Makefile

@@ -19,6 +19,7 @@ INCLUDEOPT:=-I$(CURDIR)/../genometools/src \
             -I$(CURDIR)/../genometools/src/external/zlib-1.2.8 \
             -I$(CURDIR)/../genometools/src/external/bzip2-1.0.6 \
             -I$(CURDIR)/../genometools/src/external/expat-2.0.1/lib \
+            -I$(CURDIR)/../genometools/src/external/lua-5.1.5/src \
             -I$(CURDIR)/src -I$(CURDIR)/obj \
 # these variables are exported by the configuration script
 CC:=gcc
@@ -33,7 +34,7 @@ ifneq ($(fpic),no)
 endif
 
 # ...while those starting with GTH_ are for internal purposes only
-GTH_CFLAGS:=-g -Wall -Wunused-parameter -pipe $(FPIC) -Wpointer-arith -fno-stack-protector -Wno-error=misleading-indentation
+GTH_CFLAGS:=-g -Wall -Wunused-parameter -pipe $(FPIC) -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas
 # mkvtree needs -DWITHLCP
 # rnv needs -DUNISTD_H="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION="\"1.7.8\""
 EXT_FLAGS:= -DWITHLCP -DUNISTD_H="<unistd.h>" -DEXPAT_H="<expat.h>" \
@@ -78,6 +79,12 @@ ifeq ($(wrapmemcpy),yes)
   GTH_LDFLAGS+=-Wl,--wrap=memcpy
 endif
 
+ifneq ($(SYSTEM),Darwin)
+ifneq ($(MACHINE),ARMv6_hf)
+GTH_CFLAGS+=-Wno-error=misleading-indentation
+endif
+endif
+
 # system specific stuff (concerning 64bit compilation)
 ifeq ($(SYSTEM),Darwin)
   ifeq ($(64bit),yes)
@@ -186,7 +193,7 @@ ifeq ($(wrapmemcpy),yes)
   RNVMAIN_OBJ+=../genometools/obj/src/memcpy.o
 endif
 
-LIBGENOMETHREADER_DIRS:= src/libgenomethreader
+LIBGENOMETHREADER_DIRS:= src/libgenomethreader src/gth
 
 # the GenomeThreader library
 LIBGENOMETHREADER_SRC:=$(foreach DIR,$(LIBGENOMETHREADER_DIRS),$(wildcard $(DIR)/*.c))
@@ -201,8 +208,8 @@ patch ?= patch
 
 all: lib/libgenomethreader.a bin/gth bin/gthconsensus bin/gthbssmfileinfo \
      bin/gthbssmbuild bin/gthbssmprint bin/gthbssmrmsd bin/gthbssmtrain \
-     bin/gthfilestat bin/gthsplit bin/gthunit bin/gthgetseq bin/align_dna \
-     bin/rnv
+     bin/gthfilestat bin/gthmkbssmfiles bin/gthsplit bin/gthunit \
+     bin/gthgetseq bin/align_dna bin/rnv
 
 lib/libgenomethreader.a: obj/gth_config.h $(LIBGENOMETHREADER_OBJ)
 	@echo "[link $(@F)]"
@@ -261,6 +268,10 @@ $(eval $(call PROGRAM_template, bin/gthfilestat, obj/src/gthfilestat.o \
                                 lib/libgenomethreader.a \
                                 $(GTHLIBS) ../genometools/lib/libgenometools.a))
 
+$(eval $(call PROGRAM_template, bin/gthmkbssmfiles, obj/src/gthmkbssmfiles.o \
+                                lib/libgenomethreader.a \
+                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
+
 $(eval $(call PROGRAM_template, bin/gthsplit, obj/src/gthsplit.o \
                                 lib/libgenomethreader.a \
                                 $(GTHLIBS) ../genometools/lib/libgenometools.a))
@@ -510,7 +521,7 @@ obj/train: bin/gthbssmbuild
 
 obj/old_train: ../genometools/bin/gt
 	@echo "[write old BSSMs]"
-	@../genometools/bin/gt dev gthmkbssmfiles bin/bssm
+	@bin/gthmkbssmfiles bin/bssm
 	@touch $@
 
 obj/gthdata:

