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From: <mki...@us...> - 2010-10-10 14:22:27
|
Revision: 47
http://mgfp.svn.sourceforge.net/mgfp/?rev=47&view=rev
Author: mkirchner
Date: 2010-10-10 14:22:20 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
- updated documentation
Modified Paths:
--------------
trunk/mgfp/doc/Mainpage.h
trunk/mgfp/doc/mgf_grammar.txt
Modified: trunk/mgfp/doc/Mainpage.h
===================================================================
--- trunk/mgfp/doc/Mainpage.h 2010-10-10 13:52:29 UTC (rev 46)
+++ trunk/mgfp/doc/Mainpage.h 2010-10-10 14:22:20 UTC (rev 47)
@@ -8,6 +8,8 @@
MGF processing tools:
\li mgfvalidate -- validates a given MGF file
+\li rix -- reporter ion extractor for iTRAQ4 and TMT
+\li ms2preproc -- MGF preprocessing tool (see below)
The <a href="http://steenlab.org">Steen \& Steen Lab</a> provides
the library under the terms of a BSD license for use in academic and
@@ -18,14 +20,14 @@
If you make use of \c mgfp in your own projects, please cite the
following article:<br>
-Kirchner M, Steen JAJ, Hamprecht FA, Steen H (2010).
+\li Kirchner M, Steen JAJ, Hamprecht FA, Steen H (2010).
MGFp: An open Mascot Generic Format parser library implementation.
<i>Journal of Proteome Research, 9(5):2762-2763 (2010)</i>.
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/20334363">PubMed entry</a>]
-If you use ms2preproc in your data analysis pipeline, please cite<br>
+If you use \c ms2preproc in your data analysis pipeline, please cite<br>
-Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J,
+\li Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J,
Winter D, Steen JAJ, Hamprecht FA, Steen H, When Less
Can Yield More - Computational Preprocessing of MS/MS Spectra for
Peptide Identification, <i>Proteomics 9(21):4978-4984 (2009)</i>.
@@ -39,11 +41,6 @@
\li the MGFp project page at sourceforge: http://mgfp.sf.net .
-Additional information is available on
-
-\li the Steen Lab page at http://steenlab.org/
-\li the Steen Lab software page at http://software.steenlab.org/
-
\subsection sec_install_src Building from Source
Building \c mgfp from source is straightforward. However, it requires a working
CMake build system (available from http://cmake.org/) and CMake >= 2.6.
Modified: trunk/mgfp/doc/mgf_grammar.txt
===================================================================
--- trunk/mgfp/doc/mgf_grammar.txt 2010-10-10 13:52:29 UTC (rev 46)
+++ trunk/mgfp/doc/mgf_grammar.txt 2010-10-10 14:22:20 UTC (rev 47)
@@ -23,65 +23,76 @@
16 | blocks block
17 block: "begin_ions keyword" "end of line" localparams ions "end_ions keyword" "end of line"
+ 18 | "begin_ions keyword" "end of line" localparams "end_ions keyword" "end of line"
- 18 globalparams: /* empty */
- 19 | globalparams globalparam
+ 19 globalparams: /* empty */
+ 20 | globalparams globalparam
- 20 globalparam: "enzyme keyword" '=' "string" "end of line"
- 21 | "search title keyword" '=' "string" "end of line"
- 22 | "database keyword" '=' "string" "end of line"
- 23 | "MS/MS datafile format keyword" '=' "string" "end of line"
- 24 | "MS/MS ion series keyword" '=' "string" "end of line"
- 25 | "variable modifications keyword" '=' "string" "end of line"
- 26 | "units for ITOL keyword" '=' "string" "end of line"
- 27 | "mass type (mono or avg) keyword" '=' "string" "end of line"
- 28 | "fixed modifications keyword" '=' "string" "end of line"
- 29 | "quantitation method keyword" '=' "string" "end of line"
- 30 | "maximum hits keyword" '=' "string" "end of line"
- 31 | "type of report keyword" '=' "string" "end of line"
- 32 | "type of search keyword" '=' "string" "end of line"
- 33 | "taxonomy keyword" '=' "string" "end of line"
- 34 | "tolerance units keyword" '=' "string" "end of line"
- 35 | "user keyword" '=' "string" "end of line"
- 36 | "user email keyword" '=' "string" "end of line"
- 37 | "username keyword" '=' "string" "end of line"
- 38 | "perform decoy search keyword" '=' "integer" "end of line"
- 39 | "error tolerance keyword" '=' "integer" "end of line"
- 40 | "partials keyword" '=' "integer" "end of line"
- 41 | "fragment ion tolerance keyword" '=' "double" "end of line"
- 42 | "fragment ion tolerance keyword" '=' "integer" "end of line"
- 43 | "misassigned 13C keyword" '=' "double" "end of line"
- 44 | "precursor m/z keyword" '=' "double" "end of line"
- 45 | "protein mass (kDa) keyword" '=' "double" "end of line"
- 46 | "peptide mass tolerance keyword" '=' "double" "end of line"
- 47 | "peptide mass tolerance keyword" '=' "integer" "end of line"
- 48 | "charge set keyword" '=' charges "end of line"
- 49 | "NA translation keyword" '=' csintegerlist "end of line"
- 50 | "comment" "end of line"
+ 21 globalparam: "enzyme keyword" '=' "string" "end of line"
+ 22 | "search title keyword" '=' "string" "end of line"
+ 23 | "database keyword" '=' "string" "end of line"
+ 24 | "MS/MS datafile format keyword" '=' "string" "end of line"
+ 25 | "MS/MS ion series keyword" '=' "string" "end of line"
+ 26 | "variable modifications keyword" '=' "string" "end of line"
+ 27 | "units for ITOL keyword" '=' "string" "end of line"
+ 28 | "mass type (mono or avg) keyword" '=' "string" "end of line"
+ 29 | "fixed modifications keyword" '=' "string" "end of line"
+ 30 | "quantitation method keyword" '=' "string" "end of line"
+ 31 | "maximum hits keyword" '=' "string" "end of line"
+ 32 | "type of report keyword" '=' "string" "end of line"
+ 33 | "type of search keyword" '=' "string" "end of line"
+ 34 | "taxonomy keyword" '=' "string" "end of line"
+ 35 | "tolerance units keyword" '=' "string" "end of line"
+ 36 | "user keyword" '=' "string" "end of line"
+ 37 | "user email keyword" '=' "string" "end of line"
+ 38 | "username keyword" '=' "string" "end of line"
+ 39 | "perform decoy search keyword" '=' "integer" "end of line"
+ 40 | "error tolerance keyword" '=' "integer" "end of line"
+ 41 | "partials keyword" '=' "integer" "end of line"
+ 42 | "fragment ion tolerance keyword" '=' "double" "end of line"
+ 43 | "fragment ion tolerance keyword" '=' "integer" "end of line"
+ 44 | "misassigned 13C keyword" '=' "double" "end of line"
+ 45 | "precursor m/z keyword" '=' "double" "end of line"
+ 46 | "precursor m/z keyword" '=' "integer" "end of line"
+ 47 | "protein mass (kDa) keyword" '=' "double" "end of line"
+ 48 | "protein mass (kDa) keyword" '=' "integer" "end of line"
+ 49 | "peptide mass tolerance keyword" '=' "double" "end of line"
+ 50 | "peptide mass tolerance keyword" '=' "integer" "end of line"
+ 51 | "charge set keyword" '=' charges "end of line"
+ 52 | "NA translation keyword" '=' csintegerlist "end of line"
+ 53 | "comment" "end of line"
- 51 localparams: /* empty */
- 52 | localparams localparam
+ 54 localparams: /* empty */
+ 55 | localparams localparam
- 53 localparam: "title keyword and full title string" "end of line"
- 54 | "amino acid composition keyword" '=' "string" "end of line"
- 55 | "MS/MS ion series keyword" '=' "string" "end of line"
- 56 | "variable modifications keyword" '=' "string" "end of line"
- 57 | "retention time or range keyword" '=' "double" "end of line"
- 58 | "scan number of range keyword" '=' "string" "end of line"
- 59 | "tolerance units keyword" '=' "string" "end of line"
- 60 | "amino acid sequence keyword" '=' "string" "end of line"
- 61 | "sequence tag keyword" '=' "string" "end of line"
- 62 | "error tolerant sequence keyword" '=' "string" "end of line"
- 63 | "peptide mass tolerance keyword" '=' "double" "end of line"
- 64 | "peptide mass tolerance keyword" '=' "integer" "end of line"
- 65 | "charge set keyword" '=' charges "end of line"
- 66 | "precursor mass keyword" '=' "double" "end of line"
- 67 | "precursor mass keyword" '=' "double" "double" "end of line"
- 68 | "precursor mass keyword" '=' "integer" "end of line"
- 69 | "precursor mass keyword" '=' "integer" "integer" "end of line"
- 70 | "comment" "end of line"
+ 56 localparam: "title keyword and full title string" "end of line"
+ 57 | "amino acid composition keyword" '=' "string" "end of line"
+ 58 | "MS/MS ion series keyword" '=' "string" "end of line"
+ 59 | "variable modifications keyword" '=' "string" "end of line"
+ 60 | "retention time or range keyword" '=' "double" "end of line"
+ 61 | "retention time or range keyword" '=' "integer" "end of line"
+ 62 | "retention time or range keyword" '=' "double" '-' "double" "end of line"
+ 63 | "retention time or range keyword" '=' "double" '-' "integer" "end of line"
+ 64 | "retention time or range keyword" '=' "integer" '-' "double" "end of line"
+ 65 | "retention time or range keyword" '=' "integer" '-' "integer" "end of line"
+ 66 | "scan number of range keyword" '=' "integer" "end of line"
+ 67 | "scan number of range keyword" '=' "integer" '-' "integer" "end of line"
+ 68 | "tolerance units keyword" '=' "string" "end of line"
+ 69 | "amino acid sequence keyword" '=' "string" "end of line"
+ 70 | "sequence tag keyword" '=' "string" "end of line"
+ 71 | "error tolerant sequence keyword" '=' "string" "end of line"
+ 72 | "peptide mass tolerance keyword" '=' "double" "end of line"
+ 73 | "peptide mass tolerance keyword" '=' "integer" "end of line"
+ 74 | "charge set keyword" '=' charges "end of line"
+ 75 | "precursor mass keyword" '=' "double" "end of line"
+ 76 | "precursor mass keyword" '=' "double" "double" "end of line"
+ 77 | "precursor mass keyword" '=' "double" "integer" "end of line"
+ 78 | "precursor mass keyword" '=' "integer" "end of line"
+ 79 | "precursor mass keyword" '=' "integer" "double" "end of line"
+ 80 | "precursor mass keyword" '=' "integer" "integer" "end of line"
+ 81 | "comment" "end of line"
- 71 contents: globalparams blocks "end of file"
+ 82 contents: globalparams blocks "end of file"
- 72 start: contents
+ 83 start: contents
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|
|
From: <mki...@us...> - 2010-10-10 13:52:35
|
Revision: 46
http://mgfp.svn.sourceforge.net/mgfp/?rev=46&view=rev
Author: mkirchner
Date: 2010-10-10 13:52:29 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
removing windows.h and fixing linux build
Modified Paths:
--------------
trunk/mgfp/test/include/mgfpunittest.h.in
Removed Paths:
-------------
trunk/mgfp/test/include/vigra/windows.h
Modified: trunk/mgfp/test/include/mgfpunittest.h.in
===================================================================
--- trunk/mgfp/test/include/mgfpunittest.h.in 2010-10-10 13:37:54 UTC (rev 45)
+++ trunk/mgfp/test/include/mgfpunittest.h.in 2010-10-10 13:52:29 UTC (rev 46)
@@ -1,7 +1,6 @@
#ifndef __MGFPUNITTEST_H__
#define __MGFPUNITTEST_H__
-#include "windows.h" // from VIGRA
#include "unittest.hxx" // from VIGRA
#include <string>
Deleted: trunk/mgfp/test/include/vigra/windows.h
===================================================================
--- trunk/mgfp/test/include/vigra/windows.h 2010-10-10 13:37:54 UTC (rev 45)
+++ trunk/mgfp/test/include/vigra/windows.h 2010-10-10 13:52:29 UTC (rev 46)
@@ -1,59 +0,0 @@
-/************************************************************************/
-/* */
-/* Copyright 2002-2003 by Ullrich Koethe */
-/* Cognitive Systems Group, University of Hamburg, Germany */
-/* */
-/* This file is part of the VIGRA computer vision library. */
-/* The VIGRA Website is */
-/* http://kogs-www.informatik.uni-hamburg.de/~koethe/vigra/ */
-/* Please direct questions, bug reports, and contributions to */
-/* ull...@iw... or */
-/* vi...@in... */
-/* */
-/* Permission is hereby granted, free of charge, to any person */
-/* obtaining a copy of this software and associated documentation */
-/* files (the "Software"), to deal in the Software without */
-/* restriction, including without limitation the rights to use, */
-/* copy, modify, merge, publish, distribute, sublicense, and/or */
-/* sell copies of the Software, and to permit persons to whom the */
-/* Software is furnished to do so, subject to the following */
-/* conditions: */
-/* */
-/* The above copyright notice and this permission notice shall be */
-/* included in all copies or substantial portions of the */
-/* Software. */
-/* */
-/* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND */
-/* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES */
-/* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND */
-/* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT */
-/* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, */
-/* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING */
-/* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR */
-/* OTHER DEALINGS IN THE SOFTWARE. */
-/* */
-/************************************************************************/
-
-#ifndef VIGRA_WINDOWS_H
-#define VIGRA_WINDOWS_H
-
-// prevent the global namespace to become polluted with
-// badly named Windows macros
-
-#if defined(_WIN32)
-# define VC_EXTRALEAN
-# ifndef NOMINMAX
-# define NOMINMAX
-# define _VIGRA_UNDEFINE_NOMINMAX
-# endif
-# include <windows.h>
-# ifdef _VIGRA_UNDEFINE_NOMINMAX
-# undef NOMINMAX
-# undef _VIGRA_UNDEFINE_NOMINMAX
-# endif
-# ifdef DIFFERENCE
-# undef DIFFERENCE
-# endif
-#endif
-
-#endif /* VIGRA_WINDOWS_H */
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|
|
From: <mki...@us...> - 2010-10-10 13:38:01
|
Revision: 45
http://mgfp.svn.sourceforge.net/mgfp/?rev=45&view=rev
Author: mkirchner
Date: 2010-10-10 13:37:54 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
- fixed windows compilations
- windows packages now correctly package binaries
Modified Paths:
--------------
trunk/mgfp/applications/ms2preproc/CMakeLists.txt
trunk/mgfp/applications/rix/CMakeLists.txt
trunk/mgfp/applications/rix/rix.cpp
trunk/mgfp/include/mgfp/config.h.cmake
trunk/mgfp/test/include/mgfpunittest.h.in
Modified: trunk/mgfp/applications/ms2preproc/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/ms2preproc/CMakeLists.txt 2010-10-10 12:40:29 UTC (rev 44)
+++ trunk/mgfp/applications/ms2preproc/CMakeLists.txt 2010-10-10 13:37:54 UTC (rev 45)
@@ -20,7 +20,9 @@
SET(SRCS_MS2PREPROC ms2preproc.cpp)
ADD_EXECUTABLE(ms2preproc ${SRCS_MS2PREPROC})
TARGET_LINK_LIBRARIES(ms2preproc mgfp ${Boost_PROGRAM_OPTIONS_LIBRARY})
- INSTALL(TARGETS ms2preproc RUNTIME DESTINATION bin)
+ INSTALL(TARGETS ms2preproc RUNTIME
+ DESTINATION bin
+ COMPONENT applications)
ELSE(Boost_PROGRAM_OPTIONS_FOUND)
MESSAGE(STATUS "Could not find BOOST program_options. Skipping ${CMAKE_CURRENT_SOURCE_DIR}.")
ENDIF(Boost_PROGRAM_OPTIONS_FOUND)
Modified: trunk/mgfp/applications/rix/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/rix/CMakeLists.txt 2010-10-10 12:40:29 UTC (rev 44)
+++ trunk/mgfp/applications/rix/CMakeLists.txt 2010-10-10 13:37:54 UTC (rev 45)
@@ -16,7 +16,9 @@
SET(SRCS_RIX rix.cpp)
ADD_EXECUTABLE(rix ${SRCS_RIX})
TARGET_LINK_LIBRARIES(rix mgfp ${Boost_PROGRAM_OPTIONS_LIBRARY})
- INSTALL(TARGETS rix RUNTIME DESTINATION bin)
+ INSTALL(TARGETS rix RUNTIME
+ DESTINATION bin
+ COMPONENT applications)
ELSE(Boost_PROGRAM_OPTIONS_FOUND)
MESSAGE(STATUS "Could not find BOOST program_options. Skipping ${CMAKE_CURRENT_SOURCE_DIR}.")
ENDIF(Boost_PROGRAM_OPTIONS_FOUND)
Modified: trunk/mgfp/applications/rix/rix.cpp
===================================================================
--- trunk/mgfp/applications/rix/rix.cpp 2010-10-10 12:40:29 UTC (rev 44)
+++ trunk/mgfp/applications/rix/rix.cpp 2010-10-10 13:37:54 UTC (rev 45)
@@ -1,6 +1,6 @@
/*$Id$*/
/*
- * tmtx.cpp
+ * rix.cpp
*
* Copyright (c) 2010 Marc Kirchner <mar...@ch...>
*
@@ -26,7 +26,11 @@
#include <iomanip>
#include <iostream>
#include <iterator>
+#ifdef _MSC_VER
+#include <array>
+#else
#include <tr1/array>
+#endif
#include <boost/program_options.hpp>
#include <mgfp/mgfp.h>
@@ -62,11 +66,12 @@
}
return pos1;
}
+ return end;
}
-enum LabelType { TMT, ITRAQ4, SIZE };
-static const size_t sizes[SIZE] = { 10, 8 };
-static const double masses[SIZE][10] =
+enum LabelType { TMT, ITRAQ4, LabelTypeSIZE };
+static const size_t sizes[LabelTypeSIZE] = { 10, 8 };
+static const double masses[LabelTypeSIZE][10] =
{
{ 124.0, 125.0, 126.0, 127.0, 128.0,
129.0, 130.0, 131.0, 132.0, 133.0 },
Modified: trunk/mgfp/include/mgfp/config.h.cmake
===================================================================
--- trunk/mgfp/include/mgfp/config.h.cmake 2010-10-10 12:40:29 UTC (rev 44)
+++ trunk/mgfp/include/mgfp/config.h.cmake 2010-10-10 13:37:54 UTC (rev 45)
@@ -1,9 +1,9 @@
#ifndef __MGFP_INCLUDE_CONFIG_H__
#define __MGFP_INCLUDE_CONFIG_H__
-//#ifdef _MSC_VER
-// #include "winsock2.h"
-//#endif
+#ifdef _MSC_VER
+#define NOMINMAX
+#endif
#ifdef min
#undef min
Modified: trunk/mgfp/test/include/mgfpunittest.h.in
===================================================================
--- trunk/mgfp/test/include/mgfpunittest.h.in 2010-10-10 12:40:29 UTC (rev 44)
+++ trunk/mgfp/test/include/mgfpunittest.h.in 2010-10-10 13:37:54 UTC (rev 45)
@@ -1,6 +1,7 @@
#ifndef __MGFPUNITTEST_H__
#define __MGFPUNITTEST_H__
+#include "windows.h" // from VIGRA
#include "unittest.hxx" // from VIGRA
#include <string>
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|
|
From: <mki...@us...> - 2010-10-10 12:40:35
|
Revision: 44
http://mgfp.svn.sourceforge.net/mgfp/?rev=44&view=rev
Author: mkirchner
Date: 2010-10-10 12:40:29 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
added install component descriptions
Modified Paths:
--------------
trunk/mgfp/applications/mgfvalidate/CMakeLists.txt
trunk/mgfp/src/CMakeLists.txt
Modified: trunk/mgfp/applications/mgfvalidate/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/mgfvalidate/CMakeLists.txt 2010-10-10 12:20:22 UTC (rev 43)
+++ trunk/mgfp/applications/mgfvalidate/CMakeLists.txt 2010-10-10 12:40:29 UTC (rev 44)
@@ -20,7 +20,9 @@
SET(SRCS_MGFVALIDATE mgfvalidate.cpp)
ADD_EXECUTABLE(mgfvalidate ${SRCS_MGFVALIDATE})
TARGET_LINK_LIBRARIES(mgfvalidate mgfp ${Boost_PROGRAM_OPTIONS_LIBRARY})
- INSTALL(TARGETS mgfvalidate RUNTIME DESTINATION bin)
+ INSTALL(TARGETS mgfvalidate RUNTIME
+ DESTINATION bin
+ COMPONENT applications)
ELSE(Boost_PROGRAM_OPTIONS_FOUND)
MESSAGE(STATUS "Could not find BOOST program_options. Skipping ${CMAKE_CURRENT_SOURCE_DIR}.")
ENDIF(Boost_PROGRAM_OPTIONS_FOUND)
Modified: trunk/mgfp/src/CMakeLists.txt
===================================================================
--- trunk/mgfp/src/CMakeLists.txt 2010-10-10 12:20:22 UTC (rev 43)
+++ trunk/mgfp/src/CMakeLists.txt 2010-10-10 12:40:29 UTC (rev 44)
@@ -18,5 +18,6 @@
INSTALL(TARGETS mgfp
RUNTIME DESTINATION bin
LIBRARY DESTINATION lib
- ARCHIVE DESTINATION lib)
+ ARCHIVE DESTINATION lib
+ COMPONENT libraries)
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|
|
From: <mki...@us...> - 2010-10-10 12:20:28
|
Revision: 43
http://mgfp.svn.sourceforge.net/mgfp/?rev=43&view=rev
Author: mkirchner
Date: 2010-10-10 12:20:22 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
added windows.h (VIGRA)
Added Paths:
-----------
trunk/mgfp/test/include/vigra/windows.h
Added: trunk/mgfp/test/include/vigra/windows.h
===================================================================
--- trunk/mgfp/test/include/vigra/windows.h (rev 0)
+++ trunk/mgfp/test/include/vigra/windows.h 2010-10-10 12:20:22 UTC (rev 43)
@@ -0,0 +1,59 @@
+/************************************************************************/
+/* */
+/* Copyright 2002-2003 by Ullrich Koethe */
+/* Cognitive Systems Group, University of Hamburg, Germany */
+/* */
+/* This file is part of the VIGRA computer vision library. */
+/* The VIGRA Website is */
+/* http://kogs-www.informatik.uni-hamburg.de/~koethe/vigra/ */
+/* Please direct questions, bug reports, and contributions to */
+/* ull...@iw... or */
+/* vi...@in... */
+/* */
+/* Permission is hereby granted, free of charge, to any person */
+/* obtaining a copy of this software and associated documentation */
+/* files (the "Software"), to deal in the Software without */
+/* restriction, including without limitation the rights to use, */
+/* copy, modify, merge, publish, distribute, sublicense, and/or */
+/* sell copies of the Software, and to permit persons to whom the */
+/* Software is furnished to do so, subject to the following */
+/* conditions: */
+/* */
+/* The above copyright notice and this permission notice shall be */
+/* included in all copies or substantial portions of the */
+/* Software. */
+/* */
+/* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND */
+/* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES */
+/* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND */
+/* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT */
+/* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, */
+/* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING */
+/* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR */
+/* OTHER DEALINGS IN THE SOFTWARE. */
+/* */
+/************************************************************************/
+
+#ifndef VIGRA_WINDOWS_H
+#define VIGRA_WINDOWS_H
+
+// prevent the global namespace to become polluted with
+// badly named Windows macros
+
+#if defined(_WIN32)
+# define VC_EXTRALEAN
+# ifndef NOMINMAX
+# define NOMINMAX
+# define _VIGRA_UNDEFINE_NOMINMAX
+# endif
+# include <windows.h>
+# ifdef _VIGRA_UNDEFINE_NOMINMAX
+# undef NOMINMAX
+# undef _VIGRA_UNDEFINE_NOMINMAX
+# endif
+# ifdef DIFFERENCE
+# undef DIFFERENCE
+# endif
+#endif
+
+#endif /* VIGRA_WINDOWS_H */
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|
|
From: <mki...@us...> - 2010-10-10 11:09:34
|
Revision: 42
http://mgfp.svn.sourceforge.net/mgfp/?rev=42&view=rev
Author: mkirchner
Date: 2010-10-10 11:09:27 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
updated package description in cpack.
Modified Paths:
--------------
trunk/mgfp/CMakeLists.txt
Modified: trunk/mgfp/CMakeLists.txt
===================================================================
--- trunk/mgfp/CMakeLists.txt 2010-10-10 11:08:53 UTC (rev 41)
+++ trunk/mgfp/CMakeLists.txt 2010-10-10 11:09:27 UTC (rev 42)
@@ -10,7 +10,7 @@
# versioning
#############################################################################
set(VERSION_MAJOR 2)
-set(VERSION_MINOR 0)
+set(VERSION_MINOR 1)
# get SVN revision
EXECUTE_PROCESS(
@@ -106,7 +106,7 @@
# generated prior to packaging!
set(CPACK_PACKAGE_NAME "mgfp")
-set(CPACK_PACKAGE_VENDOR "steenlab.org")
+set(CPACK_PACKAGE_VENDOR "mgfp.sf.net.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "MGF Parser")
@@ -125,7 +125,7 @@
set(CPACK_COMPONENT_DOCUMENTATION_DISPLAY_NAME "C++ Interface Documentation")
set(CPACK_COMPONENT_APPLICATIONS_DESCRIPTION
- "A simple MGF validator.")
+ "A simple MGF validator, TMT/iTRAQ reporter ion extraction and MGF preprocessing tools.")
set(CPACK_COMPONENT_LIBRARIES_DESCRIPTION
"Static libraries necessary used to build programs with MGFp.")
set(CPACK_COMPONENT_HEADERS_DESCRIPTION
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mki...@us...> - 2010-10-10 11:08:59
|
Revision: 41
http://mgfp.svn.sourceforge.net/mgfp/?rev=41&view=rev
Author: mkirchner
Date: 2010-10-10 11:08:53 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
moved tmtx to rix: the reporter ion extraction now supports iTRAQ as well and the name is misleading
Modified Paths:
--------------
trunk/mgfp/applications/CMakeLists.txt
trunk/mgfp/applications/rix/CMakeLists.txt
Added Paths:
-----------
trunk/mgfp/applications/rix/
trunk/mgfp/applications/rix/rix.cpp
Removed Paths:
-------------
trunk/mgfp/applications/rix/tmtx.cpp
trunk/mgfp/applications/tmtx/
Modified: trunk/mgfp/applications/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/CMakeLists.txt 2010-10-10 10:58:58 UTC (rev 40)
+++ trunk/mgfp/applications/CMakeLists.txt 2010-10-10 11:08:53 UTC (rev 41)
@@ -1,4 +1,4 @@
ADD_SUBDIRECTORY(mgfvalidate)
ADD_SUBDIRECTORY(ms2preproc)
-ADD_SUBDIRECTORY(tmtx)
+ADD_SUBDIRECTORY(rix)
Modified: trunk/mgfp/applications/rix/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/tmtx/CMakeLists.txt 2010-09-10 15:35:49 UTC (rev 39)
+++ trunk/mgfp/applications/rix/CMakeLists.txt 2010-10-10 11:08:53 UTC (rev 41)
@@ -4,7 +4,7 @@
${MGFP_BINARY_DIR}/include
${CMAKE_CURRENT_SOURCE_DIR}
)
-# this requres BOOST
+# this requires BOOST
IF(MSVC)
SET(Boost_USE_STATIC_LIBS ON)
SET(Boost_USE_MULTITHREAD OFF)
@@ -13,10 +13,10 @@
IF(Boost_PROGRAM_OPTIONS_FOUND)
INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
- SET(SRCS_TMTX tmtx.cpp)
- ADD_EXECUTABLE(tmtx ${SRCS_TMTX})
- TARGET_LINK_LIBRARIES(tmtx mgfp ${Boost_PROGRAM_OPTIONS_LIBRARY})
- INSTALL(TARGETS tmtx RUNTIME DESTINATION bin)
+ SET(SRCS_RIX rix.cpp)
+ ADD_EXECUTABLE(rix ${SRCS_RIX})
+ TARGET_LINK_LIBRARIES(rix mgfp ${Boost_PROGRAM_OPTIONS_LIBRARY})
+ INSTALL(TARGETS rix RUNTIME DESTINATION bin)
ELSE(Boost_PROGRAM_OPTIONS_FOUND)
MESSAGE(STATUS "Could not find BOOST program_options. Skipping ${CMAKE_CURRENT_SOURCE_DIR}.")
