Updated directory hierarchy to contain DSRC include files in 'include…

…/dsrc/' instead of raw 'include/'
refresh-bio · Mar 14, 2014 · 5bd516b · 5bd516b
1 parent 9c4ed9a
commit 5bd516b
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Showing 65 changed files with 101 additions and 103 deletions.
diff --git a/Makefile b/Makefile
@@ -10,9 +10,9 @@ CXXFLAGS += -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
 CXXFLAGS += -Wall #-pedantic
 
 # comment the line below to compile and link in shared mode
-# CXXFLAGS += -static
+CXXFLAGS += -static
 
-# compile using boost::thread 
+# by default compile using boost::thread 
 # boost::thread from 1.50+ explicitely requires boost::system library
 CXXFLAGS += -DUSE_BOOST_THREAD
 DEP_LIBS += -lboost_thread -lboost_system

diff --git a/Makefile.c++11 b/Makefile.c++11
@@ -10,7 +10,7 @@ CXXFLAGS += -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
 CXXFLAGS += -Wall #-pedantic
 
 # there are problems when statically linking with pthreads and libstdc++
-# so only shared linking is possible
+# so use only shared linking
 #CXXFLAGS += -static
 
 # compile using c++11
@@ -25,10 +25,6 @@ bin:
 lib:
 	cd src; ${MAKE} lib
 
-pylib:
-	# make sure to configure properly Jamroot file and have boost libraries installed
-	cd py; bjam
-
 examples:
 	cd examples/cpplib; ${MAKE}
 

diff --git a/examples/cpplib/Makefile b/examples/cpplib/Makefile
@@ -1,6 +1,6 @@
 all: example1 example2
 
-INC_PATH = ../../include/
+INC_PATH = ../../include/dsrc
 LIB_PATH = ../../lib/
 DSRC_LIB = -ldsrc
 

diff --git a/examples/cpplib/example1.pro b/examples/cpplib/example1.pro
@@ -6,7 +6,7 @@ CONFIG -= qt
 SOURCES += \
     example1.cpp
 
-INCLUDEPATH += ../../include/
+INCLUDEPATH += ../../include/dsrc
 
 # Specify path to DSRC library file
 LIBS += /home/lucas/dev/workspace/dsrc20-dev/lib/libdsrc.a

diff --git a/examples/cpplib/example2.pro b/examples/cpplib/example2.pro
@@ -6,7 +6,7 @@ CONFIG -= qt
 SOURCES += \
     example2.cpp
 
-INCLUDEPATH += ../../include/
+INCLUDEPATH += ../../include/dsrc
 
 # Specify path to DSRC library file
 LIBS += /home/lucas/dev/workspace/dsrc20-dev/lib/libdsrc.a

diff --git a/include/Configurable.h → include/dsrc/Configurable.h b/include/Configurable.h → include/dsrc/Configurable.h
diff --git a/include/Dsrc.h → include/dsrc/Dsrc.h b/include/Dsrc.h → include/dsrc/Dsrc.h
@@ -10,7 +10,7 @@
 #ifndef H_DSRC
 #define H_DSRC
 
-#include "../include/Globals.h"
+#include "Globals.h"
 #include "DsrcModule.h"
 #include "FastqFile.h"
 #include "DsrcArchive.h"

diff --git a/include/DsrcArchive.h → include/dsrc/DsrcArchive.h b/include/DsrcArchive.h → include/dsrc/DsrcArchive.h
diff --git a/include/DsrcModule.h → include/dsrc/DsrcModule.h b/include/DsrcModule.h → include/dsrc/DsrcModule.h
diff --git a/include/Fastq.h → include/dsrc/Fastq.h b/include/Fastq.h → include/dsrc/Fastq.h
diff --git a/include/FastqFile.h → include/dsrc/FastqFile.h b/include/FastqFile.h → include/dsrc/FastqFile.h
diff --git a/include/FastqRecord.h → include/dsrc/FastqRecord.h b/include/FastqRecord.h → include/dsrc/FastqRecord.h
diff --git a/include/Globals.h → include/dsrc/Globals.h b/include/Globals.h → include/dsrc/Globals.h
diff --git a/py/Interface.cpp b/py/Interface.cpp
@@ -19,11 +19,11 @@
 
