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MassPlusPlus: Commit

Mass++ ソースリポジトリ


Commit MetaInfo

Revision9104db045a3a262c416e472569ea0ea5cf2318de (tree)
Time2015-06-06 01:31:15
AuthorMasaki Murase
CommiterMasaki Murase

Log Message

add MsbackadjBaselineDetection Plug-in
removed MATLAB related plugin from 32bit installer configuration

Change Summary

Incremental Difference

diff -r 50db0c57ab38 -r 9104db045a3a build/msvs/solutions/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPlugin.vcxproj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/build/msvs/solutions/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPlugin.vcxproj Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,170 @@
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8+ <ProjectConfiguration Include="Release|Win32">
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16+ <ProjectConfiguration Include="Release|x64">
17+ <Configuration>Release</Configuration>
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67+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
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69+ <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
70+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
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73+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
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79+ <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(SolutionDir)$(Platform)-$(Configuration)\</OutDir>
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81+ <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(SolutionDir)$(Platform)-$(Configuration)\</OutDir>
82+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Platform)-$(Configuration)\</IntDir>
83+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Platform)-$(Configuration)\</IntDir>
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85+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(Platform)-$(Configuration)\</IntDir>
86+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</LinkIncremental>
87+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</LinkIncremental>
88+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</LinkIncremental>
89+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</LinkIncremental>
90+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Parallel-Release|x64 '">false</LinkIncremental>
91+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(ProjectName)</TargetName>
92+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(ProjectName)</TargetName>
93+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(ProjectName)</TargetName>
94+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(ProjectName)</TargetName>
95+ </PropertyGroup>
96+ <ItemDefinitionGroup>
97+ <ClCompile>
98+ <AdditionalIncludeDirectories>$(SolutionDir)..\..\..\..\include;$(SolutionDir)..\..\contrib\common\$(Platform)\boost\include;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib\msw;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\include;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\include;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\include;$(SolutionDir)..\..\contrib\forPlugins\Win32\Matlab\extern\include;$(SolutionDir)..\..\contrib\forPlugins\Win32\Matlab\BioinformaticsToolboxFuncDll;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
99+ <PrecompiledHeader>NotUsing</PrecompiledHeader>
100+ </ClCompile>
101+ <Link>
102+ <AdditionalLibraryDirectories>$(SolutionDir)..\..\..\..\lib\msvs\$(Platform)-$(Configuration);$(SolutionDir)..\..\contrib\common\$(Platform)\boost\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\lib;$(SolutionDir)..\..\contrib\forPlugins\Win32\Matlab\BioinformaticsToolboxFuncDll;$(SolutionDir)..\..\contrib\forPlugins\Win32\Matlab\extern\lib\win64\microsoft;$(SolutionDir)..\..\contrib\forPlugins\Win32\Matlab\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
103+ <ModuleDefinitionFile>$(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\$(ProjectName).def</ModuleDefinitionFile>
104+ </Link>
105+ <PostBuildEvent>
106+ <Command>mkdir "$(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)"
107+copy "$(TargetPath)" "$(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)"
108+copy "$(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\*.xml" "$(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)"
109+copy "$(SolutionDir)..\..\contrib\forPlugins\$(Platform)\MATLAB\BioinformaticsToolboxFuncDll\*.dll" "$(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\bin"</Command>
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150+ </ClCompile>
151+ </ItemDefinitionGroup>
152+ <ItemGroup>
153+ <None Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\MsbackadjBaselineDetectionPlugin.def" />
154+ <None Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\plugin.xml" />
155+ <None Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\ReadMe.txt" />
156+ <None Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\settings.xml" />
157+ </ItemGroup>
158+ <ItemGroup>
159+ <ClInclude Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\MsbackadjBaselineDetectionManager.h" />
160+ <ClInclude Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\MsbackadjBaselineDetectionPluginFunctions.h" />
161+ <ClInclude Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\stdafx.h" />
162+ </ItemGroup>
163+ <ItemGroup>
164+ <ClCompile Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\MsbackadjBaselineDetectionManager.cpp" />
165+ <ClCompile Include="..\..\..\..\..\src\common-plugin-analyze\MsbackadjBaselineDetectionPlugin\MsbackadjBaselineDetectionPluginFunctions.cpp" />
166+ </ItemGroup>
167+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
168+ <ImportGroup Label="ExtensionTargets">
169+ </ImportGroup>
170+</Project>
\ No newline at end of file
diff -r 50db0c57ab38 -r 9104db045a3a build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln
--- a/build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln Thu May 28 07:42:52 2015 +0900
+++ b/build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln Sat Jun 06 01:31:15 2015 +0900
@@ -63,6 +63,8 @@
6363 EndProject
6464 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MascotSearchPlugin", "MascotSearchPlugin\MascotSearchPlugin.vcxproj", "{3884E680-4F5C-4D72-BD7F-CC133511FBE6}"
6565 EndProject
66+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MsbackadjBaselineDetectionPlugin", "MsbackadjBaselineDetectionPlugin\MsbackadjBaselineDetectionPlugin.vcxproj", "{CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}"
67+EndProject
6668 Global
6769 GlobalSection(SolutionConfigurationPlatforms) = preSolution
6870 Debug|Win32 = Debug|Win32
@@ -567,6 +569,20 @@
567569 {3884E680-4F5C-4D72-BD7F-CC133511FBE6}.Release|Win32.Build.0 = Release|Win32
568570 {3884E680-4F5C-4D72-BD7F-CC133511FBE6}.Release|x64.ActiveCfg = Release|x64
569571 {3884E680-4F5C-4D72-BD7F-CC133511FBE6}.Release|x64.Build.0 = Release|x64
572+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Debug|Win32.ActiveCfg = Debug|Win32
573+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Debug|Win32.Build.0 = Debug|Win32
574+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Debug|x64.ActiveCfg = Debug|x64
575+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Debug|Win32.ActiveCfg = Debug|Win32
576+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Debug|Win32.Build.0 = Debug|Win32
577+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Debug|x64.ActiveCfg = Debug|x64
578+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Debug|x64.Build.0 = Debug|x64
579+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Release|Win32.ActiveCfg = Release|Win32
580+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Release|Win32.Build.0 = Release|Win32
581+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Release|x64.ActiveCfg = Release|x64
582+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Parallel-Release|x64.Build.0 = Release|x64
583+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Release|Win32.ActiveCfg = Release|Win32
584+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Release|Win32.Build.0 = Release|Win32
585+ {CE31E679-A06C-4F42-9D45-1FC9CE38ADC8}.Release|x64.ActiveCfg = Release|x64
570586 EndGlobalSection
571587 GlobalSection(SolutionProperties) = preSolution
572588 HideSolutionNode = FALSE
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionManager.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionManager.cpp Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,492 @@
1+/**
2+ * @file MsbackadjBaselineDetectionManager.cpp
3+ * @brief implements of MsbackadjBaselineDetectionManager class
4+ *
5+ * @author A.Ozaki
6+ * @date 2013.08.01
7+ *
8+ * Copyright(C) 2013-2013 Shimadzu Corporation. All rights reserved.