ENDIF(Boost_PROGRAM_OPTIONS_FOUND)
Copied: trunk/mgfp/applications/rix/rix.cpp (from rev 39, trunk/mgfp/applications/tmtx/tmtx.cpp)
===================================================================
--- trunk/mgfp/applications/rix/rix.cpp (rev 0)
+++ trunk/mgfp/applications/rix/rix.cpp 2010-10-10 11:08:53 UTC (rev 41)
@@ -0,0 +1,173 @@
+/*$Id$*/
+/*
+ * tmtx.cpp
+ *
+ * Copyright (c) 2010 Marc Kirchner <mar...@ch...>
+ *
+ * This file is part of mgfp.
+ *
+ * mgfp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ms++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with ms++. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <cmath>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <iterator>
+#include <tr1/array>
+#include <boost/program_options.hpp>
+#include <mgfp/mgfp.h>
+
+mgf::MgfSpectrum::iterator findClosestMz(mgf::MgfSpectrum::iterator begin,
+ mgf::MgfSpectrum::iterator end, double referenceMz)
+{
+ // at least one entry?
+ if (begin == end)
+ return end;
+ // find first entry that is equal or greater than the reference mz
+ typedef mgf::MgfSpectrum::iterator MSI;
+ MSI pos1 = std::lower_bound(begin, end, referenceMz, mgf::LessThanMz());
+ double dist1 = 0.0;
+ if (pos1 != end) {
+ // found equal or greater
+ dist1 = pos1->first - referenceMz;
+ if (pos1 == begin || dist1 == 0.0) {
+ return pos1;
+ }
+ } else {
+ // return the last entry in the sequence
+ pos1 = begin;
+ std::advance(pos1, std::distance(begin, end) - 1);
+ return pos1;
+ }
+ // check if the distance to the previous iterator position
+ if (pos1 != begin) {
+ MSI pos2 = begin;
+ std::advance(pos2, std::distance(begin, pos1) - 1);
+ double dist2 = referenceMz - pos2->first;
+ if (dist2 < dist1) {
+ return pos2;
+ }
+ return pos1;
+ }
+}
+
+enum LabelType { TMT, ITRAQ4, SIZE };
+static const size_t sizes[SIZE] = { 10, 8 };
+static const double masses[SIZE][10] =
+ {
+ { 124.0, 125.0, 126.0, 127.0, 128.0,
+ 129.0, 130.0, 131.0, 132.0, 133.0 },
+ { 112.1, 113.1, 114.1112, 115.1083, 116.1116,
+ 117.115, 118.1, 119.1, 0.0, 0.0 }};
+
+int main(int argc, char *argv[])
+{
+ namespace po = boost::program_options;
+ po::options_description desc("Allowed options");
+ bool verbose = false;
+ std::string inputfile;
+ size_t precision;
+ desc.add_options()
+ ("help,h", "produce help message")
+ ("verbose,v", po::value(&verbose)->zero_tokens(),
+ "verbose output (good to pinpoint parsing errors)")
+ ("type,t", po::value<std::string>(), "label type: one of TMT, ITRAQ4")
+ ("input,i", po::value<std::string>(&inputfile)->default_value("-"),
+ "input filename, defaults to stdin")
+ /*
+ ("tee,e", po::value<std::string>(), "run in tee mode: extract label "
+ "abundances to specified file and simply pipe MGF data from stdin "
+ "to stdout.")
+ */
+ ("precision,p", po::value<size_t>(&precision)->default_value(6),
+ "number of significant digits in output")
+ ;
+ po::variables_map vm;
+ po::store(po::parse_command_line(argc, argv, desc), vm);
+ po::notify(vm);
+ // check if the user asked for help
+ if (vm.count("help") || !vm.count("type")) {
+ std::cerr << desc;
+ return 1;
+ }
+ // figure put which labeling technique we use
+ LabelType labelType;
+ if (vm["type"].as<std::string>() == "TMT") {
+ labelType = TMT;
+ } else if (vm["type"].as<std::string>() == "ITRAQ4") {
+ labelType = ITRAQ4;
+ } else {
+ std::cerr << vm["type"].as<std::string>() << std::endl;
+ std::cerr << desc;
+ return 1;
+ }
+ // initialize the masses
+ std::vector<double> labelMasses(sizes[labelType]);
+ for (size_t n = 0; n < sizes[labelType]; ++n) {
+ labelMasses[n] = masses[labelType][n];
+ }
+ // prepare the parser
+ mgf::MgfFile m;
+ mgf::Driver driver(m);
+ driver.trace_parsing = verbose;
+ driver.trace_scanning = verbose;
+ // parse input
+ bool result;
+ if (inputfile == "-") {
+ result = driver.parse_stream(std::cin);
+ } else {
+ std::ifstream ifs(inputfile.c_str());
+ result = driver.parse_stream(ifs);
+ ifs.close();
+ }
+ if (!result) {
+ std::cerr << std::endl
+ << "Error parsing data stream (use -v for details)." << std::endl;
+ return -1;
+ }
+ typedef mgf::MgfFile::iterator MFI;
+ // iterate over all spectra
+ std::vector<double> obsAbundances(sizes[labelType]);
+ for (MFI i = m.begin(); i != m.end(); ++i) {
+ // sort
+ std::sort(i->begin(), i->end(), mgf::LessThanMz());
+ typedef mgf::MgfSpectrum::iterator MSI;
+ // extract TMT reproter ion intensities
+ bool atLeastOneEntry = false;
+ for (size_t n = 0; n < sizes[labelType]; ++n) {
+ MSI closestIt = findClosestMz(i->begin(), i->end(), labelMasses[n]);
+ if (closestIt != i->end()) {
+ // check if there is an MS2 centroid
+ if (std::abs(closestIt->first - labelMasses[n]) < 0.4) {
+ obsAbundances[n] = closestIt->second;
+ if (!atLeastOneEntry) atLeastOneEntry = true;
+ } else {
+ obsAbundances[n] = 0.0;
+ }
+ }
+ }
+ // extract into file
+ if (atLeastOneEntry) {
+ std::cout << i->getTITLE();
+ for (size_t n = 0; n < sizes[labelType]; ++n) {
+ std::cout << '\t' << std::setprecision(precision) << obsAbundances[n];
+ }
+ std::cout << '\n'; // don't use std::endl, save the std::flush.
+ }
+ }
+ return 0;
+}
+
Deleted: trunk/mgfp/applications/rix/tmtx.cpp
===================================================================
--- trunk/mgfp/applications/tmtx/tmtx.cpp 2010-09-10 15:35:49 UTC (rev 39)
+++ trunk/mgfp/applications/rix/tmtx.cpp 2010-10-10 11:08:53 UTC (rev 41)
@@ -1,171 +0,0 @@
-/*$Id$*/
-/*
- * tmtx.cpp
- *
- * Copyright (c) 2010 Marc Kirchner <mar...@ch...>
- *
- * This file is part of mgfp.
- *
- * mgfp is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * ms++ is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with ms++. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#include <cmath>
-#include <fstream>
-#include <iomanip>
-#include <iostream>
-#include <iterator>
-#include <tr1/array>
-#include <boost/program_options.hpp>
-#include <mgfp/mgfp.h>
-
-mgf::MgfSpectrum::iterator findClosestMz(mgf::MgfSpectrum::iterator begin,
- mgf::MgfSpectrum::iterator end, double referenceMz)
-{
- // at least one entry?
- if (begin == end)
- return end;
- // find first entry that is equal or greater than the reference mz
- typedef mgf::MgfSpectrum::iterator MSI;
- MSI pos1 = std::lower_bound(begin, end, referenceMz, mgf::LessThanMz());
- double dist1 = 0.0;
- if (pos1 != end) {
- // found equal or greater
- dist1 = pos1->first - referenceMz;
- if (pos1 == begin || dist1 == 0.0) {
- return pos1;
- }
- } else {
- // return the last entry in the sequence
- pos1 = begin;
- std::advance(pos1, std::distance(begin, end) - 1);
- return pos1;
- }
- // check if the distance to the previous iterator position
- if (pos1 != begin) {
- MSI pos2 = begin;
- std::advance(pos2, std::distance(begin, pos1) - 1);
- double dist2 = referenceMz - pos2->first;
- if (dist2 < dist1) {
- return pos2;
- }
- return pos1;
- }
-}
-
-enum LabelType { TMT, ITRAQ4, SIZE };
-static const size_t sizes[SIZE] = { 10, 8 };
-static const double masses[SIZE][10] =
- {
- { 124.0, 125.0, 126.0, 127.0, 128.0,
- 129.0, 130.0, 131.0, 132.0, 133.0 },
- { 112.1, 113.1, 114.1112, 115.1083, 116.1116,
- 117.115, 118.1, 119.1, 0.0, 0.0 }};
-
-int main(int argc, char *argv[])
-{
- namespace po = boost::program_options;
- po::options_description desc("Allowed options");
- bool verbose = false;
- std::string inputfile;
- size_t precision;
- desc.add_options()
- ("help,h", "produce help message")
- ("verbose,v", po::value(&verbose)->zero_tokens(),
- "verbose output (good to pinpoint parsing errors)")
- ("type,t", po::value<std::string>(), "label type: one of TMT, ITRAQ4")
- ("input,i", po::value<std::string>(&inputfile)->default_value("-"),
- "input filename, defaults to stdin")
- ("tee,e", po::value<std::string>(), "run in tee mode: extract label "
- "abundances to specified file and simply pipe MGF data from stdin "
- "to stdout.")
- ("precision,p", po::value<size_t>(&precision)->default_value(6),
- "number of significant digits in output")
- ;
- po::variables_map vm;
- po::store(po::parse_command_line(argc, argv, desc), vm);
- po::notify(vm);
- // check if the user asked for help
- if (vm.count("help") || !vm.count("type")) {
- std::cerr << desc;
- return 1;
- }
- // figure put which labeling technique we use
- LabelType labelType;
- if (vm["type"].as<std::string>() == "TMT") {
- labelType = TMT;
- } else if (vm["type"].as<std::string>() == "ITRAQ4") {
- labelType = ITRAQ4;
- } else {
- std::cerr << vm["type"].as<std::string>() << std::endl;
- std::cerr << desc;
- return 1;
- }
- // initialize the masses
- std::vector<double> labelMasses(sizes[labelType]);
- for (size_t n = 0; n < sizes[labelType]; ++n) {
- labelMasses[n] = masses[labelType][n];
- }
- // prepare the parser
- mgf::MgfFile m;
- mgf::Driver driver(m);
- driver.trace_parsing = verbose;
- driver.trace_scanning = verbose;
- // parse input
- bool result;
- if (inputfile == "-") {
- result = driver.parse_stream(std::cin);
- } else {
- std::ifstream ifs(inputfile.c_str());
- result = driver.parse_stream(ifs);
- ifs.close();
- }
- if (!result) {
- std::cerr << std::endl
- << "Error parsing data stream (use -v for details)." << std::endl;
- return -1;
- }
- typedef mgf::MgfFile::iterator MFI;
- // iterate over all spectra
- std::vector<double> obsAbundances(sizes[labelType]);
- for (MFI i = m.begin(); i != m.end(); ++i) {
- // sort
- std::sort(i->begin(), i->end(), mgf::LessThanMz());
- typedef mgf::MgfSpectrum::iterator MSI;
- // extract TMT reproter ion intensities
- bool atLeastOneEntry = false;
- for (size_t n = 0; n < sizes[labelType]; ++n) {
- MSI closestIt = findClosestMz(i->begin(), i->end(), labelMasses[n]);
- if (closestIt != i->end()) {
- // check if there is an MS2 centroid
- if (std::abs(closestIt->first - labelMasses[n]) < 0.4) {
- obsAbundances[n] = closestIt->second;
- if (!atLeastOneEntry) atLeastOneEntry = true;
- } else {
- obsAbundances[n] = 0.0;
- }
- }
- }
- // extract into file
- if (atLeastOneEntry) {
- std::cout << i->getTITLE();
- for (size_t n = 0; n < sizes[labelType]; ++n) {
- std::cout << '\t' << std::setprecision(precision) << obsAbundances[n];
- }
- std::cout << '\n'; // don't use std::endl, save the std::flush.
- }
- }
- return 0;
-}
-
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|
|
From: <mki...@us...> - 2010-10-10 10:59:05
|
Revision: 40
http://mgfp.svn.sourceforge.net/mgfp/?rev=40&view=rev
Author: mkirchner
Date: 2010-10-10 10:58:58 +0000 (Sun, 10 Oct 2010)
Log Message:
-----------
adding reference to Renard et al.
Modified Paths:
--------------
trunk/mgfp/doc/Mainpage.h
Modified: trunk/mgfp/doc/Mainpage.h
===================================================================
--- trunk/mgfp/doc/Mainpage.h 2010-09-10 15:35:49 UTC (rev 39)
+++ trunk/mgfp/doc/Mainpage.h 2010-10-10 10:58:58 UTC (rev 40)
@@ -4,7 +4,11 @@
\section sec_intro Introduction
\c mgfp is a flex/bison-based C++ MGF parser library.<br>
+It includes the library code as well as the following set of
+MGF processing tools:
+\li mgfvalidate -- validates a given MGF file
+
The <a href="http://steenlab.org">Steen \& Steen Lab</a> provides
the library under the terms of a BSD license for use in academic and
non-academic environments.
@@ -16,9 +20,17 @@
Kirchner M, Steen JAJ, Hamprecht FA, Steen H (2010).
MGFp: An open Mascot Generic Format parser library implementation.
-<i>Journal of Proteome Research, in press.</i>
-[<a href="http://www.ncbi.nlm.nih.gov/pubmed/20334363">PubMed</a>]
+<i>Journal of Proteome Research, 9(5):2762-2763 (2010)</i>.
+[<a href="http://www.ncbi.nlm.nih.gov/pubmed/20334363">PubMed entry</a>]
+If you use ms2preproc in your data analysis pipeline, please cite<br>
+
+Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J,
+Winter D, Steen JAJ, Hamprecht FA, Steen H, When Less
+Can Yield More - Computational Preprocessing of MS/MS Spectra for
+Peptide Identification, <i>Proteomics 9(21):4978-4984 (2009)</i>.
+[<a href="http://www.ncbi.nlm.nih.gov/pubmed/19743429">PubMed entry</a>]
+
\section sec_install Installation
\subsection sec_install_bin Obtaining the Software
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mki...@us...> - 2010-09-10 15:35:55
|
Revision: 39
http://mgfp.svn.sourceforge.net/mgfp/?rev=39&view=rev
Author: mkirchner
Date: 2010-09-10 15:35:49 +0000 (Fri, 10 Sep 2010)
Log Message:
-----------
reflect the interface change in the version number (upgrading to 2.0)
Modified Paths:
--------------
trunk/mgfp/CMakeLists.txt
Modified: trunk/mgfp/CMakeLists.txt
===================================================================
--- trunk/mgfp/CMakeLists.txt 2010-09-10 15:33:39 UTC (rev 38)
+++ trunk/mgfp/CMakeLists.txt 2010-09-10 15:35:49 UTC (rev 39)
@@ -9,8 +9,8 @@
#############################################################################
# versioning
#############################################################################
-set(VERSION_MAJOR 1)
-set(VERSION_MINOR 3)
+set(VERSION_MAJOR 2)
+set(VERSION_MINOR 0)
# get SVN revision
EXECUTE_PROCESS(
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|
|
From: <mki...@us...> - 2010-09-10 15:33:47
|
Revision: 38
http://mgfp.svn.sourceforge.net/mgfp/?rev=38&view=rev
Author: mkirchner
Date: 2010-09-10 15:33:39 +0000 (Fri, 10 Sep 2010)
Log Message:
-----------
* parser extensions: now accepting ranges for SCANS and RTINSECONDS.
* this caused an interface change. :-(
Modified Paths:
--------------
trunk/mgfp/include/mgfp/MgfSpectrum.h
trunk/mgfp/src/MgfFile.cpp
trunk/mgfp/src/MgfHeader.cpp
trunk/mgfp/src/MgfSpectrum.cpp
trunk/mgfp/src/Parser.cpp
trunk/mgfp/src/Parser.h
trunk/mgfp/src/Parser.ypp
trunk/mgfp/src/Scanner.cpp
trunk/mgfp/src/Scanner.l
Modified: trunk/mgfp/include/mgfp/MgfSpectrum.h
===================================================================
--- trunk/mgfp/include/mgfp/MgfSpectrum.h 2010-09-10 15:30:49 UTC (rev 37)
+++ trunk/mgfp/include/mgfp/MgfSpectrum.h 2010-09-10 15:33:39 UTC (rev 38)
@@ -123,31 +123,48 @@
*/
void setPEPMASS(const std::pair<double, double> pepmass);
- /** Get the retention time of the precursor.
- * @return The retention time of the precursor, in seconds.
+ /** Get the retention time range of the precursor scans.
+ * @return The retention time range of the precursor scans, in seconds.
+ * If the precursors stem from a single scan, the .second entry
+ * of the returned std::pair equals -1.0.
*/
- double getRTINSECONDS(void) const;
+ std::pair<double,double> getRTINSECONDS(void) const;
- /** Set the retention time of the precursor.
- * @param[in] rtinseconds The retention time of the precursor, in seconds.
+ /** Set the retention time range of the precursor scans.
+ * @param[in] rtinseconds The retention time of the precursor scan(s),
+ * in seconds. For single scans, use -1.0 as .second value
+ * or the alternate setRTINSECONDS function that takes a
+ * single double.
*/
+ void setRTINSECONDS(const std::pair<double,double>& rtinseconds);
+
+ /** Set the retention time range of a single precursor scan.
+ * @param[in] rtinseconds The retention time of the precursor scan,
+ * in seconds.
+ */
void setRTINSECONDS(const double rtinseconds);
- /** Get
- * @see
- * @return
+ /** Get the scan number or scan number range from which this fragmentation
+ * spectrum was generated.
+ * @see http://www.matrixscience.com/help/data_file_help.html
+ * @return A pair of scan numbers. For fragmentation spectra of single
+ * scans, the .second value of the return value equals -1.
*/
- std::string getSCANS(void) const;
+ std::pair<int, int> getSCANS(void) const;
- /** Set
- * @see
- * @param[in]
+ /** Set the scan number or scan number range from which this fragmentation
+ * spectrum was generated.
+ * @see http://www.matrixscience.com/help/data_file_help.html
+ * @param[in] A pair [start, end] of scan numbers. For single scans
+ * use [scanNumber, -1].
*/
- void setSCANS(const std::string& scans);
+ void setSCANS(const std::pair<int, int>& scans);
- /** Set
- * @see
- * @param[in]
+ /** Set the scan number from which this fragmentation
+ * spectrum was generated. This is just a convenience function wrapper
+ * for single scans.
+ * @see http://www.matrixscience.com/help/data_file_help.html
+ * @param[in] A scan number.