VERSION

-1.7.1
+1.7.2

debian/changelog

-genomethreader (1.7.1+dfsg-1) unstable; urgency=medium
+genomethreader (1.7.2+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #)
 

debian/control

@@ -7,7 +7,6 @@ Build-Depends: debhelper (>= 12),
                debhelper-compat (= 12),
                genometools,
                libgenometools0-dev,
-               libgenometools0-private-dev,
                libvmatch-dev,
                zlib1g-dev,
                libbz2-dev,

debian/patches/debian-gt-libs.patch

 --- a/Makefile
 +++ b/Makefile
-@@ -15,10 +15,8 @@
+@@ -15,19 +15,16 @@
  # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  #
  
@@ -8,12 +8,14 @@
 -            -I$(CURDIR)/../genometools/src/external/zlib-1.2.8 \
 -            -I$(CURDIR)/../genometools/src/external/bzip2-1.0.6 \
 -            -I$(CURDIR)/../genometools/src/external/expat-2.0.1/lib \
+-            -I$(CURDIR)/../genometools/src/external/lua-5.1.5/src \
 +INCLUDEOPT:=-I/usr/include/genometools \
 +	    -I/usr/include/vmatch \
              -I$(CURDIR)/src -I$(CURDIR)/obj \
  # these variables are exported by the configuration script
- CC:=gcc
-@@ -26,7 +24,7 @@
+-CC:=gcc
++#CC:=gcc
+ CXX:=g++
  EXP_CFLAGS:=$(CFLAGS)
  EXP_CXXFLAGS:=$(CXXFLAGS)
  EXP_CPPFLAGS:=$(CPPFLAGS)
@@ -22,7 +24,7 @@
  
  ifneq ($(fpic),no)
    FPIC:=-fPIC
-@@ -123,11 +121,11 @@
+@@ -130,11 +127,11 @@
  GTMAIN_DEP:=$(GTMAIN_SRC:%.c=obj/%.d)
  
  VSTREEDIR:=../vstree/src
@@ -39,17 +41,16 @@
  GTH_CPPFLAGS+=-I$(CURDIR)/$(VSTREEDIR)/include \
               -I$(CURDIR)/$(VSTREEDIR)/Vmatch \
  
-@@ -201,8 +199,7 @@
- 
+@@ -209,7 +206,7 @@
  all: lib/libgenomethreader.a bin/gth bin/gthconsensus bin/gthbssmfileinfo \
       bin/gthbssmbuild bin/gthbssmprint bin/gthbssmrmsd bin/gthbssmtrain \
--     bin/gthfilestat bin/gthsplit bin/gthunit bin/gthgetseq bin/align_dna \
--     bin/rnv
-+     bin/gthfilestat bin/gthsplit bin/gthunit bin/gthgetseq bin/align_dna
+      bin/gthfilestat bin/gthmkbssmfiles bin/gthsplit bin/gthunit \
+-     bin/gthgetseq bin/align_dna bin/rnv
++     bin/gthgetseq bin/align_dna
  