9+ */
10+
11+#include "stdafx.h"
12+#include "MsbackadjBaselineDetectionManager.h"
13+
14+#include <math.h>
15+#include <float.h>
16+
17+
18+using namespace kome::baseline::msbackadj;
19+
20+
21+#include <crtdbg.h>
22+#ifdef _DEBUG
23+ #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
24+ #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
25+#endif // _DEBUG
26+
27+
28+
29+// for use Matlab libraries
30+//
31+#include "BioinformaticsToolboxFunc.h"
32+#pragma comment( lib, "BioinformaticsToolboxFunc" )
33+#pragma comment( lib, "mclmcrrt" )
34+//
35+//
36+
37+// for Error Message on Dialog
38+#define ERROR_MESSAGE_APPL_INITIALIZE ( "BioinformaticsToolboxFunc library cannot be initialized.\nIf MATLAB Compiler Runtime Routine (MCR) ver.R2013a was not installed, please install it from flollwing web site:\nhttp://www.mathworks.com/products/compiler/mcr/index.html" )
39+#define ERROR_MESSAGE_INITIALIZE ( "BioinformaticsToolboxFunc library cannot be initialized." )
40+#define FUNCTION_NAME ( "Msbackadj" )
41+
42+
43+// constructor
44+MsbackadjBaselineDetectionManager::MsbackadjBaselineDetectionManager( void )
45+{
46+ // initialize application
47+ //
48+ m_pProgress = (kome::window::DialogProgress *)NULL;
49+
50+ // set default value
51+ m_dWindowSize = 200.0;
52+ m_dStepSize = 50.0;
53+ m_nRegressionMethod = 0;
54+ m_nEstimationMethod = 0;
55+ m_nSmoothingMethod = 0;
56+ m_dQuantile = 0.1;
57+
58+ return;
59+}
60+
61+// destructor
62+MsbackadjBaselineDetectionManager::~MsbackadjBaselineDetectionManager( void )
63+{
64+ // release application
65+ //
66+ kome::core::MsppManager &insMsppMgr = kome::core::MsppManager::getInstance( );
67+ if ( true == insMsppMgr.isInitializedMATLAB( ) )
68+ {
69+ // initialized MATLAB application
70+ try
71+ {
72+ mclTerminateApplication( );
73+
74+ // reset flag
75+ insMsppMgr.resetInitializedMATLAB( );
76+ }
77+ catch (...)
78+ {
79+ }
80+ }
81+
82+ return;
83+}
84+
85+// set window size
86+void MsbackadjBaselineDetectionManager::setWindowSize( const double dSize )
87+{
88+ m_dWindowSize = MAX( 0.0, dSize );
89+}
90+
91+// get window size
92+double MsbackadjBaselineDetectionManager::getWindowSize( void )
93+{
94+ return m_dWindowSize;
95+}
96+
97+// set step size
98+void MsbackadjBaselineDetectionManager::setStepSize( const double dSize )
99+{
100+ m_dStepSize = MAX( 0.0, dSize );
101+}
102+
103+// get step size
104+double MsbackadjBaselineDetectionManager::getStepSize( )
105+{
106+ return m_dStepSize;
107+}
108+
109+// set regression method
110+void MsbackadjBaselineDetectionManager::setRegressionMethod( const int nMethodValue )
111+{
112+ m_nRegressionMethod = MAX( 0, nMethodValue );
113+}
114+
115+// get regression method
116+int MsbackadjBaselineDetectionManager::getRegressionMethod( void )
117+{
118+ return m_nRegressionMethod;
119+}
120+
121+// set estimation method
122+void MsbackadjBaselineDetectionManager::setEstimationMethod( const int nMethodValue )
123+{
124+ m_nEstimationMethod = MAX( 0, nMethodValue );
125+}
126+
127+// get estimation method
128+int MsbackadjBaselineDetectionManager::getEstimationMethod( void )
129+{
130+ return m_nEstimationMethod;
131+}
132+
133+// set smoothing method
134+void MsbackadjBaselineDetectionManager::setSmoothingMethod( const int nMethodValue )
135+{
136+ m_nSmoothingMethod = MAX( 0, nMethodValue );
137+}
138+
139+// get smoothing method
140+int MsbackadjBaselineDetectionManager::getSmoothingMethod( void )
141+{
142+ return m_nSmoothingMethod;
143+}
144+
145+// set quantile
146+void MsbackadjBaselineDetectionManager::setQuantile( const double dQuantile )
147+{
148+ m_dQuantile = MAX( 0.0, dQuantile );
149+}
150+
151+// get quantile
152+double MsbackadjBaselineDetectionManager::getQuantile( void )
153+{
154+ return m_dQuantile;
155+}
156+
157+// initialize MATLAB application
158+bool MsbackadjBaselineDetectionManager::initializeApplication( void )
159+{
160+ kome::core::MsppManager &insMsppMgr = kome::core::MsppManager::getInstance( );
161+
162+ // check initialize
163+ bool bRet = insMsppMgr.isInitializedMATLAB( );
164+ if ( false == bRet )
165+ {
166+ // uninitialize
167+
168+ // create progress dialog
169+ if ( (kome::window::DialogProgress *)NULL != m_pProgress )
170+ {
171+ delete m_pProgress;
172+ }
173+ if ( (wxWindow *)NULL != kome::window::WindowTool::getMainWindow( ) )
174+ {