*/
void setSCANS(const int scans);
@@ -228,8 +245,9 @@
std::vector<int> charges_;
std::string comp_, etag_, instrument_, it_mods_;
std::pair<double, double> pepmass_;
- double rtinseconds_;
- std::string scans_, seq_, tag_, title_; // FIXME: scans_ should be a vector of ranges
+ std::pair<double, double> rtinseconds_;
+ std::pair<int, int> scans_;
+ std::string seq_, tag_, title_;
double tol_;
std::string tolu_;
};
Modified: trunk/mgfp/src/MgfFile.cpp
===================================================================
--- trunk/mgfp/src/MgfFile.cpp 2010-09-10 15:30:49 UTC (rev 37)
+++ trunk/mgfp/src/MgfFile.cpp 2010-09-10 15:33:39 UTC (rev 38)
@@ -22,7 +22,7 @@
std::ostream& operator<<(std::ostream& os, const MgfFile& mgf) {
os << mgf.header_;
for (MgfFile::const_iterator i = mgf.begin(); i != mgf.end(); ++i) {
- os << std::endl << *i;
+ os << '\n' << *i;
}
return os;
}
Modified: trunk/mgfp/src/MgfHeader.cpp
===================================================================
--- trunk/mgfp/src/MgfHeader.cpp 2010-09-10 15:30:49 UTC (rev 37)
+++ trunk/mgfp/src/MgfHeader.cpp 2010-09-10 15:33:39 UTC (rev 38)
@@ -203,15 +203,15 @@
std::ostream& operator<<(std::ostream& os, const MgfHeader& mgf) {
typedef std::map<std::string, std::string>::const_iterator MSSCI;
for (MSSCI i = mgf.strings.begin(); i != mgf.strings.end() ; ++i) {
- os << i->first << '=' << i->second << std::endl;
+ os << i->first << '=' << i->second << '\n';
}
typedef std::map<std::string, int>::const_iterator MSICI;
for (MSICI i = mgf.ints.begin(); i != mgf.ints.end() ; ++i) {
- os << i->first << '=' << i->second << std::endl;
+ os << i->first << '=' << i->second << '\n';
}
typedef std::map<std::string, double>::const_iterator MSDCI;
for (MSDCI i = mgf.doubles.begin(); i != mgf.doubles.end() ; ++i) {
- os << i->first << '=' << i->second << std::endl;
+ os << i->first << '=' << i->second << '\n';
}
typedef std::vector<int>::const_iterator VICI;
if (!mgf.charges_.empty()) {
@@ -227,7 +227,7 @@
os << '-';
}
}
- os << std::endl;
+ os << '\n';
}
if (!mgf.frames_.empty()) {
os << "FRAMES=";
@@ -237,7 +237,7 @@
}
os << *i;
}
- os << std::endl;
+ os << '\n';
}
return os;
}
Modified: trunk/mgfp/src/MgfSpectrum.cpp
===================================================================
--- trunk/mgfp/src/MgfSpectrum.cpp 2010-09-10 15:30:49 UTC (rev 37)
+++ trunk/mgfp/src/MgfSpectrum.cpp 2010-09-10 15:33:39 UTC (rev 38)
@@ -1,12 +1,16 @@
#include <mgfp/MgfSpectrum.h>
#include <cstdlib> // for std::abs(int)
+#include <iostream>
#include <sstream>
+#include <utility>
namespace mgf {
MgfSpectrum::MgfSpectrum() : Collection<MassAbundancePair>() {
this->clear();
+ scans_ = std::make_pair(-1, -1);
+ rtinseconds_ = std::make_pair(-1.0, -1.0);
}
std::vector<int> MgfSpectrum::getCHARGE(void) const {
@@ -58,24 +62,24 @@
pepmass_ = pepmass;
}
-double MgfSpectrum::getRTINSECONDS(void) const {
+std::pair<double, double> MgfSpectrum::getRTINSECONDS(void) const {
return rtinseconds_;
}
-void MgfSpectrum::setRTINSECONDS(const double rtinseconds) {
+void MgfSpectrum::setRTINSECONDS(const std::pair<double,double>& rtinseconds) {
rtinseconds_ = rtinseconds;
}
+void MgfSpectrum::setRTINSECONDS(const double rtinseconds) {
+ setRTINSECONDS(std::make_pair(rtinseconds, -1.0));
+}
-std::string MgfSpectrum::getSCANS(void) const {
- return scans_; // FIXME
+std::pair<int, int> MgfSpectrum::getSCANS(void) const {
+ return scans_;
}
-void MgfSpectrum::setSCANS(const std::string& scans) {
- scans_ = scans; //FIXME
+void MgfSpectrum::setSCANS(const std::pair<int, int>& scans) {
+ scans_ = scans;
}
-
-void MgfSpectrum::setSCANS(const int scans) {
- std::ostringstream oss;
- oss << scans;
- scans_ = oss.str(); //FIXME
+void MgfSpectrum::setSCANS(const int scan) {
+ setSCANS(std::make_pair(scan, -1));
}
std::string MgfSpectrum::getSEQ(void) const {
@@ -115,19 +119,20 @@
void MgfSpectrum::clear() {
charges_.clear();
- comp_ = etag_ = instrument_ = it_mods_ = scans_ = "";
+ scans_ = std::make_pair(-1, -1);
+ comp_ = etag_ = instrument_ = it_mods_;
seq_ = tag_ = title_ = tolu_ = "";
pepmass_ = std::make_pair(0.0, 0.0);
- rtinseconds_ = 0;
+ rtinseconds_ = std::make_pair(-1.0, -1.0);
tol_ = 0.0;
Collection<MassAbundancePair>::clear();
}
std::ostream& operator<<(std::ostream& os, const MgfSpectrum& mgf) {
// start with title, then A-Z
- os << "BEGIN IONS" << std::endl;
+ os << "BEGIN IONS" << '\n';
if (!mgf.title_.empty())
- os << "TITLE=" << mgf.title_ << std::endl;
+ os << "TITLE=" << mgf.title_ << '\n';
if (!mgf.charges_.empty()) {
os << "CHARGE=";
typedef std::vector<int>::const_iterator VICI;
@@ -142,39 +147,49 @@
os << '-';
}
}
- os << std::endl;
+ os << '\n';
}
if (!mgf.comp_.empty())
- os << "COMP=" << mgf.comp_ << std::endl;
+ os << "COMP=" << mgf.comp_ << '\n';
if (!mgf.etag_.empty())
- os << "ETAG=" << mgf.etag_ << std::endl;
+ os << "ETAG=" << mgf.etag_ << '\n';
if (!mgf.instrument_.empty())
- os << "INSTRUMENT=" << mgf.instrument_ << std::endl;
+ os << "INSTRUMENT=" << mgf.instrument_ << '\n';
if (!mgf.it_mods_.empty())
- os << "IT_MODS=" << mgf.it_mods_ << std::endl;
+ os << "IT_MODS=" << mgf.it_mods_ << '\n';
if (mgf.pepmass_.first > 0.0) {
os << "PEPMASS=" << mgf.pepmass_.first;
if (mgf.pepmass_.second > 0.0) {
os << " " << mgf.pepmass_.second;
}
- os << std::endl;
+ os << '\n';
}
- if (mgf.rtinseconds_ > 0)
- os << "RTINSECONDS=" << mgf.rtinseconds_ << std::endl;
- if (!mgf.scans_.empty())
- os << "SCANS=" << mgf.scans_ << std::endl;
+ if (mgf.rtinseconds_.first != -1.0) {
+ os << "RTINSECONDS=" << mgf.rtinseconds_.first;
+ if (mgf.rtinseconds_.second != -1.0) {
+ os << "-" << mgf.rtinseconds_.second;
+ }
+ os << '\n';
+ }
+ if (mgf.scans_.first != -1) {
+ os << "SCANS=" << mgf.scans_.first;
+ if (mgf.scans_.second != -1) {
+ os << "-" << mgf.scans_.second;
+ }
+ os << '\n';
+ }
if (!mgf.seq_.empty())
- os << "SEQ=" << mgf.seq_ << std::endl;
+ os << "SEQ=" << mgf.seq_ << '\n';
if (!mgf.tag_.empty())
- os << "TAG=" << mgf.tag_ << std::endl;
+ os << "TAG=" << mgf.tag_ << '\n';
if (mgf.tol_ > 0.0)
- os << "TOL=" << mgf.tol_ << std::endl;
+ os << "TOL=" << mgf.tol_ << '\n';
if (!mgf.tolu_.empty())
- os << "TOLU=" << mgf.tolu_ << std::endl;
+ os << "TOLU=" << mgf.tolu_ << '\n';
for (MgfSpectrum::const_iterator i = mgf.begin(); i != mgf.end(); ++i) {
- os << i->first << " " << i->second << std::endl;
+ os << i->first << " " << i->second << '\n';
}
- os << "END IONS" << std::endl;
+ os << "END IONS" << '\n';
return os;
}
Modified: trunk/mgfp/src/Parser.cpp
===================================================================
--- trunk/mgfp/src/Parser.cpp 2010-09-10 15:30:49 UTC (rev 37)
+++ trunk/mgfp/src/Parser.cpp 2010-09-10 15:33:39 UTC (rev 38)
@@ -47,7 +47,7 @@
/* User implementation prologue. */
/* Line 317 of lalr1.cc */
-#line 117 "Parser.ypp"
+#line 118 "Parser.ypp"
#include <mgfp/Driver.h>
#include "Scanner.h"
@@ -232,7 +232,7 @@
case 8: /* "\"string\"" */
/* Line 480 of lalr1.cc */
-#line 114 "Parser.ypp"
+#line 115 "Parser.ypp"
{ delete (yyvaluep->stringVal); };
/* Line 480 of lalr1.cc */
@@ -241,7 +241,7 @@
case 54: /* "ion" */
/* Line 480 of lalr1.cc */
-#line 115 "Parser.ypp"
+#line 116 "Parser.ypp"
{ delete (yyvaluep->doublepairnode); };
/* Line 480 of lalr1.cc */
@@ -250,7 +250,7 @@
case 55: /* "ions" */
/* Line 480 of lalr1.cc */
-#line 115 "Parser.ypp"
+#line 116 "Parser.ypp"
{ delete (yyvaluep->doublepairlistnode); };
/* Line 480 of lalr1.cc */
@@ -259,7 +259,7 @@
case 56: /* "charge" */
/* Line 480 of lalr1.cc */
-#line 115 "Parser.ypp"
+#line 116 "Parser.ypp"
{ delete (yyvaluep->integernode); };
/* Line 480 of lalr1.cc */
@@ -268,7 +268,7 @@
case 57: /* "charges" */
/* Line 480 of lalr1.cc */
-#line 115 "Parser.ypp"
+#line 116 "Parser.ypp"
{ delete (yyvaluep->integerlistnode); };
/* Line 480 of lalr1.cc */
@@ -277,7 +277,7 @@
case 58: /* "csintegerlist" */
/* Line 480 of lalr1.cc */
-#line 115 "Parser.ypp"
+#line 116 "Parser.ypp"
{ delete (yyvaluep->integerlistnode); };
/* Line 480 of lalr1.cc */
@@ -360,7 +360,7 @@
/* User initialization code. */
/* Line 553 of lalr1.cc */
-#line 39 "Parser.ypp"
+#line 40 "Parser.ypp"
{
// initialize the initial location object
yylloc.begin.filename = yylloc.end.filename = &driver.streamname;
@@ -486,105 +486,105 @@
case 2:
/* Line 678 of lalr1.cc */
-#line 130 "Parser.ypp"
+#line 131 "Parser.ypp"
{ (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].doubleVal), (yysemantic_stack_[(3) - (2)].doubleVal)); }
break;
case 3:
/* Line 678 of lalr1.cc */
-#line 131 "Parser.ypp"
+#line 132 "Parser.ypp"
{ (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].integerVal), (yysemantic_stack_[(3) - (2)].doubleVal)); }
break;
case 4:
/* Line 678 of lalr1.cc */
-#line 132 "Parser.ypp"
+#line 133 "Parser.ypp"
{ (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].doubleVal), (yysemantic_stack_[(3) - (2)].integerVal)); }
break;
case 5:
/* Line 678 of lalr1.cc */
-#line 133 "Parser.ypp"
+#line 134 "Parser.ypp"
{ (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].integerVal), (yysemantic_stack_[(3) - (2)].integerVal)); }
break;
case 6:
/* Line 678 of lalr1.cc */
-#line 135 "Parser.ypp"
+#line 136 "Parser.ypp"
{ (yyval.doublepairlistnode) = new DoublePairListNode((yysemantic_stack_[(2) - (1)].doublepairlistnode), (yysemantic_stack_[(2) - (2)].doublepairnode)); }
break;
case 7:
/* Line 678 of lalr1.cc */
-#line 136 "Parser.ypp"
+#line 137 "Parser.ypp"
{ (yyval.doublepairlistnode) = new DoublePairListNode((yysemantic_stack_[(1) - (1)].doublepairnode)); }
break;
case 8:
/* Line 678 of lalr1.cc */
-#line 138 "Parser.ypp"
+#line 139 "Parser.ypp"
{ (yyval.integernode) = new IntegerNode((yysemantic_stack_[(2) - (1)].integerVal)); }
break;
case 9:
/* Line 678 of lalr1.cc */
-#line 139 "Parser.ypp"
+#line 140 "Parser.ypp"
{ (yyval.integernode) = new IntegerNode(-(yysemantic_stack_[(2) - (1)].integerVal)); }
break;
case 10:
/* Line 678 of lalr1.cc */
-#line 141 "Parser.ypp"
+#line 142 "Parser.ypp"
{ (yyval.integerlistnode) = (yysemantic_stack_[(3) - (2)].integerlistnode); }
break;
case 11:
/* Line 678 of lalr1.cc */
-#line 142 "Parser.ypp"
+#line 143 "Parser.ypp"
{ (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integernode)); }
break;
case 12:
/* Line 678 of lalr1.cc */
-#line 143 "Parser.ypp"
+#line 144 "Parser.ypp"
{ (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integernode)); }
break;
case 13:
/* Line 678 of lalr1.cc */
-#line 144 "Parser.ypp"
+#line 145 "Parser.ypp"
{ (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(1) - (1)].integernode)); }
break;
case 14:
/* Line 678 of lalr1.cc */
-#line 146 "Parser.ypp"
+#line 147 "Parser.ypp"
{ (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integerVal)); }
break;
case 15:
/* Line 678 of lalr1.cc */
-#line 147 "Parser.ypp"
+#line 148 "Parser.ypp"
{ (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(1) - (1)].integerVal)); }
break;
case 17:
/* Line 678 of lalr1.cc */
-#line 151 "Parser.ypp"
+#line 152 "Parser.ypp"
{
driver.context.mgfFile.push_back(driver.context.currentSpectrum);
driver.context.currentSpectrum.clear();
@@ -594,353 +594,416 @@
case 18:
/* Line 678 of lalr1.cc */
-#line 157 "Parser.ypp"
+#line 158 "Parser.ypp"
{
driver.context.currentSpectrum.assign(((yysemantic_stack_[(6) - (4)].doublepairlistnode)->pairlist_)->begin(), ((yysemantic_stack_[(6) - (4)].doublepairlistnode)->pairlist_)->end());
delete (yysemantic_stack_[(6) - (4)].doublepairlistnode);
}
break;
- case 21:
+ case 22:
/* Line 678 of lalr1.cc */
-#line 165 "Parser.ypp"
+#line 167 "Parser.ypp"
{ driver.context.header.setCLE(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 22:
+ case 23:
/* Line 678 of lalr1.cc */
-#line 166 "Parser.ypp"
+#line 168 "Parser.ypp"
{ driver.context.header.setCOM(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 23:
+ case 24:
/* Line 678 of lalr1.cc */
-#line 167 "Parser.ypp"
+#line 169 "Parser.ypp"
{ driver.context.header.setDB(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 24:
+ case 25:
/* Line 678 of lalr1.cc */
-#line 168 "Parser.ypp"
+#line 170 "Parser.ypp"
{ driver.context.header.setFORMAT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 25:
+ case 26:
/* Line 678 of lalr1.cc */
-#line 169 "Parser.ypp"
+#line 171 "Parser.ypp"
{ driver.context.header.setINSTRUMENT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 26:
+ case 27:
/* Line 678 of lalr1.cc */
-#line 170 "Parser.ypp"
+#line 172 "Parser.ypp"
{ driver.context.header.setIT_MODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 27:
+ case 28:
/* Line 678 of lalr1.cc */
-#line 171 "Parser.ypp"
+#line 173 "Parser.ypp"
{ driver.context.header.setITOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 28:
+ case 29:
/* Line 678 of lalr1.cc */
-#line 172 "Parser.ypp"
+#line 174 "Parser.ypp"
{ driver.context.header.setMASS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 29:
+ case 30:
/* Line 678 of lalr1.cc */
-#line 173 "Parser.ypp"
+#line 175 "Parser.ypp"
{ driver.context.header.setMODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 30:
+ case 31:
/* Line 678 of lalr1.cc */
-#line 174 "Parser.ypp"
+#line 176 "Parser.ypp"
{ driver.context.header.setQUANTITATION(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 31:
+ case 32:
/* Line 678 of lalr1.cc */
-#line 175 "Parser.ypp"
+#line 177 "Parser.ypp"
{ driver.context.header.setREPORT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 32:
+ case 33:
/* Line 678 of lalr1.cc */
-#line 176 "Parser.ypp"
+#line 178 "Parser.ypp"
{ driver.context.header.setREPTYPE(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 33:
+ case 34:
/* Line 678 of lalr1.cc */
-#line 177 "Parser.ypp"
+#line 179 "Parser.ypp"
{ driver.context.header.setSEARCH(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 34:
+ case 35:
/* Line 678 of lalr1.cc */
-#line 178 "Parser.ypp"
+#line 180 "Parser.ypp"
{ driver.context.header.setTAXONOMY(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 35:
+ case 36:
/* Line 678 of lalr1.cc */
-#line 179 "Parser.ypp"
+#line 181 "Parser.ypp"
{ driver.context.header.setTOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 36:
+ case 37:
/* Line 678 of lalr1.cc */
-#line 180 "Parser.ypp"
+#line 182 "Parser.ypp"
{ /*driver.context.header.setUSER(*$3);*/ delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 37:
+ case 38:
/* Line 678 of lalr1.cc */
-#line 181 "Parser.ypp"
+#line 183 "Parser.ypp"
{ driver.context.header.setUSEREMAIL(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 38:
+ case 39:
/* Line 678 of lalr1.cc */
-#line 182 "Parser.ypp"
+#line 184 "Parser.ypp"
{ driver.context.header.setUSERNAME(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 39:
+ case 40:
/* Line 678 of lalr1.cc */
-#line 183 "Parser.ypp"
+#line 185 "Parser.ypp"
{ driver.context.header.setDECOY(((yysemantic_stack_[(4) - (3)].integerVal))!=0); }
break;
- case 40:
+ case 41:
/* Line 678 of lalr1.cc */
-#line 184 "Parser.ypp"
+#line 186 "Parser.ypp"
{ driver.context.header.setERRORTOLERANT(((yysemantic_stack_[(4) - (3)].integerVal))!=0); }
break;
- case 41:
+ case 42:
/* Line 678 of lalr1.cc */
-#line 185 "Parser.ypp"
+#line 187 "Parser.ypp"
{ driver.context.header.setPFA((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
- case 42:
+ case 43:
/* Line 678 of lalr1.cc */
-#line 186 "Parser.ypp"
+#line 188 "Parser.ypp"
{ driver.context.header.setITOL((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
- case 43:
+ case 44:
/* Line 678 of lalr1.cc */
-#line 187 "Parser.ypp"
+#line 189 "Parser.ypp"
{ driver.context.header.setITOL((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
- case 44:
+ case 45:
/* Line 678 of lalr1.cc */
-#line 188 "Parser.ypp"
+#line 190 "Parser.ypp"
{ driver.context.header.setPEP_ISOTOPE_ERROR((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
- case 45:
+ case 46:
/* Line 678 of lalr1.cc */
-#line 189 "Parser.ypp"
+#line 191 "Parser.ypp"
{ driver.context.header.setPRECURSOR((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
- case 46:
+ case 47:
/* Line 678 of lalr1.cc */
-#line 190 "Parser.ypp"
+#line 192 "Parser.ypp"
+ { driver.context.header.setPRECURSOR((yysemantic_stack_[(4) - (3)].integerVal)); }
+ break;
+
+ case 48:
+
+/* Line 678 of lalr1.cc */
+#line 193 "Parser.ypp"
{ driver.context.header.setSEG((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
- case 47:
+ case 49:
/* Line 678 of lalr1.cc */
-#line 191 "Parser.ypp"
+#line 194 "Parser.ypp"
+ { driver.context.header.setSEG((yysemantic_stack_[(4) - (3)].integerVal)); }
+ break;
+
+ case 50:
+
+/* Line 678 of lalr1.cc */
+#line 195 "Parser.ypp"
{ driver.context.header.setTOL((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
- case 48:
+ case 51:
/* Line 678 of lalr1.cc */
-#line 192 "Parser.ypp"
+#line 196 "Parser.ypp"
{ driver.context.header.setTOL((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
- case 49:
+ case 52:
/* Line 678 of lalr1.cc */
-#line 193 "Parser.ypp"
+#line 197 "Parser.ypp"
{ driver.context.header.setCHARGE(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); }
break;
- case 50:
+ case 53:
/* Line 678 of lalr1.cc */
-#line 194 "Parser.ypp"
+#line 198 "Parser.ypp"
{ driver.context.header.setFRAMES(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); }
break;
- case 54:
+ case 57:
/* Line 678 of lalr1.cc */
-#line 200 "Parser.ypp"
+#line 204 "Parser.ypp"
{ driver.context.currentSpectrum.setTITLE(*(yysemantic_stack_[(2) - (1)].stringVal)); delete (yysemantic_stack_[(2) - (1)].stringVal); }
break;
- case 55:
+ case 58:
/* Line 678 of lalr1.cc */
-#line 201 "Parser.ypp"
+#line 205 "Parser.ypp"
{ driver.context.currentSpectrum.setCOMP(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 56:
+ case 59:
/* Line 678 of lalr1.cc */
-#line 202 "Parser.ypp"
+#line 206 "Parser.ypp"
{ driver.context.currentSpectrum.setINSTRUMENT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 57:
+ case 60:
/* Line 678 of lalr1.cc */
-#line 203 "Parser.ypp"
+#line 207 "Parser.ypp"
{ driver.context.currentSpectrum.setIT_MODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 58:
+ case 61:
/* Line 678 of lalr1.cc */
-#line 204 "Parser.ypp"
+#line 208 "Parser.ypp"
{ driver.context.currentSpectrum.setRTINSECONDS((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
- case 59:
+ case 62:
/* Line 678 of lalr1.cc */
-#line 205 "Parser.ypp"
- { driver.context.currentSpectrum.setSCANS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
+#line 209 "Parser.ypp"
+ { driver.context.currentSpectrum.setRTINSECONDS((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
- case 60:
+ case 63:
/* Line 678 of lalr1.cc */
-#line 206 "Parser.ypp"
- { driver.context.currentSpectrum.setSCANS((yysemantic_stack_[(4) - (3)].integerVal)); }
+#line 210 "Parser.ypp"
+ { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair((yysemantic_stack_[(6) - (3)].doubleVal), (yysemantic_stack_[(6) - (5)].doubleVal))); }
break;
- case 61:
+ case 64:
/* Line 678 of lalr1.cc */
-#line 207 "Parser.ypp"
+#line 211 "Parser.ypp"
+ { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair((yysemantic_stack_[(6) - (3)].doubleVal), (yysemantic_stack_[(6) - (5)].integerVal))); }
+ break;
+
+ case 65:
+
+/* Line 678 of lalr1.cc */
+#line 212 "Parser.ypp"
+ { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair((yysemantic_stack_[(6) - (3)].integerVal), (yysemantic_stack_[(6) - (5)].doubleVal))); }
+ break;
+
+ case 66:
+
+/* Line 678 of lalr1.cc */
+#line 213 "Parser.ypp"
+ { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair((yysemantic_stack_[(6) - (3)].integerVal), (yysemantic_stack_[(6) - (5)].integerVal))); }
+ break;
+
+ case 67:
+
+/* Line 678 of lalr1.cc */
+#line 214 "Parser.ypp"
+ { driver.context.currentSpectrum.setSCANS(std::make_pair((yysemantic_stack_[(4) - (3)].integerVal), -1)); }
+ break;
+
+ case 68:
+
+/* Line 678 of lalr1.cc */
+#line 215 "Parser.ypp"
+ { driver.context.currentSpectrum.setSCANS(std::make_pair((yysemantic_stack_[(6) - (3)].integerVal), (yysemantic_stack_[(6) - (5)].integerVal))); }
+ break;
+
+ case 69:
+
+/* Line 678 of lalr1.cc */
+#line 216 "Parser.ypp"
{ driver.context.currentSpectrum.setTOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 62:
+ case 70:
/* Line 678 of lalr1.cc */
-#line 208 "Parser.ypp"
+#line 217 "Parser.ypp"
{ driver.context.currentSpectrum.setSEQ(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 63:
+ case 71:
/* Line 678 of lalr1.cc */
-#line 209 "Parser.ypp"
+#line 218 "Parser.ypp"
{ driver.context.currentSpectrum.setTAG(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 64:
+ case 72:
/* Line 678 of lalr1.cc */
-#line 210 "Parser.ypp"
+#line 219 "Parser.ypp"
{ driver.context.currentSpectrum.setETAG(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
- case 65:
+ case 73:
/* Line 678 of lalr1.cc */
-#line 211 "Parser.ypp"
+#line 220 "Parser.ypp"
{ driver.context.currentSpectrum.setTOL((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
- case 66:
+ case 74:
/* Line 678 of lalr1.cc */
-#line 212 "Parser.ypp"
+#line 221 "Parser.ypp"
{ driver.context.currentSpectrum.setTOL((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
- case 67:
+ case 75:
/* Line 678 of lalr1.cc */
-#line 213 "Parser.ypp"
+#line 222 "Parser.ypp"
{ driver.context.currentSpectrum.setCHARGE(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); }
break;
- case 68:
+ case 76:
/* Line 678 of lalr1.cc */
-#line 214 "Parser.ypp"
+#line 223 "Parser.ypp"
{ driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(4) - (3)].doubleVal), 0.0)); }
break;
- case 69:
+ case 77:
/* Line 678 of lalr1.cc */
-#line 215 "Parser.ypp"
+#line 224 "Parser.ypp"
{ driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].doubleVal), (yysemantic_stack_[(5) - (4)].doubleVal))); }
break;
- case 70:
+ case 78:
/* Line 678 of lalr1.cc */
-#line 216 "Parser.ypp"
+#line 225 "Parser.ypp"
+ { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].doubleVal), (yysemantic_stack_[(5) - (4)].integerVal))); }
+ break;
+
+ case 79:
+
+/* Line 678 of lalr1.cc */
+#line 226 "Parser.ypp"
{ driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(4) - (3)].integerVal), 0.0)); }
break;
- case 71:
+ case 80:
/* Line 678 of lalr1.cc */
-#line 217 "Parser.ypp"
+#line 227 "Parser.ypp"
+ { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].integerVal), (yysemantic_stack_[(5) - (4)].doubleVal))); }
+ break;
+
+ case 81:
+
+/* Line 678 of lalr1.cc */
+#line 228 "Parser.ypp"
{ driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].integerVal), (yysemantic_stack_[(5) - (4)].integerVal))); }
break;
- case 73:
+ case 83:
/* Line 678 of lalr1.cc */
-#line 222 "Parser.ypp"
+#line 233 "Parser.ypp"
{
driver.context.mgfFile.setHeader(driver.context.header);
driver.context.header.clear();
@@ -950,7 +1013,7 @@
/* Line 678 of lalr1.cc */
-#line 954 "Parser.cpp"
+#line 1017 "Parser.cpp"
default:
break;
}
@@ -1155,33 +1218,35 @@
/* YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
STATE-NUM. */
- const signed char Parser::yypact_ninf_ = -70;
+ const signed char Parser::yypact_ninf_ = -98;
const short int
Parser::yypact_[] =
{
- -70, 33, -70, 8, 30, -10, -6, 38, 39, 40,
- 41, 42, 43, 44, 45, 46, 48, 49, 50, 51,