  lib/libgenomethreader.a: obj/gth_config.h $(LIBGENOMETHREADER_OBJ)
  	@echo "[link $(@F)]"
-@@ -224,63 +221,63 @@
+@@ -231,67 +228,67 @@
  $(1): $(2)
  	@echo "[link $$(@F)]"
  	@test -d $$(@D) || mkdir -p $$(@D)
@@ -62,62 +63,67 @@
  $(eval $(call PROGRAM_template, bin/gth, obj/src/gth.o \
                                  lib/libgenomethreader.a \
 -                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
-+                                $(GTHLIBS) /usr/lib/libgenometools.a))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthconsensus, obj/src/gthconsensus.o \
                                  lib/libgenomethreader.a \
 -                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
-+                                $(GTHLIBS) /usr/lib/libgenometools.a))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthbssmfileinfo, obj/src/gthbssmfileinfo.o \
                                  lib/libgenomethreader.a \
 -                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
-+                                /usr/lib/libgenometools.a $(GTHLIBS)))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthbssmbuild, obj/src/gthbssmbuild.o \
                                  lib/libgenomethreader.a \
 -                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
-+                                /usr/lib/libgenometools.a $(GTHLIBS)))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthbssmprint, obj/src/gthbssmprint.o \
                                  lib/libgenomethreader.a \
 -                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
-+                                /usr/lib/libgenometools.a $(GTHLIBS)))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthbssmrmsd, obj/src/gthbssmrmsd.o \
                                  lib/libgenomethreader.a \
 -                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
-+                                /usr/lib/libgenometools.a $(GTHLIBS)))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthbssmtrain, obj/src/gthbssmtrain.o \
                                  lib/libgenomethreader.a \
 -                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
-+                                /usr/lib/libgenometools.a $(GTHLIBS)))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthfilestat, obj/src/gthfilestat.o \
                                  lib/libgenomethreader.a \
 -                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
-+                                $(GTHLIBS) /usr/lib/libgenometools.a))
++                                $(GTHLIBS)))
+ 
+ $(eval $(call PROGRAM_template, bin/gthmkbssmfiles, obj/src/gthmkbssmfiles.o \
+                                 lib/libgenomethreader.a \
+-                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthsplit, obj/src/gthsplit.o \
                                  lib/libgenomethreader.a \
 -                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
-+                                $(GTHLIBS) /usr/lib/libgenometools.a))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthunit, obj/src/gthunit.o \
                                  lib/libgenomethreader.a \
 -                                $(GTHLIBS) ../genometools/lib/libgenometools.a))
-+                                $(GTHLIBS) /usr/lib/libgenometools.a))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/gthgetseq, obj/src/gthgetseq.o \
                                  lib/libgenomethreader.a \
 -                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
-+                                /usr/lib/libgenometools.a $(GTHLIBS)))
++                                $(GTHLIBS)))
  
  $(eval $(call PROGRAM_template, bin/align_dna, obj/src/align_dna.o \
                                  lib/libgenomethreader.a \
 -                                ../genometools/lib/libgenometools.a $(GTHLIBS)))
-+                                /usr/lib/libgenometools.a $(GTHLIBS)))
++                                $(GTHLIBS)))
  
 -bin/rnv: $(RNVMAIN_OBJ) lib/librnv.a ../genometools/lib/libexpat.a
 -	@echo "[link $(@F)]"
@@ -130,7 +136,7 @@
  
  obj/gth_config.h: VERSION
  	@echo '[create $@]'
-@@ -310,9 +307,9 @@
+@@ -321,9 +318,9 @@
  $(1): $(2)
  	@echo "[compile $$(@F)]"
  	@test -d $$(@D) || mkdir -p $$(@D)
@@ -142,7 +148,7 @@
          $(3) -MM -MP -MT $$@
  endef
  
-@@ -321,17 +318,17 @@
+@@ -332,17 +329,17 @@
  obj/%.o: %.cxx
  	@echo "[compile $(@F)]"
  	@test -d $(@D) || mkdir -p $(@D)
@@ -164,15 +170,3 @@
  	  -MT $@
  
  obj/src/core/versionfunc.o: obj/gth_config.h
-@@ -508,9 +505,9 @@
-                           -gtdonor -agacceptor -gzip
- 	@touch $@
- 
--obj/old_train: ../genometools/bin/gt
-+obj/old_train:
- 	@echo "[write old BSSMs]"
--	@../genometools/bin/gt dev gthmkbssmfiles bin/bssm
-+	@gt dev gthmkbssmfiles bin/bssm
- 	@touch $@
- 
- obj/gthdata:

