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412 lines
12 KiB
412 lines
12 KiB
Makefile.am | 9 +++---
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ajax/Makefile.am | 4 +--
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ajax/acd/Makefile.am | 8 +++--
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ajax/ajaxdb/Makefile.am | 6 ++--
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ajax/core/Makefile.am | 6 ++--
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ajax/core/ajreg.h | 7 ++--
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ajax/ensembl/Makefile.am | 6 ++--
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ajax/graphics/Makefile.am | 8 +++--
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configure.ac | 82 ++++++++++++++++++++++++++---------------------
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emboss/Makefile.am | 13 +++++---
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jemboss/lib/Makefile.am | 2 +-
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m4/idxdbs.m4 | 17 +++-------
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nucleus/Makefile.am | 8 +++--
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13 files changed, 100 insertions(+), 76 deletions(-)
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diff --git a/Makefile.am b/Makefile.am
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index 177dec5..18dd99a 100644
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--- a/Makefile.am
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+++ b/Makefile.am
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@@ -12,8 +12,11 @@ LICENSE \
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ONEWS \
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PROBLEMS
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-SUBDIRS = \
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-plplot \
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+SUBDIRS =
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+if !ESYSTEMLIBS
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+SUBDIRS += plplot
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+endif
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+SUBDIRS += \
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ajax \
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nucleus \
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emboss \
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@@ -33,5 +36,3 @@ dist-hook:
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tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; )
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tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf )
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-install-exec-hook:
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- $(bindir)/embossupdate
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diff --git a/ajax/Makefile.am b/ajax/Makefile.am
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index f27472c..de34e17 100644
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--- a/ajax/Makefile.am
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+++ b/ajax/Makefile.am
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@@ -1,7 +1,7 @@
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## Process this file with automake to produce Makefile.in
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-SUBDIRS = pcre
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+SUBDIRS =
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if !ESYSTEMLIBS
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-SUBDIRS += expat zlib
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+SUBDIRS += pcre expat zlib
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endif
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SUBDIRS += core graphics ensembl ajaxdb acd
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diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
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index 9f0f700..3295a1d 100644
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--- a/ajax/acd/Makefile.am
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+++ b/ajax/acd/Makefile.am
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@@ -3,16 +3,20 @@
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lib_LTLIBRARIES = libacd.la
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libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
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+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
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libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb
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+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
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libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
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libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
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-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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if !ESYSTEMLIBS
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+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
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libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
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-endif
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libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
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+else
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+libacd_la_CFLAGS += $(PLPLOT_CFLAGS)
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+endif
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libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
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libacd_la_LDFLAGS = -version-info 6:5:0
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diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
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index c2b0c00..9de14fe 100644
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--- a/ajax/ajaxdb/Makefile.am
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+++ b/ajax/ajaxdb/Makefile.am
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@@ -3,14 +3,16 @@
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lib_LTLIBRARIES = libajaxdb.la
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libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
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+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
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libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl
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-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core
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if !ESYSTEMLIBS
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+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
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libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
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-endif
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libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
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+endif
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libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
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libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS)
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diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
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index 2906837..3189c34 100644
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--- a/ajax/core/Makefile.am
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+++ b/ajax/core/Makefile.am
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@@ -3,13 +3,15 @@
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lib_LTLIBRARIES = libajax.la
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libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
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+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS)
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-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
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+libajax_la_CPPFLAGS =
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if !ESYSTEMLIBS
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+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
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libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
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-endif
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libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
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+endif
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libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
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libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS)
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libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS)
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diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
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index 1623c82..5d928cf 100644
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--- a/ajax/core/ajreg.h
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+++ b/ajax/core/ajreg.h
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@@ -39,9 +39,8 @@
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#include "ajdefine.h"
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#include "ajstr.h"
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-#include "pcre_config.h"
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-#include "pcre_internal.h"
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-#include "pcreposix.h"
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+#include <pcre.h>
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+#include <pcreposix.h>
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AJ_BEGIN_DECLS
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@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS
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typedef struct AjSRegexp
