Commit b89724d9 authored by Filippo Rusconi's avatar Filippo Rusconi

New upstream version 82

parent 046a1875
<?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="$(ConfigurationName)"
ConfigurationType="1"
CharacterSet="1"
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<Tool
Name="VCPreBuildEventTool"
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<Tool
Name="VCCustomBuildTool"
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<Tool
Name="VCXMLDataGeneratorTool"
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<Tool
Name="VCWebServiceProxyGeneratorTool"
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<Tool
Name="VCMIDLTool"
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<Tool
Name="VCCLCompilerTool"
Optimization="0"
PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
MinimalRebuild="true"
BasicRuntimeChecks="3"
RuntimeLibrary="3"
UsePrecompiledHeader="0"
WarningLevel="3"
DebugInformationFormat="4"
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<Tool
Name="VCManagedResourceCompilerTool"
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<Tool
Name="VCResourceCompilerTool"
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<Tool
Name="VCPreLinkEventTool"
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<Tool
Name="VCLinkerTool"
LinkIncremental="2"
GenerateDebugInformation="true"
SubSystem="1"
TargetMachine="1"
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<Tool
Name="VCALinkTool"
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<Tool
Name="VCManifestTool"
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<Tool
Name="VCXDCMakeTool"
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<Tool
Name="VCBscMakeTool"
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<Tool
Name="VCFxCopTool"
/>
<Tool
Name="VCAppVerifierTool"
/>
<Tool
Name="VCPostBuildEventTool"
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</Configuration>
<Configuration
Name="Release|Win32"
OutputDirectory="$(SolutionDir)$(ConfigurationName)"
IntermediateDirectory="$(ConfigurationName)"
ConfigurationType="1"
CharacterSet="1"
WholeProgramOptimization="1"
>
<Tool
Name="VCPreBuildEventTool"
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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="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"
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<Tool
Name="VCXDCMakeTool"
/>
<Tool
Name="VCBscMakeTool"
/>
<Tool
Name="VCFxCopTool"
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<Tool
Name="VCAppVerifierTool"
/>
<Tool
Name="VCPostBuildEventTool"
/>
</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>
</Filter>
<Filter
Name="Header Files"
Filter="h;hpp;hxx;hm;inl;inc;xsd"
UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
>
</Filter>
<Filter
Name="Resource Files"
Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav"
UniqueIdentifier="{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}"
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libmstoolkit (82-1) unstable; urgency=medium
* New upstream version. Fixes problems I reported on the github site.
-- Filippo Rusconi <lopippo@debian.org> Thu, 14 Sep 2017 17:01:11 +0200
libmstoolkit (77.0.0-1) unstable; urgency=medium
* New upstream version;
......
......@@ -4,12 +4,12 @@ Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Build-Depends: debhelper (>= 9.2),
dpkg-dev (>= 1.16.1~),
libzip-dev (>= 0.11.2),
zlib1g-dev (>=1:1.2.8),
libhdf5-dev (>=1.8.13),
libsqlite3-dev (>= 3.8.6),
libexpat1-dev (>= 2.1.0),
docbook-to-man
Standards-Version: 4.0.1
Standards-Version: 4.1.1
Section: libs
Homepage: https://github.com/mhoopmann/mstoolkit
Vcs-Git: https://anonscm.debian.org/git/debichem/packages/libmstoolkit.git
......@@ -19,7 +19,7 @@ Package: libmstoolkit-dev
Section: libdevel
Architecture: any
Depends: ${misc:Depends},
libmstoolkit78 (= ${binary:Version}),
libmstoolkit82 (= ${binary:Version}),
libzip-dev (>= 0.11.2),
libhdf5-dev (>=1.8.13),
libsqlite3-dev (>= 3.8.6),
......@@ -46,7 +46,7 @@ Description: libraries for manipulating mass spectrometry data - dev files
- Sequential or random-access file reading.
Package: libmstoolkit78
Package: libmstoolkit82
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
......@@ -76,34 +76,3 @@ Description: libraries for manipulating mass spectrometry data - runtime
- libmstoolkit;
- libmstoolkitlite;
Package: libmstoolkit78-dbg
Section: debug
Priority: extra
Architecture: any
Depends: libmstoolkit78 (= ${binary:Version}),
${misc:Depends}
Conflicts: libmstoolkit77
Description: libraries for manipulating mass spectrometry data - debug symbols
The MSToolkit is a light-weight C++ library for reading, writing, and
manipulating mass spectrometry data. The MSToolkit is easily linked
to virtually any C++ algorithm for simple, fast file reading and
analysis.
