From 43a8a4dc1b2f9d2ad26316113a6acf44a40e866b Mon Sep 17 00:00:00 2001
From: DetlevCM <detlevcm@googlemail.com>
Date: Fri, 3 Jul 2015 22:12:13 +0200
Subject: [PATCH] regression patch

patched regression where the ouput switch would crash the code
---
 .cproject                                     | 12 ++++++++---
 source/Main.cpp                               | 20 +++++++++++++------
 .../Species_Class_Mapping.cpp                 |  4 ++--
 3 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/.cproject b/.cproject
index dadd7bd..01d0ced 100644
--- a/.cproject
+++ b/.cproject
@@ -22,11 +22,13 @@
 							</tool>
 							<tool id="cdt.managedbuild.tool.gnu.archiver.mingw.base.319273247" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.mingw.base"/>
 							<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.mingw.exe.debug.285252123" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.mingw.exe.debug">
-								<option id="gnu.cpp.compiler.mingw.exe.debug.option.optimization.level.160749690" name="Optimization Level" superClass="gnu.cpp.compiler.mingw.exe.debug.option.optimization.level" value="gnu.cpp.compiler.optimization.level.none" valueType="enumerated"/>
+								<option id="gnu.cpp.compiler.mingw.exe.debug.option.optimization.level.160749690" name="Optimization Level" superClass="gnu.cpp.compiler.mingw.exe.debug.option.optimization.level" value="gnu.cpp.compiler.optimization.level.more" valueType="enumerated"/>
 								<option id="gnu.cpp.compiler.mingw.exe.debug.option.debugging.level.1052191191" name="Debug Level" superClass="gnu.cpp.compiler.mingw.exe.debug.option.debugging.level" value="gnu.cpp.compiler.debugging.level.max" valueType="enumerated"/>
 								<option id="gnu.cpp.compiler.option.include.paths.434808899" name="Include paths (-I)" superClass="gnu.cpp.compiler.option.include.paths" valueType="includePath">
 									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/${ProjName}/headers}&quot;"/>
 								</option>
+								<option id="gnu.cpp.compiler.option.dialect.std.1756808621" name="Language standard" superClass="gnu.cpp.compiler.option.dialect.std" value="gnu.cpp.compiler.dialect.default" valueType="enumerated"/>
+								<option id="gnu.cpp.compiler.option.dialect.flags.1965329902" name="Other dialect flags" superClass="gnu.cpp.compiler.option.dialect.flags" value="-std=c++14" valueType="string"/>
 								<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.655957808" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>
 							</tool>
 							<tool id="cdt.managedbuild.tool.gnu.c.compiler.mingw.exe.debug.995030329" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.mingw.exe.debug">
@@ -89,7 +91,7 @@
 							<tool id="cdt.managedbuild.tool.gnu.c.compiler.mingw.exe.release.1194885499" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.mingw.exe.release">
 								<option defaultValue="gnu.c.optimization.level.most" id="gnu.c.compiler.mingw.exe.release.option.optimization.level.347302575" name="Optimization Level" superClass="gnu.c.compiler.mingw.exe.release.option.optimization.level" useByScannerDiscovery="false" valueType="enumerated"/>
 								<option id="gnu.c.compiler.mingw.exe.release.option.debugging.level.1471167164" name="Debug Level" superClass="gnu.c.compiler.mingw.exe.release.option.debugging.level" useByScannerDiscovery="false" value="gnu.c.debugging.level.none" valueType="enumerated"/>
-								<option id="gnu.c.compiler.option.dialect.std.1229277554" superClass="gnu.c.compiler.option.dialect.std" value="gnu.c.compiler.dialect.default" valueType="enumerated"/>
+								<option id="gnu.c.compiler.option.dialect.std.1229277554" name="Language standard" superClass="gnu.c.compiler.option.dialect.std" value="gnu.c.compiler.dialect.default" valueType="enumerated"/>
 								<inputType id="cdt.managedbuild.tool.gnu.c.compiler.input.1494902871" superClass="cdt.managedbuild.tool.gnu.c.compiler.input"/>
 							</tool>
 							<tool id="cdt.managedbuild.tool.gnu.c.linker.mingw.exe.release.913906878" name="MinGW C Linker" superClass="cdt.managedbuild.tool.gnu.c.linker.mingw.exe.release"/>
@@ -100,7 +102,7 @@
 								<option id="gnu.cpp.link.option.paths.2071182915" name="Library search path (-L)" superClass="gnu.cpp.link.option.paths" valueType="libPaths">
 									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/${ProjName}/libraries}&quot;"/>
 								</option>
-								<option id="gnu.cpp.link.option.flags.1767542147" superClass="gnu.cpp.link.option.flags" value="-static" valueType="string"/>
+								<option id="gnu.cpp.link.option.flags.1767542147" name="Linker flags" superClass="gnu.cpp.link.option.flags" value="-static" valueType="string"/>
 								<inputType id="cdt.managedbuild.tool.gnu.cpp.linker.input.1358711304" superClass="cdt.managedbuild.tool.gnu.cpp.linker.input">
 									<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>
 									<additionalInput kind="additionalinput" paths="$(LIBS)"/>
@@ -145,11 +147,14 @@
 								<option id="gnu.cpp.compiler.option.other.verbose.258431376" name="Verbose (-v)" superClass="gnu.cpp.compiler.option.other.verbose" useByScannerDiscovery="false" value="true" valueType="boolean"/>
 								<option id="gnu.cpp.compiler.option.optimization.flags.842389400" name="Other optimization flags" superClass="gnu.cpp.compiler.option.optimization.flags" useByScannerDiscovery="false" value="-m64 -march=native" valueType="string"/>
 								<option id="gnu.cpp.compiler.option.dialect.flags.2028087826" name="Other dialect flags" superClass="gnu.cpp.compiler.option.dialect.flags" value="-std=c++14" valueType="string"/>
+								<option id="gnu.cpp.compiler.option.warnings.extrawarn.1480377328" name="Extra warnings (-Wextra)" superClass="gnu.cpp.compiler.option.warnings.extrawarn" value="false" valueType="boolean"/>
+								<option id="gnu.cpp.compiler.option.other.pic.217907667" name="Position Independent Code (-fPIC)" superClass="gnu.cpp.compiler.option.other.pic" value="false" valueType="boolean"/>
 								<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.1087350520" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>
 							</tool>
 							<tool id="cdt.managedbuild.tool.gnu.c.compiler.mingw.exe.release.1890043214" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.mingw.exe.release">
 								<option defaultValue="gnu.c.optimization.level.most" id="gnu.c.compiler.mingw.exe.release.option.optimization.level.1499234231" name="Optimization Level" superClass="gnu.c.compiler.mingw.exe.release.option.optimization.level" useByScannerDiscovery="false" valueType="enumerated"/>
 								<option id="gnu.c.compiler.mingw.exe.release.option.debugging.level.1531068451" name="Debug Level" superClass="gnu.c.compiler.mingw.exe.release.option.debugging.level" useByScannerDiscovery="false" value="gnu.c.debugging.level.none" valueType="enumerated"/>
+								<option id="gnu.c.compiler.option.dialect.std.1361701275" name="Language standard" superClass="gnu.c.compiler.option.dialect.std" value="gnu.c.compiler.dialect.default" valueType="enumerated"/>
 								<inputType id="cdt.managedbuild.tool.gnu.c.compiler.input.923693020" superClass="cdt.managedbuild.tool.gnu.c.compiler.input"/>
 							</tool>
 							<tool id="cdt.managedbuild.tool.gnu.c.linker.mingw.exe.release.1485766447" name="MinGW C Linker" superClass="cdt.managedbuild.tool.gnu.c.linker.mingw.exe.release"/>
@@ -160,6 +165,7 @@
 								<option id="gnu.cpp.link.option.paths.2099848798" name="Library search path (-L)" superClass="gnu.cpp.link.option.paths" valueType="libPaths">
 									<listOptionValue builtIn="false" value="&quot;${workspace_loc:/${ProjName}/libraries}&quot;"/>
 								</option>
+								<option id="gnu.cpp.link.option.flags.1186658786" name="Linker flags" superClass="gnu.cpp.link.option.flags" value="" valueType="string"/>
 								<inputType id="cdt.managedbuild.tool.gnu.cpp.linker.input.1315145987" superClass="cdt.managedbuild.tool.gnu.cpp.linker.input">
 									<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>
 									<additionalInput kind="additionalinput" paths="$(LIBS)"/>
diff --git a/source/Main.cpp b/source/Main.cpp
index eeefa67..a15cbd3 100644
--- a/source/Main.cpp
+++ b/source/Main.cpp
@@ -21,15 +21,21 @@ int main(int argc, char* argv[])
 