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{
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- real_pcre *pcre;
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+ struct real_pcre *pcre;
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pcre_extra *extra;
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int *ovector;
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const char* orig;
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diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
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index 0d1250b..5484c02 100644
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--- a/ajax/ensembl/Makefile.am
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+++ b/ajax/ensembl/Makefile.am
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@@ -3,13 +3,15 @@
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lib_LTLIBRARIES = libensembl.la
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libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
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+libensembl_la_LIBADD = ../core/libajax.la
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-libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
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+libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core
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if !ESYSTEMLIBS
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+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
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libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
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-endif
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libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
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+endif
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libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
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libensembl_la_LDFLAGS = -version-info 6:5:0
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diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
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index a4f202b..1114c2c 100644
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--- a/ajax/graphics/Makefile.am
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+++ b/ajax/graphics/Makefile.am
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@@ -3,12 +3,16 @@
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lib_LTLIBRARIES = libajaxg.la
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libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
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+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS)
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-libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
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+libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core
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if !ESYSTEMLIBS
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+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
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-endif
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libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
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+else
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+libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS)
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+endif
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libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
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libajaxg_la_LDFLAGS = -version-info 6:5:0
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diff --git a/configure.ac b/configure.ac
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index a7bd9c6..9ba3121 100644
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--- a/configure.ac
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+++ b/configure.ac
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@@ -629,32 +629,6 @@ AS_CASE([${host_os}],
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-
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-dnl PCRE library definitions - see the MAJOR and MINOR values
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-dnl to see which version's configure.in these lines come from
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-
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-dnl Provide the current PCRE version information. Do not use numbers
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-dnl with leading zeros for the minor version, as they end up in a C
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-dnl macro, and may be treated as octal constants. Stick to single
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-dnl digits for minor numbers less than 10. There are unlikely to be
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-dnl that many releases anyway.
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-
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-PCRE_MAJOR="7"
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-PCRE_MINOR="9"
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-PCRE_DATE="11-Apr-2009"
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-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
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-
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-dnl Default values for miscellaneous macros
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-
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-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
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-
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-dnl Provide versioning information for libtool shared libraries that
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-dnl are built by default on Unix systems.
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-
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-PCRE_LIB_VERSION="0:1:0"
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-PCRE_POSIXLIB_VERSION="0:0:0"
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-
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-
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dnl Define where the EMBOSS package is located
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AC_SUBST([AJAX_FIXED_ROOT])
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AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
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@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL
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-dnl "Export" these variables for PCRE
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-AC_SUBST([HAVE_MEMMOVE])
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-AC_SUBST([HAVE_STRERROR])
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-AC_SUBST([PCRE_MAJOR])
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-AC_SUBST([PCRE_MINOR])
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-AC_SUBST([PCRE_DATE])
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-AC_SUBST([PCRE_VERSION])
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-AC_SUBST([PCRE_LIB_VERSION])
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-AC_SUBST([PCRE_POSIXLIB_VERSION])
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-AC_SUBST([POSIX_MALLOC_THRESHOLD])
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@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs],
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AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
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+AS_IF([test "x${enable_systemlibs}" = "xyes"],
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+[
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+dnl using system libraries
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+ PKG_CHECK_MODULES([PCRE], [libpcre])
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+ PKG_CHECK_MODULES([EXPAT], [expat])
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+ PKG_CHECK_MODULES([ZLIB], [zlib])
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+ PKG_CHECK_MODULES([PLPLOT], [plplotd],
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+ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
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+ )
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+],
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+[
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+dnl using bundled libraries
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+ dnl PCRE library definitions - see the MAJOR and MINOR values
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+ dnl to see which version's configure.ac these lines come from
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+ dnl Provide the current PCRE version information. Do not use numbers
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+ dnl with leading zeros for the minor version, as they end up in a C
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+ dnl macro, and may be treated as octal constants. Stick to single
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+ dnl digits for minor numbers less than 10. There are unlikely to be
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+ dnl that many releases anyway.
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+
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+ PCRE_MAJOR="7"
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+ PCRE_MINOR="9"
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+ PCRE_DATE="11-Apr-2009"
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+ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
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+
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+ dnl Default values for miscellaneous macros
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+
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+ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
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+
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+ dnl Provide versioning information for libtool shared libraries that
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+ dnl are built by default on Unix systems.