.
Supported File Formats:
-----------------------
- read-only mzML including internal compression (zlib and numpress)
and external compression (.mzML.gz) read-only;
- read-only mzXML including internal compression (zlib) and external
compression (.mzXML.gz)
- read/write mgf, ms1, ms2, bms1, bms2, cms1, cms2
.
Simple Interface:
------------------
- Open any file format from a single function call;
- Store any spectrum in a simple, comprehensive data structure;
- Sequential or random-access file reading.
.
This package provides the debugging symbols for libmstoolkit and
libmstoolkitlite.
usr/lib/libmstoolkit.so.77.0.0 usr/lib/libmstoolkit.so
usr/lib/libmstoolkitlite.so.77.0.0 usr/lib/libmstoolkitlite.so
usr/lib/libmstoolkit.so.82.0.0 usr/lib/libmstoolkit.so
usr/lib/libmstoolkitlite.so.82.0.0 usr/lib/libmstoolkitlite.so
usr/share/man/man3/libmstoolkit.3.gz usr/share/man/man3/libmstoolkit-dev.3.gz
......@@ -29,7 +29,7 @@ manpage.1: manpage.sgml
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
<!ENTITY LIBVERSION "77">
<!ENTITY LIBVERSION "82">
]>
<refentry>
......
libmstoolkit.so.77.0.0 usr/lib
libmstoolkitlite.so.77.0.0 usr/lib
usr/lib/libmstoolkit.so.77.0.0 usr/lib/libmstoolkit.so.77
usr/lib/libmstoolkitlite.so.77.0.0 usr/lib/libmstoolkitlite.so.77
spelling-error-in-binary usr/lib/libmstoolkit.so.77.0.0 dont don't
spelling-error-in-binary usr/lib/libmstoolkitlite.so.77.0.0 dont don't
\ No newline at end of file
libmstoolkit.so.82.0.0 usr/lib
libmstoolkitlite.so.82.0.0 usr/lib
usr/lib/libmstoolkit.so.82.0.0 usr/lib/libmstoolkit.so.82
usr/lib/libmstoolkitlite.so.82.0.0 usr/lib/libmstoolkitlite.so.82
spelling-error-in-binary usr/lib/libmstoolkit.so.82.0.0 dont don't
spelling-error-in-binary usr/lib/libmstoolkitlite.so.82.0.0 dont don't
Ensure the building of both static and shared libs.
diff --git a/Makefile b/Makefile
index 0c4d94e..11ae972 100644
index 8f8f087..12724ff 100644
--- a/Makefile
+++ b/Makefile
@@ -1,80 +1,78 @@
-#Set your paths here.
-ZLIB_PATH = ./src/zLib-1.2.5
@@ -1,79 +1,68 @@
#Set your paths here.
-ZLIB_PATH = ./src/zlib-1.2.8
MZPARSER_PATH = ./src/mzParser
-EXPAT_PATH = ./src/expat-2.0.1
-EXPAT_PATH = ./src/expat-2.2.0
-SQLITE_PATH = ./src/sqlite-3.7.7.1
MST_PATH = ./src/MSToolkit
-HEADER_PATH = ./include
+HEADER_PATH = -I./include -I/usr/include/hdf5/serial/
HEADER_PATH = ./include
MZPARSER = mzp.MSNumpress.o mzp.mzp_base64.o mzp.BasicSpectrum.o mzp.mzParser.o mzp.RAMPface.o mzp.saxhandler.o mzp.saxmzmlhandler.o \
mzp.saxmzxmlhandler.o mzp.Czran.o mzp.mz5handler.o mzp.mzpMz5Config.o mzp.mzpMz5Structs.o mzp.BasicChromatogram.o mzp.PWIZface.o
......@@ -22,116 +20,106 @@ index 0c4d94e..11ae972 100644
-EXPAT = xmlparse.o xmlrole.o xmltok.o
-ZLIB = adler32.o compress.o crc32.o deflate.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o
+
MSTOOLKIT = Spectrum.o MSObject.o
MSTOOLKIT = Spectrum.o MSObject.o mzMLWriter.o pepXMLWriter.o
+
READER = MSReader.o
+
READERLITE = MSReaderLite.o
-SQLITE = sqlite3.o
CC = g++
GCC = gcc
-NOSQLITE = -D_NOSQLITE
+MZ5 = -DMST_MZ5 -DMZP_MZ5
NOSQLITE = -D_NOSQLITE
-CFLAGS = -O3 -static -I. -I$(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
-LIBS = -lm -lpthread -ldl
+SOVER = 77
+RELVER = $(SOVER).0.0
-
-all: $(ZLIB) $(MZPARSER) $(MZPARSERLITE) $(MSTOOLKIT) $(READER) $(READERLITE) $(EXPAT) $(SQLITE)