175+// m_pProgress = new kome::window::DialogProgress( kome::window::WindowTool::getMainWindow( ), FUNCTION_NAME );
176+ }
177+ if ( (kome::window::DialogProgress *)NULL != m_pProgress )
178+ {
179+ m_pProgress->setStatus( "MATLAB application initialzing..." );
180+ m_pProgress->setRange( 1, 4 );
181+ m_pProgress->setPosition( 2 );
182+ }
183+
184+ // initialize application
185+ //
186+ if ( true == mclInitializeApplication( NULL, 0 ) )
187+ {
188+ // success
189+ insMsppMgr.setInitializedMATLAB( );
190+ bRet = true;
191+ }
192+ else
193+ {
194+ // failure
195+ LOG_ERROR( FMT( "mclInitializeApplication function failure." ) );
196+
197+ wxMessageBox( wxT( ERROR_MESSAGE_APPL_INITIALIZE ), wxT( FUNCTION_NAME ), wxOK );
198+
199+ if ( (kome::core::Progress *)NULL != m_pProgress )
200+ {
201+ m_pProgress->fill( );
202+ delete m_pProgress;
203+ m_pProgress = (kome::window::DialogProgress *)NULL;
204+ }
205+ }
206+
207+ if ( (kome::window::DialogProgress *)NULL != m_pProgress )
208+ {
209+ m_pProgress->setPosition( 3 );
210+ }
211+
212+ }
213+
214+ return bRet;
215+}
216+// get baseline
217+void MsbackadjBaselineDetectionManager::getMsbackadj
218+(
219+ kome::core::XYData &src,
220+ kome::core::XYData &baseline
221+)
222+{
223+ // initialize application for MATLAB
224+ if ( false == initializeApplication( ) )
225+ {
226+ LOG_ERROR( FMT( "initializeApplication function failure." ) );
227+ return;
228+ }
229+
230+ while ( 1 )
231+ {
232+ int nIndex = 0;
233+
234+ const int nRowTemp = src.getLength( );
235+ const int nColumn = 2; // 行列（m/zの１次元配列、intensityの１次元配列からなる２列）
236+ const int nDataSizeTemp = nRowTemp * nColumn;
237+
238+ double *pdDataArray = (double *)NULL;
239+
240+ pdDataArray = new double[nDataSizeTemp];
241+ if ( (double *)NULL == pdDataArray )
242+ {
243+ LOG_ERROR( FMT( "can not allocate data array.(size:%dx%d)", sizeof( double ), nDataSizeTemp ) );
244+ break;
245+ }
246+
247+ memset( (void *)pdDataArray, 0x00, sizeof( double ) * nDataSizeTemp );
248+
249+ // m/z、intensityを設定します
250+ // ただし、intensityの値がゼロのものは、省いて設定する必要があります
251+ //
252+ int nRow = 0;
253+ int nIndexTemp = 0;
254+
255+ // 強度の値が0のところを省く
256+ for ( nIndex = 0 ; nIndex < nRowTemp ; nIndex++ )
257+ {
258+ if ( 0 < src.getY( nIndex ) )
259+ {
260+ *(pdDataArray + nRow) = src.getX( nIndex );
261+ nRow++;
262+ }
263+ }
264+ for ( nIndex = 0 ; nIndex < nRowTemp ; nIndex++ )
265+ {
266+ if ( 0 < src.getY( nIndex ) )
267+ {
268+ *(pdDataArray + nIndexTemp + nRow) = src.getY( nIndex );
269+ nIndexTemp++;
270+ }
271+ }
272+ const int nDataSize = nRow * nColumn;
273+
274+ // nRowTemp...raw dataのデータポイント数
275+ // nRow、nIndexTemp....強度が0のデータポイントを除いたデータポイント数
276+
277+ // データ数の確認
278+ if ( 0 >= nDataSize )
279+ {
280+ LOG_ERROR( FMT( "illegal data size (%d)", nDataSize ) );
281+ break;
282+ }
283+
284+ mwArray insArrayData( nRow, nColumn, mxDOUBLE_CLASS, mxREAL );
285+
286+ // dDataArray -> insArrayData
287+ insArrayData.SetData( pdDataArray, nDataSize );
288+
289+ //
290+ delete[] pdDataArray;
291+
292+ mwArray insWindowSize( m_dWindowSize );
293+ mwArray insStepSize( m_dStepSize );
294+ mwArray insRegressionMethod( m_nRegressionMethod );
295+ mwArray insEstimationMethod( m_nEstimationMethod );
296+ mwArray insSmoothingMethod( m_nSmoothingMethod );
297+ mwArray insQuantile( m_dQuantile);
298+
299+ const int nArgOut = 1; // size of return values
300+
301+ mwArray insBackadj; // return
302+
303+ bool bSuccess = true;
304+
305+
306+ // initialize MATLAB function libray
307+ //
308+ if ( (kome::window::DialogProgress *)NULL != m_pProgress )
309+ {
310+ m_pProgress->setPosition( 3 );
311+ m_pProgress->setStatus( "MATLAB function initializing..." );
312+ }
313+ if ( false == BioinformaticsToolboxFuncInitialize( ) )
314+ {
315+ // initialize false
316+ LOG_ERROR( FMT( "BioinformaticsToolboxFuncInitialize function failure." ) );
317+
318+ wxMessageBox( wxT( ERROR_MESSAGE_INITIALIZE ), wxT( FUNCTION_NAME ), wxOK );
319+
320+ break;
321+ }
322+
323+ // execute MATLAB function
324+ if ( (kome::window::DialogProgress *)NULL != m_pProgress )
325+ {
326+ m_pProgress->setPosition( 4 );
327+ m_pProgress->setStatus( "Processing..." );
328+ }
329+ try
330+ {
331+ MatlabMsbackadj( nArgOut, insBackadj, insArrayData,
332+ insWindowSize, insStepSize, insRegressionMethod, insEstimationMethod,
333+ insSmoothingMethod, insQuantile );
334+
335+ std::string strTemp;
336+ }
337+ catch (...)