- 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,
- 62, 63, 64, 27, -70, -70, -70, 5, 109, 110,
- 32, 111, 112, 113, 114, 115, 116, 117, 118, 119,
- 120, 121, 122, 123, 124, 125, 126, 129, 130, 34,
- 131, 133, 134, 135, 137, -70, 141, -70, -3, 5,
- -70, -2, 142, 143, 144, 145, 146, 147, 148, 149,
- 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
- 160, 161, 162, 163, 164, 165, 166, 167, 168, 169,
- -70, 2, -70, -70, -70, 1, -70, 170, 170, -70,
- -70, -70, -70, -70, -70, -70, -70, -70, -70, -70,
- -70, -70, -70, -70, -70, -70, -70, -70, -70, -70,
- -70, -70, -70, -70, -70, -70, -70, -70, 171, 3,
- -70, -70, -70, -70, 172, 74, 76, 85, 88, 127,
- 128, 132, 136, 138, 139, 140, 173, 175, 174, 176,
- -70, 22, -70, -70, 178, 179, 180, 182, 5, 181,
- 185, 186, 187, 78, 189, 24, 190, 191, -70, 80,
- 192, 183, -70, -70, -70, -70, -70, -1, 184, 194,
- 198, 199, 9, 28, 200, 201, 202, 203, 204, 205,
- 206, 207, -70, -70, -70, -70, -70, -70, -70, 208,
- -70, 209, -70, -70, -70, -70, -70, -70, -70, -70,
- -70, -70
+ -98, 53, -98, 59, 104, 14, 56, 57, 60, 61,
+ 62, 64, 66, 68, 69, 70, 71, 72, 73, 74,
+ 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,
+ 85, 86, 87, 34, -98, -98, -98, 9, 102, 103,
+ 12, 107, 109, 111, 132, 133, 134, 135, 136, 137,
+ 138, 139, 140, 141, 142, 143, 144, 147, 148, 31,
+ 55, 149, 33, 54, 150, -98, 154, -98, -40, 9,
+ -98, -2, 155, 156, 157, 158, 159, 160, 161, 162,
+ 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ 173, 174, 175, 176, 177, 178, 179, 180, 181, 182,
+ 183, 184, -98, 2, -98, -98, -98, 1, -98, 185,
+ 185, -98, -98, -98, -98, -98, -98, -98, -98, -98,
+ -98, -98, -98, -98, -98, -98, -98, -98, -98, -98,
+ -98, -98, -98, -98, -98, -98, -98, -98, -98, -98,
+ -98, -98, 186, 10, -98, -98, -98, -98, 187, 58,
+ 63, 145, 146, 190, 151, 152, 153, 188, 189, 191,
+ 192, 193, 196, 194, 195, -98, 29, -98, -98, 197,
+ 198, 199, 203, 9, 200, -98, 201, 202, 204, 65,
+ 67, 205, 206, 207, -98, 94, 208, 210, -98, -98,
+ -98, -98, -98, -1, 214, 215, 216, 217, 39, 41,
+ 6, 7, 8, 218, 219, 220, 221, 222, -98, -98,
+ -98, -98, -98, -98, -98, 223, 224, -98, 225, 226,
+ -98, 96, -98, 99, -98, 227, -98, -98, -98, -98,
+ -98, -98, -98, -98, -98, 228, 229, 231, 232, 233,
+ -98, -98, -98, -98, -98
};
/* YYDEFACT[S] -- default rule to reduce with in state S when YYTABLE
@@ -1190,45 +1255,47 @@
const unsigned char
Parser::yydefact_[] =
{
- 19, 16, 74, 0, 0, 0, 0, 0, 0, 0,
+ 20, 16, 84, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 20, 1, 51, 0, 0, 0,
+ 0, 0, 0, 0, 21, 1, 54, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 73, 0, 17, 0, 0,
+ 0, 0, 0, 0, 0, 83, 0, 17, 0, 0,
13, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 15, 0, 52, 8, 9, 0, 49, 0, 0, 25,
- 26, 48, 47, 35, 21, 22, 23, 24, 27, 28,
- 29, 30, 31, 32, 33, 34, 36, 37, 38, 39,
- 40, 43, 42, 44, 41, 45, 46, 50, 0, 0,
- 10, 12, 11, 14, 0, 0, 0, 0, 0, 0,
+ 0, 0, 15, 0, 55, 8, 9, 0, 52, 0,
+ 0, 26, 27, 51, 50, 36, 22, 23, 24, 25,
+ 28, 29, 30, 31, 32, 33, 34, 35, 37, 38,
+ 39, 40, 41, 44, 43, 45, 42, 47, 46, 49,
+ 48, 53, 0, 0, 10, 12, 11, 14, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 7, 0, 53, 72, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 54, 0,
- 0, 0, 6, 5, 3, 4, 2, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 18, 67, 55, 64, 56, 57, 70, 0,
- 68, 0, 58, 60, 59, 62, 63, 66, 65, 61,
- 71, 69
+ 0, 0, 0, 0, 0, 7, 0, 56, 82, 0,
+ 0, 0, 0, 0, 0, 19, 0, 0, 0, 0,
+ 0, 0, 0, 0, 57, 0, 0, 0, 6, 5,
+ 3, 4, 2, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 18, 75,
+ 58, 72, 59, 60, 79, 0, 0, 76, 0, 0,
+ 62, 0, 61, 0, 67, 0, 70, 71, 74, 73,
+ 69, 81, 80, 78, 77, 0, 0, 0, 0, 0,
+ 66, 65, 64, 63, 68
};
/* YYPGOTO[NTERM-NUM]. */
const signed char
Parser::yypgoto_[] =
{
- -70, 12, -70, -19, -69, -70, -70, -70, -70, -70,
- -70, -70, -70, -70
+ -98, 22, -98, -97, -69, -98, -98, -98, -98, -98,
+ -98, -98, -98, -98
};
/* YYDEFGOTO[NTERM-NUM]. */
const short int
Parser::yydefgoto_[] =
{
- -1, 160, 161, 70, 71, 101, 33, 67, 1, 34,
- 139, 162, 2, 3
+ -1, 165, 166, 70, 71, 103, 33, 67, 1, 34,
+ 143, 167, 2, 3
};
/* YYTABLE[YYPACT[STATE-NUM]]. What to do in state STATE-NUM. If
@@ -1238,58 +1305,62 @@
const unsigned char
Parser::yytable_[] =
{
- 105, 106, 203, 107, 107, 137, 107, 144, 35, 145,
- 146, 68, 208, 147, 148, 209, 149, 150, 151, 152,
- 153, 154, 155, 156, 157, 158, 159, 65, 145, 146,
- 195, 210, 196, 36, 181, 211, 66, 4, 74, 75,
- 94, 95, 37, 5, 103, 104, 38, 6, 7, 108,
- 108, 140, 108, 138, 69, 8, 9, 10, 11, 12,
+ 107, 108, 209, 109, 109, 141, 109, 105, 106, 220,
+ 222, 224, 145, 146, 148, 68, 149, 150, 74, 75,
+ 151, 152, 153, 154, 155, 156, 157, 158, 159, 160,
+ 161, 162, 163, 164, 65, 149, 150, 94, 95, 98,
+ 99, 187, 214, 66, 217, 215, 216, 218, 219, 110,
+ 110, 144, 110, 142, 221, 223, 225, 4, 69, 35,
+ 100, 101, 96, 5, 169, 170, 37, 6, 7, 171,
+ 172, 198, 199, 200, 201, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
- 164, 165, 166, 167, 192, 193, 199, 200, 141, 142,
- 39, 40, 41, 42, 43, 44, 45, 46, 47, 187,
- 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
- 58, 59, 60, 61, 62, 63, 64, 72, 73, 76,
- 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
- 87, 88, 89, 90, 91, 92, 93, 168, 96, 97,
- 169, 98, 99, 100, 102, 109, 110, 111, 112, 113,
- 114, 115, 116, 117, 118, 119, 120, 121, 122, 123,
- 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,
- 134, 135, 136, 182, 0, 163, 68, 143, 178, 170,
- 171, 183, 184, 185, 172, 186, 202, 204, 173, 188,
- 174, 175, 176, 189, 190, 191, 194, 205, 197, 198,
- 201, 206, 207, 212, 213, 214, 215, 216, 217, 218,
- 219, 220, 221, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 177, 179, 0, 180
+ 205, 206, 235, 236, 193, 237, 238, 36, 38, 39,
+ 72, 73, 40, 41, 42, 76, 43, 77, 44, 78,
+ 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
+ 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
+ 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,
+ 89, 90, 91, 92, 93, 97, 102, 104, 111, 112,
+ 113, 114, 115, 116, 117, 118, 119, 120, 121, 122,
+ 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ 133, 134, 135, 136, 137, 138, 139, 140, 188, 0,
+ 168, 68, 147, 175, 0, 0, 0, 173, 174, 184,
+ 189, 190, 191, 176, 177, 178, 192, 0, 194, 195,
+ 196, 202, 197, 208, 203, 204, 207, 210, 211, 212,
+ 213, 226, 227, 228, 229, 230, 231, 232, 233, 234,
+ 0, 240, 241, 239, 242, 243, 244, 0, 0, 0,
+ 179, 180, 0, 181, 182, 183, 185, 186
};
/* YYCHECK. */
const short int
Parser::yycheck_[] =
{
- 69, 3, 3, 5, 5, 3, 5, 4, 0, 6,
- 7, 6, 3, 10, 11, 6, 13, 14, 15, 16,
- 17, 18, 19, 20, 21, 22, 23, 0, 6, 7,
- 6, 3, 8, 3, 12, 7, 9, 4, 6, 7,
- 6, 7, 52, 10, 47, 48, 52, 14, 15, 51,
- 51, 50, 51, 51, 49, 22, 23, 24, 25, 26,
+ 69, 3, 3, 5, 5, 3, 5, 47, 48, 3,
+ 3, 3, 109, 110, 4, 6, 6, 7, 6, 7,
+ 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
+ 20, 21, 22, 23, 0, 6, 7, 6, 7, 6,
+ 7, 12, 3, 9, 3, 6, 7, 6, 7, 51,
+ 51, 50, 51, 51, 48, 48, 48, 4, 49, 0,
+ 6, 7, 7, 10, 6, 7, 52, 14, 15, 6,
+ 7, 6, 7, 6, 7, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
37, 38, 39, 40, 41, 42, 43, 44, 45, 46,
- 6, 7, 6, 7, 6, 7, 6, 7, 107, 108,
- 52, 52, 52, 52, 52, 52, 52, 52, 52, 168,
+ 6, 7, 6, 7, 173, 6, 7, 3, 52, 52,
+ 8, 8, 52, 52, 52, 8, 52, 8, 52, 8,
52, 52, 52, 52, 52, 52, 52, 52, 52, 52,
- 52, 52, 52, 52, 52, 52, 52, 8, 8, 8,
+ 52, 52, 52, 52, 52, 52, 52, 52, 52, 52,
8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
- 8, 8, 8, 8, 8, 6, 6, 52, 7, 6,
- 52, 7, 7, 6, 3, 3, 3, 3, 3, 3,
+ 8, 8, 8, 6, 6, 6, 6, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
- 3, 3, 3, 161, -1, 3, 6, 6, 3, 52,
- 52, 3, 3, 3, 52, 3, 3, 3, 52, 8,
- 52, 52, 52, 8, 8, 8, 7, 3, 8, 8,
- 8, 3, 3, 3, 3, 3, 3, 3, 3, 3,
- 3, 3, 3, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, 52, 52, -1, 52
+ 3, 3, 3, 3, 3, 3, 3, 3, 166, -1,
+ 3, 6, 6, 3, -1, -1, -1, 52, 52, 3,
+ 3, 3, 3, 52, 52, 52, 3, -1, 8, 8,
+ 8, 6, 8, 3, 8, 8, 8, 3, 3, 3,
+ 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
+ -1, 3, 3, 6, 3, 3, 3, -1, -1, -1,
+ 52, 52, -1, 52, 52, 52, 52, 52
};
/* STOS_[STATE-NUM] -- The (internal number of the) accessing
@@ -1306,20 +1377,22 @@
52, 52, 52, 52, 52, 0, 9, 60, 6, 49,
56, 57, 8, 8, 6, 7, 8, 8, 8, 8,
8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
- 8, 8, 6, 6, 6, 7, 7, 6, 7, 7,
- 6, 58, 3, 47, 48, 57, 3, 5, 51, 3,
+ 8, 8, 6, 6, 6, 7, 7, 6, 6, 7,
+ 6, 7, 6, 58, 3, 47, 48, 57, 3, 5,
+ 51, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
- 3, 3, 3, 3, 3, 3, 3, 3, 51, 63,
- 50, 56, 56, 6, 4, 6, 7, 10, 11, 13,
- 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
- 54, 55, 64, 3, 6, 7, 6, 7, 52, 52,
- 52, 52, 52, 52, 52, 52, 52, 52, 3, 52,
- 52, 12, 54, 3, 3, 3, 3, 57, 8, 8,
- 8, 8, 6, 7, 7, 6, 8, 8, 8, 6,
- 7, 8, 3, 3, 3, 3, 3, 3, 3, 6,
- 3, 7, 3, 3, 3, 3, 3, 3, 3, 3,
- 3, 3
+ 3, 3, 51, 63, 50, 56, 56, 6, 4, 6,
+ 7, 10, 11, 12, 13, 14, 15, 16, 17, 18,
+ 19, 20, 21, 22, 23, 54, 55, 64, 3, 6,
+ 7, 6, 7, 52, 52, 3, 52, 52, 52, 52,
+ 52, 52, 52, 52, 3, 52, 52, 12, 54, 3,
+ 3, 3, 3, 57, 8, 8, 8, 8, 6, 7,
+ 6, 7, 6, 8, 8, 6, 7, 8, 3, 3,
+ 3, 3, 3, 3, 3, 6, 7, 3, 6, 7,
+ 3, 48, 3, 48, 3, 48, 3, 3, 3, 3,
+ 3, 3, 3, 3, 3, 6, 7, 6, 7, 6,
+ 3, 3, 3, 3, 3
};
#if YYDEBUG
@@ -1342,12 +1415,13 @@
Parser::yyr1_[] =
{
0, 53, 54, 54, 54, 54, 55, 55, 56, 56,
- 57, 57, 57, 57, 58, 58, 59, 59, 60, 61,
- 61, 62, 62, 62, 62, 62, 62, 62, 62, 62,
+ 57, 57, 57, 57, 58, 58, 59, 59, 60, 60,
+ 61, 61, 62, 62, 62, 62, 62, 62, 62, 62,
62, 62, 62, 62, 62, 62, 62, 62, 62, 62,
62, 62, 62, 62, 62, 62, 62, 62, 62, 62,
- 62, 62, 63, 63, 64, 64, 64, 64, 64, 64,
+ 62, 62, 62, 62, 62, 63, 63, 64, 64, 64,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
+ 64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
64, 64, 64, 65, 66
};
@@ -1356,13 +1430,14 @@
Parser::yyr2_[] =
{
0, 2, 3, 3, 3, 3, 2, 1, 2, 2,
- 3, 3, 3, 1, 3, 1, 0, 2, 6, 0,
- 2, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 3, 3, 3, 1, 3, 1, 0, 2, 6, 5,
+ 0, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 4, 2, 0, 2, 2, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 5,
- 4, 5, 2, 3, 1
+ 4, 4, 4, 4, 2, 0, 2, 2, 4, 4,
+ 4, 4, 4, 6, 6, 6, 6, 4, 6, 4,
+ 4, 4, 4, 4, 4, 4, 4, 5, 5, 4,
+ 5, 5, 2, 3, 1
};
#if YYDEBUG || YYERROR_VERBOSE || YYTOKEN_TABLE
@@ -1409,33 +1484,39 @@
49, 57, 50, -1, 57, 51, 56, -1, 57, 5,
56, -1, 56, -1, 58, 51, 6, -1, 6, -1,
-1, 59, 60, -1, 9, 3, 63, 55, 12, 3,
- -1, -1, 61, 62, -1, 24, 52, 8, 3, -1,
- 25, 52, 8, 3, -1, 26, 52, 8, 3, -1,
- 27, 52, 8, 3, -1, 14, 52, 8, 3, -1,
- 15, 52, 8, 3, -1, 28, 52, 8, 3, -1,
- 29, 52, 8, 3, -1, 30, 52, 8, 3, -1,
- 31, 52, 8, 3, -1, 32, 52, 8, 3, -1,
- 33, 52, 8, 3, -1, 34, 52, 8, 3, -1,
- 35, 52, 8, 3, -1, 23, 52, 8, 3, -1,
- 36, 52, 8, 3, -1, 37, 52, 8, 3, -1,
- 38, 52, 8, 3, -1, 39, 52, 6, 3, -1,
- 40, 52, 6, 3, -1, 43, 52, 6, 3, -1,
- 41, 52, 7, 3, -1, 41, 52, 6, 3, -1,
- 42, 52, 7, 3, -1, 44, 52, 7, 3, -1,
- 45, 52, 7, 3, -1, 22, 52, 7, 3, -1,
- 22, 52, 6, 3, -1, 10, 52, 57, 3, -1,
- 46, 52, 58, 3, -1, 4, 3, -1, -1, 63,
- 64, -1, 21, 3, -1, 11, 52, 8, 3, -1,
- 14, 52, 8, 3, -1, 15, 52, 8, 3, -1,
- 17, 52, 7, 3, -1, 18, 52, 8, 3, -1,
- 18, 52, 6, 3, -1, 23, 52, 8, 3, -1,
- 19, 52, 8, 3, -1, 20, 52, 8, 3, -1,
- 13, 52, 8, 3, -1, 22, 52, 7, 3, -1,
- 22, 52, 6, 3, -1, 10, 52, 57, 3, -1,
- 16, 52, 7, 3, -1, 16, 52, 7, 7, 3,
- -1, 16, 52, 6, 3, -1, 16, 52, 6, 6,
- 3, -1, 4, 3, -1, 61, 59, 0, -1, 65,
- -1
+ -1, 9, 3, 63, 12, 3, -1, -1, 61, 62,
+ -1, 24, 52, 8, 3, -1, 25, 52, 8, 3,
+ -1, 26, 52, 8, 3, -1, 27, 52, 8, 3,
+ -1, 14, 52, 8, 3, -1, 15, 52, 8, 3,
+ -1, 28, 52, 8, 3, -1, 29, 52, 8, 3,
+ -1, 30, 52, 8, 3, -1, 31, 52, 8, 3,
+ -1, 32, 52, 8, 3, -1, 33, 52, 8, 3,
+ -1, 34, 52, 8, 3, -1, 35, 52, 8, 3,
+ -1, 23, 52, 8, 3, -1, 36, 52, 8, 3,
+ -1, 37, 52, 8, 3, -1, 38, 52, 8, 3,
+ -1, 39, 52, 6, 3, -1, 40, 52, 6, 3,
+ -1, 43, 52, 6, 3, -1, 41, 52, 7, 3,
+ -1, 41, 52, 6, 3, -1, 42, 52, 7, 3,
+ -1, 44, 52, 7, 3, -1, 44, 52, 6, 3,
+ -1, 45, 52, 7, 3, -1, 45, 52, 6, 3,
+ -1, 22, 52, 7, 3, -1, 22, 52, 6, 3,
+ -1, 10, 52, 57, 3, -1, 46, 52, 58, 3,
+ -1, 4, 3, -1, -1, 63, 64, -1, 21, 3,
+ -1, 11, 52, 8, 3, -1, 14, 52, 8, 3,
+ -1, 15, 52, 8, 3, -1, 17, 52, 7, 3,
+ -1, 17, 52, 6, 3, -1, 17, 52, 7, 48,
+ 7, 3, -1, 17, 52, 7, 48, 6, 3, -1,
+ 17, 52, 6, 48, 7, 3, -1, 17, 52, 6,
+ 48, 6, 3, -1, 18, 52, 6, 3, -1, 18,
+ 52, 6, 48, 6, 3, -1, 23, 52, 8, 3,
+ -1, 19, 52, 8, 3, -1, 20, 52, 8, 3,
+ -1, 13, 52, 8, 3, -1, 22, 52, 7, 3,
+ -1, 22, 52, 6, 3, -1, 10, 52, 57, 3,
+ -1, 16, 52, 7, 3, -1, 16, 52, 7, 7,
+ 3, -1, 16, 52, 7, 6, 3, -1, 16, 52,
+ 6, 3, -1, 16, 52, 6, 7, 3, -1, 16,
+ 52, 6, 6, 3, -1, 4, 3, -1, 61, 59,
+ 0, -1, 65, -1
};
/* YYPRHS[YYN] -- Index of the first RHS symbol of rule number YYN in
@@ -1445,26 +1526,28 @@
{
0, 0, 3, 7, 11, 15, 19, 22, 24, 27,
30, 34, 38, 42, 44, 48, 50, 51, 54, 61,
- 62, 65, 70, 75, 80, 85, 90, 95, 100, 105,
- 110, 115, 120, 125, 130, 135, 140, 145, 150, 155,
- 160, 165, 170, 175, 180, 185, 190, 195, 200, 205,
- 210, 215, 218, 219, 222, 225, 230, 235, 240, 245,
- 250, 255, 260, 265, 270, 275, 280, 285, 290, 295,
- 301, 306, 312, 315, 319
+ 67, 68, 71, 76, 81, 86, 91, 96, 101, 106,
+ 111, 116, 121, 126, 131, 136, 141, 146, 151, 156,
+ 161, 166, 171, 176, 181, 186, 191, 196, 201, 206,
+ 211, 216, 221, 226, 231, 234, 235, 238, 241, 246,
+ 251, 256, 261, 266, 273, 280, 287, 294, 299, 306,
+ 311, 316, 321, 326, 331, 336, 341, 346, 352, 358,
+ 363, 369, 375, 378, 382
};
/* YYRLINE[YYN] -- Source line where rule number YYN was defined. */
const unsigned char
Parser::yyrline_[] =
{
- 0, 130, 130, 131, 132, 133, 135, 136, 138, 139,
- 141, 142, 143, 144, 146, 147, 149, 150, 156, 162,
- 163, 165, 166, 167, 168, 169, 170, 171, 172, 173,
- 174, 175, 176, 177, 178, 179, 180, 181, 182, 183,
- 184, 185, 186, 187, 188, 189, 190, 191, 192, 193,
- 194, 195, 197, 198, 200, 201, 202, 203, 204, 205,
- 206, 207, 208, 209, 210, 211, 212, 213, 214, 215,
- 216, 217, 218, 221, 227
+ 0, 131, 131, 132, 133, 134, 136, 137, 139, 140,
+ 142, 143, 144, 145, 147, 148, 150, 151, 157, 162,
+ 164, 165, 167, 168, 169, 170, 171, 172, 173, 174,
+ 175, 176, 177, 178, 179, 180, 181, 182, 183, 184,
+ 185, 186, 187, 188, 189, 190, 191, 192, 193, 194,
+ 195, 196, 197, 198, 199, 201, 202, 204, 205, 206,
+ 207, 208, 209, 210, 211, 212, 213, 214, 215, 216,
+ 217, 218, 219, 220, 221, 222, 223, 224, 225, 226,
+ 227, 228, 229, 232, 238
};
// Print the state stack on the debug stream.
@@ -1543,7 +1626,7 @@
}
const int Parser::yyeof_ = 0;
- const int Parser::yylast_ = 228;
+ const int Parser::yylast_ = 247;
const int Parser::yynnts_ = 14;
const int Parser::yyempty_ = -2;
const int Parser::yyfinal_ = 35;
@@ -1561,11 +1644,11 @@
} // mgf
/* Line 1054 of lalr1.cc */
-#line 1565 "Parser.cpp"
+#line 1648 "Parser.cpp"
/* Line 1056 of lalr1.cc */
-#line 229 "Parser.ypp"
+#line 240 "Parser.ypp"
/*** Additional Code ***/
void mgf::Parser::error(const Parser::location_type& l, const std::string& m)
Modified: trunk/mgfp/src/Parser.h
===================================================================
--- trunk/mgfp/src/Parser.h 2010-09-10 15:30:49 UTC (rev 37)
+++ trunk/mgfp/src/Parser.h 2010-09-10 15:33:39 UTC (rev 38)
@@ -47,6 +47,7 @@
#include <cstdio>
#include <string>
+#include <utility>
#include <vector>
using namespace mgf;
@@ -55,7 +56,7 @@
/* Line 35 of lalr1.cc */
-#line 59 "Parser.h"
+#line 60 "Parser.h"
#include <string>
@@ -69,7 +70,7 @@
namespace mgf {
/* Line 35 of lalr1.cc */
-#line 73 "Parser.h"
+#line 74 "Parser.h"
class position;
class location;
@@ -79,7 +80,7 @@
} // mgf
/* Line 35 of lalr1.cc */
-#line 83 "Parser.h"
+#line 84 "Parser.h"
#include "location.h"
@@ -127,7 +128,7 @@
namespace mgf {
/* Line 35 of lalr1.cc */
-#line 131 "Parser.h"
+#line 132 "Parser.h"
/// A Bison parser.
class Parser
@@ -139,7 +140,7 @@
{
/* Line 35 of lalr1.cc */
-#line 52 "Parser.ypp"
+#line 53 "Parser.ypp"
int integerVal;
double doubleVal;
@@ -152,7 +153,7 @@
/* Line 35 of lalr1.cc */
-#line 156 "Parser.h"
+#line 157 "Parser.h"
};
#else
typedef YYSTYPE semantic_type;
@@ -385,7 +386,7 @@
} // mgf
/* Line 35 of lalr1.cc */
-#line 389 "Parser.h"
+#line 390 "Parser.h"
Modified: trunk/mgfp/src/Parser.ypp
===================================================================
--- trunk/mgfp/src/Parser.ypp 2010-09-10 15:30:49 UTC (rev 37)
+++ trunk/mgfp/src/Parser.ypp 2010-09-10 15:33:39 UTC (rev 38)
@@ -6,6 +6,7 @@
#include <cstdio>
#include <string>
+#include <utility>
#include <vector>
using namespace mgf;
@@ -158,6 +159,7 @@
driver.context.currentSpectrum.assign(($4->pairlist_)->begin(), ($4->pairlist_)->end());
delete $4;
}
+ | BEGIN_IONS EOL localparams END_IONS EOL
globalparams : /*empty*/
| globalparams globalparam
@@ -187,7 +189,9 @@
| ITOL '=' INTEGER EOL { driver.context.header.setITOL($3); }
| PEP_ISOTOPE_ERROR '=' DOUBLE EOL { driver.context.header.setPEP_ISOTOPE_ERROR($3); }
| PRECURSOR '=' DOUBLE EOL { driver.context.header.setPRECURSOR($3); }
+ | PRECURSOR '=' INTEGER EOL { driver.context.header.setPRECURSOR($3); }
| SEG '=' DOUBLE EOL { driver.context.header.setSEG($3); }
+ | SEG '=' INTEGER EOL { driver.context.header.setSEG($3); }
| TOL '=' DOUBLE EOL { driver.context.header.setTOL($3); }
| TOL '=' INTEGER EOL { driver.context.header.setTOL($3); }
| CHARGE '=' charges EOL { driver.context.header.setCHARGE(*($3->integers_)); delete $3; }
@@ -202,8 +206,13 @@
| INSTRUMENT '=' STRING EOL { driver.context.currentSpectrum.setINSTRUMENT(*$3); delete $3; }
| IT_MODS '=' STRING EOL { driver.context.currentSpectrum.setIT_MODS(*$3); delete $3; }
| RTINSECONDS '=' DOUBLE EOL { driver.context.currentSpectrum.setRTINSECONDS($3); }
- | SCANS '=' STRING EOL { driver.context.currentSpectrum.setSCANS(*$3); delete $3; }
- | SCANS '=' INTEGER EOL { driver.context.currentSpectrum.setSCANS($3); }
+ | RTINSECONDS '=' INTEGER EOL { driver.context.currentSpectrum.setRTINSECONDS($3); }
+ | RTINSECONDS '=' DOUBLE '-' DOUBLE EOL { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair($3, $5)); }
+ | RTINSECONDS '=' DOUBLE '-' INTEGER EOL { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair($3, $5)); }
+ | RTINSECONDS '=' INTEGER '-' DOUBLE EOL { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair($3, $5)); }
+ | RTINSECONDS '=' INTEGER '-' INTEGER EOL { driver.context.currentSpectrum.setRTINSECONDS(std::make_pair($3, $5)); }
+ | SCANS '=' INTEGER EOL { driver.context.currentSpectrum.setSCANS(std::make_pair($3, -1)); }
+ | SCANS '=' INTEGER '-' INTEG...
[truncated message content] |
|
From: <mki...@us...> - 2010-09-10 15:30:56
|
Revision: 37
http://mgfp.svn.sourceforge.net/mgfp/?rev=37&view=rev
Author: mkirchner
Date: 2010-09-10 15:30:49 +0000 (Fri, 10 Sep 2010)
Log Message:
-----------
- bugfix and generalization to TMT and iTRAQ-4
Modified Paths:
--------------
trunk/mgfp/applications/tmtx/tmtx.cpp
Modified: trunk/mgfp/applications/tmtx/tmtx.cpp
===================================================================
--- trunk/mgfp/applications/tmtx/tmtx.cpp 2010-09-09 21:29:45 UTC (rev 36)
+++ trunk/mgfp/applications/tmtx/tmtx.cpp 2010-09-10 15:30:49 UTC (rev 37)
@@ -22,6 +22,8 @@
*/
#include <cmath>
+#include <fstream>
+#include <iomanip>
#include <iostream>
#include <iterator>
#include <tr1/array>
@@ -62,35 +64,73 @@
}
}
-static const double tmtMasses[10] =
- { 124.0, 125.0, 126.0, 127.0, 128.0,
- 129.0, 130.0, 131.0, 132.0, 133.0 };
+enum LabelType { TMT, ITRAQ4, SIZE };
+static const size_t sizes[SIZE] = { 10, 8 };
+static const double masses[SIZE][10] =
+ {
+ { 124.0, 125.0, 126.0, 127.0, 128.0,
+ 129.0, 130.0, 131.0, 132.0, 133.0 },
+ { 112.1, 113.1, 114.1112, 115.1083, 116.1116,
+ 117.115, 118.1, 119.1, 0.0, 0.0 }};
int main(int argc, char *argv[])
{
namespace po = boost::program_options;
po::options_description desc("Allowed options");
bool verbose = false;
+ std::string inputfile;
+ size_t precision;
desc.add_options()
("help,h", "produce help message")
("verbose,v", po::value(&verbose)->zero_tokens(),
"verbose output (good to pinpoint parsing errors)")
+ ("type,t", po::value<std::string>(), "label type: one of TMT, ITRAQ4")
+ ("input,i", po::value<std::string>(&inputfile)->default_value("-"),
+ "input filename, defaults to stdin")
+ ("tee,e", po::value<std::string>(), "run in tee mode: extract label "
+ "abundances to specified file and simply pipe MGF data from stdin "
+ "to stdout.")
+ ("precision,p", po::value<size_t>(&precision)->default_value(6),
+ "number of significant digits in output")
;
po::variables_map vm;
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
// check if the user asked for help
- if (vm.count("help")) {
+ if (vm.count("help") || !vm.count("type")) {
std::cerr << desc;
return 1;
}
+ // figure put which labeling technique we use
+ LabelType labelType;
+ if (vm["type"].as<std::string>() == "TMT") {
+ labelType = TMT;
+ } else if (vm["type"].as<std::string>() == "ITRAQ4") {
+ labelType = ITRAQ4;
+ } else {
+ std::cerr << vm["type"].as<std::string>() << std::endl;
+ std::cerr << desc;
+ return 1;
+ }
+ // initialize the masses
+ std::vector<double> labelMasses(sizes[labelType]);
+ for (size_t n = 0; n < sizes[labelType]; ++n) {
+ labelMasses[n] = masses[labelType][n];
+ }
// prepare the parser
mgf::MgfFile m;
mgf::Driver driver(m);
driver.trace_parsing = verbose;
driver.trace_scanning = verbose;
- // parse input
- bool result = driver.parse_stream(std::cin);
+ // parse input
+ bool result;
+ if (inputfile == "-") {
+ result = driver.parse_stream(std::cin);
+ } else {
+ std::ifstream ifs(inputfile.c_str());
+ result = driver.parse_stream(ifs);
+ ifs.close();
+ }
if (!result) {
std::cerr << std::endl
<< "Error parsing data stream (use -v for details)." << std::endl;
@@ -98,27 +138,33 @@
}
typedef mgf::MgfFile::iterator MFI;
// iterate over all spectra
+ std::vector<double> obsAbundances(sizes[labelType]);
for (MFI i = m.begin(); i != m.end(); ++i) {
// sort
std::sort(i->begin(), i->end(), mgf::LessThanMz());
typedef mgf::MgfSpectrum::iterator MSI;
// extract TMT reproter ion intensities
- double obsTmtAbundances[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
- for (size_t n = 0; n < 6; ++n) {
- MSI closestIt = findClosestMz(i->begin(), i->end(), tmtMasses[n]);
- // check if there is a MS2 centroid
- if (std::abs(closestIt->first - tmtMasses[n]) < 0.4) {
- obsTmtAbundances[n] = closestIt->second;
- } else {
- obsTmtAbundances[n] = 0.0;
+ bool atLeastOneEntry = false;
+ for (size_t n = 0; n < sizes[labelType]; ++n) {
+ MSI closestIt = findClosestMz(i->begin(), i->end(), labelMasses[n]);
+ if (closestIt != i->end()) {
+ // check if there is an MS2 centroid
+ if (std::abs(closestIt->first - labelMasses[n]) < 0.4) {
+ obsAbundances[n] = closestIt->second;
+ if (!atLeastOneEntry) atLeastOneEntry = true;
+ } else {
+ obsAbundances[n] = 0.0;
+ }
}
}
// extract into file
- std::cout << i->getTITLE();
- for (size_t n = 0; n < 6; ++n) {
- std::cout << '\t' << obsTmtAbundances[n];
+ if (atLeastOneEntry) {
+ std::cout << i->getTITLE();
+ for (size_t n = 0; n < sizes[labelType]; ++n) {
+ std::cout << '\t' << std::setprecision(precision) << obsAbundances[n];
+ }
+ std::cout << '\n'; // don't use std::endl, save the std::flush.