- ar rcs libmstoolkitlite.a $(ZLIB) $(EXPAT) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE)
- ar rcs libmstoolkit.a $(ZLIB) $(EXPAT) $(MZPARSER) $(MSTOOLKIT) $(READER) $(SQLITE)
-# $(CC) $(CFLAGS) MSTDemo.cpp -L. -lmstoolkitlite -o MSTDemo
- $(CC) $(CFLAGS) -I./include MSSingleScan/MSSingleScan.cpp -L. -lmstoolkitlite -o msSingleScan
-# $(CC) $(CFLAGS) MSConvertFile.cpp -L. -lmstoolkitlite -o MSConvertFile
+LIBS = -lm -lpthread -ldl -lhdf5_serial -lzip -lsqlite3 -lexpat
+LIB_PATH := -L./
-
-lite: $(ZLIB) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE) $(EXPAT)
- ar rcs libmstoolkitlite.a $(ZLIB) $(EXPAT) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE)
- $(CC) $(CFLAGS) -I./include MSSingleScan/MSSingleScan.cpp -L. -lmstoolkitlite -o msSingleScan
+CLEAN_LIBS = libmstoolkitlite.a libmstoolkitlite.so libmstoolkitlite.so.$(SOVER)* libmstoolkit.a libmstoolkit.so libmstoolkit.so.$(SOVER)*
-
-clean:
- rm -f *.o libmstoolkitlite.a libmstoolkit.a msSingleScan
+arlib: CFLAGS += -O3 -static -I. $(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
+arlib:
+ make clean_objects
+ CFLAGS="$(CFLAGS)" make -e all
+SOVER = 82
+RELVER = $(SOVER).0.0
-# zLib objects
+ ar rcs libmstoolkitlite.a $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE)
+ ar rcs libmstoolkit.a $(MZPARSER) $(MSTOOLKIT) $(READER)
+LIBS = -lm -lpthread -ldl -lz -lsqlite3 -lexpat
+LIB_PATH := -L./
-adler32.o : $(ZLIB_PATH)/adler32.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/adler32.c -c
+solib: CFLAGS += -shared -fPIC -g $(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
+solib:
+ make clean
+ CFLAGS="$(CFLAGS)" make -e all
+CLEAN_LIBS = libmstoolkitlite.a libmstoolkitlite.so libmstoolkitlite.so.$(SOVER)* libmstoolkit.a libmstoolkit.so libmstoolkit.so.$(SOVER)*
-compress.o : $(ZLIB_PATH)/compress.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/compress.c -c
+ $(CC) $(CFLAGS) -o libmstoolkitlite.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmstoolkitlite.so.$(SOVER) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE) $(LIB_PATH) $(LIBS)
+ ln -sf libmstoolkitlite.so.$(RELVER) libmstoolkitlite.so.$(SOVER)
+ ln -sf libmstoolkitlite.so.$(SOVER) libmstoolkitlite.so
+# Original version
+# CFLAGS = -O3 -static -I. -I$(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
-crc32.o : $(ZLIB_PATH)/crc32.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/crc32.c -c
+ $(CC) $(CFLAGS) -o libmstoolkit.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmstoolkit.so.$(SOVER) $(MZPARSER) $(MSTOOLKIT) $(READER) $(LIB_PATH) $(LIBS)
+ ln -sf libmstoolkit.so.$(RELVER) libmstoolkit.so.$(SOVER)
+ ln -sf libmstoolkit.so.$(SOVER) libmstoolkit.so
+.PHONY: objects
+objects: CFLAGS += -O3 -static -I. -I$(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
+objects: $(MZPARSER) $(MZPARSERLITE) $(MSTOOLKIT) $(READER) $(READERLITE)
-deflate.o : $(ZLIB_PATH)/deflate.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/deflate.c -c
+ $(CC) $(CFLAGS) -I./include MSSingleScan/MSSingleScan.cpp $(LIB_PATH) -lmstoolkitlite -o msSingleScan
+arlib: CFLAGS += -O3 -static -I. -I$(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
+arlib: clean_objects objects
-inffast.o : $(ZLIB_PATH)/inffast.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/inffast.c -c