 	// Add a switch to have regular ouput to a log file or debug to command line
 	// http://stackoverflow.com/questions/12774207/fastest-way-to-check-if-a-file-exist-using-standard-c-c11-c
-	ifstream file_exists("debug");
+	ifstream debug_file_exists("debug");
 	// File does not exist, so redirect to log file
-			// http://stackoverflow.com/questions/10150468/how-to-redirect-cin-and-cout-to-files
-			std::ofstream out("log.txt");
-	if (!file_exists.good()){
-		//std::streambuf *coutbuf = std::cout.rdbuf(); //save old buf
+	// http://stackoverflow.com/questions/10150468/how-to-redirect-cin-and-cout-to-files
+	std::ofstream out("log.txt");
+	std::streambuf *coutbuf = std::cout.rdbuf(); //save old buffer
+	if (!debug_file_exists.good()){
 		std::cout.rdbuf(out.rdbuf());
+	}//*
+	else
+	{
+		std::cout.rdbuf(coutbuf);
 	}
-	file_exists.close();
+	//*/
+	debug_file_exists.close();
+
 
 
 
@@ -245,6 +251,8 @@ int main(int argc, char* argv[])
 
 	}
 
+	out.close(); // close output stream
+	std::cout.rdbuf(coutbuf); // reassign buffer to avoid crash
 	// And it is done. Return 0 as the code has finished.
 	return 0;
 }
diff --git a/source/mechanism_reduction/Species_Class_Mapping.cpp b/source/mechanism_reduction/Species_Class_Mapping.cpp
index 5c98e55..75b2493 100644
--- a/source/mechanism_reduction/Species_Class_Mapping.cpp
+++ b/source/mechanism_reduction/Species_Class_Mapping.cpp
@@ -65,8 +65,8 @@ vector< int > Map_Species_Classes(
 	NumberOfClasses = CountUnmappedSpecies + BiggestClass; // sum of unmapped species and the number of classes
 
 	cout << "The Mapping consists of " << CountUnmappedSpecies << " unmapped Species, and "
-		 << BiggestClass << "dedicated class mappings, resulting in " << NumberOfClasses
-		 << "Species Classes. \n";
+		 << BiggestClass << " dedicated class mappings, resulting in " << NumberOfClasses
+		 << " Species Classes. \n";
 
 	// Classed species have a number, unclassed species get identified via a negative ID:
 	// This will only work if I coded the rest well as position 0 drops out