 #include <Python.h>
 
-#include "../include/Globals.h"
-#include "../include/FastqRecord.h"
-#include "../include/FastqFile.h"
-#include "../include/DsrcModule.h"
-#include "../include/DsrcArchive.h"
+#include "../include/dsrc/Globals.h"
+#include "../include/dsrc/FastqRecord.h"
+#include "../include/dsrc/FastqFile.h"
+#include "../include/dsrc/DsrcModule.h"
+#include "../include/dsrc/DsrcArchive.h"
 
 namespace dsrc
 {

diff --git a/py/Jamroot b/py/Jamroot
@@ -3,17 +3,19 @@
 #
 
 import python ;
-
 
-# User-specified path to the Boost project
+#
+# Important!
+#
+# To compile DSRC Python module please specify your boost installation directory below
+#
 use-project boost 
-  : /home/andrzej/dev/lib/boost_1_49_0/ ;
+  : /absolute/path/to/user/boost/directory/ ;
 
 
 # Project-wide requirements
 project
-  : requirements <library>/boost/python//boost_python <library>/boost/thread//boost_thread ;
-
+  : requirements <library>/boost/python//boost_python <library>/boost/thread//boost_thread <library>/boost/thread//boost_system ;
 
 # Extension modules
 python-extension pydsrc

diff --git a/src/BitMemory.h b/src/BitMemory.h
@@ -10,7 +10,7 @@
 #ifndef H_BITMEMORY
 #define H_BITMEMORY
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <vector>
 #include <algorithm>

diff --git a/src/BlockCompressor.h b/src/BlockCompressor.h
@@ -10,7 +10,7 @@
 #ifndef H_BLOCKCOMPRESSOR
 #define H_BLOCKCOMPRESSOR
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <vector>
 

diff --git a/src/BlockCompressorExt.h b/src/BlockCompressorExt.h
@@ -10,8 +10,8 @@
 #ifndef BLOCKCOMPRESSOREXT_H
 #define BLOCKCOMPRESSOREXT_H
 
-#include "../include/Globals.h"
-#include "../include/FastqRecord.h"
+#include "../include/dsrc/Globals.h"
+#include "../include/dsrc/FastqRecord.h"
 
 #include "BlockCompressor.h"
 

diff --git a/src/Buffer.h b/src/Buffer.h
@@ -10,7 +10,7 @@
 #ifndef BUFFER_H
 #define BUFFER_H
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <algorithm>
 

diff --git a/src/Common.h b/src/Common.h
@@ -10,7 +10,7 @@
 #ifndef H_COMMON
 #define H_COMMON
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #ifndef NDEBUG
 #	define DEBUG 1

diff --git a/src/Configurable.cpp b/src/Configurable.cpp
@@ -10,7 +10,7 @@
 #ifndef CPP_CONFIGURABLE
 #define CPP_CONFIGURABLE
 
-#include "../include/Configurable.h"
+#include "../include/dsrc/Configurable.h"
 
 #include "Common.h"
 

diff --git a/src/Crc32.h b/src/Crc32.h
@@ -10,7 +10,7 @@
 #ifndef CRC32_H
 #define CRC32_H
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <vector>
 #include <string>

diff --git a/src/DataPool.h b/src/DataPool.h
@@ -10,7 +10,7 @@
 #ifndef H_DATA_POOL
 #define H_DATA_POOL
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <vector>
 

diff --git a/src/DataQueue.h b/src/DataQueue.h
@@ -10,7 +10,7 @@
 #ifndef H_DATAQUEUE
 #define H_DATAQUEUE
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <queue>
 

diff --git a/src/DataStream.h b/src/DataStream.h
@@ -10,7 +10,7 @@
 #ifndef H_DATASTREAM
 #define H_DATASTREAM
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 namespace dsrc
 {

diff --git a/src/DnaModeler.h b/src/DnaModeler.h
@@ -10,7 +10,7 @@
 #ifndef H_DNAMODELER
 #define H_DNAMODELER
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "Common.h"
 

diff --git a/src/DnaModelerBasicB2.h b/src/DnaModelerBasicB2.h
@@ -10,7 +10,7 @@
 #ifndef H_DNAMODELERBASICB2
 #define H_DNAMODELERBASICB2
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "DnaModeler.h"
 #include "Stats.h"

diff --git a/src/DnaModelerHuffman.h b/src/DnaModelerHuffman.h
@@ -1,7 +1,7 @@
 #ifndef DNAMODELHUFFMAN_H
 #define DNAMODELHUFFMAN_H
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "DnaModeler.h"
 #include "Stats.h"

diff --git a/src/DnaModelerProxy.h b/src/DnaModelerProxy.h
@@ -10,7 +10,7 @@
 #ifndef H_DNAMODELERPROXY
 #define H_DNAMODELERPROXY
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "Stats.h"
 #include "DnaModelerBasicB2.h"

diff --git a/src/DnaModelerRCO.h b/src/DnaModelerRCO.h
@@ -10,7 +10,7 @@
 #ifndef H_DNAMODELRCO
 #define H_DNAMODELRCO
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "DnaModeler.h"
 #include "Fastq.h"

diff --git a/src/DsrcArchive.cpp b/src/DsrcArchive.cpp
@@ -7,7 +7,7 @@
   Version: 2.00
 */
 