+all: $(MZPARSER) $(MZPARSERLITE) $(MSTOOLKIT) $(READER) $(READERLITE)
+ ar rcs libmstoolkitlite.a $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE)
+ ar rcs libmstoolkit.a $(MZPARSER) $(MSTOOLKIT) $(READER)
-inflate.o : $(ZLIB_PATH)/inflate.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/inflate.c -c
+# Not found in the source tree
+# $(CC) $(CFLAGS) MSTDemo.cpp $(LIB_PATH) -lmstoolkitlite -o MSTDemo
+solib: CFLAGS += -shared -fPIC -g -I. -I$(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
+solib: clean_objects objects
-infback.o : $(ZLIB_PATH)/infback.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/infback.c -c
+# $(CC) $(CFLAGS) -I./include MSSingleScan/MSSingleScan.cpp $(LIB_PATH) -lmstoolkitlite -o msSingleScan
+ $(CC) $(CFLAGS) -o libmstoolkitlite.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmstoolkitlite.so.$(SOVER) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE) $(LIB_PATH) $(LIBS)
+ ln -sf libmstoolkitlite.so.$(RELVER) libmstoolkitlite.so.$(SOVER)
+ ln -sf libmstoolkitlite.so.$(SOVER) libmstoolkitlite.so
-inftrees.o : $(ZLIB_PATH)/inftrees.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/inftrees.c -c
+# Not found in the source tree
+# $(CC) $(CFLAGS) MSConvertFile.cpp $(LIB_PATH) -lmstoolkitlite -o MSConvertFile
+ $(CC) $(CFLAGS) -o libmstoolkit.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmstoolkit.so.$(SOVER) $(MZPARSER) $(MSTOOLKIT) $(READER) $(LIB_PATH) $(LIBS)
+ ln -sf libmstoolkit.so.$(RELVER) libmstoolkit.so.$(SOVER)
+ ln -sf libmstoolkit.so.$(SOVER) libmstoolkit.so
-trees.o : $(ZLIB_PATH)/trees.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/trees.c -c
+all: CFLAGS += -shared -fPIC -g -I. -I$(HEADER_PATH) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H
+all: solib
+ $(CC) $(CFLAGS) -I. -I./include MSSingleScan/MSSingleScan.cpp -L. -lmstoolkitlite -o msSingleScan
-uncompr.o : $(ZLIB_PATH)/uncompr.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/uncompr.c -c
+#lite: $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE)
+#
+# ar rcs libmstoolkitlite.a $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE)
+# $(CC) $(LIB_PATH) $(CFLAGS) -o libmstoolkitlite.so.$(RELVER) -Wl,-z,relro -Wl,-soname,libmstoolkitlite.so.$(SOVER) $(MZPARSERLITE) $(MSTOOLKIT) $(READERLITE) $(LIBS)
+# ln -sf libmstoolkitlite.so.$(RELVER) libmstoolkitlite.so.$(SOVER)
+# ln -sf libmstoolkitlite.so.$(SOVER) libmstoolkitlite.so
-zutil.o : $(ZLIB_PATH)/zutil.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/zutil.c -c
+clean_objects:
+ rm -f *.o msSingleScan
-zutil.o : $(ZLIB_PATH)/zutil.c
- $(GCC) $(CFLAGS) $(ZLIB_PATH)/zutil.c -c
+clean_libs:
+ rm -f $(CLEAN_LIBS)
+clean: clean_libs clean_objects
#mzParser objects
mzp.%.o : $(MZPARSER_PATH)/%.cpp
@@ -84,26 +82,7 @@ mzp.%.o : $(MZPARSER_PATH)/%.cpp
mzp.%_lite.o : $(MZPARSER_PATH)/%.cpp
@@ -85,23 +74,6 @@ mzp.%_lite.o : $(MZPARSER_PATH)/%.cpp
$(CC) $(CFLAGS) $< -c -o $@
-
-#expat objects
-xmlparse.o : $(EXPAT_PATH)/xmlparse.c
- $(GCC) $(CFLAGS) $(EXPAT_PATH)/xmlparse.c -c
......@@ -150,7 +138,5 @@ index 0c4d94e..11ae972 100644
-
-
#MSToolkit objects
-
Spectrum.o : $(MST_PATH)/Spectrum.cpp
$(CC) $(CFLAGS) $(MST_PATH)/Spectrum.cpp -c
Spectrum.o : $(MST_PATH)/Spectrum.cpp
Remove code making call to getenv. We hardcode the path to the lib data.
