Merge branch 'emboss-split' into emboss

src/clibs/emboss/README

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+BioLib R mapping functions
+
+Note: EMBOSS redefines the assert function - for DEBUG mode you'll need to 
+include 
+
+  ${CONTRIB_PATH}/ajax/ajassert.c
+
+in the ./src/files.txt
+
+A writeup on the EMBOSS mapping can be found at
+
+  http://biolib.open-bio.org/wiki/Mapping_EMBOSS 
+

src/clibs/emboss/src/CMakeLists.txt

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+# Module CMake file - builds library in ./contrib
+
+cmake_minimum_required(VERSION 2.6)
+
+PROJECT(Biolib_emboss)
+SET (M_NAME emboss)
+# SET (M_VERSION 6.1.0)
+
+IF(NOT BUILD_LIBS)
+  SET (MAP_ROOT ../../../..)
+  SET (CMAKE_MODULE_PATH ${MAP_ROOT}/tools/cmake-support/modules)
+ENDIF()
+
+FIND_PACKAGE(Map)
+
+SET(CONTRIB_PATH ${MAP_ROOT}/contrib/EMBOSS)
+
+MESSAGE("CONTRIB_PATH=${CONTRIB_PATH}")
+
+SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY ../build)
+
+INCLUDE_DIRECTORIES(.)
+INCLUDE_DIRECTORIES(${CONTRIB_PATH}/emboss/function)
+INCLUDE_DIRECTORIES(${CONTRIB_PATH}/ajax/core)
+INCLUDE_DIRECTORIES(${CONTRIB_PATH}/ajax/pcre)
+INCLUDE_DIRECTORIES(${CONTRIB_PATH}/ajax/ajaxdb)
+INCLUDE_DIRECTORIES(${CONTRIB_PATH}/ajax/graphics)
+INCLUDE_DIRECTORIES(${CONTRIB_PATH}/plplot)
+
+# INCLUDE_DIRECTORIES(${BOOST_PATH})
+add_definitions(-DVERSION="6.1" -DLINK_SIZE=4 -DHAVE_MEMMOVE -DPOSIX_MALLOC_THRESHOLD=10)
+
+# Here a hack to get EMBOSS to compile without running configure (may change
+# later and run ./configure once)
+add_definitions(-DMAX_NAME_COUNT=10000 -DNEWLINE=10 -DMAX_NAME_SIZE=32 -DMATCH_LIMIT=10000000 -DMATCH_LIMIT_RECURSION=MATCH_LIMIT -DBUILD_DIR="${CONTRIB_PATH}/" -DEMBOSS_TOP="${CONTRIB_PATH}/" -DPREFIX="/usr/local")
+
+BUILD_CLIB()
+
+FILE(STRINGS files.txt CONTRIB_FILES)
+
+ADD_LIBRARY(${LIBNAME} SHARED
+  ${CONTRIB_FILES}
+)
+
+# ---- The following may be required for OSX
+# TARGET_LINK_LIBRARIES(${LIBNAME} ${ZLIB_NAME})
+
+INSTALL_CLIB()
+