338+ {
339+ LOG_ERROR( FMT( "MatlabMsbackadj function failure." ) );
340+ bSuccess = false;
341+ }
342+
343+ // release MATLAB function libray
344+ //
345+ try
346+ {
347+ BioinformaticsToolboxFuncTerminate( );
348+ }
349+ catch (...)
350+ {
351+ }
352+
353+ // prot process
354+ //
355+ if ( true == bSuccess )
356+ {
357+ mwArray insSize = insBackadj.GetDimensions( );
358+
359+ int nGetSize[1];
360+
361+ insSize.GetData( nGetSize, _countof( nGetSize ) );
362+
363+ int nCountOfBackadj= nGetSize[0];
364+
365+ // 入力したデータポイント数と、出力されてきたデータポイント数が異なればエラー
366+ // check values
367+ if ( nRow != nCountOfBackadj )
368+ {
369+ // error
370+ LOG_ERROR( FMT( "unmatch row size (%d:%d)", nRow, nDataSize ) );
371+ break;
372+ }
373+
374+ double *pdBackadj = new double[nCountOfBackadj];
375+ if ( (double *)NULL == pdBackadj )
376+ {
377+ LOG_ERROR( FMT( "can not allocate data array.(size:%dx%d)", sizeof( double ), nCountOfBackadj ) );
378+ break;
379+ }
380+
381+ // メモリの確保
382+ memset( (void *)pdBackadj, 0x00, sizeof( double ) * nCountOfBackadj );
383+
384+ // store
385+ insBackadj.GetData( pdBackadj, nCountOfBackadj ); // pdBackadjにベースラインサブトラクト後のピーク強度が入る。
386+
387+ baseline.reserve( nRowTemp );
388+
389+ // ベースラインの値を baseline に格納
390+ int nRow_index = 0;
391+ for ( nIndex = 0 ; nIndex < nRowTemp ; nIndex++ )
392+ {
393+ if ( 0 < src.getY( nIndex ) ) // 元の配列において、強度が0でなければ
394+ {
395+ baseline.addPoint( src.getX( nIndex ), src.getY( nIndex )- pdBackadj[nRow_index]);
396+ nRow_index++;
397+ }
398+ else // 元の配列において、強度が0以下ならば
399+ {
400+ baseline.addPoint( src.getX( nIndex ), 0);
401+
402+ }
403+ }
404+
405+ // 強度が0以外の点数を確認します
406+ if ( nRow != nRow_index )
407+ {
408+ // error
409+ LOG_ERROR( FMT( "unmatch row size without zero value (%d:%d)", nRow, nRow_index ) );
410+ delete[] pdBackadj; // @Date:2014/02/21 <Add> A.Ozaki
411+ break;
412+ }
413+
414+ /* baseline除去後のデータをbaselineに渡していたので、削除 <del> 2014-2-7 Fujita
415+ baseline.reserve( nRow );
416+
417+ nRow
418+ for ( nIndex = 0 ; nIndex < nRow ; nIndex++ )
419+ {
420+ if ( 0 < src.getY( nIndex ){ // 元の配列において、強度が0でなければ
421+ baseline.addPoint( src.getX( nIndex ), *( pdBackadj + nIndex ) );
422+ }
423+ }
424+ */
425+
426+ delete[] pdBackadj;
427+ }
428+
429+ break;
430+ }
431+
432+ // clean up progress
433+ //
434+ if ( (kome::window::DialogProgress *)NULL != m_pProgress )
435+ {
436+ m_pProgress->fill( );
437+
438+ delete m_pProgress;
439+ m_pProgress = (kome::window::DialogProgress *)NULL;
440+ }
441+
442+ return;
443+}
444+
445+// get noise threshold
446+double MsbackadjBaselineDetectionManager::getNoiseThreshold( kome::core::XYData& src )
447+{
448+ // noise threshold
449+ return 0.0;
450+}
451+
452+// get instance
453+MsbackadjBaselineDetectionManager &MsbackadjBaselineDetectionManager::getInstance( void )
454+{
455+ // create object
456+ static MsbackadjBaselineDetectionManager mgr;
457+
458+ return mgr;
459+}
460+
461+// release MATLAB application
462+void MsbackadjBaselineDetectionManager::releaseMatlab( void )
463+{
464+ kome::core::MsppManager &insMsppMgr = kome::core::MsppManager::getInstance( );
465+
466+ // check initialize
467+ bool bRet = insMsppMgr.isInitializedMATLAB( );
468+ if ( true == bRet )
469+ {
470+ // already initialized
471+ try
472+ {
473+ // release application
474+ //
475+ mclTerminateApplication( );
476+ }
477+ catch (...)
478+ {
479+ // failure
480+ LOG_ERROR( FMT( "mclTerminateApplication function failure." ) );
481+ }
482+
483+ // reset initialized flag
484+ //
485+ insMsppMgr.resetInitializedMATLAB( );
486+ }
487+
488+ return;
489+}
490+
491+
492+//
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionManager.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionManager.h Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,186 @@
1+/**
2+ * @file MsbackadjBaselineDetectionManager.h
3+ * @brief interfaces of MsbackadjBaselineDetectionManager class
4+ *
5+ * @author A.Ozaki
6+ * @date 2013.08.01
7+ *
8+ * Copyright(C) 2013-2013 Shimadzu Corporation. All rights reserved.