--- a/LibApplications/Wm5Application.cpp
+++ b/LibApplications/Wm5Application.cpp
@@ -40,7 +40,10 @@
// WM5_PATH environment variable in order for the applications to find
// various data files.
#ifndef __APPLE__
- Application::WM5Path = Environment::GetVariable("WM5_PATH");
+ // Debian packaging modifs by FR <lopippo@debian.org>.
+ // We do not want to handle paths with environment variables.
+ // Application::WM5Path = Environment::GetVariable("WM5_PATH");
+ Application::WM5Path = "/usr/share/libmstoolkit/";
#else
// Mac OS X Lion returns NULL on any getenv call (such as the one in
// Environment::GetVariable). This hack works around the problem.
......@@ -8,8 +8,8 @@ export DH_VERBOSE=1
DEBIAN_DIR = $(CURDIR)/debian
BUILD_DIR = $(CURDIR)
LIB_PACKAGE = libmstoolkit77
VERSION = 77.0.0
LIB_PACKAGE = libmstoolkit82
VERSION = 82.0.0
LIB_VERSION = $(VERSION)
# This is the only method that actually worked...
......
......@@ -93,7 +93,7 @@ class MSReader {
void setPrecisionInt(int i);
void setPrecisionMZ(int i);
void writeFile(const char* c, bool text, MSObject& m);
void writeFile(const char* c, MSFileFormat ff, MSObject& m, char* sha1Report='\0');
void writeFile(const char* c, MSFileFormat ff, MSObject& m, const char* sha1Report="\0");
bool readMGFFile(const char* c, Spectrum& s); //Note, no random-access of MGF files.
bool readMSTFile(const char* c, bool text, Spectrum& s, int scNum=0);
......@@ -193,7 +193,7 @@ class MSReader {
void sql_stmt(const char* stmt);
bool executeSqlStmt(Spectrum& s, char* zSql);
void appendFile(Spectrum& s);
void writeSqlite(const char* c, MSObject& m, char* sha1Report);
void writeSqlite(const char* c, MSObject& m, const char* sha1Report);
void readChargeTable(int scanID, Spectrum& s);
vector<int> estimateCharge(Spectrum& s);
#endif
......
#ifndef AMIGACONFIG_H
#define AMIGACONFIG_H
/* 1234 = LIL_ENDIAN, 4321 = BIGENDIAN */
#define BYTEORDER 4321
/* Define to 1 if you have the `bcopy' function. */
#define HAVE_BCOPY 1
/* Define to 1 if you have the `memmove' function. */
#define HAVE_MEMMOVE 1
/* Define to 1 if you have the <unistd.h> header file. */
#define HAVE_UNISTD_H 1
/* whether byteorder is bigendian */
#define WORDS_BIGENDIAN
/* Define to specify how much context to retain around the current parse
point. */
#define XML_CONTEXT_BYTES 1024
/* Define to make parameter entity parsing functionality available. */
#define XML_DTD
/* Define to make XML Namespaces functionality available. */
#define XML_NS
#endif /* AMIGACONFIG_H */
/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
See the file COPYING for copying permission.