}
- std::cout << std::endl;
}
return 0;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mki...@us...> - 2010-09-09 21:29:53
|
Revision: 36
http://mgfp.svn.sourceforge.net/mgfp/?rev=36&view=rev
Author: mkirchner
Date: 2010-09-09 21:29:45 +0000 (Thu, 09 Sep 2010)
Log Message:
-----------
now allowing numbers for SCANS
Modified Paths:
--------------
trunk/mgfp/include/mgfp/MgfSpectrum.h
trunk/mgfp/src/MgfSpectrum.cpp
trunk/mgfp/src/Parser.cpp
trunk/mgfp/src/Parser.h
trunk/mgfp/src/Parser.ypp
trunk/mgfp/src/Scanner.cpp
trunk/mgfp/src/location.h
trunk/mgfp/src/position.h
trunk/mgfp/src/stack.h
Modified: trunk/mgfp/include/mgfp/MgfSpectrum.h
===================================================================
--- trunk/mgfp/include/mgfp/MgfSpectrum.h 2010-09-08 03:51:39 UTC (rev 35)
+++ trunk/mgfp/include/mgfp/MgfSpectrum.h 2010-09-09 21:29:45 UTC (rev 36)
@@ -145,6 +145,12 @@
*/
void setSCANS(const std::string& scans);
+ /** Set
+ * @see
+ * @param[in]
+ */
+ void setSCANS(const int scans);
+
/** Get the amino acid sequence. Please consult the detailed description in
* the Mascot documentation (see link).
* @see http://www.matrixscience.com/help/sq_help.html#SEQ
Modified: trunk/mgfp/src/MgfSpectrum.cpp
===================================================================
--- trunk/mgfp/src/MgfSpectrum.cpp 2010-09-08 03:51:39 UTC (rev 35)
+++ trunk/mgfp/src/MgfSpectrum.cpp 2010-09-09 21:29:45 UTC (rev 36)
@@ -1,6 +1,7 @@
#include <mgfp/MgfSpectrum.h>
#include <cstdlib> // for std::abs(int)
+#include <sstream>
namespace mgf {
@@ -71,6 +72,12 @@
scans_ = scans; //FIXME
}
+void MgfSpectrum::setSCANS(const int scans) {
+ std::ostringstream oss;
+ oss << scans;
+ scans_ = oss.str(); //FIXME
+}
+
std::string MgfSpectrum::getSEQ(void) const {
return seq_ ;
}
Modified: trunk/mgfp/src/Parser.cpp
===================================================================
--- trunk/mgfp/src/Parser.cpp 2010-09-08 03:51:39 UTC (rev 35)
+++ trunk/mgfp/src/Parser.cpp 2010-09-09 21:29:45 UTC (rev 36)
@@ -1,23 +1,23 @@
-/* A Bison parser, made by GNU Bison 2.3. */
+/* A Bison parser, made by GNU Bison 2.4.1. */
+
/* Skeleton implementation for Bison LALR(1) parsers in C++
-
- Copyright (C) 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
-
- This program is free software; you can redistribute it and/or modify
+
+ Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software
+ Foundation, Inc.
+
+ This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2, or (at your option)
- any later version.
-
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
-
+
You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor,
- Boston, MA 02110-1301, USA. */
+ along with this program. If not, see <http://www.gnu.org/licenses/>. */
/* As a special exception, you may create a larger work that contains
part or all of the Bison parser skeleton and distribute that work
@@ -28,18 +28,27 @@
special exception, which will cause the skeleton and the resulting
Bison output files to be licensed under the GNU General Public
License without this special exception.
-
+
This special exception was added by the Free Software Foundation in
version 2.2 of Bison. */
// Take the name prefix into account.
#define yylex mgflex
+/* First part of user declarations. */
+
+
+/* Line 311 of lalr1.cc */
+#line 43 "Parser.cpp"
+
+
#include "Parser.h"
/* User implementation prologue. */
-#line 127 "Parser.ypp"
+/* Line 317 of lalr1.cc */
+#line 117 "Parser.ypp"
+
#include <mgfp/Driver.h>
#include "Scanner.h"
@@ -50,11 +59,11 @@
#define yylex driver.lexer->lex
-/* Line 317 of lalr1.cc. */
-#line 55 "Parser.cpp"
+/* Line 317 of lalr1.cc */
+#line 64 "Parser.cpp"
#ifndef YY_
-# if defined YYENABLE_NLS && YYENABLE_NLS
+# if YYENABLE_NLS
# if ENABLE_NLS
# include <libintl.h> /* FIXME: INFRINGES ON USER NAME SPACE */
# define YY_(msgid) dgettext ("bison-runtime", msgid)
@@ -68,14 +77,12 @@
/* Suppress unused-variable warnings by "using" E. */
#define YYUSE(e) ((void) (e))
-/* A pseudo ostream that takes yydebug_ into account. */
-# define YYCDEBUG \
- for (bool yydebugcond_ = yydebug_; yydebugcond_; yydebugcond_ = false) \
- (*yycdebug_)
-
/* Enable debugging if requested. */
#if YYDEBUG
+/* A pseudo ostream that takes yydebug_ into account. */
+# define YYCDEBUG if (yydebug_) (*yycdebug_)
+
# define YY_SYMBOL_PRINT(Title, Type, Value, Location) \
do { \
if (yydebug_) \
@@ -100,18 +107,29 @@
#else /* !YYDEBUG */
+# define YYCDEBUG if (false) std::cerr
# define YY_SYMBOL_PRINT(Title, Type, Value, Location)
# define YY_REDUCE_PRINT(Rule)
# define YY_STACK_PRINT()
#endif /* !YYDEBUG */
+#define yyerrok (yyerrstatus_ = 0)
+#define yyclearin (yychar = yyempty_)
+
#define YYACCEPT goto yyacceptlab
#define YYABORT goto yyabortlab
#define YYERROR goto yyerrorlab
+#define YYRECOVERING() (!!yyerrstatus_)
-namespace mgf
-{
+
+/* Line 380 of lalr1.cc */
+#line 1 "[Bison:b4_percent_define_default]"
+
+namespace mgf {
+
+/* Line 380 of lalr1.cc */
+#line 133 "Parser.cpp"
#if YYERROR_VERBOSE
/* Return YYSTR after stripping away unnecessary quotes and
@@ -155,8 +173,11 @@
/// Build a parser object.
Parser::Parser (Driver& driver_yyarg)
- : yydebug_ (false),
+ :
+#if YYDEBUG
+ yydebug_ (false),
yycdebug_ (&std::cerr),
+#endif
driver (driver_yyarg)
{
}
@@ -194,7 +215,7 @@
yy_symbol_value_print_ (yytype, yyvaluep, yylocationp);
*yycdebug_ << ')';
}
-#endif /* ! YYDEBUG */
+#endif
void
Parser::yydestruct_ (const char* yymsg,
@@ -209,34 +230,58 @@
switch (yytype)
{
case 8: /* "\"string\"" */
-#line 124 "Parser.ypp"
+
+/* Line 480 of lalr1.cc */
+#line 114 "Parser.ypp"
{ delete (yyvaluep->stringVal); };
-#line 215 "Parser.cpp"
+
+/* Line 480 of lalr1.cc */
+#line 240 "Parser.cpp"
break;
case 54: /* "ion" */
-#line 125 "Parser.ypp"
+
+/* Line 480 of lalr1.cc */
+#line 115 "Parser.ypp"
{ delete (yyvaluep->doublepairnode); };
-#line 220 "Parser.cpp"
+
+/* Line 480 of lalr1.cc */
+#line 249 "Parser.cpp"
break;
case 55: /* "ions" */
-#line 125 "Parser.ypp"
+
+/* Line 480 of lalr1.cc */
+#line 115 "Parser.ypp"
{ delete (yyvaluep->doublepairlistnode); };
-#line 225 "Parser.cpp"
+
+/* Line 480 of lalr1.cc */
+#line 258 "Parser.cpp"
break;
case 56: /* "charge" */
-#line 125 "Parser.ypp"
+
+/* Line 480 of lalr1.cc */
+#line 115 "Parser.ypp"
{ delete (yyvaluep->integernode); };
-#line 230 "Parser.cpp"
+
+/* Line 480 of lalr1.cc */
+#line 267 "Parser.cpp"
break;
case 57: /* "charges" */
-#line 125 "Parser.ypp"
+
+/* Line 480 of lalr1.cc */
+#line 115 "Parser.ypp"
{ delete (yyvaluep->integerlistnode); };
-#line 235 "Parser.cpp"
+
+/* Line 480 of lalr1.cc */
+#line 276 "Parser.cpp"
break;
case 58: /* "csintegerlist" */
-#line 125 "Parser.ypp"
+
+/* Line 480 of lalr1.cc */
+#line 115 "Parser.ypp"
{ delete (yyvaluep->integerlistnode); };
-#line 240 "Parser.cpp"
+
+/* Line 480 of lalr1.cc */
+#line 285 "Parser.cpp"
break;
default:
@@ -252,6 +297,7 @@
yylocation_stack_.pop (n);
}
+#if YYDEBUG
std::ostream&
Parser::debug_stream () const
{
@@ -276,12 +322,12 @@
{
yydebug_ = l;
}
+#endif
-
int
Parser::parse ()
{
- /// Look-ahead and look-ahead in internal form.
+ /// Lookahead and lookahead in internal form.
int yychar = yyempty_;
int yytoken = 0;
@@ -294,12 +340,12 @@
int yynerrs_ = 0;
int yyerrstatus_ = 0;
- /// Semantic value of the look-ahead.
+ /// Semantic value of the lookahead.
semantic_type yylval;
- /// Location of the look-ahead.
+ /// Location of the lookahead.
location_type yylloc;
/// The locations where the error started and ended.
- location yyerror_range[2];
+ location_type yyerror_range[2];
/// $$.
semantic_type yyval;
@@ -312,13 +358,17 @@
/* User initialization code. */
- #line 49 "Parser.ypp"
+
+/* Line 553 of lalr1.cc */
+#line 39 "Parser.ypp"
{
// initialize the initial location object
yylloc.begin.filename = yylloc.end.filename = &driver.streamname;
}
- /* Line 555 of yacc.c. */
-#line 322 "Parser.cpp"
+
+/* Line 553 of lalr1.cc */
+#line 371 "Parser.cpp"
+
/* Initialize the stacks. The initial state will be pushed in
yynewstate, since the latter expects the semantical and the
location values to have been already stored, initialize these
@@ -333,17 +383,22 @@
yynewstate:
yystate_stack_.push (yystate);
YYCDEBUG << "Entering state " << yystate << std::endl;
+
+ /* Accept? */
+ if (yystate == yyfinal_)
+ goto yyacceptlab;
+
goto yybackup;
/* Backup. */
yybackup:
- /* Try to take a decision without look-ahead. */
+ /* Try to take a decision without lookahead. */
yyn = yypact_[yystate];
if (yyn == yypact_ninf_)
goto yydefault;
- /* Read a look-ahead token. */
+ /* Read a lookahead token. */
if (yychar == yyempty_)
{
YYCDEBUG << "Reading a token: ";
@@ -379,16 +434,11 @@
goto yyreduce;
}
- /* Accept? */
- if (yyn == yyfinal_)
- goto yyacceptlab;
-
- /* Shift the look-ahead token. */
+ /* Shift the lookahead token. */
YY_SYMBOL_PRINT ("Shifting", yytoken, &yylval, &yylloc);
- /* Discard the token being shifted unless it is eof. */
- if (yychar != yyeof_)
- yychar = yyempty_;
+ /* Discard the token being shifted. */
+ yychar = yyempty_;
yysemantic_stack_.push (yylval);
yylocation_stack_.push (yylloc);
@@ -434,338 +484,475 @@
switch (yyn)
{
case 2:
-#line 140 "Parser.ypp"
- { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].doubleVal), (yysemantic_stack_[(3) - (2)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 130 "Parser.ypp"
+ { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].doubleVal), (yysemantic_stack_[(3) - (2)].doubleVal)); }
break;
case 3:
-#line 141 "Parser.ypp"
- { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].integerVal), (yysemantic_stack_[(3) - (2)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 131 "Parser.ypp"
+ { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].integerVal), (yysemantic_stack_[(3) - (2)].doubleVal)); }
break;
case 4:
-#line 142 "Parser.ypp"
- { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].doubleVal), (yysemantic_stack_[(3) - (2)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 132 "Parser.ypp"
+ { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].doubleVal), (yysemantic_stack_[(3) - (2)].integerVal)); }
break;
case 5:
-#line 143 "Parser.ypp"
- { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].integerVal), (yysemantic_stack_[(3) - (2)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 133 "Parser.ypp"
+ { (yyval.doublepairnode) = new DoublePairNode((yysemantic_stack_[(3) - (1)].integerVal), (yysemantic_stack_[(3) - (2)].integerVal)); }
break;
case 6:
-#line 145 "Parser.ypp"
- { (yyval.doublepairlistnode) = new DoublePairListNode((yysemantic_stack_[(2) - (1)].doublepairlistnode), (yysemantic_stack_[(2) - (2)].doublepairnode)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 135 "Parser.ypp"
+ { (yyval.doublepairlistnode) = new DoublePairListNode((yysemantic_stack_[(2) - (1)].doublepairlistnode), (yysemantic_stack_[(2) - (2)].doublepairnode)); }
break;
case 7:
-#line 146 "Parser.ypp"
- { (yyval.doublepairlistnode) = new DoublePairListNode((yysemantic_stack_[(1) - (1)].doublepairnode)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 136 "Parser.ypp"
+ { (yyval.doublepairlistnode) = new DoublePairListNode((yysemantic_stack_[(1) - (1)].doublepairnode)); }
break;
case 8:
-#line 148 "Parser.ypp"
- { (yyval.integernode) = new IntegerNode((yysemantic_stack_[(2) - (1)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 138 "Parser.ypp"
+ { (yyval.integernode) = new IntegerNode((yysemantic_stack_[(2) - (1)].integerVal)); }
break;
case 9:
-#line 149 "Parser.ypp"
- { (yyval.integernode) = new IntegerNode(-(yysemantic_stack_[(2) - (1)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 139 "Parser.ypp"
+ { (yyval.integernode) = new IntegerNode(-(yysemantic_stack_[(2) - (1)].integerVal)); }
break;
case 10:
-#line 151 "Parser.ypp"
- { (yyval.integerlistnode) = (yysemantic_stack_[(3) - (2)].integerlistnode); ;}
+
+/* Line 678 of lalr1.cc */
+#line 141 "Parser.ypp"
+ { (yyval.integerlistnode) = (yysemantic_stack_[(3) - (2)].integerlistnode); }
break;
case 11:
-#line 152 "Parser.ypp"
- { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integernode)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 142 "Parser.ypp"
+ { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integernode)); }
break;
case 12:
-#line 153 "Parser.ypp"
- { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integernode)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 143 "Parser.ypp"
+ { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integernode)); }
break;
case 13:
-#line 154 "Parser.ypp"
- { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(1) - (1)].integernode)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 144 "Parser.ypp"
+ { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(1) - (1)].integernode)); }
break;
case 14:
-#line 156 "Parser.ypp"
- { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 146 "Parser.ypp"
+ { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(3) - (1)].integerlistnode), (yysemantic_stack_[(3) - (3)].integerVal)); }
break;
case 15:
-#line 157 "Parser.ypp"
- { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(1) - (1)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 147 "Parser.ypp"
+ { (yyval.integerlistnode) = new IntegerListNode((yysemantic_stack_[(1) - (1)].integerVal)); }
break;
case 17:
-#line 161 "Parser.ypp"
+
+/* Line 678 of lalr1.cc */
+#line 151 "Parser.ypp"
{
driver.context.mgfFile.push_back(driver.context.currentSpectrum);
driver.context.currentSpectrum.clear();
- ;}
+ }
break;
case 18:
-#line 167 "Parser.ypp"
+
+/* Line 678 of lalr1.cc */
+#line 157 "Parser.ypp"
{
driver.context.currentSpectrum.assign(((yysemantic_stack_[(6) - (4)].doublepairlistnode)->pairlist_)->begin(), ((yysemantic_stack_[(6) - (4)].doublepairlistnode)->pairlist_)->end());
delete (yysemantic_stack_[(6) - (4)].doublepairlistnode);
- ;}
+ }
break;
case 21:
-#line 175 "Parser.ypp"
- { driver.context.header.setCLE(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 165 "Parser.ypp"
+ { driver.context.header.setCLE(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 22:
-#line 176 "Parser.ypp"
- { driver.context.header.setCOM(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 166 "Parser.ypp"
+ { driver.context.header.setCOM(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 23:
-#line 177 "Parser.ypp"
- { driver.context.header.setDB(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 167 "Parser.ypp"
+ { driver.context.header.setDB(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 24:
-#line 178 "Parser.ypp"
- { driver.context.header.setFORMAT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 168 "Parser.ypp"
+ { driver.context.header.setFORMAT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 25:
-#line 179 "Parser.ypp"
- { driver.context.header.setINSTRUMENT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 169 "Parser.ypp"
+ { driver.context.header.setINSTRUMENT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 26:
-#line 180 "Parser.ypp"
- { driver.context.header.setIT_MODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 170 "Parser.ypp"
+ { driver.context.header.setIT_MODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 27:
-#line 181 "Parser.ypp"
- { driver.context.header.setITOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 171 "Parser.ypp"
+ { driver.context.header.setITOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 28:
-#line 182 "Parser.ypp"
- { driver.context.header.setMASS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 172 "Parser.ypp"
+ { driver.context.header.setMASS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 29:
-#line 183 "Parser.ypp"
- { driver.context.header.setMODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 173 "Parser.ypp"
+ { driver.context.header.setMODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 30:
-#line 184 "Parser.ypp"
- { driver.context.header.setQUANTITATION(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 174 "Parser.ypp"
+ { driver.context.header.setQUANTITATION(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 31:
-#line 185 "Parser.ypp"
- { driver.context.header.setREPORT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 175 "Parser.ypp"
+ { driver.context.header.setREPORT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 32:
-#line 186 "Parser.ypp"
- { driver.context.header.setREPTYPE(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 176 "Parser.ypp"
+ { driver.context.header.setREPTYPE(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 33:
-#line 187 "Parser.ypp"
- { driver.context.header.setSEARCH(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 177 "Parser.ypp"
+ { driver.context.header.setSEARCH(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 34:
-#line 188 "Parser.ypp"
- { driver.context.header.setTAXONOMY(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 178 "Parser.ypp"
+ { driver.context.header.setTAXONOMY(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 35:
-#line 189 "Parser.ypp"
- { driver.context.header.setTOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 179 "Parser.ypp"
+ { driver.context.header.setTOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 36:
-#line 190 "Parser.ypp"
- { /*driver.context.header.setUSER(*$3);*/ delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 180 "Parser.ypp"
+ { /*driver.context.header.setUSER(*$3);*/ delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 37:
-#line 191 "Parser.ypp"
- { driver.context.header.setUSEREMAIL(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 181 "Parser.ypp"
+ { driver.context.header.setUSEREMAIL(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 38:
-#line 192 "Parser.ypp"
- { driver.context.header.setUSERNAME(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 182 "Parser.ypp"
+ { driver.context.header.setUSERNAME(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 39:
-#line 193 "Parser.ypp"
- { driver.context.header.setDECOY(((yysemantic_stack_[(4) - (3)].integerVal))!=0); ;}
+
+/* Line 678 of lalr1.cc */
+#line 183 "Parser.ypp"
+ { driver.context.header.setDECOY(((yysemantic_stack_[(4) - (3)].integerVal))!=0); }
break;
case 40:
-#line 194 "Parser.ypp"
- { driver.context.header.setERRORTOLERANT(((yysemantic_stack_[(4) - (3)].integerVal))!=0); ;}
+
+/* Line 678 of lalr1.cc */
+#line 184 "Parser.ypp"
+ { driver.context.header.setERRORTOLERANT(((yysemantic_stack_[(4) - (3)].integerVal))!=0); }
break;
case 41:
-#line 195 "Parser.ypp"
- { driver.context.header.setPFA((yysemantic_stack_[(4) - (3)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 185 "Parser.ypp"
+ { driver.context.header.setPFA((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
case 42:
-#line 196 "Parser.ypp"
- { driver.context.header.setITOL((yysemantic_stack_[(4) - (3)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 186 "Parser.ypp"
+ { driver.context.header.setITOL((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
case 43:
-#line 197 "Parser.ypp"
- { driver.context.header.setITOL((yysemantic_stack_[(4) - (3)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 187 "Parser.ypp"
+ { driver.context.header.setITOL((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
case 44:
-#line 198 "Parser.ypp"
- { driver.context.header.setPEP_ISOTOPE_ERROR((yysemantic_stack_[(4) - (3)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 188 "Parser.ypp"
+ { driver.context.header.setPEP_ISOTOPE_ERROR((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
case 45:
-#line 199 "Parser.ypp"
- { driver.context.header.setPRECURSOR((yysemantic_stack_[(4) - (3)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 189 "Parser.ypp"
+ { driver.context.header.setPRECURSOR((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
case 46:
-#line 200 "Parser.ypp"
- { driver.context.header.setSEG((yysemantic_stack_[(4) - (3)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 190 "Parser.ypp"
+ { driver.context.header.setSEG((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
case 47:
-#line 201 "Parser.ypp"
- { driver.context.header.setTOL((yysemantic_stack_[(4) - (3)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 191 "Parser.ypp"
+ { driver.context.header.setTOL((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
case 48:
-#line 202 "Parser.ypp"
- { driver.context.header.setTOL((yysemantic_stack_[(4) - (3)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 192 "Parser.ypp"
+ { driver.context.header.setTOL((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
case 49:
-#line 203 "Parser.ypp"
- { driver.context.header.setCHARGE(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); ;}
+
+/* Line 678 of lalr1.cc */
+#line 193 "Parser.ypp"
+ { driver.context.header.setCHARGE(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); }
break;
case 50:
-#line 204 "Parser.ypp"
- { driver.context.header.setFRAMES(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); ;}
+
+/* Line 678 of lalr1.cc */
+#line 194 "Parser.ypp"
+ { driver.context.header.setFRAMES(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); }
break;
case 54:
-#line 210 "Parser.ypp"
- { driver.context.currentSpectrum.setTITLE(*(yysemantic_stack_[(2) - (1)].stringVal)); delete (yysemantic_stack_[(2) - (1)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 200 "Parser.ypp"
+ { driver.context.currentSpectrum.setTITLE(*(yysemantic_stack_[(2) - (1)].stringVal)); delete (yysemantic_stack_[(2) - (1)].stringVal); }
break;
case 55:
-#line 211 "Parser.ypp"
- { driver.context.currentSpectrum.setCOMP(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 201 "Parser.ypp"
+ { driver.context.currentSpectrum.setCOMP(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 56:
-#line 212 "Parser.ypp"
- { driver.context.currentSpectrum.setINSTRUMENT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 202 "Parser.ypp"
+ { driver.context.currentSpectrum.setINSTRUMENT(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 57:
-#line 213 "Parser.ypp"
- { driver.context.currentSpectrum.setIT_MODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 203 "Parser.ypp"
+ { driver.context.currentSpectrum.setIT_MODS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 58:
-#line 214 "Parser.ypp"
- { driver.context.currentSpectrum.setRTINSECONDS((yysemantic_stack_[(4) - (3)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 204 "Parser.ypp"
+ { driver.context.currentSpectrum.setRTINSECONDS((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
case 59:
-#line 215 "Parser.ypp"
- { driver.context.currentSpectrum.setSCANS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 205 "Parser.ypp"
+ { driver.context.currentSpectrum.setSCANS(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 60:
-#line 216 "Parser.ypp"
- { driver.context.currentSpectrum.setTOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 206 "Parser.ypp"
+ { driver.context.currentSpectrum.setSCANS((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
case 61:
-#line 217 "Parser.ypp"
- { driver.context.currentSpectrum.setSEQ(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 207 "Parser.ypp"
+ { driver.context.currentSpectrum.setTOLU(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 62:
-#line 218 "Parser.ypp"
- { driver.context.currentSpectrum.setTAG(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 208 "Parser.ypp"
+ { driver.context.currentSpectrum.setSEQ(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 63:
-#line 219 "Parser.ypp"
- { driver.context.currentSpectrum.setETAG(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); ;}
+
+/* Line 678 of lalr1.cc */
+#line 209 "Parser.ypp"
+ { driver.context.currentSpectrum.setTAG(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 64:
-#line 220 "Parser.ypp"
- { driver.context.currentSpectrum.setTOL((yysemantic_stack_[(4) - (3)].doubleVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 210 "Parser.ypp"
+ { driver.context.currentSpectrum.setETAG(*(yysemantic_stack_[(4) - (3)].stringVal)); delete (yysemantic_stack_[(4) - (3)].stringVal); }
break;
case 65:
-#line 221 "Parser.ypp"
- { driver.context.currentSpectrum.setTOL((yysemantic_stack_[(4) - (3)].integerVal)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 211 "Parser.ypp"
+ { driver.context.currentSpectrum.setTOL((yysemantic_stack_[(4) - (3)].doubleVal)); }
break;
case 66:
-#line 222 "Parser.ypp"
- { driver.context.currentSpectrum.setCHARGE(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); ;}
+
+/* Line 678 of lalr1.cc */
+#line 212 "Parser.ypp"
+ { driver.context.currentSpectrum.setTOL((yysemantic_stack_[(4) - (3)].integerVal)); }
break;
case 67:
-#line 223 "Parser.ypp"
- { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(4) - (3)].doubleVal), 0.0)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 213 "Parser.ypp"
+ { driver.context.currentSpectrum.setCHARGE(*((yysemantic_stack_[(4) - (3)].integerlistnode)->integers_)); delete (yysemantic_stack_[(4) - (3)].integerlistnode); }
break;
case 68:
-#line 224 "Parser.ypp"
- { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].doubleVal), (yysemantic_stack_[(5) - (4)].doubleVal))); ;}
+
+/* Line 678 of lalr1.cc */
+#line 214 "Parser.ypp"
+ { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(4) - (3)].doubleVal), 0.0)); }
break;
case 69:
-#line 225 "Parser.ypp"
- { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(4) - (3)].integerVal), 0.0)); ;}
+
+/* Line 678 of lalr1.cc */
+#line 215 "Parser.ypp"
+ { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].doubleVal), (yysemantic_stack_[(5) - (4)].doubleVal))); }
break;
case 70:
-#line 226 "Parser.ypp"
- { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].integerVal), (yysemantic_stack_[(5) - (4)].integerVal))); ;}
+
+/* Line 678 of lalr1.cc */
+#line 216 "Parser.ypp"
+ { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(4) - (3)].integerVal), 0.0)); }
break;
- case 72:
-#line 231 "Parser.ypp"
+ case 71:
+
+/* Line 678 of lalr1.cc */
+#line 217 "Parser.ypp"
+ { driver.context.currentSpectrum.setPEPMASS(std::make_pair((yysemantic_stack_[(5) - (3)].integerVal), (yysemantic_stack_[(5) - (4)].integerVal))); }
+ break;
+
+ case 73:
+
+/* Line 678 of lalr1.cc */
+#line 222 "Parser.ypp"
{
driver.context.mgfFile.setHeader(driver.context.header);
driver.context.header.clear();
- ;}
+ }
break;
- /* Line 675 of lalr1.cc. */
-#line 768 "Parser.cpp"
- default: break;
+
+/* Line 678 of lalr1.cc */
+#line 954 "Parser.cpp"
+ default:
+ break;
}
YY_SYMBOL_PRINT ("-> $$ =", yyr1_[yyn], &yyval, &yyloc);
@@ -800,7 +987,7 @@
yyerror_range[0] = yylloc;
if (yyerrstatus_ == 3)
{
- /* If just tried and failed to reuse look-ahead token after an
+ /* If just tried and failed to reuse lookahead token after an
error, discard it. */
if (yychar <= yyeof_)
@@ -816,7 +1003,7 @@
}
}
- /* Else will try to reuse look-ahead token after shifting the error
+ /* Else will try to reuse lookahead token after shifting the error
token. */
goto yyerrlab1;
@@ -873,19 +1060,16 @@
YY_STACK_PRINT ();
}
- if (yyn == yyfinal_)
- goto yyacceptlab;
-
yyerror_range[1] = yylloc;
// Using YYLLOC is tempting, but would change the location of
- // the look-ahead. YYLOC is available though.
+ // the lookahead. YYLOC is available though.