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+
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+ PCRE_LIB_VERSION="0:1:0"
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+ PCRE_POSIXLIB_VERSION="0:0:0"
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+
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+ dnl "Export" these variables for PCRE
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+ AC_SUBST([HAVE_MEMMOVE])
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+ AC_SUBST([HAVE_STRERROR])
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+ AC_SUBST([PCRE_MAJOR])
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+ AC_SUBST([PCRE_MINOR])
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+ AC_SUBST([PCRE_DATE])
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+ AC_SUBST([PCRE_VERSION])
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+ AC_SUBST([PCRE_LIB_VERSION])
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+ AC_SUBST([PCRE_POSIXLIB_VERSION])
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+ AC_SUBST([POSIX_MALLOC_THRESHOLD])
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+])
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# Enable the purify tool: --enable-purify, sets CC and LIBTOOL
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diff --git a/emboss/Makefile.am b/emboss/Makefile.am
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index 89ada78..f987d40 100644
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--- a/emboss/Makefile.am
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+++ b/emboss/Makefile.am
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@@ -28,15 +28,18 @@ endif
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AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd
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AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
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+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core
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AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
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AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
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+if !ESYSTEMLIBS
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AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
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-if !ESYSTEMLIBS
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AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
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AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
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-endif
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-AM_CPPFLAGS += -I$(top_srcdir)/nucleus
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|
AM_CPPFLAGS += -I$(top_srcdir)/plplot
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|
+else
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|
+AM_CFLAGS += $(PLPLOT_CFLAGS)
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|
+endif
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|
+AM_CPPFLAGS += -I$(top_srcdir)/nucleus
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|
AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
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|
AM_CPPFLAGS += $(JAVA_CPPFLAGS)
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|
|
|
@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la
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if !ESYSTEMLIBS
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LDADD += ../ajax/zlib/libezlib.la
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|
LDADD += ../ajax/expat/libeexpat.la
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-endif
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|
LDADD += ../ajax/pcre/libepcre.la
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|
LDADD += ../plplot/libeplplot.la
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|
+else
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|
+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS)
|
|
+endif
|
|
LDADD += $(XLIB)
|
|
|
|
#if PURIFY
|
|
diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am
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|
index 5f7e21e..8b45ce2 100644
|
|
--- a/jemboss/lib/Makefile.am
|
|
+++ b/jemboss/lib/Makefile.am
|
|
@@ -12,7 +12,7 @@ mail.jar \
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|
jalviewApplet.jar \
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|
jemboss.jar
|
|
|
|
-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java
|
|
+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java
|
|
if JAVA_BUILD
|
|
$(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes;
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endif
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|
diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4
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|
index 0ca7ea9..9b54f2a 100644
|
|
--- a/m4/idxdbs.m4
|
|
+++ b/m4/idxdbs.m4
|
|
@@ -1,17 +1,8 @@
|
|
AC_DEFUN([CHECK_IDXDBS],
|
|
[
|
|
-AC_MSG_CHECKING(for EMBOSS pre-indexed databases)
|
|
+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases)
|
|
|
|
-
|
|
-if test -f ./emboss/index/edam.xac; then
|
|
-AC_MSG_RESULT(yes)
|
|
-else
|
|
-AC_MSG_RESULT(no)
|
|
-echo ""
|
|
-echo "Pre-indexed edam, taxon + drcat databases not found."
|
|
-echo "Please download them from within this directory using:"
|
|
-echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ."
|
|
-echo "and then repeat the configure step."
|
|
-exit 1
|
|
-fi
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|
+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac],
|
|
+ [],
|
|
+ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])])
|
|
])
|
|
diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
|
|
index 37b8543..5819c89 100644
|
|
--- a/nucleus/Makefile.am
|
|
+++ b/nucleus/Makefile.am
|
|
@@ -3,6 +3,7 @@
|
|
lib_LTLIBRARIES = libnucleus.la
|
|
|
|
libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
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|
+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
|
|
|
|
if ISSHARED
|
|
if ISAIXIA64
|
|
@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm
|
|
endif
|
|
endif
|
|
|
|
-libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot
|
|
-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
+libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core
|
|
if !ESYSTEMLIBS
|
|
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot
|
|
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
|
|
+else
|
|
+libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS)
|
|
endif
|
|
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
|
|
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
|