9+ */
10+
11+
12+#ifndef __KOME_BASELINE_MSBACKADJ_MANAGER_H__
13+#define __KOME_BASELINE_MSBACKADJ_MANAGER_H__
14+
15+
16+namespace kome {
17+ namespace baseline {
18+ namespace msbackadj {
19+
20+ /**
21+ * @class AbcBaselineDetectionManager
22+ * @brief weighted average baseline class
23+ */
24+ class MsbackadjBaselineDetectionManager {
25+ protected:
26+ /**
27+ * @fn MsbackadjBaselineDetectionManager( void )
28+ * @brief constructor
29+ */
30+ MsbackadjBaselineDetectionManager( void );
31+
32+ /**
33+ * @fn virtual ~MsbackadjBaselineDetectionManager( void )
34+ * @brief destructor
35+ */
36+ virtual ~MsbackadjBaselineDetectionManager( void );
37+
38+ protected:
39+ /** window size */
40+ double m_dWindowSize;
41+
42+ /** step size */
43+ double m_dStepSize;
44+
45+ /** regression method */
46+ int m_nRegressionMethod;
47+
48+ /** estimation method */
49+ int m_nEstimationMethod;
50+
51+ /** smoothing method */
52+ int m_nSmoothingMethod;
53+
54+ /** quantile */
55+ double m_dQuantile;
56+
57+ public:
58+ /**
59+ * @fn void setWindowSize( const double dSize )
60+ * @brief sets window size
61+ * @param dSize window size
62+ */
63+ void setWindowSize( const double dSize );
64+
65+ /**
66+ * @fn double getWindowSize( void )
67+ * @brief gets window size
68+ * @return window size
69+ */
70+ double getWindowSize( void );
71+
72+ /**
73+ * @fn void setStepSize( const double dSize )
74+ * @brief sets step size
75+ * @param dSize step size
76+ */
77+ void setStepSize( const double dSize );
78+
79+ /**
80+ * @fn double getStepSize( void )
81+ * @brief gets step size
82+ * @return step size
83+ */
84+ double getStepSize( void );
85+
86+ /**
87+ * @fn void setRegressionMethod( const ind nMethodValue )
88+ * @brief sets regression method
89+ * @param nMethodValue number of regression method
90+ */
91+ void setRegressionMethod( const int nMethodValue );
92+
93+ /**
94+ * @fn double getRegressionMethod( void )
95+ * @brief gets regression method
96+ * @return number of regresstion method
97+ */
98+ int getRegressionMethod( void );
99+
100+ /**
101+ * @fn void setEstimationMethod( const ind nMethodValue )
102+ * @brief sets estimation method
103+ * @param nMethodValue number of estimation method
104+ */
105+ void setEstimationMethod( const int nMethodValue );
106+
107+ /**
108+ * @fn double getEstimationMethod( void )
109+ * @brief gets estimation method
110+ * @return number of estimation method
111+ */
112+ int getEstimationMethod( void );
113+
114+ /**
115+ * @fn void setSmoothingMethod( const ind nMethodValue )
116+ * @brief sets smoothing method
117+ * @param nMethodValue number of smoothing method
118+ */
119+ void setSmoothingMethod( const int nMethodValue );
120+
121+ /**
122+ * @fn double getSmoothingMethod( void )
123+ * @brief gets smoothing method
124+ * @return number of smoothing method
125+ */
126+ int getSmoothingMethod( void );
127+
128+ /**
129+ * @fn void setSQuantile( const double dQuantile )
130+ * @brief sets quantile
131+ * @param dQuantile quantile
132+ */
133+ void setQuantile( const double dQuantile );
134+
135+ /**
136+ * @fn int getQuantile( void )
137+ * @brief gets quantile
138+ * @return quantile
139+ */
140+ double getQuantile( void );
141+
142+ public:
143+ /**
144+ * @fn void getMsbackadj( kome::core::XYData& src, kome::core::XYData& baseline )
145+ * @brief gets baseline
146+ * @param src source data points
147+ * @param baseline the object to store baseline
148+ */
149+ void getMsbackadj( kome::core::XYData& src, kome::core::XYData& baseline );
150+
151+ /**
152+ * @fn void releaseMatlab( void )
153+ * @brief release MATLAB application
154+ */
155+ void releaseMatlab( void );
156+
157+ protected:
158+ /**
159+ * @fn double getNoiseThreshold( kome::core::XYData& src )
160+ * @brief gets noise threshold
161+ * @param src source data points
162+ * @return noise threshold
163+ */
164+ double getNoiseThreshold( kome::core::XYData& src );
165+
166+ private:
167+ /** Progress */
168+ kome::window::DialogProgress *m_pProgress;
169+
170+ private:
171+ /** initialize application */
172+ bool initializeApplication( void );
173+
174+ public:
175+ /**
176+ * @fn static MsbackadjBaselineDetectionManager& getInstance( void )
177+ * @brief gets MsbackadjBaselineDetectionManager object
178+ * @return AbcBaselineDetectionManager object (This is the only object.)
179+ */
180+ static MsbackadjBaselineDetectionManager& getInstance( void );
181+ };
182+ }
183+ }
184+}
185+
186+#endif // __KOME_BASELINE_MSBACKADJ_MANAGER_H__
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPlugin.def
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPlugin.def Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,3 @@
1+EXPORTS
2+ msbackadjBaselineDetection
3+ exitPlugin
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPluginFunctions.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPluginFunctions.cpp Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,115 @@
1+/**
2+ * @file MsbackadjBaselineDetectionPluginFunctions.cpp
3+ * @brief implementation of plug-in functions
4+ *
5+ * @author ozaki
6+ * @date 2013.07.31
7+ *
8+ * Copyright(C) 2006-2014 Shimadzu Corporation All rights reserved.