YYLLOC_DEFAULT (yyloc, (yyerror_range - 1), 2);
yysemantic_stack_.push (yylval);
yylocation_stack_.push (yyloc);
/* Shift the error token. */
YY_SYMBOL_PRINT ("Shifting", yystos_[yyn],
- &yysemantic_stack_[0], &yylocation_stack_[0]);
+ &yysemantic_stack_[0], &yylocation_stack_[0]);
yystate = yyn;
goto yynewstate;
@@ -901,7 +1085,7 @@
goto yyreturn;
yyreturn:
- if (yychar != yyeof_ && yychar != yyempty_)
+ if (yychar != yyempty_)
yydestruct_ ("Cleanup: discarding lookahead", yytoken, &yylval, &yylloc);
/* Do not reclaim the symbols of the rule which action triggered
@@ -975,28 +1159,29 @@
const short int
Parser::yypact_[] =
{
- -70, 33, -70, 8, 39, -22, -6, 36, 37, 40,
+ -70, 33, -70, 8, 30, -10, -6, 38, 39, 40,
41, 42, 43, 44, 45, 46, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61,
- 62, 63, 64, 27, -70, -70, -70, 5, 82, 83,
- 26, 109, 110, 111, 112, 113, 114, 115, 116, 117,
- 118, 119, 120, 121, 122, 123, 124, 127, 128, 32,
- 129, 131, 132, 133, 135, -70, 139, -70, -7, 5,
- -70, -2, 140, 141, 142, 143, 144, 145, 146, 147,
- 148, 149, 150, 151, 152, 153, 154, 155, 156, 157,
- 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,
- -70, 2, -70, -70, -70, 1, -70, 168, 168, -70,
+ 62, 63, 64, 27, -70, -70, -70, 5, 109, 110,
+ 32, 111, 112, 113, 114, 115, 116, 117, 118, 119,
+ 120, 121, 122, 123, 124, 125, 126, 129, 130, 34,
+ 131, 133, 134, 135, 137, -70, 141, -70, -3, 5,
+ -70, -2, 142, 143, 144, 145, 146, 147, 148, 149,
+ 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
+ 160, 161, 162, 163, 164, 165, 166, 167, 168, 169,
+ -70, 2, -70, -70, -70, 1, -70, 170, 170, -70,
-70, -70, -70, -70, -70, -70, -70, -70, -70, -70,
-70, -70, -70, -70, -70, -70, -70, -70, -70, -70,
- -70, -70, -70, -70, -70, -70, -70, -70, 169, 3,
- -70, -70, -70, -70, 170, 38, 74, 86, 125, 126,
- 130, 134, 136, 137, 138, 171, 172, 173, 174, 175,
- -70, 22, -70, -70, 176, 177, 178, 180, 5, 179,
- 183, 184, 185, 76, 187, 188, 189, 190, -70, 78,
- 191, 181, -70, -70, -70, -70, -70, -1, 182, 192,
- 197, 198, 9, 28, 199, 200, 201, 202, 203, 204,
- 205, -70, -70, -70, -70, -70, -70, -70, 206, -70,
- 207, -70, -70, -70, -70, -70, -70, -70, -70, -70
+ -70, -70, -70, -70, -70, -70, -70, -70, 171, 3,
+ -70, -70, -70, -70, 172, 74, 76, 85, 88, 127,
+ 128, 132, 136, 138, 139, 140, 173, 175, 174, 176,
+ -70, 22, -70, -70, 178, 179, 180, 182, 5, 181,
+ 185, 186, 187, 78, 189, 24, 190, 191, -70, 80,
+ 192, 183, -70, -70, -70, -70, -70, -1, 184, 194,
+ 198, 199, 9, 28, 200, 201, 202, 203, 204, 205,
+ 206, 207, -70, -70, -70, -70, -70, -70, -70, 208,
+ -70, 209, -70, -70, -70, -70, -70, -70, -70, -70,
+ -70, -70
};
/* YYDEFACT[S] -- default rule to reduce with in state S when YYTABLE
@@ -1005,13 +1190,13 @@
const unsigned char
Parser::yydefact_[] =
{
- 19, 16, 73, 0, 0, 0, 0, 0, 0, 0,
+ 19, 16, 74, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 20, 1, 51, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 72, 0, 17, 0, 0,
+ 0, 0, 0, 0, 0, 73, 0, 17, 0, 0,
13, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
@@ -1021,19 +1206,20 @@
40, 43, 42, 44, 41, 45, 46, 50, 0, 0,
10, 12, 11, 14, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 7, 0, 53, 71, 0, 0, 0, 0, 0, 0,
+ 7, 0, 53, 72, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 54, 0,
0, 0, 6, 5, 3, 4, 2, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 18, 66, 55, 63, 56, 57, 69, 0, 67,
- 0, 58, 59, 61, 62, 65, 64, 60, 70, 68
+ 0, 0, 18, 67, 55, 64, 56, 57, 70, 0,
+ 68, 0, 58, 60, 59, 62, 63, 66, 65, 61,
+ 71, 69
};
/* YYPGOTO[NTERM-NUM]. */
const signed char
Parser::yypgoto_[] =
{
- -70, -26, -70, -21, -69, -70, -70, -70, -70, -70,
+ -70, 12, -70, -19, -69, -70, -70, -70, -70, -70,
-70, -70, -70, -70
};
@@ -1052,29 +1238,29 @@
const unsigned char
Parser::yytable_[] =
{
- 105, 106, 202, 107, 107, 137, 107, 144, 35, 145,
- 146, 68, 207, 147, 148, 208, 149, 150, 151, 152,
+ 105, 106, 203, 107, 107, 137, 107, 144, 35, 145,
+ 146, 68, 208, 147, 148, 209, 149, 150, 151, 152,
153, 154, 155, 156, 157, 158, 159, 65, 145, 146,
- 37, 209, 74, 75, 181, 210, 66, 4, 94, 95,
- 103, 104, 36, 5, 164, 165, 38, 6, 7, 108,
+ 195, 210, 196, 36, 181, 211, 66, 4, 74, 75,
+ 94, 95, 37, 5, 103, 104, 38, 6, 7, 108,
108, 140, 108, 138, 69, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
- 166, 167, 192, 193, 198, 199, 141, 142, 39, 40,
- 72, 73, 41, 42, 43, 44, 45, 46, 47, 187,
+ 164, 165, 166, 167, 192, 193, 199, 200, 141, 142,
+ 39, 40, 41, 42, 43, 44, 45, 46, 47, 187,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
- 58, 59, 60, 61, 62, 63, 64, 76, 77, 78,
- 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,
- 89, 90, 91, 92, 93, 182, 96, 97, 168, 98,
- 99, 100, 102, 109, 110, 111, 112, 113, 114, 115,
- 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,
- 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
- 136, 0, 0, 163, 68, 143, 178, 169, 170, 183,
- 184, 185, 171, 186, 201, 203, 172, 188, 173, 174,
- 175, 189, 190, 191, 194, 204, 195, 196, 197, 200,
- 205, 206, 211, 212, 213, 214, 215, 216, 217, 218,
- 219, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 176, 177, 0, 179, 180
+ 58, 59, 60, 61, 62, 63, 64, 72, 73, 76,
+ 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
+ 87, 88, 89, 90, 91, 92, 93, 168, 96, 97,
+ 169, 98, 99, 100, 102, 109, 110, 111, 112, 113,
+ 114, 115, 116, 117, 118, 119, 120, 121, 122, 123,
+ 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,
+ 134, 135, 136, 182, 0, 163, 68, 143, 178, 170,
+ 171, 183, 184, 185, 172, 186, 202, 204, 173, 188,
+ 174, 175, 176, 189, 190, 191, 194, 205, 197, 198,
+ 201, 206, 207, 212, 213, 214, 215, 216, 217, 218,
+ 219, 220, 221, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 177, 179, 0, 180
};
/* YYCHECK. */
@@ -1084,26 +1270,26 @@
69, 3, 3, 5, 5, 3, 5, 4, 0, 6,
7, 6, 3, 10, 11, 6, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 0, 6, 7,
- 52, 3, 6, 7, 12, 7, 9, 4, 6, 7,
- 47, 48, 3, 10, 6, 7, 52, 14, 15, 51,
+ 6, 3, 8, 3, 12, 7, 9, 4, 6, 7,
+ 6, 7, 52, 10, 47, 48, 52, 14, 15, 51,
51, 50, 51, 51, 49, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
37, 38, 39, 40, 41, 42, 43, 44, 45, 46,
- 6, 7, 6, 7, 6, 7, 107, 108, 52, 52,
- 8, 8, 52, 52, 52, 52, 52, 52, 52, 168,
+ 6, 7, 6, 7, 6, 7, 6, 7, 107, 108,
+ 52, 52, 52, 52, 52, 52, 52, 52, 52, 168,
52, 52, 52, 52, 52, 52, 52, 52, 52, 52,
52, 52, 52, 52, 52, 52, 52, 8, 8, 8,
8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
- 8, 8, 8, 6, 6, 161, 7, 6, 52, 7,
- 7, 6, 3, 3, 3, 3, 3, 3, 3, 3,
+ 8, 8, 8, 8, 8, 6, 6, 52, 7, 6,
+ 52, 7, 7, 6, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
- 3, -1, -1, 3, 6, 6, 3, 52, 52, 3,
- 3, 3, 52, 3, 3, 3, 52, 8, 52, 52,
- 52, 8, 8, 8, 7, 3, 8, 8, 8, 8,
- 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
- 3, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, 52, 52, -1, 52, 52
+ 3, 3, 3, 161, -1, 3, 6, 6, 3, 52,
+ 52, 3, 3, 3, 52, 3, 3, 3, 52, 8,
+ 52, 52, 52, 8, 8, 8, 7, 3, 8, 8,
+ 8, 3, 3, 3, 3, 3, 3, 3, 3, 3,
+ 3, 3, 3, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, 52, 52, -1, 52
};
/* STOS_[STATE-NUM] -- The (internal number of the) accessing
@@ -1130,9 +1316,10 @@
54, 55, 64, 3, 6, 7, 6, 7, 52, 52,
52, 52, 52, 52, 52, 52, 52, 52, 3, 52,
52, 12, 54, 3, 3, 3, 3, 57, 8, 8,
- 8, 8, 6, 7, 7, 8, 8, 8, 6, 7,
- 8, 3, 3, 3, 3, 3, 3, 3, 6, 3,
- 7, 3, 3, 3, 3, 3, 3, 3, 3, 3
+ 8, 8, 6, 7, 7, 6, 8, 8, 8, 6,
+ 7, 8, 3, 3, 3, 3, 3, 3, 3, 6,
+ 3, 7, 3, 3, 3, 3, 3, 3, 3, 3,
+ 3, 3
};
#if YYDEBUG
@@ -1161,7 +1348,7 @@
62, 62, 62, 62, 62, 62, 62, 62, 62, 62,
62, 62, 63, 63, 64, 64, 64, 64, 64, 64,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
- 64, 64, 65, 66
+ 64, 64, 64, 65, 66
};
/* YYR2[YYN] -- Number of symbols composing right hand side of rule YYN. */
@@ -1174,8 +1361,8 @@
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 2, 0, 2, 2, 4, 4, 4, 4, 4,
- 4, 4, 4, 4, 4, 4, 4, 4, 5, 4,
- 5, 2, 3, 1
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 5,
+ 4, 5, 2, 3, 1
};
#if YYDEBUG || YYERROR_VERBOSE || YYTOKEN_TABLE
@@ -1241,13 +1428,14 @@
64, -1, 21, 3, -1, 11, 52, 8, 3, -1,
14, 52, 8, 3, -1, 15, 52, 8, 3, -1,
17, 52, 7, 3, -1, 18, 52, 8, 3, -1,
- 23, 52, 8, 3, -1, 19, 52, 8, 3, -1,
- 20, 52, 8, 3, -1, 13, 52, 8, 3, -1,
- 22, 52, 7, 3, -1, 22, 52, 6, 3, -1,
- 10, 52, 57, 3, -1, 16, 52, 7, 3, -1,
- 16, 52, 7, 7, 3, -1, 16, 52, 6, 3,
- -1, 16, 52, 6, 6, 3, -1, 4, 3, -1,
- 61, 59, 0, -1, 65, -1
+ 18, 52, 6, 3, -1, 23, 52, 8, 3, -1,
+ 19, 52, 8, 3, -1, 20, 52, 8, 3, -1,
+ 13, 52, 8, 3, -1, 22, 52, 7, 3, -1,
+ 22, 52, 6, 3, -1, 10, 52, 57, 3, -1,
+ 16, 52, 7, 3, -1, 16, 52, 7, 7, 3,
+ -1, 16, 52, 6, 3, -1, 16, 52, 6, 6,
+ 3, -1, 4, 3, -1, 61, 59, 0, -1, 65,
+ -1
};
/* YYPRHS[YYN] -- Index of the first RHS symbol of rule number YYN in
@@ -1261,22 +1449,22 @@
110, 115, 120, 125, 130, 135, 140, 145, 150, 155,
160, 165, 170, 175, 180, 185, 190, 195, 200, 205,
210, 215, 218, 219, 222, 225, 230, 235, 240, 245,
- 250, 255, 260, 265, 270, 275, 280, 285, 290, 296,
- 301, 307, 310, 314
+ 250, 255, 260, 265, 270, 275, 280, 285, 290, 295,
+ 301, 306, 312, 315, 319
};
/* YYRLINE[YYN] -- Source line where rule number YYN was defined. */
const unsigned char
Parser::yyrline_[] =
{
- 0, 140, 140, 141, 142, 143, 145, 146, 148, 149,
- 151, 152, 153, 154, 156, 157, 159, 160, 166, 172,
- 173, 175, 176, 177, 178, 179, 180, 181, 182, 183,
+ 0, 130, 130, 131, 132, 133, 135, 136, 138, 139,
+ 141, 142, 143, 144, 146, 147, 149, 150, 156, 162,
+ 163, 165, 166, 167, 168, 169, 170, 171, 172, 173,
+ 174, 175, 176, 177, 178, 179, 180, 181, 182, 183,
184, 185, 186, 187, 188, 189, 190, 191, 192, 193,
- 194, 195, 196, 197, 198, 199, 200, 201, 202, 203,
- 204, 205, 207, 208, 210, 211, 212, 213, 214, 215,
- 216, 217, 218, 219, 220, 221, 222, 223, 224, 225,
- 226, 227, 230, 236
+ 194, 195, 197, 198, 200, 201, 202, 203, 204, 205,
+ 206, 207, 208, 209, 210, 211, 212, 213, 214, 215,
+ 216, 217, 218, 221, 227
};
// Print the state stack on the debug stream.
@@ -1298,7 +1486,7 @@
int yynrhs = yyr2_[yyrule];
/* Print the symbols being reduced, and their result. */
*yycdebug_ << "Reducing stack by rule " << yyrule - 1
- << " (line " << yylno << "), ";
+ << " (line " << yylno << "):" << std::endl;
/* The symbols being reduced. */
for (int yyi = 0; yyi < yynrhs; yyi++)
YY_SYMBOL_PRINT (" $" << yyi + 1 << " =",
@@ -1355,7 +1543,7 @@
}
const int Parser::yyeof_ = 0;
- const int Parser::yylast_ = 227;
+ const int Parser::yylast_ = 228;
const int Parser::yynnts_ = 14;
const int Parser::yyempty_ = -2;
const int Parser::yyfinal_ = 35;
@@ -1366,9 +1554,18 @@
const unsigned int Parser::yyuser_token_number_max_ = 301;
const Parser::token_number_type Parser::yyundef_token_ = 2;
-} // namespace mgf
-#line 238 "Parser.ypp"
+/* Line 1054 of lalr1.cc */
+#line 1 "[Bison:b4_percent_define_default]"
+
+} // mgf
+
+/* Line 1054 of lalr1.cc */
+#line 1565 "Parser.cpp"
+
+
+/* Line 1056 of lalr1.cc */
+#line 229 "Parser.ypp"
/*** Additional Code ***/
void mgf::Parser::error(const Parser::location_type& l, const std::string& m)
Modified: trunk/mgfp/src/Parser.h
===================================================================
--- trunk/mgfp/src/Parser.h 2010-09-08 03:51:39 UTC (rev 35)
+++ trunk/mgfp/src/Parser.h 2010-09-09 21:29:45 UTC (rev 36)
@@ -1,23 +1,23 @@
-/* A Bison parser, made by GNU Bison 2.3. */
+/* A Bison parser, made by GNU Bison 2.4.1. */
+
/* Skeleton interface for Bison LALR(1) parsers in C++
-
- Copyright (C) 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
-
- This program is free software; you can redistribute it and/or modify
+
+ Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software
+ Foundation, Inc.
+
+ This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2, or (at your option)
- any later version.
-
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
-
+
You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor,
- Boston, MA 02110-1301, USA. */
+ along with this program. If not, see <http://www.gnu.org/licenses/>. */
/* As a special exception, you may create a larger work that contains
part or all of the Bison parser skeleton and distribute that work
@@ -28,7 +28,7 @@
special exception, which will cause the skeleton and the resulting
Bison output files to be licensed under the GNU General Public
License without this special exception.
-
+
This special exception was added by the Free Software Foundation in
version 2.2 of Bison. */
@@ -37,20 +37,11 @@
#ifndef PARSER_HEADER_H
# define PARSER_HEADER_H
-#include <string>
-#include <iostream>
-#include "stack.h"
+/* "%code requires" blocks. */
-namespace mgf
-{
- class position;
- class location;
-}
-
-/* First part of user declarations. */
-#line 6 "Parser.ypp"
-
-
+/* Line 35 of lalr1.cc */
+#line 3 "Parser.ypp"
+
#include <mgfp/Driver.h>
#include "Nodes.h"
@@ -63,9 +54,33 @@
-/* Line 303 of lalr1.cc. */
-#line 68 "Parser.h"
+/* Line 35 of lalr1.cc */
+#line 59 "Parser.h"
+
+#include <string>
+#include <iostream>
+#include "stack.h"
+
+
+/* Line 35 of lalr1.cc */
+#line 1 "[Bison:b4_percent_define_default]"
+
+namespace mgf {
+
+/* Line 35 of lalr1.cc */
+#line 73 "Parser.h"
+ class position;
+ class location;
+
+/* Line 35 of lalr1.cc */
+#line 1 "[Bison:b4_percent_define_default]"
+
+} // mgf
+
+/* Line 35 of lalr1.cc */
+#line 83 "Parser.h"
+
#include "location.h"
/* Enabling traces. */
@@ -105,9 +120,15 @@
} while (false)
#endif
-namespace mgf
-{
+/* Line 35 of lalr1.cc */
+#line 1 "[Bison:b4_percent_define_default]"
+
+namespace mgf {
+
+/* Line 35 of lalr1.cc */
+#line 131 "Parser.h"
+
/// A Bison parser.
class Parser
{
@@ -115,8 +136,11 @@
/// Symbol semantic values.
#ifndef YYSTYPE
union semantic_type
-#line 62 "Parser.ypp"
-{
+ {
+
+/* Line 35 of lalr1.cc */
+#line 52 "Parser.ypp"
+
int integerVal;
double doubleVal;
std::string* stringVal;
@@ -124,10 +148,12 @@
DoublePairListNode* doublepairlistnode;
IntegerNode* integernode;
IntegerListNode* integerlistnode;
-}
-/* Line 303 of lalr1.cc. */
-#line 130 "Parser.h"
- ;
+
+
+
+/* Line 35 of lalr1.cc */
+#line 156 "Parser.h"
+ };
#else
typedef YYSTYPE semantic_type;
#endif
@@ -197,6 +223,7 @@
/// \returns 0 iff parsing succeeded.
virtual int parse ();
+#if YYDEBUG
/// The current debugging stream.
std::ostream& debug_stream () const;
/// Set the current debugging stream.
@@ -208,6 +235,7 @@
debug_level_type debug_level () const;
/// Set the current debugging level.
void set_debug_level (debug_level_type l);
+#endif
private:
/// Report a syntax error.
@@ -217,7 +245,7 @@
/// Generate an error message.
/// \param state the state where the error occurred.
- /// \param tok the look-ahead token.
+ /// \param tok the lookahead token.
virtual std::string yysyntax_error_ (int yystate, int tok);
#if YYDEBUG
@@ -235,7 +263,7 @@
virtual void yy_symbol_print_ (int yytype,
const semantic_type* yyvaluep,
const location_type* yylocationp);
-#endif /* ! YYDEBUG */
+#endif
/// State numbers.
@@ -312,6 +340,10 @@
virtual void yy_reduce_print_ (int r);
/// Print the state stack on the debug stream.
virtual void yystack_print_ ();
+
+ /* Debugging. */
+ int yydebug_;
+ std::ostream* yycdebug_;
#endif
/// Convert a scanner token number \a t to a symbol number.
@@ -343,15 +375,18 @@
static const unsigned int yyuser_token_number_max_;
static const token_number_type yyundef_token_;
- /* Debugging. */
- int yydebug_;
- std::ostream* yycdebug_;
-
-
/* User arguments. */
Driver& driver;
};
-}
+/* Line 35 of lalr1.cc */
+#line 1 "[Bison:b4_percent_define_default]"
+} // mgf
+
+/* Line 35 of lalr1.cc */
+#line 389 "Parser.h"
+
+
+
#endif /* ! defined PARSER_HEADER_H */
Modified: trunk/mgfp/src/Parser.ypp
===================================================================
--- trunk/mgfp/src/Parser.ypp 2010-09-08 03:51:39 UTC (rev 35)
+++ trunk/mgfp/src/Parser.ypp 2010-09-09 21:29:45 UTC (rev 36)
@@ -1,10 +1,6 @@
/* $Id$ */
-/*
- * C/C++ Declarations
- */
-%{
-
+%code requires {
#include <mgfp/Driver.h>
#include "Nodes.h"
@@ -14,26 +10,20 @@
using namespace mgf;
using namespace mgf::detail;
+}
-%}
-
-/*
- * yacc/bison Declarations
- */
-
/* Require bison 2.3 or later */
%require "2.3"
-/* add debug output code to generated parser. disable this for release
- * versions. */
-%debug
-
/* start symbol is named "start" */
%start start
-/* write out a header file containing the token defines */
+/* write a header file containing macro definitions */
%defines
+/* add debug output code to generated parser. */
+%debug
+
/* use newer C++ skeleton file */
%skeleton "lalr1.cc"
@@ -213,6 +203,7 @@
| IT_MODS '=' STRING EOL { driver.context.currentSpectrum.setIT_MODS(*$3); delete $3; }
| RTINSECONDS '=' DOUBLE EOL { driver.context.currentSpectrum.setRTINSECONDS($3); }
| SCANS '=' STRING EOL { driver.context.currentSpectrum.setSCANS(*$3); delete $3; }
+ | SCANS '=' INTEGER EOL { driver.context.currentSpectrum.setSCANS($3); }
| TOLU '=' STRING EOL { driver.context.currentSpectrum.setTOLU(*$3); delete $3; }
| SEQ '=' STRING EOL { driver.context.currentSpectrum.setSEQ(*$3); delete $3; }/* FIXME: multiple */
| TAG '=' STRING EOL { driver.context.currentSpectrum.setTAG(*$3); delete $3; }/* FIXME: multiple */
Modified: trunk/mgfp/src/Scanner.cpp
===================================================================
--- trunk/mgfp/src/Scanner.cpp 2010-09-08 03:51:39 UTC (rev 35)
+++ trunk/mgfp/src/Scanner.cpp 2010-09-09 21:29:45 UTC (rev 36)
@@ -58,7 +58,6 @@
typedef unsigned char flex_uint8_t;
typedef unsigned short int flex_uint16_t;
typedef unsigned int flex_uint32_t;
-#endif /* ! C99 */
/* Limits of integral types. */
#ifndef INT8_MIN
@@ -89,12 +88,15 @@
#define UINT32_MAX (4294967295U)
#endif
+#endif /* ! C99 */
+
#endif /* ! FLEXINT_H */
/* begin standard C++ headers. */
#include <iostream>
#include <errno.h>
#include <cstdlib>
+#include <cstdio>
#include <cstring>
/* end standard C++ headers. */
@@ -152,7 +154,15 @@
/* Size of default input buffer. */
#ifndef YY_BUF_SIZE
+#ifdef __ia64__
+/* On IA-64, the buffer size is 16k, not 8k.
+ * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
+ * Ditto for the __ia64__ case accordingly.
+ */
+#define YY_BUF_SIZE 32768
+#else
#define YY_BUF_SIZE 16384
+#endif /* __ia64__ */
#endif
/* The state buf must be large enough to hold one state per character in the main buffer.
@@ -164,13 +174,8 @@
typedef struct yy_buffer_state *YY_BUFFER_STATE;
#endif
-#ifndef YY_TYPEDEF_YY_SIZE_T
-#define YY_TYPEDEF_YY_SIZE_T
-typedef size_t yy_size_t;
-#endif
+extern int yyleng;
-extern yy_size_t yyleng;
-
#define EOB_ACT_CONTINUE_SCAN 0
#define EOB_ACT_END_OF_FILE 1
#define EOB_ACT_LAST_MATCH 2
@@ -193,6 +198,11 @@
#define unput(c) yyunput( c, (yytext_ptr) )
+#ifndef YY_TYPEDEF_YY_SIZE_T
+#define YY_TYPEDEF_YY_SIZE_T
+typedef size_t yy_size_t;
+#endif
+
#ifndef YY_STRUCT_YY_BUFFER_STATE
#define YY_STRUCT_YY_BUFFER_STATE
struct yy_buffer_state
@@ -211,7 +221,7 @@
/* Number of characters read into yy_ch_buf, not including EOB
* characters.
...
[truncated message content] |
|
From: <mki...@us...> - 2010-09-08 03:51:46
|
Revision: 35
http://mgfp.svn.sourceforge.net/mgfp/?rev=35&view=rev
Author: mkirchner
Date: 2010-09-08 03:51:39 +0000 (Wed, 08 Sep 2010)
Log Message:
-----------
adding a very simple TMT extraction application
Added Paths:
-----------
trunk/mgfp/applications/tmtx/
trunk/mgfp/applications/tmtx/CMakeLists.txt
trunk/mgfp/applications/tmtx/tmtx.cpp
Added: trunk/mgfp/applications/tmtx/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/tmtx/CMakeLists.txt (rev 0)
+++ trunk/mgfp/applications/tmtx/CMakeLists.txt 2010-09-08 03:51:39 UTC (rev 35)
@@ -0,0 +1,23 @@
+# make sure we find the headers
+INCLUDE_DIRECTORIES(
+ ${MGFP_SOURCE_DIR}/include
+ ${MGFP_BINARY_DIR}/include
+ ${CMAKE_CURRENT_SOURCE_DIR}
+)
+# this requres BOOST
+IF(MSVC)
+ SET(Boost_USE_STATIC_LIBS ON)
+ SET(Boost_USE_MULTITHREAD OFF)
+ENDIF(MSVC)
+FIND_PACKAGE(Boost COMPONENTS program_options)
+IF(Boost_PROGRAM_OPTIONS_FOUND)
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
+ SET(SRCS_TMTX tmtx.cpp)
+ ADD_EXECUTABLE(tmtx ${SRCS_TMTX})
+ TARGET_LINK_LIBRARIES(tmtx mgfp ${Boost_PROGRAM_OPTIONS_LIBRARY})
+ INSTALL(TARGETS tmtx RUNTIME DESTINATION bin)
+ELSE(Boost_PROGRAM_OPTIONS_FOUND)
+ MESSAGE(STATUS "Could not find BOOST program_options. Skipping ${CMAKE_CURRENT_SOURCE_DIR}.")
