </enum>
31+ <enum>
32+ <enum-name>6</enum-name>
33+ <enum-value>6</enum-value>
34+ </enum>
35+ <enum>
36+ <enum-name>7</enum-name>
37+ <enum-value>7</enum-value>
38+ </enum>
39+ <enum>
40+ <enum-name>8</enum-name>
41+ <enum-value>8</enum-value>
42+ </enum>
43+ <enum>
44+ <enum-name>9</enum-name>
45+ <enum-value>9</enum-value>
46+ </enum>
47+ </value>
48+ <value id="4" type="string" required="true">
49+ <enum-call>enzymes</enum-call>
50+ </value>
51+ <value id="5" type="string" default="Monoisotopic" required="true">
52+ <enum>
53+ <enum-name>Monoisotopic</enum-name>
54+ <enum-value>Monoisotopic</enum-value>
55+ </enum>
56+ <enum>
57+ <enum-name>Average</enum-name>
58+ <enum-value>Average</enum-value>
59+ </enum>
60+ </value>
61+ <value id="6" type="bool" default="false" />
62+ <value id="7" type="list" hideAllChk="true" parent="6" required="false" />
63+ <value id="8" type="bool" list="7">
64+ <enum-call>modifications</enum-call>
65+ <value-name>Modification Name</value-name>
66+ </value>
67+ <value id="9" type="list" hideAllChk="true" parent="6" required="false" />
68+ <value id="10" type="bool" list="9">
69+ <enum-call>modifications</enum-call>
70+ <value-name>Modification Name</value-name>
71+ </value>
72+ <value id="11" type="double" default="1.2" minExclusive="0.0" required="true" />
73+ <value id="12" type="string" default="Da" required="true">
74+ <enum>
75+ <enum-name>Da</enum-name>
76+ <enum-value>Da</enum-value>
77+ </enum>
78+ <enum>
79+ <enum-name>mmu</enum-name>
80+ <enum-value>mmu</enum-value>
81+ </enum>
82+ <enum>
83+ <enum-name>%</enum-name>
84+ <enum-value>%</enum-value>
85+ </enum>
86+ <enum>
87+ <enum-name>ppm</enum-name>
88+ <enum-value>ppm</enum-value>
89+ </enum>
90+ </value>
91+ <value id="13" type="string" default="0" required="true">
92+ <enum>
93+ <enum-name>0</enum-name>
94+ <enum-value>0</enum-value>
95+ </enum>
96+ <enum>
97+ <enum-name>1</enum-name>
98+ <enum-value>1</enum-value>
99+ </enum>
100+ <enum>
101+ <enum-name>2</enum-name>
102+ <enum-value>2</enum-value>
103+ </enum>
104+ </value>
105+ <value id="14" type="double" default="0.6" minExclusive="0.0" required="true" />
106+ <value id="15" type="string" default="Da" required="true">
107+ <enum>
108+ <enum-name>Da</enum-name>
109+ <enum-value>Da</enum-value>
110+ </enum>
111+ <enum>
112+ <enum-name>mmu</enum-name>
113+ <enum-value>mmu</enum-value>
114+ </enum>
115+ </value>
116+ <value id="18" type="string" default="(None)" required="false">
117+ <enum>
118+ <enum-name>Error Tolerant</enum-name>
119+ <enum-value>Error Tolerant</enum-value>
120+ </enum>
121+ <enum>
122+ <enum-name>Decoy</enum-name>
123+ <enum-value>Decoy</enum-value>
124+ </enum>
125+ </value>
126+ <value id="19" type="string" default="AUTO" required="true">
127+ <enum>
128+ <enum-name>AUTO</enum-name>
129+ <enum-value>AUTO</enum-value>
130+ </enum>
131+ <enum>
132+ <enum-name>5</enum-name>
133+ <enum-value>5</enum-value>
134+ </enum>
135+ <enum>
136+ <enum-name>10</enum-name>
137+ <enum-value>10</enum-value>
138+ </enum>
139+ <enum>
140+ <enum-name>20</enum-name>
141+ <enum-value>20</enum-value>
142+ </enum>
143+ <enum>
144+ <enum-name>30</enum-name>
145+ <enum-value>30</enum-value>
146+ </enum>
147+ <enum>
148+ <enum-name>50</enum-name>
149+ <enum-value>50</enum-value>
150+ </enum>
151+ <enum>
152+ <enum-name>100</enum-name>
153+ <enum-value>100</enum-value>
154+ </enum>
155+ <enum>
156+ <enum-name>200</enum-name>
157+ <enum-value>200</enum-value>
158+ </enum>
159+ </value>
160+ <value id="20" type="string" required="true">
161+ <enum-call>pmf_db</enum-call>
162+ </value>
163+ <value id="22" type="string" required="true">