-#include "../include/DsrcArchive.h"
+#include "../include/dsrc/DsrcArchive.h"
 
 #include "BlockCompressorExt.h"
 #include "DsrcFile.h"

diff --git a/src/DsrcFile.h b/src/DsrcFile.h
@@ -9,7 +9,7 @@
 #ifndef H_DSRCFILE
 #define H_DSRCFILE
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <vector>
 

diff --git a/src/DsrcIo.h b/src/DsrcIo.h
@@ -10,7 +10,7 @@
 #ifndef H_DSRCWRITER
 #define H_DSRCWRITER
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "Buffer.h"
 #include "DataQueue.h"

diff --git a/src/DsrcModule.cpp b/src/DsrcModule.cpp
@@ -7,7 +7,7 @@
   Version: 2.00
 */
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <iostream>
 
@@ -19,7 +19,7 @@ namespace th = boost;
 namespace th = std;
 #endif
 
-#include "../include/DsrcModule.h"
+#include "../include/dsrc/DsrcModule.h"
 
 #include "DsrcOperator.h"
 

diff --git a/src/DsrcOperator.h b/src/DsrcOperator.h
@@ -10,7 +10,7 @@
 #ifndef H_DSRCOPERATOR
 #define H_DSRCOPERATOR
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include <string>
 

diff --git a/src/DsrcWorker.cpp b/src/DsrcWorker.cpp
@@ -7,7 +7,7 @@
   Version: 2.00
 */
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "DsrcWorker.h"
 #include "DsrcIo.h"

diff --git a/src/DsrcWorker.h b/src/DsrcWorker.h
@@ -10,7 +10,7 @@
 #ifndef H_DSRCWORKER
 #define H_DSRCWORKER
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "Fastq.h"
 #include "BitMemory.h"

diff --git a/src/ErrorHandler.h b/src/ErrorHandler.h
@@ -10,7 +10,7 @@
 #ifndef H_ERRORHANDLER
 #define H_ERRORHANDLER
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #ifdef USE_BOOST_THREAD
 #include <boost/thread.hpp>

diff --git a/src/Fastq.h b/src/Fastq.h
@@ -10,7 +10,7 @@
 #ifndef H_FASTQ_SRC
 #define H_FASTQ_SRC
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 #include "Common.h"
 
 #include <vector>

diff --git a/src/FastqFile.cpp b/src/FastqFile.cpp
@@ -7,7 +7,7 @@
   Version: 2.00
 */
 
-#include "../include/FastqFile.h"
+#include "../include/dsrc/FastqFile.h"
 
 #include "Common.h"
 #include "Buffer.h"

diff --git a/src/FastqIo.h b/src/FastqIo.h
@@ -10,7 +10,7 @@
 #ifndef H_FASTQREADER
 #define H_FASTQREADER
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "Common.h"
 #include "Fastq.h"

diff --git a/src/FastqParser.h b/src/FastqParser.h
@@ -10,7 +10,7 @@
 #ifndef H_FASTQPARSER
 #define H_FASTQPARSER
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "Common.h"
 #include "Fastq.h"

diff --git a/src/FastqStream.h b/src/FastqStream.h
@@ -9,7 +9,7 @@
 #ifndef H_FASTQSTREAM
 #define H_FASTQSTREAM
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 //#include "Common.h"
 #include "Fastq.h"

diff --git a/src/FileStream.h b/src/FileStream.h
@@ -9,7 +9,7 @@
 #ifndef H_FILESTREAM
 #define H_FILESTREAM
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "DataStream.h"
 

diff --git a/src/Makefile b/src/Makefile
@@ -1,6 +1,6 @@
 all: bin lib
 
-INC_DIR = ../include
+INC_DIR = ../include/dsrc
 SRC_DIR = .
 LIB_DIR = ../lib
 BIN_DIR = ../bin

diff --git a/src/QualityEncoder.h b/src/QualityEncoder.h
@@ -10,7 +10,7 @@
 #ifndef H_QUALITYENCODER
 #define H_QUALITYENCODER
 
-#include "../include/Globals.h"
+#include "../include/dsrc/Globals.h"
 
 #include "RangeCoder.h"
 #include "SymbolCoderRC.h"