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Commits (17)
<?xml version="1.0" encoding="Windows-1252"?>
<VisualStudioProject
ProjectType="Visual C++"
Version="9.00"
Name="MSSingleScan"
ProjectGUID="{24C852FB-C978-4957-BC4D-92F27FD031AE}"
RootNamespace="MSSingleScan"
Keyword="Win32Proj"
TargetFrameworkVersion="196613"
>
<Platforms>
<Platform
Name="Win32"
/>
</Platforms>
<ToolFiles>
</ToolFiles>
<Configurations>
<Configuration
Name="Debug|Win32"
OutputDirectory="$(SolutionDir)$(ConfigurationName)"
IntermediateDirectory="$(ConfigurationName)"
ConfigurationType="1"
CharacterSet="1"
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<Tool
Name="VCPreBuildEventTool"
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<Tool
Name="VCCustomBuildTool"
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<Tool
Name="VCXMLDataGeneratorTool"
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<Tool
Name="VCWebServiceProxyGeneratorTool"
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<Tool
Name="VCMIDLTool"
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<Tool
Name="VCCLCompilerTool"
Optimization="0"
PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
MinimalRebuild="true"
BasicRuntimeChecks="3"
RuntimeLibrary="3"
UsePrecompiledHeader="0"
WarningLevel="3"
DebugInformationFormat="4"
/>
<Tool
Name="VCManagedResourceCompilerTool"
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<Tool
Name="VCResourceCompilerTool"
/>
<Tool
Name="VCPreLinkEventTool"
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<Tool
Name="VCLinkerTool"
LinkIncremental="2"
GenerateDebugInformation="true"
SubSystem="1"
TargetMachine="1"
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<Tool
Name="VCALinkTool"
/>
<Tool
Name="VCManifestTool"
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<Tool
Name="VCXDCMakeTool"
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<Tool
Name="VCBscMakeTool"
/>
<Tool
Name="VCFxCopTool"
/>
<Tool
Name="VCAppVerifierTool"
/>
<Tool
Name="VCPostBuildEventTool"
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</Configuration>
<Configuration
Name="Release|Win32"
OutputDirectory="$(SolutionDir)$(ConfigurationName)"
IntermediateDirectory="$(ConfigurationName)"
ConfigurationType="1"
CharacterSet="1"
WholeProgramOptimization="1"
>
<Tool
Name="VCPreBuildEventTool"
/>
<Tool
Name="VCCustomBuildTool"
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<Tool
Name="VCXMLDataGeneratorTool"
/>
<Tool
Name="VCWebServiceProxyGeneratorTool"
/>
<Tool
Name="VCMIDLTool"
/>
<Tool
Name="VCCLCompilerTool"
Optimization="2"
EnableIntrinsicFunctions="true"
AdditionalIncludeDirectories="../include"
PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
RuntimeLibrary="2"
EnableFunctionLevelLinking="true"
UsePrecompiledHeader="0"
WarningLevel="3"
DebugInformationFormat="3"
/>
<Tool
Name="VCManagedResourceCompilerTool"
/>
<Tool
Name="VCResourceCompilerTool"
/>
<Tool
Name="VCPreLinkEventTool"
/>
<Tool
Name="VCLinkerTool"
AdditionalDependencies="MSToolkitLite.lib"
LinkIncremental="1"
AdditionalLibraryDirectories="&quot;C:\Users\mhoopman\Documents\Software Development\MSToolkit\Release&quot;"
GenerateDebugInformation="true"
SubSystem="1"
OptimizeReferences="2"
EnableCOMDATFolding="2"
TargetMachine="1"
/>
<Tool
Name="VCALinkTool"
/>
<Tool
Name="VCManifestTool"
/>
<Tool
Name="VCXDCMakeTool"
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<Tool
Name="VCBscMakeTool"
/>
<Tool
Name="VCFxCopTool"
/>
<Tool
Name="VCAppVerifierTool"
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<Tool
Name="VCPostBuildEventTool"
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</Configuration>
</Configurations>
<References>
</References>
<Files>
<Filter
Name="Source Files"
Filter="cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx"
UniqueIdentifier="{4FC737F1-C7A5-4376-A066-2A32D752A2FF}"
>
<File
RelativePath=".\MSSingleScan.cpp"
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</File>
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<Filter
Name="Header Files"
Filter="h;hpp;hxx;hm;inl;inc;xsd"
UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
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</Filter>
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Name="Resource Files"
Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav"
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......@@ -3,7 +3,18 @@ libmstoolkit (82-2) unstable; urgency=medium
* Fix the missing license/copyright stanzas from a number of files. The
stanzas have been added by Michael Hoopmann as a response to a private
mail request by me. The files were modified on GitHub. I added these license
stanzas to the files in the form of a patch.
stanzas to the files in the form of a patch. The version of the library
was not updated and probably won't for some time. This is a compromise
that should be acceptable.