164+ <enum-call>pmf_taxonomy</enum-call>
165+ </value>
166+ <value id="24" type="bool" default="off" required="true" />
167+ <value id="25" type="string" required="true">
168+ <enum>
169+ <enum-name>MH+</enum-name>
170+ <enum-value>1+</enum-value>
171+ </enum>
172+ <enum>
173+ <enum-name>Mr</enum-name>
174+ <enum-value>Mr</enum-value>
175+ </enum>
176+ <enum>
177+ <enum-name>MH-</enum-name>
178+ <enum-value>1-</enum-value>
179+ </enum>
180+ </value>
181+ <value id="26" type="double" required="false" minExclusive="0.0" />
182+ <!-- @date 2013.06.20 <Mod> M.Izumi -->
183+ <value id="27" type="double" required="true" default="0.25" minInclusive="0.0" />
184+ <value id="28" type="int" required="true" default="999" minInclusive="1" maxInclusive="999" />
185+ <value id="29" type="string" required="true" default="da">
186+ <enum>
187+ <enum-name>Da</enum-name>
188+ <enum-value>da</enum-value>
189+ </enum>
190+ <enum>
191+ <enum-name>ppm</enum-name>
192+ <enum-value>ppm</enum-value>
193+ </enum>
194+ </value>
195+ <value id="30" type="double" required="true" default="0.05" minInclusive="0.0" maxExclusive="1.0" />
196+ </values>
197+ <params>
198+ <param id="0" value="0">
199+ <param-name>USERNAME</param-name>
200+ <param-section>Mascot Search</param-section>
201+ <param-key>NAME</param-key>
202+ </param>
203+ <param id="1" value="1">
204+ <param-name>USEREMAIL</param-name>
205+ <param-section>Mascot Search</param-section>
206+ <param-key>EMAIL</param-key>
207+ </param>
208+ <param id="4" value="4">
209+ <param-name>CLE</param-name>
210+ <param-section>Mascot Search</param-section>
211+ <param-key>ENZYME</param-key>
212+ </param>
213+ <param id="5" value="2">
214+ <param-name>PFA</param-name>
215+ <param-section>Mascot Search</param-section>
216+ <param-key>ALLOWED_MISSED_CLEAVAGES</param-key>
217+ </param>
218+ <param id="7" value="7">
219+ <param-name>MODS</param-name>
220+ <param-section>Mascot Search</param-section>
221+ <param-key>FIXED_MODS</param-key>
222+ </param>
223+ <param id="8" value="9">
224+ <param-name>IT_MODS</param-name>
225+ <param-section>Mascot Search</param-section>
226+ <param-key>VARIABLE_MODS</param-key>
227+ </param>
228+ <param id="9" value="11">
229+ <param-name>TOL</param-name>
230+ <param-section>Mascot Search</param-section>
231+ <param-key>PEPTIDE_TOL</param-key>
232+ </param>
233+ <param id="10" value="12">
234+ <param-name>TOLU</param-name>
235+ <param-section>Mascot Search</param-section>
236+ <param-key>PEPTIDE_TOL_UNIT</param-key>
237+ </param>
238+ <param id="11" value="13">
239+ <param-name>PEP_ISOTOPE_ERROR</param-name>
240+ <param-section>Mascot Search</param-section>
241+ <param-key>PEPTIDE_ISOTOPE_ERROR</param-key>
242+ </param>
243+ <param id="12" value="14">
244+ <param-name>ITOL</param-name>
245+ <param-section>Mascot Search</param-section>
246+ <param-key>MSMS_TOL</param-key>
247+ </param>
248+ <param id="13" value="15">
249+ <param-name>ITOLU</param-name>
250+ <param-section>Mascot Search</param-section>
251+ <param-key>MSMS_TOL_UNIT</param-key>
252+ </param>
253+ <param id="15" value="5">
254+ <param-name>MASS</param-name>
255+ <param-section>Mascot Search</param-section>
256+ <param-key>MASS</param-key>
257+ </param>
258+ <param id="17" value="18">
259+ <param-name>ErrorTolerant/Decoy</param-name>
260+ <param-section>Mascot Search</param-section>
261+ <param-key>ERROR_TOL_DECOY</param-key>
262+ </param>
263+ <param id="18" value="19">
264+ <param-name>REPORT</param-name>
265+ <param-section>Mascot Search</param-section>
266+ <param-key>REPORT_NUM</param-key>
267+ </param>
268+ <param id="19" value="20">