9+ */
10+
11+
12+#include "stdafx.h"
13+#include "MsbackadjBaselineDetectionPluginFunctions.h"
14+#include "MsbackadjBaselineDetectionManager.h"
15+
16+
17+using namespace kome::baseline::msbackadj;
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+// Define parameter names
29+#define PARAM_NAME_WINDOW_SIZE ( "window_size" )
30+#define PARAM_NAME_STEP_SIZE ( "step_size" )
31+#define PARAM_NAME_REGRESSION_METHOD ( "regression_method" )
32+#define PARAM_NAME_ESTIMATION_METHOD ( "estimation_method" )
33+#define PARAM_NAME_SMOOTHING_METHOD ( "smoothing_method" )
34+#define PARAM_NAME_QUANTILE ( "quantile" )
35+
36+// Define parameter initial value
37+#define PARAM_INIT_WINDOW_SIZE ( 200.0 )
38+#define PARAM_INIT_STEP_SIZE ( 50.0 )
39+#define PARAM_INIT_REGRESSION_METHOD ( 0 )
40+#define PARAM_INIT_ESTIMATION_METHOD ( 0 )
41+#define PARAM_INIT_SMOOTHING_METHOD ( 0 )
42+#define PARAM_INIT_QUANTILE ( 0.1 )
43+
44+// detect baseline
45+kome::objects::Variant msbackadjBaselineDetection( kome::objects::Parameters* params )
46+{
47+ // return value
48+ kome::objects::Variant ret;
49+
50+ // get object
51+ kome::core::XYData* src = kome::plugin::PluginCallTool::getXYData( params );
52+ if( src == NULL ) {
53+ return ret;
54+ }
55+ kome::core::XYData* baseline = kome::plugin::PluginCallTool::getBaseline( params );
56+ if( baseline == NULL ) {
57+ return ret;
58+ }
59+
60+ kome::objects::SettingParameterValues* settings = kome::plugin::PluginCallTool::getSettingValues( params );
61+
62+ // manager
63+ MsbackadjBaselineDetectionManager &insManager = MsbackadjBaselineDetectionManager::getInstance( );
64+
65+ wxBeginBusyCursor( );
66+
67+ // set parameters
68+ double dWindowSize = PARAM_INIT_WINDOW_SIZE;
69+ double dStepSize = PARAM_INIT_STEP_SIZE;
70+ int nRegressionMethod = PARAM_INIT_REGRESSION_METHOD;
71+ int nEstimationMethod = PARAM_INIT_ESTIMATION_METHOD;
72+ int nSmoothingMethod = PARAM_INIT_SMOOTHING_METHOD;
73+ double dQuantile = PARAM_INIT_QUANTILE;
74+
75+ if ( (kome::objects::SettingParameterValues *)NULL != settings )
76+ {
77+ dWindowSize = settings->getDoubleValue( PARAM_NAME_WINDOW_SIZE, dWindowSize );
78+ dStepSize = settings->getDoubleValue( PARAM_NAME_STEP_SIZE, dStepSize );
79+ nRegressionMethod = settings->getIntValue( PARAM_NAME_REGRESSION_METHOD, nRegressionMethod );
80+ nEstimationMethod = settings->getIntValue( PARAM_NAME_ESTIMATION_METHOD, nEstimationMethod );
81+ nSmoothingMethod = settings->getIntValue( PARAM_NAME_SMOOTHING_METHOD, nSmoothingMethod );
82+ dQuantile = settings->getDoubleValue( PARAM_NAME_QUANTILE, dQuantile );
83+ }
84+
85+ insManager.setWindowSize( dWindowSize );
86+ insManager.setStepSize( dStepSize );
87+ insManager.setRegressionMethod( nRegressionMethod );
88+ insManager.setEstimationMethod( nEstimationMethod );
89+ insManager.setSmoothingMethod( nSmoothingMethod );
90+ insManager.setQuantile( dQuantile );
91+
92+ // get baseline
93+ insManager.getMsbackadj( *src, *baseline );
94+
95+ wxEndBusyCursor( );
96+
97+ return ret;
98+}
99+
100+// exit plugin
101+kome::objects::Variant exitPlugin( kome::objects::Parameters* params )
102+{
103+ // retrun value
104+ kome::objects::Variant ret;
105+
106+ // get manager
107+ MsbackadjBaselineDetectionManager &insManager = MsbackadjBaselineDetectionManager::getInstance( );
108+
109+ // release MATLAB application
110+ insManager.releaseMatlab( );
111+
112+ return ret;
113+}
114+
115+//
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPluginFunctions.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/MsbackadjBaselineDetectionPluginFunctions.h Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,41 @@
1+/**
2+ * @file MsbackadjBaselineDetectionPluginFunctions.h
3+ * @brief interfaces of plug-in functions
4+ *
5+ * @author ozaki
6+ * @date 2013.07.31
7+ *
8+ * Copyright(C) 2013-2013 Shimadzu Corporation All rights reserved.
9+ */
10+
11+
12+#ifndef __KOME_MSBACKADJ_BASELINE_DETECTION_PLUGIN_FUNCTIONS_H__
13+#define __KOME_MSBACKADJ_BASELINE_DETECTION_PLUGIN_FUNCTIONS_H__
14+
15+
16+#ifdef __unix
17+ extern "C" {
18+#endif // __unix
19+
20+/**
21+ * @fn kome::objects::Variant msbackadjBaselineDetection( kome::objects::Parameters* params )
22+ * @brief detects baseline
23+ * @param params parameters information
24+ * @return return value (This value has no meanings.)
25+ */
26+kome::objects::Variant msbackadjBaselineDetection( kome::objects::Parameters* params );
27+
28+/**
29+ * @fn kome::objects::Variant exitPlugin( kome::objects::Parameters* params )
30+ * @brief detect peaks
31+ * @param[in] params parameters
32+ * @return This value has no meanings.