* Update debian/copyright for the MSSingleScan.cpp file and all the others
that got new license notices in the patch above.
* debian/compat 11.
* mv source.lintian-overrides source/lintian-overrides.
* debian/control: Standards-Version: 4.1.3
-- Filippo Rusconi <lopippo@debian.org> Mon, 26 Feb 2018 20:41:29 +0100
......@@ -16,14 +27,14 @@ libmstoolkit (82-1) unstable; urgency=medium
libmstoolkit (77.0.0-1) unstable; urgency=medium
* New upstream version;
* Fix debian/copyright to reflect source modifications in upstream and
to fix lintian-detected glitches;
debian/control & debian copyright: change the projet home website url.
* Better cleaning up of the source tarball (libs not required, .svn and
other cruft);
* Still closing the ITP bug (Closes: #763747).
-- Filippo Rusconi <lopippo@debian.org> Tue, 13 Jan 2015 10:25:07 +0100
......@@ -42,19 +53,20 @@ libmstoolkit (73~svn-2) unstable; urgency=medium
* Fixes to the debian/copyright file so as to document some shipped
include files;
* Add source lintian overrides file.
* Initial packaging (Closes: #763747);
-- Filippo Rusconi <lopippo@debian.org> Tue, 04 Nov 2014 11:27:08 +0100
libmstoolkit (73~svn-1) unstable; urgency=low
* Initial packaging (Closes: #763747);
* The main modification is related to the Makefile which has been
changed so as to produce first-class citizen UNIX/LINUX/POSIX shared
object libraries.
-- Filippo Rusconi <lopippo@debian.org> Thu, 02 Oct 2014 12:40:10 +0200
......@@ -2,13 +2,13 @@ Source: libmstoolkit
Priority: optional
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Build-Depends: debhelper (>= 9.2),
Build-Depends: debhelper (>= 11),
dpkg-dev (>= 1.16.1~),
zlib1g-dev (>=1:1.2.8),
libsqlite3-dev (>= 3.8.6),
libexpat1-dev (>= 2.1.0),
docbook-to-man
Standards-Version: 4.1.1
Standards-Version: 4.1.3
Section: libs
Homepage: https://github.com/mhoopmann/mstoolkit
Vcs-Git: https://anonscm.debian.org/git/debichem/packages/libmstoolkit.git
......
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: libmstoolkit
Source: https://github.com/mhoopmann/mstoolkit
......@@ -283,6 +283,10 @@ License: Zlib
(deflate format) and rfc1952.txt (gzip format).
Files: MSSingleScan/MSSingleScan.cpp
Copyright: 2011 Michael R. Hoopmann, Institute for Systems Biology
License: Apache
Files: src/MSToolkit/*
Copyright: 2005-2016 Michael R. Hoopmann
License: Apache
......@@ -317,6 +321,14 @@ Files: src/mzParser/Czran.cpp
Copyright: 2005 Mark Adler
License: Zlib
Files: src/mzParser/BasicChromatogram.cpp src/mzParser/PWIZface.cpp src/mzParser/RAMPface.cpp src/mzParser/mz5handler.cpp src/mzParser/mzMLReader.cpp src/mzParser/mzpMz5Config.cpp src/mzParser/mzpMz5Structs.cpp
Copyright: 2011 Mike Hoopmann, Institute for Systems Biology
License: BSD-3-Clause
Files: src/mzParser/mzp_base64.cpp
Copyright: The Global Proteome Machine Organization
License: Artistic
Files: include/MSObject.h include/MSReader.h include/MSToolkitTypes.h include/RAWReader.h include/Spectrum.h include/mzMLWriter.h include/mzParser.h include/pepXMLWriter.h
Copyright: 2005-2016, Michael R. Hoopmann
License: Apache
......
Patch that adds all the missing license stanzas as published on GitHub following
private mail-based requests exchanged by me with the author of the software,
Michael Hoopmann.
Patch that add the various missing copyright notices in the source files.
This patch will go away as soon as a new version of the library is released.