269+ <param-name>DB</param-name>
270+ <param-section>Mascot Search</param-section>
271+ <param-key>PMF_DB</param-key>
272+ </param>
273+ <param id="20" value="22">
274+ <param-name>TAXONOMY</param-name>
275+ <param-section>Mascot Search</param-section>
276+ <param-key>PMF_TAXONOMY</param-key>
277+ </param>
278+ <param id="21" value="24">
279+ <param-name>DECOY</param-name>
280+ <param-section>Mascot Search</param-section>
281+ <param-key>DECOY</param-key>
282+ </param>
283+ <param id="22" value="25">
284+ <param-name>CHARGE</param-name>
285+ <param-section>Mascot Search</param-section>
286+ <param-key>MASS_VALUES</param-key>
287+ </param>
288+ <param id="23" value="26">
289+ <param-name>SEG</param-name>
290+ <param-section>Mascot Search</param-section>
291+ <param-key>PROTEIN_MASS</param-key>
292+ </param>
293+ <param id="24" value="6">
294+ <param-name>allmod</param-name>
295+ <param-section>Identification</param-section>
296+ <param-key>SHOW_ALL_MODIFICATION</param-key>
297+ </param>
298+ <param id="25" value="27">
299+ <param-name>peak_tol</param-name>
300+ <param-section>Identification</param-section>
301+ <param-key>PEAK_LIST_TOLERANCE</param-key>
302+ </param>
303+ <param id="26" value="28">
304+ <param-name>peak_num</param-name>
305+ <param-section>Identification</param-section>
306+ <param-key>PEAK_LIST_NUM</param-key>
307+ </param>
308+ <param id="27" value="29">
309+ <param-name>peak_tol_unit</param-name>
310+ <param-section>Identification</param-section>
311+ <param-key>PEAK_LIST_TOLERANCE_UNIT</param-key>
312+ </param>
313+ <param id="28" value="30">
314+ <param-name>min_probability</param-name>
315+ <param-section>Identification</param-section>
316+ <param-key>MASCOT_MIN_PROBABILITY</param-key>
317+ </param>
318+ </params>
319+ <groups>
320+ <group id="0">
321+ <group-name>User</group-name>
322+ </group>
323+ <group id="1">
324+ <group-name></group-name>
325+ </group>
326+ <group id="2">
327+ <group-name></group-name>
328+ </group>
329+ <group id="3">
330+ <group-name></group-name>
331+ </group>
332+ <group id="4">
333+ <group-name>Peptide Tolerance</group-name>
334+ </group>
335+ <group id="5">
336+ <group-name></group-name>
337+ </group>
338+ <group id="6">
339+ <group-name>MS/MS Tolerance</group-name>
340+ </group>
341+ <group id="7">
342+ <group-name></group-name>
343+ </group>
344+ <group id="8">
345+ <group-name>Peak List</group-name>
346+ </group>
347+ </groups>
348+ <pages>
349+ <page common="false">
350+ <page-name>pmf</page-name>
351+ <page-title>Mascot Peptide Mass Fingerprint</page-title>
352+ <check-functions>
353+ <check-fun>pmf_lcms_mods</check-fun>
354+ </check-functions>
355+ <forms>
356+ <form id="0" param="0" group="0">
357+ <form-title>Name</form-title>
358+ <form-desc>On the free, public Mascot server, your name and email address must be entered in these fields. This information will nobe be used by us, Matrix Science or anyone else to send you "spam" or junk mail.</form-desc>
359+ </form>
360+ <form id="1" param="1" group="0">
361+ <form-title>Email</form-title>
362+ <form-desc>On the free, public Mascot server, your name and email address must be entered in these fields. This information will nobe be used by us, Matrix Science or anyone else to send you "spam" or junk mail.</form-desc>
363+ </form>
364+ <form id="2" param="25" group="8">
365+ <form-title>m/z Tol.</form-title>
366+ </form>
367+ <form id="3" param="27" group="8">
368+ <form-title>m/z Tol. Unit</form-title>
369+ </form>
370+ <form id="4" param="26" group="8">
371+ <form-title>Max Peak Num.</form-title>
372+ </form>
373+ <form id="5" param="19" group="1">