+ENDIF(Boost_PROGRAM_OPTIONS_FOUND)
+
Added: trunk/mgfp/applications/tmtx/tmtx.cpp
===================================================================
--- trunk/mgfp/applications/tmtx/tmtx.cpp (rev 0)
+++ trunk/mgfp/applications/tmtx/tmtx.cpp 2010-09-08 03:51:39 UTC (rev 35)
@@ -0,0 +1,125 @@
+/*$Id$*/
+/*
+ * tmtx.cpp
+ *
+ * Copyright (c) 2010 Marc Kirchner <mar...@ch...>
+ *
+ * This file is part of mgfp.
+ *
+ * mgfp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ms++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with ms++. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <cmath>
+#include <iostream>
+#include <iterator>
+#include <tr1/array>
+#include <boost/program_options.hpp>
+#include <mgfp/mgfp.h>
+
+mgf::MgfSpectrum::iterator findClosestMz(mgf::MgfSpectrum::iterator begin,
+ mgf::MgfSpectrum::iterator end, double referenceMz)
+{
+ // at least one entry?
+ if (begin == end)
+ return end;
+ // find first entry that is equal or greater than the reference mz
+ typedef mgf::MgfSpectrum::iterator MSI;
+ MSI pos1 = std::lower_bound(begin, end, referenceMz, mgf::LessThanMz());
+ double dist1 = 0.0;
+ if (pos1 != end) {
+ // found equal or greater
+ dist1 = pos1->first - referenceMz;
+ if (pos1 == begin || dist1 == 0.0) {
+ return pos1;
+ }
+ } else {
+ // return the last entry in the sequence
+ pos1 = begin;
+ std::advance(pos1, std::distance(begin, end) - 1);
+ return pos1;
+ }
+ // check if the distance to the previous iterator position
+ if (pos1 != begin) {
+ MSI pos2 = begin;
+ std::advance(pos2, std::distance(begin, pos1) - 1);
+ double dist2 = referenceMz - pos2->first;
+ if (dist2 < dist1) {
+ return pos2;
+ }
+ return pos1;
+ }
+}
+
+static const double tmtMasses[10] =
+ { 124.0, 125.0, 126.0, 127.0, 128.0,
+ 129.0, 130.0, 131.0, 132.0, 133.0 };
+
+int main(int argc, char *argv[])
+{
+ namespace po = boost::program_options;
+ po::options_description desc("Allowed options");
+ bool verbose = false;
+ desc.add_options()
+ ("help,h", "produce help message")
+ ("verbose,v", po::value(&verbose)->zero_tokens(),
+ "verbose output (good to pinpoint parsing errors)")
+ ;
+ po::variables_map vm;
+ po::store(po::parse_command_line(argc, argv, desc), vm);
+ po::notify(vm);
+ // check if the user asked for help
+ if (vm.count("help")) {
+ std::cerr << desc;
+ return 1;
+ }
+ // prepare the parser
+ mgf::MgfFile m;
+ mgf::Driver driver(m);
+ driver.trace_parsing = verbose;
+ driver.trace_scanning = verbose;
+ // parse input
+ bool result = driver.parse_stream(std::cin);
+ if (!result) {
+ std::cerr << std::endl
+ << "Error parsing data stream (use -v for details)." << std::endl;
+ return -1;
+ }
+ typedef mgf::MgfFile::iterator MFI;
+ // iterate over all spectra
+ for (MFI i = m.begin(); i != m.end(); ++i) {
+ // sort
+ std::sort(i->begin(), i->end(), mgf::LessThanMz());
+ typedef mgf::MgfSpectrum::iterator MSI;
+ // extract TMT reproter ion intensities
+ double obsTmtAbundances[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
+ for (size_t n = 0; n < 6; ++n) {
+ MSI closestIt = findClosestMz(i->begin(), i->end(), tmtMasses[n]);
+ // check if there is a MS2 centroid
+ if (std::abs(closestIt->first - tmtMasses[n]) < 0.4) {
+ obsTmtAbundances[n] = closestIt->second;
+ } else {
+ obsTmtAbundances[n] = 0.0;
+ }
+ }
+ // extract into file
+ std::cout << i->getTITLE();
+ for (size_t n = 0; n < 6; ++n) {
+ std::cout << '\t' << obsTmtAbundances[n];
+ }
+ std::cout << std::endl;
+ }
+ return 0;
+}
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mki...@us...> - 2010-09-08 03:36:59
|
Revision: 34
http://mgfp.svn.sourceforge.net/mgfp/?rev=34&view=rev
Author: mkirchner
Date: 2010-09-08 03:36:53 +0000 (Wed, 08 Sep 2010)
Log Message:
-----------
renaming tools
Added Paths:
-----------
trunk/mgfp/applications/tmtadducts/
trunk/mgfp/applications/tmtadducts/tmtadducts.cpp
Removed Paths:
-------------
trunk/mgfp/applications/tmtadducts/tmtx.cpp
trunk/mgfp/applications/tmtx/
Copied: trunk/mgfp/applications/tmtadducts/tmtadducts.cpp (from rev 31, trunk/mgfp/applications/tmtx/tmtx.cpp)
===================================================================
--- trunk/mgfp/applications/tmtadducts/tmtadducts.cpp (rev 0)
+++ trunk/mgfp/applications/tmtadducts/tmtadducts.cpp 2010-09-08 03:36:53 UTC (rev 34)
@@ -0,0 +1,166 @@
+/*$Id$*/
+/*
+ * tmtx.cpp
+ *
+ * Copyright (c) 2010 Marc Kirchner <mar...@ch...>
+ *
+ * This file is part of mgfp.
+ *
+ * mgfp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ms++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with ms++. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <cmath>
+#include <iostream>
+#include <iterator>
+#include <tr1/array>
+#include <boost/program_options.hpp>
+#include <mgfp/mgfp.h>
+
+mgf::MgfSpectrum::iterator findClosestMz(mgf::MgfSpectrum::iterator begin,
+ mgf::MgfSpectrum::iterator end, double referenceMz)
+{
+ // at least one entry?
+ if (begin == end)
+ return end;
+ // find first entry that is equal or greater than the reference mz
+ typedef mgf::MgfSpectrum::iterator MSI;
+ MSI pos1 = std::lower_bound(begin, end, referenceMz, mgf::LessThanMz());
+ double dist1 = 0.0;
+ if (pos1 != end) {
+ // found equal or greater
+ dist1 = pos1->first - referenceMz;
+ if (pos1 == begin || dist1 == 0.0) {
+ return pos1;
+ }
+ } else {
+ // return the last entry in the sequence
+ pos1 = begin;
+ std::advance(pos1, std::distance(begin, end) - 1);
+ return pos1;
+ }
+ // check if the distance to the previous iterator position
+ if (pos1 != begin) {
+ MSI pos2 = begin;
+ std::advance(pos2, std::distance(begin, pos1) - 1);
+ double dist2 = referenceMz - pos2->first;
+ if (dist2 < dist1) {
+ return pos2;
+ }
+ return pos1;
+ }
+}
+
+static const double adductMasses[6] =
+ { 155.0, 156.0, 157.0, 158.0, 159.0, 160.0 };
+static const double tmtMasses[6] =
+ { 126.0, 127.0, 128.0, 129.0, 130.0, 131.0 };
+
+int main(int argc, char *argv[])
+{
+ namespace po = boost::program_options;
+ po::options_description desc("Allowed options");
+ bool replace = false;
+ bool verbose = false;
+ desc.add_options()
+ ("help,h", "produce help message")
+ ("verbose,v", po::value(&verbose)->zero_tokens(),
+ "verbose output (good to pinpoint parsing errors)")
+ ("replace,r", po::value(&replace)->zero_tokens(),
+ "replace TMT intensities in original MGF, output new MGF to stdout.")
+ ;
+ po::variables_map vm;
+ po::store(po::parse_command_line(argc, argv, desc), vm);
+ po::notify(vm);
+ // check if the user asked for help
+ if (vm.count("help")) {
+ std::cerr << desc;
+ return 1;
+ }
+ // prepare the parser
+ mgf::MgfFile m;
+ mgf::Driver driver(m);
+ driver.trace_parsing = verbose;
+ driver.trace_scanning = verbose;
+ // parse input
+ bool result = driver.parse_stream(std::cin);
+ if (!result) {
+ std::cerr << std::endl
+ << "Error parsing data stream (use -v for details)." << std::endl;
+ return -1;
+ }
+ typedef mgf::MgfFile::iterator MFI;
+ // iterate over all spectra
+ for (MFI i = m.begin(); i != m.end(); ++i) {
+ // sort
+ std::sort(i->begin(), i->end(), mgf::LessThanMz());
+ // extract adduct intensities
+ double obsAdductAbundances[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
+ typedef mgf::MgfSpectrum::iterator MSI;
+ for (size_t n = 0; n < 6; ++n) {
+ MSI closestIt = findClosestMz(i->begin(), i->end(), adductMasses[n]);
+ // check if there is a MS2 centroid
+ if (std::abs(closestIt->first - adductMasses[n]) < 0.5) {
+ obsAdductAbundances[n] = closestIt->second;
+ if (replace) {
+ // if the replace option is on, remove the observed value
+ // from the spectrum
+ i->erase(closestIt);
+ }
+ } else {
+ obsAdductAbundances[n] = 0.0;
+ }
+ }
+ // extract TMT reproter ion intensities
+ double obsTmtAbundances[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
+ for (size_t n = 0; n < 6; ++n) {
+ MSI closestIt = findClosestMz(i->begin(), i->end(), tmtMasses[n]);
+ // check if there is a MS2 centroid
+ if (std::abs(closestIt->first - tmtMasses[n]) < 0.5) {
+ obsTmtAbundances[n] = closestIt->second;
+ if (replace) {
+ // if the replace option is on, remove the observed value
+ // from the spectrum
+ i->erase(closestIt);
+ }
+ } else {
+ obsTmtAbundances[n] = 0.0;
+ }
+ }
+ // add on TMTs
+ if (replace) {
+ // re-insert
+ for (size_t n = 0; n < 6; ++n) {
+ i->push_back(std::make_pair(tmtMasses[n], obsTmtAbundances[n] +
+ obsAdductAbundances[n]));
+ }
+ } else {
+ // extract into file
+ std::cout << i->getTITLE();
+ for (size_t n = 0; n < 6; ++n) {
+ std::cout << '\t' << obsTmtAbundances[n];
+ }
+ for (size_t n = 0; n < 6; ++n) {
+ std::cout << '\t' << obsAdductAbundances[n];
+ }
+ std::cout << std::endl;
+ }
+ }
+ // if replacement is in effect, output the whole modified file at once.
+ if (replace) {
+ std::cout << m;
+ }
+ return 0;
+}
+
Deleted: trunk/mgfp/applications/tmtadducts/tmtx.cpp
===================================================================
--- trunk/mgfp/applications/tmtx/tmtx.cpp 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/applications/tmtadducts/tmtx.cpp 2010-09-08 03:36:53 UTC (rev 34)
@@ -1,166 +0,0 @@
-/*$Id$*/
-/*
- * tmtx.cpp
- *
- * Copyright (c) 2010 Marc Kirchner <mar...@ch...>
- *
- * This file is part of mgfp.
- *
- * mgfp is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * ms++ is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with ms++. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#include <cmath>
-#include <iostream>
-#include <iterator>
-#include <tr1/array>
-#include <boost/program_options.hpp>
-#include <mgfp/mgfp.h>
-
-mgf::MgfSpectrum::iterator findClosestMz(mgf::MgfSpectrum::iterator begin,
- mgf::MgfSpectrum::iterator end, double referenceMz)
-{
- // at least one entry?
- if (begin == end)
- return end;
- // find first entry that is equal or greater than the reference mz
- typedef mgf::MgfSpectrum::iterator MSI;
- MSI pos1 = std::lower_bound(begin, end, referenceMz, mgf::LessThanMz());
- double dist1 = 0.0;
- if (pos1 != end) {
- // found equal or greater
- dist1 = pos1->first - referenceMz;
- if (pos1 == begin || dist1 == 0.0) {
- return pos1;
- }
- } else {
- // return the last entry in the sequence
- pos1 = begin;
- std::advance(pos1, std::distance(begin, end) - 1);
- return pos1;
- }
- // check if the distance to the previous iterator position
- if (pos1 != begin) {
- MSI pos2 = begin;
- std::advance(pos2, std::distance(begin, pos1) - 1);
- double dist2 = referenceMz - pos2->first;
- if (dist2 < dist1) {
- return pos2;
- }
- return pos1;
- }
-}
-
-static const double adductMasses[6] =
- { 155.0, 156.0, 157.0, 158.0, 159.0, 160.0 };
-static const double tmtMasses[6] =
- { 126.0, 127.0, 128.0, 129.0, 130.0, 131.0 };
-
-int main(int argc, char *argv[])
-{
- namespace po = boost::program_options;
- po::options_description desc("Allowed options");
- bool replace = false;
- bool verbose = false;
- desc.add_options()
- ("help,h", "produce help message")
- ("verbose,v", po::value(&verbose)->zero_tokens(),
- "verbose output (good to pinpoint parsing errors)")
- ("replace,r", po::value(&replace)->zero_tokens(),
- "replace TMT intensities in original MGF, output new MGF to stdout.")
- ;
- po::variables_map vm;
- po::store(po::parse_command_line(argc, argv, desc), vm);
- po::notify(vm);
- // check if the user asked for help
- if (vm.count("help")) {
- std::cerr << desc;
- return 1;
- }
- // prepare the parser
- mgf::MgfFile m;
- mgf::Driver driver(m);
- driver.trace_parsing = verbose;
- driver.trace_scanning = verbose;
- // parse input
- bool result = driver.parse_stream(std::cin);
- if (!result) {
- std::cerr << std::endl
- << "Error parsing data stream (use -v for details)." << std::endl;
- return -1;
- }
- typedef mgf::MgfFile::iterator MFI;
- // iterate over all spectra
- for (MFI i = m.begin(); i != m.end(); ++i) {
- // sort
- std::sort(i->begin(), i->end(), mgf::LessThanMz());
- // extract adduct intensities
- double obsAdductAbundances[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
- typedef mgf::MgfSpectrum::iterator MSI;
- for (size_t n = 0; n < 6; ++n) {
- MSI closestIt = findClosestMz(i->begin(), i->end(), adductMasses[n]);
- // check if there is a MS2 centroid
- if (std::abs(closestIt->first - adductMasses[n]) < 0.5) {
- obsAdductAbundances[n] = closestIt->second;
- if (replace) {
- // if the replace option is on, remove the observed value
- // from the spectrum
- i->erase(closestIt);
- }
- } else {
- obsAdductAbundances[n] = 0.0;
- }
- }
- // extract TMT reproter ion intensities
- double obsTmtAbundances[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
- for (size_t n = 0; n < 6; ++n) {
- MSI closestIt = findClosestMz(i->begin(), i->end(), tmtMasses[n]);
- // check if there is a MS2 centroid
- if (std::abs(closestIt->first - tmtMasses[n]) < 0.5) {
- obsTmtAbundances[n] = closestIt->second;
- if (replace) {
- // if the replace option is on, remove the observed value
- // from the spectrum
- i->erase(closestIt);
- }
- } else {
- obsTmtAbundances[n] = 0.0;
- }
- }
- // add on TMTs
- if (replace) {
- // re-insert
- for (size_t n = 0; n < 6; ++n) {
- i->push_back(std::make_pair(tmtMasses[n], obsTmtAbundances[n] +
- obsAdductAbundances[n]));
- }
- } else {
- // extract into file
- std::cout << i->getTITLE();
- for (size_t n = 0; n < 6; ++n) {
- std::cout << '\t' << obsTmtAbundances[n];
- }
- for (size_t n = 0; n < 6; ++n) {
- std::cout << '\t' << obsAdductAbundances[n];
- }
- std::cout << std::endl;
- }
- }
- // if replacement is in effect, output the whole modified file at once.
- if (replace) {
- std::cout << m;
- }
- return 0;
-}
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mki...@us...> - 2010-08-12 22:18:25
|
Revision: 33
http://mgfp.svn.sourceforge.net/mgfp/?rev=33&view=rev
Author: mkirchner
Date: 2010-08-12 22:18:18 +0000 (Thu, 12 Aug 2010)
Log Message:
-----------
* initial import of the ms2preproc code into the mgfp package.
* ms2preproc itself is still a bit of a hack but at least it now resides where it belongs.
Modified Paths:
--------------
trunk/mgfp/applications/CMakeLists.txt
trunk/mgfp/applications/mgfvalidate/CMakeLists.txt
Added Paths:
-----------
trunk/mgfp/applications/ms2preproc/
trunk/mgfp/applications/ms2preproc/CMakeLists.txt
trunk/mgfp/applications/ms2preproc/ms2preproc.cpp
Modified: trunk/mgfp/applications/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/CMakeLists.txt 2010-08-05 22:12:58 UTC (rev 32)
+++ trunk/mgfp/applications/CMakeLists.txt 2010-08-12 22:18:18 UTC (rev 33)
@@ -1,3 +1,4 @@
ADD_SUBDIRECTORY(mgfvalidate)
+ADD_SUBDIRECTORY(ms2preproc)
ADD_SUBDIRECTORY(tmtx)
Modified: trunk/mgfp/applications/mgfvalidate/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/mgfvalidate/CMakeLists.txt 2010-08-05 22:12:58 UTC (rev 32)
+++ trunk/mgfp/applications/mgfvalidate/CMakeLists.txt 2010-08-12 22:18:18 UTC (rev 33)
@@ -1,10 +1,14 @@
+#############################################################################
# make sure we find the headers
+#############################################################################
INCLUDE_DIRECTORIES(
${MGFP_SOURCE_DIR}/include
${MGFP_BINARY_DIR}/include
${CMAKE_CURRENT_SOURCE_DIR}
)
+#############################################################################
# this requres BOOST
+#############################################################################
IF(MSVC)
SET(Boost_USE_STATIC_LIBS ON)
SET(Boost_USE_MULTITHREAD OFF)
Added: trunk/mgfp/applications/ms2preproc/CMakeLists.txt
===================================================================
--- trunk/mgfp/applications/ms2preproc/CMakeLists.txt (rev 0)
+++ trunk/mgfp/applications/ms2preproc/CMakeLists.txt 2010-08-12 22:18:18 UTC (rev 33)
@@ -0,0 +1,27 @@
+#############################################################################
+# make sure we find the headers
+#############################################################################
+INCLUDE_DIRECTORIES(
+ ${MGFP_SOURCE_DIR}/include
+ ${MGFP_BINARY_DIR}/include
+ ${CMAKE_CURRENT_SOURCE_DIR}
+)
+#############################################################################
+# require boost
+#############################################################################
+IF(MSVC)
+ SET(Boost_USE_STATIC_LIBS ON)
+ SET(Boost_USE_MULTITHREAD OFF)
+ENDIF(MSVC)
+FIND_PACKAGE(Boost COMPONENTS program_options)
+IF(Boost_PROGRAM_OPTIONS_FOUND)
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
+ SET(SRCS_MS2PREPROC ms2preproc.cpp)
+ ADD_EXECUTABLE(ms2preproc ${SRCS_MS2PREPROC})
+ TARGET_LINK_LIBRARIES(ms2preproc mgfp ${Boost_PROGRAM_OPTIONS_LIBRARY})
+ INSTALL(TARGETS ms2preproc RUNTIME DESTINATION bin)
+ELSE(Boost_PROGRAM_OPTIONS_FOUND)
+ MESSAGE(STATUS "Could not find BOOST program_options. Skipping ${CMAKE_CURRENT_SOURCE_DIR}.")
+ENDIF(Boost_PROGRAM_OPTIONS_FOUND)
+
Added: trunk/mgfp/applications/ms2preproc/ms2preproc.cpp
===================================================================
--- trunk/mgfp/applications/ms2preproc/ms2preproc.cpp (rev 0)
+++ trunk/mgfp/applications/ms2preproc/ms2preproc.cpp 2010-08-12 22:18:18 UTC (rev 33)
@@ -0,0 +1,479 @@
+/*$Id: ms2preproc.cpp 2725 2009-11-30 22:27:57Z mar...@ch... $*/
+
+/*
+ * ms2preproc.cpp
+ *
+ * Copyright (c) 2010 Marc Kirchner <mar...@ch...>
+ * Copyright (c) 2009 Marc Kirchner <mar...@ch...>
+ *
+ * This file is part of mgfp.
+ *
+ * ms++ is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ms++ is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with ms++. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <iostream>
+#include <iterator>
+#include <iomanip>
+#include <fstream>
+#include <sstream>
+#include <exception>
+#include <stdexcept>
+#include <algorithm>
+
+#include <boost/program_options.hpp>
+
+#include <mgfp/Driver.h>
+#include <mgfp/Context.h>
+#include <mgfp/MgfFile.h>
+
+// #define DEBUG
+
+struct LessThanMass
+{
+ bool operator()(const mgf::MassAbundancePair& lhs, const mgf::MassAbundancePair& rhs) {
+ return lhs.first < rhs.first;
+ }
+ bool operator()(const double lhs, const mgf::MassAbundancePair& rhs) {
+ return lhs < rhs.first;
+ }
+ bool operator()(const mgf::MassAbundancePair& lhs, const double rhs) {
+ return lhs.first < rhs;
+ }
+};
+
+struct LessThanAbundance
+{
+ bool operator()(const mgf::MassAbundancePair& lhs, const mgf::MassAbundancePair& rhs) {
+ return lhs.second < rhs.second;
+ }
+ bool operator()(const double lhs, const mgf::MassAbundancePair& rhs) {
+ return lhs < rhs.second;
+ }
+ bool operator()(const mgf::MassAbundancePair& lhs, const double rhs) {
+ return lhs.second < rhs;
+ }
+};
+
+namespace Ms2Preproc {
+
+
+/** Functor to determine the top X peaks in a given set of peaks.
+ */
+class TopX
+{
+ public:
+ TopX(unsigned int x) : x_(x)
+ {}
+
+ template<class In, class Out, class Comp>
+ Out operator()(In begin, In end, Out out, Comp comp) {
+ typename In::difference_type size = std::distance(begin, end);
+#ifdef DEBUG
+if (size > 0) {
+ std::cerr << "range " << begin->first << " - " << (end-1)->first << std::endl;
+}
+#endif
+
+ // FIXME: Make the static_cast in the next step safe.
+ if (static_cast<unsigned int>(size) > x_) {
+ // sort a copy
+ std::vector<typename In::value_type> v(begin, end);
+ std::sort(v.begin(), v.end(), comp);
+ std::copy(v.rbegin(), v.rbegin()+x_, out);
+#ifdef DEBUG
+if (size > 0) {
+ for (typename std::vector<typename In::value_type>::iterator i = v.end()-x_; i != v.end() ; ++i) {
+ std::cerr << '\t' << i->first << " " << i->second << std::endl;
+ }
+}
+#endif
+ std::advance(out, x_);
+ } else {
+#ifdef DEBUG
+if (size > 0) {
+ for (In i = begin; i != end ; ++i) {
+ std::cerr << '\t' << i->first << " " << i->second << std::endl;
+ }
+}
+#endif
+ // accept all peaks
+ std::copy(begin, end, out);
+ std::advance(out, size);
+ }
+ return out;
+ }
+ protected:
+ unsigned int x_;
+};
+
+/** Functor to determine the top X peaks in Y regions for a given set of peaks.
+ */
+class TopXInYRegions
+{
+ public:
+ TopXInYRegions(unsigned int x, unsigned int y) : x_(x), y_(y)
+ {}
+
+ template<class In, class Out, class MassComp, class AbundanceComp>
+ Out operator()(In begin, In end, Out out, MassComp massComp, AbundanceComp abundanceComp) {
+ // sort a copy
+ std::vector<typename In::value_type> v(begin, end);
+ std::sort(v.begin(), v.end(), massComp);
+ // split the m/z domain in y_ equisized regions
+ double maxMz = (v.end()-1)->first;
+ double minMz = (v.begin())->first;
+ double increment = (maxMz - minMz) / static_cast<double>(y_);
+ TopX topX(x_);
+ if (increment > 2.5) {
+ for (unsigned int k = 0; k < y_; ++k) {
+#ifdef DEBUG
+std::cerr << '#' << minMz + k*increment - 2.5 << " - " << minMz + (k+1)*increment + 2.5 << std::endl;
+#endif
+ // iterate over all regions and apply TopX
+ double regionBegin = minMz + k*increment - 2.5;
+ regionBegin = regionBegin > minMz ? regionBegin : minMz;
+ double regionEnd = minMz + (k+1)*increment + 2.5;
+ In regionBeginIt = lower_bound(v.begin(), v.end(), regionBegin, massComp);
+ In regionEndIt = upper_bound(v.begin(), v.end(), regionEnd, massComp);
+ // run TopX on region
+ Out nout = topX(regionBeginIt, regionEndIt, out, abundanceComp);
+#ifdef DEBUG
+std::cerr << "step " << k << " of " << y_ << ": topX returned " << nout-out << " peaks." << std::endl;
+#endif
+ out = nout;
+
+ }
+ } else {
+ Out nout = topX(v.begin(), v.end(), out, abundanceComp);
+#ifdef DEBUG
+std::cerr << "increment too small: topX returned " << nout-out << " peaks." << std::endl;
+#endif
+ out = nout;
+ }
+ return out;
+ }
+ private:
+ unsigned int x_, y_;
+};
+
+/** Functor to determine the top X peaks in windows of size Z.
+ */
+class TopXInWindowsOfSizeZ
+{
+ public:
+ TopXInWindowsOfSizeZ(unsigned int x, double z) : x_(x), z_(z)
+ {
+#ifdef DEBUG
+std::cerr << "got: " << z_ << std::endl;
+#endif
+ }
+
+ template <class In, class Out, class MassComp, class AbundanceComp>
+ Out operator()(In begin, In end, Out out, MassComp massComp, AbundanceComp abundanceComp) {
+ // get a copy
+ std::vector<typename In::value_type> v(begin, end);
+ TopX topX(x_);
+
+ while (!v.empty()) {
+ // sort by abundance
+ std::sort(v.begin(), v.end(), abundanceComp);
+ double maxAbundanceMass = v[v.size()-1].first;
+ // sort by mass
+ std::sort(v.begin(), v.end(), massComp);
+ // define window
+#ifdef DEBUG
+std::cerr << '#' << maxAbundanceMass - z_ << '-' << maxAbundanceMass + z_ << std::endl;
+#endif
+ In regionBegin = lower_bound(v.begin(), v.end(), maxAbundanceMass - z_, massComp);
+ In regionEnd = upper_bound(regionBegin, v.end(), maxAbundanceMass + z_, massComp);
+ // get TopX
+ out = topX(regionBegin, regionEnd, out, abundanceComp);
+ // erase entries in window
+ v.erase(regionBegin, regionEnd);
+ }
+ return out;
+ }
+
+ private:
+ unsigned int x_;
+ double z_;
+};
+
+}
+
+namespace dta {
+
+/** A DTA spectrum. Quick hack for the ms2preproc executable until we have a better concept for annotated spectra.
+ */
+class DtaSpectrum : public mgf::Collection<mgf::MassAbundancePair> {
+ public:
+ void setPrecursorMass(const double m) { precursorMass_ = m; }
+ double getPrecursorMass() const { return precursorMass_; }
+ void setCharge(const int c) { charge_ = c; }
+ int getCharge() const { return charge_; }
+ void setScans(const std::pair<unsigned int, unsigned int>& scans) { scans_ = scans; }
+ std::pair<unsigned int, unsigned int> getScans() const { return scans_; }
+ void clear() {
+ precursorMass_ = 0.0;
+ charge_ = 0;
+ scans_ = std::make_pair(0,0);
+ mgf::Collection<mgf::MassAbundancePair>::clear();
+ }
+ private:
+ MGFP_EXPORT friend std::ostream& operator<<(std::ostream& os, DtaSpectrum& s);
+ double precursorMass_;
+ int charge_;
+ std::pair<unsigned int, unsigned int> scans_;
+};
+
+/** A DTA parser that fills a DTA spectrum. Should also be integrated with ms++. Implementation trivial.