See debian/changelog for an explanation
diff --git a/MSSingleScan/MSSingleScan.cpp b/MSSingleScan/MSSingleScan.cpp
index 9f2b6f3..6b73152 100644
--- a/MSSingleScan/MSSingleScan.cpp
+++ b/MSSingleScan/MSSingleScan.cpp
@@ -1,70 +1,84 @@
-#include <iostream>
-#include <iomanip>
-#include <cmath>
-#include "MSToolkitTypes.h"
-#include "MSReader.h"
-#include "MSObject.h"
-#include "Spectrum.h"
-
-using namespace std;
-using namespace MSToolkit;
-
-int main(int argc, char *argv[]){
-
- //Here are all the variable we are going to need
- MSReader r;
- Spectrum s;
- int j;
-
- if(argc==1){
- printf("DESCRIPTION: Reads an MS/MS spectrum from any MSToolkit supported file type and outputs to screen in MS2 format.\n\n");
- printf("USAGE: MSSingleScan [scan number] [file]\n");
- exit(0);
- }
-
-
- r.setFilter(MS1);
- r.addFilter(MS2);
- r.addFilter(MSX);
- r.addFilter(SRM);
-
- char nativeID[256];
- r.readFile(argv[2],s,atoi(argv[1]));
- if(s.getScanNumber()==0) exit(-1);
-
-
- char szNativeID[128];
- if (s.getNativeID(szNativeID, 128))
- printf("success: scan %d nativeID: %s\n", s.getScanNumber(), szNativeID);
- else
- printf("failure: scan %d\n", s.getScanNumber());
-
- printf("size: %d\n", s.sizeMZ());
-
- s.getNativeID(nativeID, 256);
- printf("%s\n",nativeID);
- printf("S\t%d\t%d",s.getScanNumber(),s.getScanNumber());
- for(j=0;j<s.sizeMZ();j++){
- printf("\t%.*lf",4,s.getMZ(j));
- }
- printf("\n");
- if(s.getRTime()>0) printf("I\tRTime\t%.*f\n",4,s.getRTime());
- //printf("I\tConvA\t%.6lf\n",s.getConversionA());
- //printf("I\tConvB\t%.6lf\n",s.getConversionB());
- //printf("I\tConvC\t%.6lf\n",s.getConversionC());
- //printf("I\tConvD\t%.6lf\n",s.getConversionD());
- //printf("I\tConvE\t%.6lf\n",s.getConversionE());
- //printf("I\tConvI\t%.6lf\n",s.getConversionI());
- for(j=0;j<s.sizeZ();j++){
- printf("Z\t%d\t%.*f\n",s.atZ(j).z,6,s.atZ(j).mh);
- }
-
- for(j=0;j<s.size();j++){
- printf("%.4f %.4f\n",s.at(j).mz,s.at(j).intensity);
- }
-
- return 0;
-
-}
-
-
+/*
+Copyright 2011, Michael R. Hoopmann, Institute for Systems Biology
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+ http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
+#include <iostream>
+#include <iomanip>
+#include <cmath>
+#include "MSToolkitTypes.h"
+#include "MSReader.h"
+#include "MSObject.h"
+#include "Spectrum.h"
+
+using namespace std;
+using namespace MSToolkit;
+
+int main(int argc, char *argv[]){
+
+ //Here are all the variable we are going to need
+ MSReader r;
+ Spectrum s;
+ int j;
+
+ if(argc==1){
+ printf("DESCRIPTION: Reads an MS/MS spectrum from any MSToolkit supported file type and outputs to screen in MS2 format.\n\n");
+ printf("USAGE: MSSingleScan [scan number] [file]\n");
+ exit(0);
+ }
+
+
+ r.setFilter(MS1);
+ r.addFilter(MS2);
+ r.addFilter(MSX);
+ r.addFilter(SRM);
+
+ char nativeID[256];
+ r.readFile(argv[2],s,atoi(argv[1]));
+ if(s.getScanNumber()==0) exit(-1);
+
+
+ char szNativeID[128];
+ if (s.getNativeID(szNativeID, 128))
+ printf("success: scan %d nativeID: %s\n", s.getScanNumber(), szNativeID);
+ else
+ printf("failure: scan %d\n", s.getScanNumber());
+
+ printf("size: %d\n", s.sizeMZ());
+
+ s.getNativeID(nativeID, 256);
+ printf("%s\n",nativeID);
+ printf("S\t%d\t%d",s.getScanNumber(),s.getScanNumber());
+ for(j=0;j<s.sizeMZ();j++){
+ printf("\t%.*lf",4,s.getMZ(j));
+ }
+ printf("\n");
+ if(s.getRTime()>0) printf("I\tRTime\t%.*f\n",4,s.getRTime());
+ //printf("I\tConvA\t%.6lf\n",s.getConversionA());
+ //printf("I\tConvB\t%.6lf\n",s.getConversionB());
+ //printf("I\tConvC\t%.6lf\n",s.getConversionC());
+ //printf("I\tConvD\t%.6lf\n",s.getConversionD());
+ //printf("I\tConvE\t%.6lf\n",s.getConversionE());
+ //printf("I\tConvI\t%.6lf\n",s.getConversionI());
+ for(j=0;j<s.sizeZ();j++){
+ printf("Z\t%d\t%.*f\n",s.atZ(j).z,6,s.atZ(j).mh);
+ }
+
+ for(j=0;j<s.size();j++){
+ printf("%.4f %.4f\n",s.at(j).mz,s.at(j).intensity);
+ }
+
+ return 0;
+
+}
+
+
diff --git a/src/mzParser/BasicChromatogram.cpp b/src/mzParser/BasicChromatogram.cpp
index ac49ad4..284311e 100644
--- a/src/mzParser/BasicChromatogram.cpp
......
debian-watch-file-is-missing