374+ <form-title>Database</form-title>
375+ <form-desc>Select the sequence database to be searched.</form-desc>
376+ </form>
377+ <form id="6" param="20" group="1">
378+ <form-title>Taxonomy</form-title>
379+ <form-desc>The Taxonomy parameter allows searches to bee limited to entries from particular specied or groups of species. This can spped up a search, and ensures that the hits list will only contain entries from the selected spcies.</form-desc>
380+ </form>
381+ <form id="7" param="4" group="2">
382+ <form-title>Enzyme</form-title>
383+ <form-desc>Select the enzyme used in sample prepatation.</form-desc>
384+ </form>
385+ <form id="8" param="5" group="2">
386+ <form-title>Allowed Missed Cleavages</form-title>
387+ <form-desc>Setting the number of allowed missed cleavage sites to zero similates a limit digest.</form-desc>
388+ </form>
389+ <form id="9" param="7" group="3">
390+ <form-title>Fixed Modifications</form-title>
391+ <form-desc>Select any known or suspected modifications. Fixed modifications are applied universally, to every instance of the spefified redidue(s) or terminus.</form-desc>
392+ </form>
393+ <form id="10" param="8" group="3">
394+ <form-title>Variable Modifications</form-title>
395+ <form-desc>Select any known or suspected modifications. Variable modifications are those which may or may not be present.</form-desc>
396+ </form>
397+ <form id="11" param="24" group="3">
398+ <form-title>Display all modifications</form-title>
399+ </form>
400+ <form id="12" param="23" group="5">
401+ <form-title>Protein Mass (kDa)</form-title>
402+ <form-desc>The mass of the intact protein in Da applied as a sliding window.</form-desc>
403+ </form>
404+ <form id="13" param="9" group="4">
405+ <form-title>Peptide Tol.</form-title>
406+ <form-desc>The mass of the intact protein in Da applied as a sliding window.</form-desc>
407+ </form>
408+ <form id="14" param="10" group="4">
409+ <form-title>Peptide Tol. Unit</form-title>
410+ <form-desc>The error window on experimantal peptide mass values.</form-desc>
411+ </form>
412+ <form id="15" param="22" group="7">
413+ <form-title>Mass Values</form-title>
414+ <form-desc>Specifies whether experimental peptide mass values in a speptide mass fingerpring search include the mass of the charge carrier, MH+ or M-H-, or whether they correspond to neutral, Mr Values.</form-desc>
415+ </form>
416+ <form id="16" param="15" group="7">
417+ <form-title>Mass</form-title>
418+ <form-desc>Specify wheter the expeimental mass values area average of monoisotopic.</form-desc>
419+ </form>
420+ <form id="17" param="21" group="7">
421+ <form-title>Decoy</form-title>
422+ <form-desc>During the Decoy Search, every time a protein sequence from the target database in tested, a decoy sequence of the same length is automatically generated and tested.</form-desc>
423+ </form>
424+ <form id="18" param="18" group="7">
425+ <form-title>Report Num.</form-title>
426+ <form-desc>This parameter determines the maximum number of hits displayed in a search results report.</form-desc>
427+ </form>
428+ <form id="19" param="28">
429+ <form-title>Min. Probalility</form-title>
430+ </form>
431+ </forms>
432+ </page>
433+ </pages>
434+</settings>
diff -r c58797fa5711 -r 619a409b044a src/common-plugin-analyze/MascotPMFForLCMSPlugin/stdafx.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MascotPMFForLCMSPlugin/stdafx.h Sun Jun 07 21:52:12 2015 +0900
@@ -0,0 +1,141 @@
1+/**
2+ * @file stdafx.h
3+ * @brief common header file
4+ *
5+ * @author Parry
6+ * @date 2012.01.16
7+ *
8+ * Copyright(C) 2006-2014 Shimadzu Corporation All rights reserved.