+ */
+class DtaParser {
+ public:
+ void parse(const std::string& filename, DtaSpectrum& s) {
+ // TODO: add some filename parsing here to obtain the
+ // scan numbers (DTA is *such* a horrible format).
+
+ // open file and parse contents
+ std::ifstream ifs(filename.c_str());
+ if (ifs) {
+ s.clear();
+ // first line is precursor mass and charge
+ double precursorMass;
+ int charge;
+ ifs >> precursorMass >> charge;
+ s.setPrecursorMass(precursorMass);
+ s.setCharge(charge);
+ // afterwards there are mass/abundance pairs
+ double m, ab;
+ ifs >> m >> ab;
+ while(!ifs.eof()) {
+ s.push_back(std::make_pair(m, ab));
+ ifs >> m >> ab;
+ }
+ } else {
+ throw std::invalid_argument("file not found.");
+ }
+ }
+};
+
+std::ostream& operator<<(std::ostream& os, DtaSpectrum& s) {
+ os << s.precursorMass_ << " " << s.charge_ << std::endl;
+ for (DtaSpectrum::const_iterator i = s.begin(); i != s.end(); ++i) {
+ os << i-> first << " " << i->second << std::endl;
+ }
+ return os;
+}
+
+}
+
+namespace po = boost::program_options;
+
+int main(int argc, char* argv[]) {
+ try {
+
+ // Declare the supported options.
+ // FIXME: add version info.
+ po::options_description desc("MS/MS preprocessor executable, Copyright 2009-10 Marc Kirchner.\n"
+ "Please cite as:\n"
+ " Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J,\n"
+ " Winter D, Steen JAJ, Hamprecht FA, Steen H, When Less Can Yield\n"
+ " More - Computational Preprocessing of MS/MS Spectra for\n"
+ " Peptide Identification, Proteomics (2009).\n\nValid arguments are"
+ );
+ unsigned int precision(0);
+ std::string format;
+ desc.add_options()
+ ("help,h", "produce this help message")
+ ("infile,i", po::value<std::string>(), "name of the MGF/DTA input file")
+ ("outfile,o", po::value<std::string>(), "name of the MGF output file")
+ ("format,f", po::value<std::string>(&format)->default_value(std::string("mgf")), "input format: (dta|mgf)")
+ ("top,X", po::value<int>(), "number of highest intensity ions to keep")
+ ("nregions,Y", po::value<int>(), "number of equal-sized regions the MS/MS spectrum is split into")
+ ("winsize,Z", po::value<double>(), "m/z window (+/-Z) around high-intensity peaks in which the top X are selected")
+ ("verbose,v", "toggle verbose output")
+ ("precision,p", po::value<unsigned int>(&precision)->default_value(4), "precision of output")
+ ;
+
+ po::variables_map vm;
+ po::store(po::parse_command_line(argc, argv, desc), vm);
+ po::notify(vm);
+
+ if (vm.count("help")) {
+ std::cerr << desc << std::endl;
+ return 1;
+ }
+
+ // input sanity checking
+ if (!(vm.count("infile") && vm.count("outfile"))) {
+ std::cerr << desc << std::endl << "ERROR: "
+ "Need 'infile' and 'outfile' arguments." << std::endl;
+ return 1;
+ }
+ if (!(vm.count("top"))) {
+ std::cerr << desc << std::endl << "ERROR: "
+ "Need 'top,X' argument." << std::endl;
+ return 1;
+ }
+ if (vm.count("nregions") > 0 && vm.count("winsize") > 0) {
+ std::cerr << desc << std::endl << "ERROR: "
+ "Parameters 'nregions' and 'winsize' cannot be specified together." << std::endl;
+ return 1;
+ }
+ if (!(format == "mgf" || format == "dta")) {
+ std::cerr << desc << std::endl << "ERROR: "
+ "Format must be one of 'mgf' or 'dta'." << std::endl;
+ return 1;
+ }
+ // logging/debug output
+ bool trace = vm.count("verbose") > 0 ? true : false;
+ // I/O
+ std::string infilename(vm["infile"].as<std::string>());
+ std::string outfilename(vm["outfile"].as<std::string>());
+ std::ofstream out(outfilename.c_str());
+ if (!out.good()) {
+ return -1;
+ }
+ // check format
+ // common variables
+ int x = vm["top"].as<int>();
+ // check which format we are dealing with: in the case of MGF
+ // we need to invoke the parser, read a whole collection of
+ // spectra and apply the operators to each spectrum. In the
+ // case of DTA, we deal with a single spectrum only.
+ //
+ // This is some ugly code duplication between the two cases; oh, well...
+ //
+ if (format == "mgf") {
+ // set up context
+ mgf::MgfFile s;
+ mgf::Driver driver(s);
+ driver.trace_parsing = trace;
+ driver.trace_scanning = trace;
+
+ // I/O: input
+ std::ifstream in(infilename.c_str());
+ if (!in.good()) {
+ return -1;
+ }
+
+ // parse input into memory
+ bool result = driver.parse_stream(in);
+ if (!result) {
+ return -1;
+ }
+
+ // set info
+ out << "# MGF created using ms2preproc, (c) 2009 Marc Kirchner.\n"
+ << "# This program accompanies Renard BY, Kirchner M, Monigatti F, Invanov AR,\n"
+ << "# Rappsilber J, Winter D, Steen JAJ, Hamprecht FA, Steen H, When Less\n"
+ << "# Can Yield More - Computational Preprocessing of MS/MS Spectra for\n"
+ << "# Peptide Identification, Proteomics (2009).\n"
+ << "# Command: " << argv[0];
+ for (int i = 1; i < argc; ++i) {
+ out << " " << argv[i];
+ }
+ out << "." << std::endl;
+
+ // get a handle to the data
+ typedef mgf::MgfFile::iterator Iterator;
+
+ if (vm.count("nregions")) {
+ // Top X in Y regions
+ int y = vm["nregions"].as<int>();
+ Ms2Preproc::TopXInYRegions topXInYRegions(static_cast<unsigned int>(x), static_cast<unsigned int>(y));
+ for (Iterator i = s.begin(); i != s.end(); ++i) {
+ // get a temporary object and make sure it is big enough
+ mgf::MgfSpectrum m;
+ m.resize(2*i->size());
+ // get the top X in Y regions, including duplicated from overlaps
+ mgf::MgfSpectrum::iterator sEnd = topXInYRegions(i->begin(), i->end(), m.begin(), LessThanMass(), LessThanAbundance());
+ // make sure we have enough space in the original object
+ i->resize(std::distance(m.begin(), sEnd));
+ // unique copy expectes a sorted range
+ std::sort(m.begin(), sEnd, LessThanMass());
+ // copy all unique peaks back into the original MgfSpectrum
+ mgf::MgfSpectrum::iterator iEnd = std::unique_copy(m.begin(), sEnd, i->begin());
+ // crop to fit
+ i->resize(std::distance(i->begin(), iEnd));
+ }
+ } else if (vm.count("winsize")) {
+ // Top X in windows of size Z
+ double z = vm["winsize"].as<int>();
+ Ms2Preproc::TopXInWindowsOfSizeZ topXInWindowsOfSizeZ(static_cast<unsigned int>(x), z);
+ for (Iterator i = s.begin(); i != s.end(); ++i) {
+ mgf::MgfSpectrum::iterator trash = topXInWindowsOfSizeZ(i->begin(), i->end(), i->begin(), LessThanMass(), LessThanAbundance());
+ i->erase(trash, i->end());
+ std::sort(i->begin(), i->end(), LessThanMass()); // not necessary
+ }
+ } else {
+ // Top X
+ Ms2Preproc::TopX topX(static_cast<unsigned int>(x));
+ for (Iterator i = s.begin(); i != s.end(); ++i) {
+ mgf::MgfSpectrum::iterator trash = topX(i->begin(), i->end(), i->begin(), LessThanAbundance());
+ i->erase(trash, i->end());
+ std::sort(i->begin(), i->end(), LessThanMass());
+ }
+ }
+ out.setf(std::ios_base::fixed, std::ios_base::floatfield);
+ out.precision(precision);
+ out << s << std::endl;
+ } else if (format == "dta") {
+ dta::DtaParser parser;
+ dta::DtaSpectrum s;
+ // read DTA spectrum
+ parser.parse(infilename, s);
+ if (vm.count("nregions")) {
+ // Top X in Y regions
+ int y = vm["nregions"].as<int>();
+ Ms2Preproc::TopXInYRegions topXInYRegions(static_cast<unsigned int>(x), static_cast<unsigned int>(y));
+ // get a temporary object and make sure it is big enough
+ mgf::MgfSpectrum tmp;
+ tmp.resize(2*s.size());
+ // get the top X in Y regions, including duplicated from overlaps
+ mgf::MgfSpectrum::iterator tmpEnd = topXInYRegions(s.begin(), s.end(), tmp.begin(), LessThanMass(), LessThanAbundance());
+ // make sure we have enough space in the original object
+ s.resize(std::distance(tmp.begin(), tmpEnd));
+ // unique copy expectes a sorted range
+ std::sort(tmp.begin(), tmpEnd, LessThanMass());
+ // copy all unique peaks back into the original MgfSpectrum
+ mgf::MgfSpectrum::iterator sEnd = std::unique_copy(tmp.begin(), tmpEnd, s.begin());
+ // crop to fit
+ s.resize(std::distance(s.begin(), sEnd));
+ } else if (vm.count("winsize")) {
+ // Top X in windows of size Z
+ double z = vm["winsize"].as<int>();
+ Ms2Preproc::TopXInWindowsOfSizeZ topXInWindowsOfSizeZ(static_cast<unsigned int>(x), z);
+ mgf::MgfSpectrum::iterator trash = topXInWindowsOfSizeZ(s.begin(), s.end(), s.begin(), LessThanMass(), LessThanAbundance());
+ s.erase(trash, s.end());
+ std::sort(s.begin(), s.end(), LessThanMass()); // not necessary
+ } else {
+ // Top X
+ Ms2Preproc::TopX topX(static_cast<unsigned int>(x));
+ mgf::MgfSpectrum::iterator trash = topX(s.begin(), s.end(), s.begin(), LessThanAbundance());
+ s.erase(trash, s.end());
+ std::sort(s.begin(), s.end(), LessThanMass());
+ }
+ out.setf(std::ios_base::fixed, std::ios_base::floatfield);
+ out.precision(precision);
+ out << s << std::endl;
+ }
+ return 0;
+ } catch (std::exception& e) {
+ std::cerr << e.what() << std::endl;
+ }
+ return (-1);
+}
+
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|
|
From: <mki...@us...> - 2010-08-05 22:13:04
|
Revision: 32
http://mgfp.svn.sourceforge.net/mgfp/?rev=32&view=rev
Author: mkirchner
Date: 2010-08-05 22:12:58 +0000 (Thu, 05 Aug 2010)
Log Message:
-----------
* changed include guard names to less collision-prone names
* we now define Collection<T> inside the mgf namespace
Modified Paths:
--------------
trunk/mgfp/include/mgfp/Collection.h
trunk/mgfp/include/mgfp/Context.h
trunk/mgfp/include/mgfp/Driver.h
trunk/mgfp/include/mgfp/MassAbundancePair.h
trunk/mgfp/include/mgfp/MgfFile.h
trunk/mgfp/include/mgfp/MgfHeader.h
trunk/mgfp/include/mgfp/MgfSpectrum.h
trunk/mgfp/include/mgfp/config.h.cmake
trunk/mgfp/include/mgfp/mgfp.h
trunk/mgfp/include/mgfp/utils.h
trunk/mgfp/test/Collection-test.cpp
Modified: trunk/mgfp/include/mgfp/Collection.h
===================================================================
--- trunk/mgfp/include/mgfp/Collection.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/Collection.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,15 +1,18 @@
/*$Id$*/
-#ifndef __COLLECTION_H__
-#define __COLLECTION_H__
+#ifndef __MGFP_INCLUDE_COLLECTION_H__
+#define __MGFP_INCLUDE_COLLECTION_H__
#include <vector>
#include <mgfp/config.h>
+
#ifdef REGRESSION_TEST_BUILD
- struct CollectionTestSuite;
+struct CollectionTestSuite;
#endif
+namespace mgf {
+
/** A std::vector<T> composite.
* The STL std::vector<T> does not have a virtual destructor, hence it is not
* possible for vector-like classes to derive in order to inherit the
@@ -187,4 +190,6 @@
lhs.c_.swap(rhs.c_);
}
+} // namespace mgf
+
#endif
Modified: trunk/mgfp/include/mgfp/Context.h
===================================================================
--- trunk/mgfp/include/mgfp/Context.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/Context.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,6 +1,6 @@
// $Id$
-#ifndef __CONTEXT_H__
-#define __CONTEXT_H__
+#ifndef __MGFP_INCLUDE_CONTEXT_H__
+#define __MGFP_INCLUDE_CONTEXT_H__
#include <mgfp/MgfFile.h>
#include <mgfp/MgfHeader.h>
@@ -23,4 +23,4 @@
}
-#endif // __CONTEXT_H__
+#endif // __MGFP_INCLUDE_CONTEXT_H__
Modified: trunk/mgfp/include/mgfp/Driver.h
===================================================================
--- trunk/mgfp/include/mgfp/Driver.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/Driver.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,7 +1,7 @@
/* $Id$ */
-#ifndef __DRIVER_H__
-#define __DRIVER_H__
+#ifndef __MGFP_INCLUDE_DRIVER_H__
+#define __MGFP_INCLUDE_DRIVER_H__
#include <string>
#include <vector>
@@ -81,4 +81,4 @@
} // namespace mgf
-#endif // __DRIVER_H__
+#endif // __MGFP_INCLUDE_DRIVER_H__
Modified: trunk/mgfp/include/mgfp/MassAbundancePair.h
===================================================================
--- trunk/mgfp/include/mgfp/MassAbundancePair.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/MassAbundancePair.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,5 +1,5 @@
-#ifndef __MASSABUNDANCEPAIR_H__
-#define __MASSABUNDANCEPAIR_H__
+#ifndef __MGFP_INCLUDE_MASSABUNDANCEPAIR_H__
+#define __MGFP_INCLUDE_MASSABUNDANCEPAIR_H__
#include <mgfp/config.h>
Modified: trunk/mgfp/include/mgfp/MgfFile.h
===================================================================
--- trunk/mgfp/include/mgfp/MgfFile.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/MgfFile.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,7 +1,7 @@
/* $Id$ */
-#ifndef __MGFFILE_H__
-#define __MGFFILE_H__
+#ifndef __MGFP_INCLUDE_MGFFILE_H__
+#define __MGFP_INCLUDE_MGFFILE_H__
#include <mgfp/config.h>
Modified: trunk/mgfp/include/mgfp/MgfHeader.h
===================================================================
--- trunk/mgfp/include/mgfp/MgfHeader.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/MgfHeader.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,5 +1,5 @@
-#ifndef __MGFHEADER_H__
-#define __MGFHEADER_H__
+#ifndef __MGFP_INCLUDE_MGFHEADER_H__
+#define __MGFP_INCLUDE_MGFHEADER_H__
#include <mgfp/config.h>
Modified: trunk/mgfp/include/mgfp/MgfSpectrum.h
===================================================================
--- trunk/mgfp/include/mgfp/MgfSpectrum.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/MgfSpectrum.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,5 +1,5 @@
-#ifndef __MGFSPECTRUM_H__
-#define __MGFSPECTRUM_H__
+#ifndef __MGFP_INCLUDE_MGFSPECTRUM_H__
+#define __MGFP_INCLUDE_MGFSPECTRUM_H__
#include <mgfp/config.h>
Modified: trunk/mgfp/include/mgfp/config.h.cmake
===================================================================
--- trunk/mgfp/include/mgfp/config.h.cmake 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/config.h.cmake 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,5 +1,5 @@
-#ifndef __CONFIG_H__
-#define __CONFIG_H__
+#ifndef __MGFP_INCLUDE_CONFIG_H__
+#define __MGFP_INCLUDE_CONFIG_H__
//#ifdef _MSC_VER
// #include "winsock2.h"
@@ -26,5 +26,5 @@
#define MGFP_EXPORT
#endif
-#endif // __CONFIG_H__
+#endif // __MGFP_INCLUDE_CONFIG_H__
Modified: trunk/mgfp/include/mgfp/mgfp.h
===================================================================
--- trunk/mgfp/include/mgfp/mgfp.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/mgfp.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,5 +1,5 @@
-#ifndef __MGFPARSER_H__
-#define __MGFPARSER_H__
+#ifndef __MGFP_INCLUDE_MGFP_H__
+#define __MGFP_INCLUDE_MGFP_H__
#include <mgfp/Context.h>
#include <mgfp/Driver.h>
Modified: trunk/mgfp/include/mgfp/utils.h
===================================================================
--- trunk/mgfp/include/mgfp/utils.h 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/include/mgfp/utils.h 2010-08-05 22:12:58 UTC (rev 32)
@@ -1,5 +1,5 @@
-#ifndef __UTILS_H__
-#define __UTILS_H__
+#ifndef __MGFP_INCLUDE_UTILS_H__
+#define __MGFP_INCLUDE_UTILS_H__
#include <mgfp/config.h>
Modified: trunk/mgfp/test/Collection-test.cpp
===================================================================
--- trunk/mgfp/test/Collection-test.cpp 2010-03-31 03:03:44 UTC (rev 31)
+++ trunk/mgfp/test/Collection-test.cpp 2010-08-05 22:12:58 UTC (rev 32)
@@ -29,6 +29,7 @@
#include "unittest.hxx"
+using namespace mgf;
struct CollectionTestSuite : vigra::test_suite {
CollectionTestSuite() : vigra::test_suite("Collection") {
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|
|
From: <mki...@us...> - 2010-03-31 03:03:50
|
Revision: 31
http://mgfp.svn.sourceforge.net/mgfp/?rev=31&view=rev
Author: mkirchner
Date: 2010-03-31 03:03:44 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
adapted docs to publication and sf.net launch
Modified Paths:
--------------
trunk/mgfp/doc/Mainpage.h
Modified: trunk/mgfp/doc/Mainpage.h
===================================================================
--- trunk/mgfp/doc/Mainpage.h 2010-03-31 01:36:40 UTC (rev 30)
+++ trunk/mgfp/doc/Mainpage.h 2010-03-31 03:03:44 UTC (rev 31)
@@ -1,30 +1,36 @@
/*!
-\image html mgfp_small.png
-
\mainpage mgfp: Mascot Generic Format (MGF) Parser
-\author Marc Kirchner <fir...@ch...>
-
\section sec_intro Introduction
\c mgfp is a flex/bison-based C++ MGF parser library.<br>
-The library is provided
-under the terms of a BSD license and can thus be used in academic and
+The <a href="http://steenlab.org">Steen \& Steen Lab</a> provides
+the library under the terms of a BSD license for use in academic and
non-academic environments.
+\section sec_citation Citation
+
+If you make use of \c mgfp in your own projects, please cite the
+following article:<br>
+
+Kirchner M, Steen JAJ, Hamprecht FA, Steen H (2010).
+MGFp: An open Mascot Generic Format parser library implementation.
+<i>Journal of Proteome Research, in press.</i>
+[<a href="http://www.ncbi.nlm.nih.gov/pubmed/20334363">PubMed</a>]
+
\section sec_install Installation
-\subsection sec_install_bin Obtaining a Binary Package
+\subsection sec_install_bin Obtaining the Software
Binary packages for Microsoft Windows, Linux (64 bit, built on Ubuntu 10.4) and
MacOS X (Snow Leopard) are available for download from
-\li the Steen Lab software page at http://software.steenlab.org/mgfp .
+\li the MGFp project page at sourceforge: http://mgfp.sf.net .
-Additionally, we are in the process of migrating MGFp to sourceforge.
-This will allow SVN access for anyone who wants to contribute.
+Additional information is available on
-\li (Future) MGFp project page at sourceforge: http://mgfp.sf.net .
+\li the Steen Lab page at http://steenlab.org/
+\li the Steen Lab software page at http://software.steenlab.org/
\subsection sec_install_src Building from Source
Building \c mgfp from source is straightforward. However, it requires a working
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|
|
From: <mki...@us...> - 2010-03-31 01:36:47
|
Revision: 30
http://mgfp.svn.sourceforge.net/mgfp/?rev=30&view=rev
Author: mkirchner
Date: 2010-03-31 01:36:40 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
-sync scripts to upload htdocs to sf.net
-final touches on the webpage
Modified Paths:
--------------
trunk/mgfp/CMakeLists.txt
trunk/mgfp/doc/Mainpage.h
trunk/mgfp/htdocs/index.html
trunk/mgfp/htdocs/style.css
Modified: trunk/mgfp/CMakeLists.txt
===================================================================
--- trunk/mgfp/CMakeLists.txt 2010-03-30 06:00:39 UTC (rev 29)
+++ trunk/mgfp/CMakeLists.txt 2010-03-31 01:36:40 UTC (rev 30)
@@ -60,7 +60,14 @@
@ONLY IMMEDIATE
)
FIND_PACKAGE(Doxygen)
+
+# target for doxygen
ADD_CUSTOM_TARGET(doc COMMAND ${DOXYGEN} ${MGFP_BINARY_DIR}/doc/Doxyfile)
+
+# convenience targets for synchronisation: htdocs and docs
+ADD_CUSTOM_TARGET(synchtdocs COMMAND rsync -Cavz ${MGFP_SOURCE_DIR}/htdocs mkirchner,mg...@we...:/home/groups/m/mg/mgfp/)
+ADD_CUSTOM_TARGET(syncdocs COMMAND rsync -Cavz ${MGFP_BINARY_DIR}/doc/html mkirchner,mg...@we...:/home/groups/m/mg/mgfp/htdocs/doc)
+
# FIXME: add target for pdf generation
#############################################################################
Modified: trunk/mgfp/doc/Mainpage.h
===================================================================
--- trunk/mgfp/doc/Mainpage.h 2010-03-30 06:00:39 UTC (rev 29)
+++ trunk/mgfp/doc/Mainpage.h 2010-03-31 01:36:40 UTC (rev 30)
@@ -4,7 +4,7 @@
\mainpage mgfp: Mascot Generic Format (MGF) Parser
-\author Marc Kirchner <mar...@ch...>
+\author Marc Kirchner <fir...@ch...>
\section sec_intro Introduction
\c mgfp is a flex/bison-based C++ MGF parser library.<br>
Modified: trunk/mgfp/htdocs/index.html
===================================================================
--- trunk/mgfp/htdocs/index.html 2010-03-30 06:00:39 UTC (rev 29)
+++ trunk/mgfp/htdocs/index.html 2010-03-31 01:36:40 UTC (rev 30)
@@ -16,8 +16,9 @@
<td class="links">
<a href="http://sourceforge.net/projects/mgfp/">mgfp project page</a><br>
<a href="http://sourceforge.net/projects/mgfp/files/">download</a><br>
-<a href="doc/">documentation</a><br>
-<a href="http://sourceforge.net/apps/trac/mgfp/wiki">development (trac)</a>
+<a href="doc/html/">documentation</a><br>
+<a href="http://sourceforge.net/apps/trac/mgfp/wiki">development (trac)</a><br>
+<a href="http://steenlab.org">steen & steen lab</a><br>
</td>
</tr>
</table>
Modified: trunk/mgfp/htdocs/style.css
===================================================================
--- trunk/mgfp/htdocs/style.css 2010-03-30 06:00:39 UTC (rev 29)
+++ trunk/mgfp/htdocs/style.css 2010-03-31 01:36:40 UTC (rev 30)
@@ -1,33 +1,33 @@
body {
- font-size: 10pt;
font-family: sans-serif;
- background-color: #7b8276;
- color: #333333;
+ background-color: #ffffff;
+ color: #64747c;
}
table.canopy {
- background-color: #7b8276;
+ background-color: #ffffff;
width=50%;
margin-top:15%;
margin-left:auto;
margin-right:auto;
- border: 1px solid #aaaaaa;
+ /* border: 1px solid #eef0e3;*/
padding: 25px;
+ vertical-align: middle;
}
a {
text-decoration:none;
- color:#333333;
+ color:#64747c;
}
td.links {
- color: #333333;
- font-size: 1.6em;
+ color: #64747c;
+ font-size: 1.1em;
font-weight: bold;
}
td.content {
- background-color: #7b8276;
+ background-color: #ffffff;
text-align: left;
margin: 15px;
border: 10px solid #ffffff;
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|
|
From: <mki...@us...> - 2010-03-30 06:00:45
|
Revision: 29
http://mgfp.svn.sourceforge.net/mgfp/?rev=29&view=rev
Author: mkirchner
Date: 2010-03-30 06:00:39 +0000 (Tue, 30 Mar 2010)
Log Message:
-----------
added simplistic homepage
Added Paths:
-----------
trunk/mgfp/htdocs/
trunk/mgfp/htdocs/index.html
trunk/mgfp/htdocs/mgfp_small.png
trunk/mgfp/htdocs/style.css
Removed Paths:
-------------
trunk/mgfp/doc/images/mgfp_small.png
Deleted: trunk/mgfp/doc/images/mgfp_small.png
===================================================================
(Binary files differ)
Added: trunk/mgfp/htdocs/index.html
===================================================================
--- trunk/mgfp/htdocs/index.html (rev 0)
+++ trunk/mgfp/htdocs/index.html 2010-03-30 06:00:39 UTC (rev 29)
@@ -0,0 +1,33 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" >
+<title>Mascot Generic Format (MGF) parser</title>
+<link rel="stylesheet" type="text/css" href="style.css">
+<link rel="icon" type="image/png" href="favicon.ico">
+</head>
+</head>
+<body>
+<table class="canopy">
+<tr>
+<td class="logo">
+<img src="mgfp_small.png">
+</td>
+<td class="links">
+<a href="http://sourceforge.net/projects/mgfp/">mgfp project page</a><br>
+<a href="http://sourceforge.net/projects/mgfp/files/">download</a><br>
+<a href="doc/">documentation</a><br>
+<a href="http://sourceforge.net/apps/trac/mgfp/wiki">development (trac)</a>
+</td>
+</tr>
+</table>
+<table align="center">
+<tr>
+<td colspan=2 align="center">
+<br><br>
+<img src="http://sflogo.sourceforge.net/sflogo.php?group_id=312035&type=2">
+</td>
+</tr>
+</table>
+</body>
+</html>
Copied: trunk/mgfp/htdocs/mgfp_small.png (from rev 28, trunk/mgfp/doc/images/mgfp_small.png)
===================================================================
(Binary files differ)
Added: trunk/mgfp/htdocs/style.css
===================================================================
--- trunk/mgfp/htdocs/style.css (rev 0)
+++ trunk/mgfp/htdocs/style.css 2010-03-30 06:00:39 UTC (rev 29)
@@ -0,0 +1,35 @@
+body {
+ font-size: 10pt;
+ font-family: sans-serif;
+ background-color: #7b8276;
+ color: #333333;
+}
+
+table.canopy {
+ background-color: #7b8276;
+ width=50%;
+ margin-top:15%;
+ margin-left:auto;
+ margin-right:auto;
+ border: 1px solid #aaaaaa;
+ padding: 25px;
+}
+
+a {
+ text-decoration:none;
+ color:#333333;
+}
+
+td.links {
+ color: #333333;
+ font-size: 1.6em;
+ font-weight: bold;
+}
+
+td.content {
+ background-color: #7b8276;
+ text-align: left;
+ margin: 15px;
+ border: 10px solid #ffffff;
+}
+
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