33+ */
34+kome::objects::Variant exitPlugin( kome::objects::Parameters* params );
35+
36+#ifdef __unix
37+ }
38+#endif // __unix
39+
40+
41+#endif // __KOME_MSBACKADJ_BASELINE_DETECTION_PLUGIN_FUNCTIONS_H__
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/ReadMe.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/ReadMe.txt Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,19 @@
1+========================================================================
2+ Mass++ plug-in for common Shimadzu [C/C++]:
3+ MsbackadjBaselineDetectionPlugin Project
4+========================================================================
5+
6+plugin.xml
7+ plug-in definition file
8+
9+stdafx.h
10+ common header file
11+
12+MsbackadjBaselineDetectionPlugin.def
13+ the list of exported functions
14+
15+MsbackadjBaselineDetectionPluginFunctions.h
16+ header file of plug-in functions
17+
18+MsbackadjBaselineDetectionPluginFunctions.cpp
19+ implementation of plug-in functions
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/plugin.xml Sat Jun 06 01:31:15 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>MsbackadjBaselineDetectionPlugin</name>
8+ <version>1.00</version>
9+ <provider>Shimadzu Corporation</provider>
10+ <link>MsbackadjBaselineDetectionPlugin</link>
11+ <function>
12+ <call type="xydata_baseline">
13+ <call-name>detectBaseline</call-name>
14+ <call-function>msbackadjBaselineDetection</call-function>
15+ <packages>
16+ <package>Data Processing</package>
17+ </packages>
18+ <params>
19+ <param>
20+ <param-name>long name</param-name>
21+ <param-value>Msbackadj</param-value>
22+ </param>
23+ <param>
24+ <param-name>short name</param-name>
25+ <param-value>msbackadj</param-value>
26+ </param>
27+ <param>
28+ <param-name>page</param-name>
29+ <param-value>Baseline</param-value>
30+ </param>
31+ </params>
32+ <call-description>detect baseline</call-description>
33+ </call>
34+ <call type="exit" ifloaded="true">
35+ <call-name>exit plugin</call-name>
36+ <call-function>exitPlugin</call-function>
37+ <call-description>exit plugin</call-description>
38+ </call>
39+ </function>
40+ <components>
41+ <component>
42+ <component-name>MATLAB Function</component-name>
43+ <component-desc>Baseline detection using MATLAB function(msbackadj)</component-desc>
44+ <component-calls>
45+ <component-call>detectBaseline</component-call>
46+ <component-call>exit plugin</component-call>
47+ </component-calls>
48+ </component>
49+ </components>
50+ <packages>
51+ <package>
52+ <package-name>Quantitation</package-name>
53+ <package-components>
54+ <package-component>MATLAB Function</package-component>
55+ </package-components>
56+ </package>
57+ <package>
58+ <package-name>Data Processing</package-name>
59+ <package-components>
60+ <package-component>MATLAB Function</package-component>
61+ </package-components>
62+ </package>
63+ </packages>
64+ <parameters>
65+ <parameters-file>settings.xml</parameters-file>
66+ </parameters>
67+</plugin>
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/settings.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/settings.xml Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,138 @@
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="double" default="200.0" minInclusive="0" required="true" />
9+ <value id="1" type="double" default="200.0" minInclusive="0" required="true" />
10+ <value id="2" type="string" default="0" required="true">
11+ <enum>
12+ <enum-name>pchip</enum-name>
13+ <enum-value>0</enum-value>
14+ </enum>
15+ <enum>
16+ <enum-name>liner</enum-name>
17+ <enum-value>1</enum-value>
18+ </enum>
19+ <enum>
20+ <enum-name>spline</enum-name>
21+ <enum-value>2</enum-value>
22+ </enum>
23+ </value>
24+ <value id="3" type="string" default="0" required="true">
25+ <enum>
26+ <enum-name>quantile</enum-name>
27+ <enum-value>0</enum-value>
28+ </enum>
29+ <enum>
30+ <enum-name>em</enum-name>
31+ <enum-value>1</enum-value>
32+ </enum>
33+ </value>
34+ <value id="4" type="string" default="0" required="true">
35+ <enum>
36+ <enum-name>none</enum-name>
37+ <enum-value>0</enum-value>
38+ </enum>
39+ <enum>
40+ <enum-name>lowess</enum-name>
41+ <enum-value>1</enum-value>
42+ </enum>
43+ <enum>
44+ <enum-name>loess</enum-name>
45+ <enum-value>2</enum-value>
46+ </enum>
47+ <enum>
48+ <enum-name>rlowess</enum-name>
49+ <enum-value>3</enum-value>
50+ </enum>
51+ <enum>
52+ <enum-name>rloess</enum-name>
53+ <enum-value>4</enum-value>
54+ </enum>
55+ </value>
56+ <value id="5" type="double" default="0.1" minInclusive="0" required="true" />
57+ </values>
58+ <params>
59+ <param id="0" value="0">
60+ <param-name>window_size</param-name>
61+ <param-section>Msbackadj Baseline Detection</param-section>
62+ <param-key>WINDOW_SIZE</param-key>
63+ </param>
64+ <param id="1" value="1">
65+ <param-name>step_size</param-name>
66+ <param-section>Msbackadj Baseline Detection</param-section>
67+ <param-key>STEP_SIZE</param-key>
68+ </param>
69+ <param id="2" value="2">
70+ <param-name>regression_method</param-name>
71+ <param-section>Msbackadj Baseline Detection</param-section>
72+ <param-key>REGRESSION_METHOD</param-key>
73+ </param>
74+ <param id="3" value="3">
75+ <param-name>estimation_method</param-name>
76+ <param-section>Msbackadj Baseline Detection</param-section>
77+ <param-key>ESTIMATION_METHOD</param-key>
78+ </param>
79+ <param id="4" value="4">
80+ <param-name>smoothing_method</param-name>
81+ <param-section>Msbackadj Baseline Detection</param-section>
82+ <param-key>SMOOTHING_METHOD</param-key>
83+ </param>
84+ <param id="5" value="5">
85+ <param-name>quantile</param-name>
86+ <param-section>Msbackadj Baseline Detection</param-section>
87+ <param-key>QUANTILE</param-key>
88+ </param>
89+ </params>
90+ <pages>
91+ <page common="false">
92+ <page-name>Baseline</page-name>
93+ <page-title>Msbackadj Baseline</page-title>
94+ <forms>
95+ <form id="6" param="0">
96+ <form-title>Window Size (separation unit)</form-title>
97+ <form-desc>Specify the width for the shifting window.