*/
#define ASCII_A 0x41
#define ASCII_B 0x42
#define ASCII_C 0x43
#define ASCII_D 0x44
#define ASCII_E 0x45
#define ASCII_F 0x46
#define ASCII_G 0x47
#define ASCII_H 0x48
#define ASCII_I 0x49
#define ASCII_J 0x4A
#define ASCII_K 0x4B
#define ASCII_L 0x4C
#define ASCII_M 0x4D
#define ASCII_N 0x4E
#define ASCII_O 0x4F
#define ASCII_P 0x50
#define ASCII_Q 0x51
#define ASCII_R 0x52
#define ASCII_S 0x53
#define ASCII_T 0x54
#define ASCII_U 0x55
#define ASCII_V 0x56
#define ASCII_W 0x57
#define ASCII_X 0x58
#define ASCII_Y 0x59
#define ASCII_Z 0x5A
#define ASCII_a 0x61
#define ASCII_b 0x62
#define ASCII_c 0x63
#define ASCII_d 0x64
#define ASCII_e 0x65
#define ASCII_f 0x66
#define ASCII_g 0x67
#define ASCII_h 0x68
#define ASCII_i 0x69
#define ASCII_j 0x6A
#define ASCII_k 0x6B
#define ASCII_l 0x6C
#define ASCII_m 0x6D
#define ASCII_n 0x6E
#define ASCII_o 0x6F
#define ASCII_p 0x70
#define ASCII_q 0x71
#define ASCII_r 0x72
#define ASCII_s 0x73
#define ASCII_t 0x74
#define ASCII_u 0x75
#define ASCII_v 0x76
#define ASCII_w 0x77
#define ASCII_x 0x78
#define ASCII_y 0x79
#define ASCII_z 0x7A
#define ASCII_0 0x30
#define ASCII_1 0x31
#define ASCII_2 0x32
#define ASCII_3 0x33
#define ASCII_4 0x34
#define ASCII_5 0x35
#define ASCII_6 0x36
#define ASCII_7 0x37
#define ASCII_8 0x38
#define ASCII_9 0x39
#define ASCII_TAB 0x09
#define ASCII_SPACE 0x20
#define ASCII_EXCL 0x21
#define ASCII_QUOT 0x22
#define ASCII_AMP 0x26
#define ASCII_APOS 0x27
#define ASCII_MINUS 0x2D
#define ASCII_PERIOD 0x2E
#define ASCII_COLON 0x3A
#define ASCII_SEMI 0x3B
#define ASCII_LT 0x3C
#define ASCII_EQUALS 0x3D
#define ASCII_GT 0x3E
#define ASCII_LSQB 0x5B
#define ASCII_RSQB 0x5D
#define ASCII_UNDERSCORE 0x5F
#define ASCII_LPAREN 0x28
#define ASCII_RPAREN 0x29
#define ASCII_FF 0x0C
#define ASCII_SLASH 0x2F
#define ASCII_HASH 0x23
#define ASCII_PIPE 0x7C
#define ASCII_COMMA 0x2C
/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
See the file COPYING for copying permission.
*/
/* 0x00 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x04 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x08 */ BT_NONXML, BT_S, BT_LF, BT_NONXML,
/* 0x0C */ BT_NONXML, BT_CR, BT_NONXML, BT_NONXML,
/* 0x10 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x14 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x18 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x1C */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x20 */ BT_S, BT_EXCL, BT_QUOT, BT_NUM,
/* 0x24 */ BT_OTHER, BT_PERCNT, BT_AMP, BT_APOS,
/* 0x28 */ BT_LPAR, BT_RPAR, BT_AST, BT_PLUS,
/* 0x2C */ BT_COMMA, BT_MINUS, BT_NAME, BT_SOL,
/* 0x30 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT,
/* 0x34 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT,
/* 0x38 */ BT_DIGIT, BT_DIGIT, BT_COLON, BT_SEMI,
/* 0x3C */ BT_LT, BT_EQUALS, BT_GT, BT_QUEST,
/* 0x40 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX,
/* 0x44 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT,
/* 0x48 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x4C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x50 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x54 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x58 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_LSQB,
/* 0x5C */ BT_OTHER, BT_RSQB, BT_OTHER, BT_NMSTRT,
/* 0x60 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX,
/* 0x64 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT,
/* 0x68 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x6C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x70 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x74 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x78 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER,
/* 0x7C */ BT_VERBAR, BT_OTHER, BT_OTHER, BT_OTHER,
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/* expat_config.h. Generated by configure. */
/* expat_config.h.in. Generated from configure.in by autoheader. */
/* 1234 = LIL_ENDIAN, 4321 = BIGENDIAN */
#define BYTEORDER 1234
/* Define to 1 if you have the `bcopy' function. */
#define HAVE_BCOPY 1
/* Define to 1 if you have the <dlfcn.h> header file. */
#define HAVE_DLFCN_H 1
/* Define to 1 if you have the <fcntl.h> header file. */
#define HAVE_FCNTL_H 1
/* Define to 1 if you have the `getpagesize' function. */
#define HAVE_GETPAGESIZE 1