src/clibs/emboss/src/files.txt

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+${CONTRIB_PATH}/emboss/function/emboss_transeq.c
+${CONTRIB_PATH}/plplot/plctrl.c
+${CONTRIB_PATH}/plplot/data.c
+${CONTRIB_PATH}/plplot/pbm.c
+${CONTRIB_PATH}/plplot/plhist.c
+${CONTRIB_PATH}/plplot/plsym.c
+${CONTRIB_PATH}/plplot/dg300.c
+${CONTRIB_PATH}/plplot/pdfutils.c
+${CONTRIB_PATH}/plplot/plimage.c
+${CONTRIB_PATH}/plplot/pltick.c
+${CONTRIB_PATH}/plplot/gd.c
+${CONTRIB_PATH}/plplot/plargs.c
+${CONTRIB_PATH}/plplot/plline.c
+${CONTRIB_PATH}/plplot/plvect.c
+${CONTRIB_PATH}/plplot/gdpng.c
+${CONTRIB_PATH}/plplot/plbox.c
+${CONTRIB_PATH}/plplot/plmap.c
+${CONTRIB_PATH}/plplot/plvpor.c
+${CONTRIB_PATH}/plplot/hpgl.c
+${CONTRIB_PATH}/plplot/plbuf.c
+${CONTRIB_PATH}/plplot/plmeta.c
+${CONTRIB_PATH}/plplot/plwind.c
+${CONTRIB_PATH}/plplot/impress.c
+${CONTRIB_PATH}/plplot/plcont.c
+${CONTRIB_PATH}/plplot/plot3d.c
+${CONTRIB_PATH}/plplot/ps.c
+${CONTRIB_PATH}/plplot/linuxvga.c
+${CONTRIB_PATH}/plplot/plcore.c
+${CONTRIB_PATH}/plplot/plpage.c
+${CONTRIB_PATH}/plplot/tek.c
+${CONTRIB_PATH}/plplot/ljii.c
+${CONTRIB_PATH}/plplot/plsdef.c
+${CONTRIB_PATH}/plplot/xfig.c
+${CONTRIB_PATH}/plplot/ljiip.c
+${CONTRIB_PATH}/plplot/plcvt.c
+${CONTRIB_PATH}/plplot/plshade.c
+${CONTRIB_PATH}/plplot/xwin.c
+${CONTRIB_PATH}/plplot/next.c
+${CONTRIB_PATH}/plplot/pldtik.c
+${CONTRIB_PATH}/plplot/plstdio.c
+${CONTRIB_PATH}/plplot/null.c
+${CONTRIB_PATH}/plplot/plfill.c
+${CONTRIB_PATH}/plplot/plstripc.c
+${CONTRIB_PATH}/ajax/graphics/ajgraph.c
+${CONTRIB_PATH}/ajax/graphics/ajhist.c
+${CONTRIB_PATH}/ajax/pcre/pcre_chartables.c
+${CONTRIB_PATH}/ajax/pcre/pcre_info.c
+${CONTRIB_PATH}/ajax/pcre/pcre_compile.c
+${CONTRIB_PATH}/ajax/pcre/pcre_newline.c
+${CONTRIB_PATH}/ajax/pcre/pcre_exec.c
+${CONTRIB_PATH}/ajax/pcre/pcreposix.c
+${CONTRIB_PATH}/ajax/pcre/pcre_fullinfo.c
+${CONTRIB_PATH}/ajax/pcre/pcre_study.c
+${CONTRIB_PATH}/ajax/pcre/pcre_get.c
+${CONTRIB_PATH}/ajax/pcre/pcre_tables.c
+${CONTRIB_PATH}/ajax/pcre/pcre_globals.c
+${CONTRIB_PATH}/ajax/pcre/pcre_try_flipped.c
+${CONTRIB_PATH}/ajax/acd/ajacd.c
+${CONTRIB_PATH}/ajax/core/ajfeat.c
+${CONTRIB_PATH}/ajax/core/ajmatrices.c
+${CONTRIB_PATH}/ajax/core/ajseqabi.c
+${CONTRIB_PATH}/ajax/core/ajtree.c
+${CONTRIB_PATH}/ajax/core/ajalign.c
+${CONTRIB_PATH}/ajax/core/ajfile.c
+${CONTRIB_PATH}/ajax/core/ajmem.c
+${CONTRIB_PATH}/ajax/core/ajseq.c
+${CONTRIB_PATH}/ajax/core/ajutil.c
+${CONTRIB_PATH}/ajax/core/ajarr.c
+${CONTRIB_PATH}/ajax/core/ajfiledata.c
+${CONTRIB_PATH}/ajax/core/ajmess.c
+${CONTRIB_PATH}/ajax/ajaxdb/ajseqdb.c
+${CONTRIB_PATH}/ajax/core/ajvector.c
+${CONTRIB_PATH}/ajax/core/ajfileio.c
+${CONTRIB_PATH}/ajax/core/ajnam.c
+${CONTRIB_PATH}/ajax/core/ajseqread.c
+${CONTRIB_PATH}/ajax/core/ajbase.c
+${CONTRIB_PATH}/ajax/core/ajfmt.c
+${CONTRIB_PATH}/ajax/core/ajnexus.c
+${CONTRIB_PATH}/ajax/core/ajseqtype.c
+${CONTRIB_PATH}/ajax/core/ajcall.c
+${CONTRIB_PATH}/ajax/core/ajpat.c
+${CONTRIB_PATH}/ajax/core/ajseqwrite.c
+${CONTRIB_PATH}/ajax/core/ajcod.c
+${CONTRIB_PATH}/ajax/core/ajpdb.c
+${CONTRIB_PATH}/ajax/core/ajsort.c
+${CONTRIB_PATH}/ajax/core/ajdan.c
+${CONTRIB_PATH}/ajax/core/ajpdbio.c
+${CONTRIB_PATH}/ajax/core/ajstr.c
+${CONTRIB_PATH}/ajax/core/ajdmx.c
+${CONTRIB_PATH}/ajax/core/ajindex.c
+${CONTRIB_PATH}/ajax/core/ajphylo.c
+${CONTRIB_PATH}/ajax/core/ajsys.c
+${CONTRIB_PATH}/ajax/core/ajdomain.c
+${CONTRIB_PATH}/ajax/core/ajjava.c
+${CONTRIB_PATH}/ajax/core/ajrange.c
+${CONTRIB_PATH}/ajax/core/ajtable.c
+${CONTRIB_PATH}/ajax/core/ajdom.c
+${CONTRIB_PATH}/ajax/core/ajlist.c
+${CONTRIB_PATH}/ajax/core/ajreg.c
+${CONTRIB_PATH}/ajax/core/ajtime.c
+${CONTRIB_PATH}/ajax/core/ajexcept.c
+${CONTRIB_PATH}/ajax/core/ajmath.c
+${CONTRIB_PATH}/ajax/core/ajreport.c
+${CONTRIB_PATH}/ajax/core/ajtranslate.c

src/clibs/emboss/src/skipping.txt

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+
+${CONTRIB_PATH}/ajax/pcreposix.c
+${CONTRIB_PATH}/ajax/ajgraph.c
+${CONTRIB_PATH}/ajax/ajhist.c
+${CONTRIB_PATH}/ajax/pcre_printint.c