98+Refer "msbackadj" function of Matlab Bioinfomatics Toolbox for more detail. </form-desc>
99+ </form>
100+ <form id="7" param="1">
101+ <form-title>Step Size (separation unit)</form-title>
102+ <form-desc>Specify the steps for the shifting window.
103+Refer "msbackadj" function of Matlab Bioinfomatics Toolbox for more detail.</form-desc>
104+ </form>
105+ <form id="8" param="2">
106+ <form-title>Regression Method</form-title>
107+ <form-desc>Specifiy the method for regression line from following:
108+・pchip
109+・liner
110+・spline
111+Refer "msbackadj" function of Matlab Bioinfomatics Toolbox for more detail.</form-desc>
112+ </form>
113+ <form id="9" param="3">
114+ <form-title>Estimation Method</form-title>
115+ <form-desc>Specify the method for finding the likely baseline value in every window.
116+
117+Refer "msbackadj" function of Matlab Bioinfomatics Toolbox for more detail.</form-desc>
118+ </form>
119+ <form id="10" param="4">
120+ <form-title>Smoothing Method</form-title>
121+ <form-desc>Specify the smoothing method from following:
122+・none
123+・lowess
124+・loess
125+・rlowess
126+・rloess
127+
128+Refer "msbackadj" function of Matlab Bioinfomatics Toolbox for more detail.</form-desc>
129+ </form>
130+ <form id="11" param="5">
131+ <form-title>Quantile Value</form-title>
132+ <form-desc>Specify the quantile value.
133+Refer "msbackadj" function of Matlab Bioinfomatics Toolbox for more detail.</form-desc>
134+ </form>
135+ </forms>
136+ </page>
137+ </pages>
138+</settings>
diff -r 50db0c57ab38 -r 9104db045a3a src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/stdafx.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/MsbackadjBaselineDetectionPlugin/stdafx.h Sat Jun 06 01:31:15 2015 +0900
@@ -0,0 +1,136 @@
1+/**
2+ * @file stdafx.h
3+ * @brief common header file
4+ *
5+ * @author ozaki
6+ * @date 2013.07.31
7+ *
8+ * Copyright(C) 2006-2014 Shimadzu Corporation All rights reserved.
9+ */
10+
11+
12+
13+#ifndef __KOME_MSBACKADJ_BASELINE_DETECTION_PLUGIN_STD_AFX_H__
14+#define __KOME_MSBACKADJ_BASELINE_DETECTION_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, "EventManager" )
63+ #pragma comment( lib, "WindowManager" )
64+ #pragma comment( lib, "XMLTools" )
65+ #pragma comment( lib, "NetworkTools" )
66+ #pragma comment( lib, "GLTools" )
67+ #pragma comment( lib, "JavaTools" )
68+ #pragma comment( lib, "IdentificationTools" )
69+
70+ #ifdef _DEBUG
71+ #pragma comment( lib, "wxbase28d" )
72+ #pragma comment( lib, "wxbase28d_net" )
73+ #pragma comment( lib, "wxbase28d_xml" )
74+ #pragma comment( lib, "wxexpatd" )
75+ #pragma comment( lib, "wxjpegd" )
76+ #pragma comment( lib, "wxmsw28d_adv" )
77+ #pragma comment( lib, "wxmsw28d_aui" )
78+ #pragma comment( lib, "wxmsw28d_core" )
79+ #pragma comment( lib, "wxmsw28d_gl" )
80+ #pragma comment( lib, "wxmsw28d_html" )
81+ #pragma comment( lib, "wxmsw28d_media" )
82+ #pragma comment( lib, "wxmsw28d_qa" )
83+ #pragma comment( lib, "wxmsw28d_richtext" )
84+ #pragma comment( lib, "wxmsw28d_xrc" )
85+ #pragma comment( lib, "wxpngd" )
86+ #pragma comment( lib, "wxregexd" )
87+ #pragma comment( lib, "wxtiffd" )
88+ #pragma comment( lib, "wxzlibd" )
89+
90+ #pragma comment( lib, "xerces-c_3D" )
91+ #else
92+ #pragma comment( lib, "wxbase28" )
93+ #pragma comment( lib, "wxbase28_net" )
94+ #pragma comment( lib, "wxbase28_xml" )
95+ #pragma comment( lib, "wxexpat" )
96+ #pragma comment( lib, "wxjpeg" )
97+ #pragma comment( lib, "wxmsw28_adv" )
98+ #pragma comment( lib, "wxmsw28_aui" )
99+ #pragma comment( lib, "wxmsw28_core" )
100+ #pragma comment( lib, "wxmsw28_gl" )
101+ #pragma comment( lib, "wxmsw28_html" )
102+ #pragma comment( lib, "wxmsw28_media" )
103+ #pragma comment( lib, "wxmsw28_qa" )
104+ #pragma comment( lib, "wxmsw28_richtext" )
105+ #pragma comment( lib, "wxmsw28_xrc" )
106+ #pragma comment( lib, "wxpng" )
107+ #pragma comment( lib, "wxregex" )
108+ #pragma comment( lib, "wxtiff" )
109+ #pragma comment( lib, "wxzlib" )
110+
111+ #pragma comment( lib, "xerces-c_3" )
112+ #endif // _DEBUG
113+#endif // _MSC_VER
114+
115+
116+//
117+// includes
118+//
119+
120+#include "kome/CoreFunctions.h"
121+#include "kome/CoreToolkits.h"
122+#include "kome/DataObjects.h"
123+#include "kome/ImageManager.h"
124+#include "kome/PluginTools.h"
125+#include "kome/DbTools.h"
126+#include "kome/DataOperation.h"
127+#include "kome/EventManager.h"
128+#include "kome/WindowManager.h"
129+#include "kome/XMLTools.h"
130+#include "kome/NetworkTools.h"
131+#include "kome/GLTools.h"
132+#include "kome/JavaTools.h"
133+#include "kome/IdentificationTools.h"
134+
135+
136+#endif // __KOME_MSBACKADJ_BASELINE_DETECTION_PLUGIN_STD_AFX_H__
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