9+ */
10+
11+
12+
13+#ifndef __KOME_MASCOT_SEARCH_PLUGIN_STD_AFX_H__
14+#define __KOME_MASCOT_SEARCH_PLUGIN_STD_AFX_H__
15+
16+
17+
18+//
19+// namespace
20+//
21+
22+/// kome project namespace
23+namespace kome {
24+}
25+
26+
27+//
28+// macros
29+//
30+
31+#define WXUSINGDLL
32+
33+
34+//
35+// message
36+//
37+
38+#ifdef _MSC_VER
39+ #pragma warning( disable:4190 )
40+ #pragma warning( disable:4244 )
41+ #pragma warning( disable:4251 )
42+ #pragma warning( disable:4267 )
43+ #pragma warning( disable:4561 )
44+ #pragma warning( disable:4793 )
45+ #pragma warning( disable:4819 )
46+ #pragma warning( disable:4996 )
47+#endif // _MSC_VER
48+
49+
50+//
51+// libraries
52+//
53+
54+#ifdef _MSC_VER
55+ #pragma comment( lib, "CoreFunctions" )
56+ #pragma comment( lib, "CoreToolkits" )
57+ #pragma comment( lib, "DataObjects" )
58+ #pragma comment( lib, "ImageManager" )
59+ #pragma comment( lib, "PluginTools" )
60+ #pragma comment( lib, "DbTools" )
61+ #pragma comment( lib, "DataOperation" )
62+ #pragma comment( lib, "IdentificationTools" )
63+ #pragma comment( lib, "EventManager" )
64+ #pragma comment( lib, "WindowManager" )
65+ #pragma comment( lib, "XMLTools" )
66+ #pragma comment( lib, "NetworkTools" )
67+ #pragma comment( lib, "GLTools" )
68+
69+ #ifdef _DEBUG
70+ #pragma comment( lib, "wxbase28d" )
71+ #pragma comment( lib, "wxbase28d_net" )
72+ #pragma comment( lib, "wxbase28d_xml" )
73+ #pragma comment( lib, "wxexpatd" )
74+ #pragma comment( lib, "wxjpegd" )
75+ #pragma comment( lib, "wxmsw28d_adv" )
76+ #pragma comment( lib, "wxmsw28d_aui" )
77+ #pragma comment( lib, "wxmsw28d_core" )
78+ #pragma comment( lib, "wxmsw28d_gl" )
79+ #pragma comment( lib, "wxmsw28d_html" )
80+ #pragma comment( lib, "wxmsw28d_media" )
81+ #pragma comment( lib, "wxmsw28d_qa" )
82+ #pragma comment( lib, "wxmsw28d_richtext" )
83+ #pragma comment( lib, "wxmsw28d_xrc" )
84+ #pragma comment( lib, "wxpngd" )
85+ #pragma comment( lib, "wxregexd" )
86+ #pragma comment( lib, "wxtiffd" )
87+ #pragma comment( lib, "wxzlibd" )
88+
89+ #pragma comment( lib, "xerces-c_3D" )
90+ #else
91+ #pragma comment( lib, "wxbase28" )
92+ #pragma comment( lib, "wxbase28_net" )
93+ #pragma comment( lib, "wxbase28_xml" )
94+ #pragma comment( lib, "wxexpat" )
95+ #pragma comment( lib, "wxjpeg" )
96+ #pragma comment( lib, "wxmsw28_adv" )
97+ #pragma comment( lib, "wxmsw28_aui" )
98+ #pragma comment( lib, "wxmsw28_core" )
99+ #pragma comment( lib, "wxmsw28_gl" )
100+ #pragma comment( lib, "wxmsw28_html" )
101+ #pragma comment( lib, "wxmsw28_media" )
102+ #pragma comment( lib, "wxmsw28_qa" )
103+ #pragma comment( lib, "wxmsw28_richtext" )
104+ #pragma comment( lib, "wxmsw28_xrc" )
105+ #pragma comment( lib, "wxpng" )
106+ #pragma comment( lib, "wxregex" )
107+ #pragma comment( lib, "wxtiff" )
108+ #pragma comment( lib, "wxzlib" )
109+
110+ #pragma comment( lib, "xerces-c_3" )
111+ #endif // _DEBUG
112+#endif // _MSC_VER
113+
114+
115+//
116+// includes
117+//
118+
119+#include "kome/CoreFunctions.h"
120+#include "kome/CoreToolkits.h"
121+#include "kome/DataObjects.h"
122+#include "kome/ImageManager.h"
123+#include "kome/PluginTools.h"
124+#include "kome/DbTools.h"
125+#include "kome/DataOperation.h"
126+#include "kome/IdentificationTools.h"
127+#include "kome/EventManager.h"
128+#include "kome/WindowManager.h"
129+#include "kome/XMLTools.h"
130+#include "kome/NetworkTools.h"
131+#include "MascotLib.h"
132+
133+//
134+// Global variables
135+//
136+
137+// Indicates whether it is necessary to load Mascot parameters next time the dialog is opened.
138+extern bool g_bMustLoadMascotParameters;
139+
140+
141+#endif // __KOME_MASCOT_SEARCH_PLUGIN_STD_AFX_H__
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