debian/patches/headers-api.patch

+--- a/src/gth/bssm_helper.c
++++ b/src/gth/bssm_helper.c
+@@ -14,7 +14,7 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/alphabet.h"
++#include "core/alphabet_api.h"
+ #include "core/grep_api.h"
+ #include "gth/bssm_helper.h"
+ 
+--- a/src/gth/bssm_train_visitor.c
++++ b/src/gth/bssm_train_visitor.c
+@@ -14,13 +14,13 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/alphabet.h"
++#include "core/alphabet_api.h"
+ #include "core/cstr_api.h"
+ #include "core/ma_api.h"
+ #include "core/warning_api.h"
+ #include "core/xansi_api.h"
+ #include "extended/feature_node_iterator_api.h"
+-#include "extended/feature_type.h"
++#include "extended/feature_type_api.h"
+ #include "extended/node_visitor_api.h"
+ #include "extended/reverse_api.h"
+ #include "gth/bssm_helper.h"
+--- a/src/gth/dp_param.h
++++ b/src/gth/dp_param.h
+@@ -18,7 +18,7 @@
+ #ifndef DP_PARAM_H
+ #define DP_PARAM_H
+ 
+-#include "core/alphabet.h"
++#include "core/alphabet_api.h"
+ #include "gth/gthchain.h"
+ #include "gth/splice_site_model.h"
+ 
+--- a/src/gth/seq_con.h
++++ b/src/gth/seq_con.h
+@@ -17,7 +17,7 @@
+ #ifndef SEQ_CON_H
+ #define SEQ_CON_H
+ 
+-#include "core/alphabet.h"
++#include "core/alphabet_api.h"
+ #include "core/file_api.h"
+ #include "core/range_api.h"
+ #include "core/str_api.h"
+--- a/src/gth/bssm_train_stream.c
++++ b/src/gth/bssm_train_stream.c
+@@ -14,7 +14,7 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "extended/genome_node.h"
++#include "extended/genome_node_api.h"
+ #include "extended/node_stream_api.h"
+ #include "gth/bssm_train_stream.h"
+ #include "gth/bssm_train_visitor.h"
+--- a/src/gth/gff3_pgl_visitor.c
++++ b/src/gth/gff3_pgl_visitor.c
+@@ -16,9 +16,9 @@
+ */
+ 
+ #include "core/unused_api.h"
+-#include "extended/cds_visitor.h"
+-#include "extended/feature_type.h"
+-#include "extended/genome_node.h"
++#include "extended/cds_visitor_api.h"
++#include "extended/feature_type_api.h"
++#include "extended/genome_node_api.h"
+ #include "gth/ags.h"
+ #include "gth/gff3_pgl_visitor.h"
+ #include "gth/pgl_visitor_rep.h"
+--- a/src/gth/gff3_sa_visitor.c
++++ b/src/gth/gff3_sa_visitor.c
+@@ -16,8 +16,8 @@
+ */
+ 
+ #include "core/unused_api.h"
+-#include "extended/feature_type.h"
+-#include "extended/genome_node.h"
++#include "extended/feature_type_api.h"
++#include "extended/genome_node_api.h"
+ #include "gth/gff3_sa_visitor.h"
+ #include "gth/sa_visitor_rep.h"
+ #include "gth/region_factory.h"
+--- a/src/gth/gt_gthbssmtrain.c
++++ b/src/gth/gt_gthbssmtrain.c
+@@ -15,19 +15,19 @@
+ */
+ 
+ #include "core/compat_api.h"
+-#include "core/cstr_array.h"
++#include "core/cstr_array_api.h"
+ #include "core/ma_api.h"
+-#include "core/output_file.h"
++#include "core/output_file_api.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
+-#include "core/yarandom.h"
++#include "core/yarandom_api.h"
+ #include "core/warning_api.h"
+ #include "extended/add_introns_stream_api.h"
+-#include "extended/buffer_stream.h"
+-#include "extended/feature_type.h"
++#include "extended/buffer_stream_api.h"
++#include "extended/feature_type_api.h"
+ #include "extended/gff3_in_stream_api.h"
+-#include "extended/seqid2file.h"
+-#include "extended/splice_site_info_stream.h"
++#include "extended/seqid2file_api.h"
++#include "extended/splice_site_info_stream_api.h"
+ #include "gth/bssm_train_stream.h"
+ #include "gth/gt_gthbssmtrain.h"
+ 
+--- a/src/gth/pgl_collection.c
++++ b/src/gth/pgl_collection.c
+@@ -15,10 +15,10 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/parseutils.h"
++#include "core/parseutils_api.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
+-#include "extended/consensus_sa.h"
++#include "extended/consensus_sa_api.h"
+ #include "gth/ags_build.h"
+ #include "gth/pgl_collection.h"
+ #include "gth/gthcluster.h"
+--- a/src/gth/sa.c
++++ b/src/gth/sa.c
+@@ -15,12 +15,12 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/mathsupport.h"
+-#include "core/md5_seqid.h"
++#include "core/mathsupport_api.h"
++#include "core/md5_seqid_api.h"
+ #include "core/safearith_api.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
+-#include "extended/gff3_escaping.h"
++#include "extended/gff3_escaping_api.h"
+ #include "gth/default.h"
+ #include "gth/sa.h"
+ #include "gth/txt_sa_visitor.h"
+--- a/src/gth/gthchain.h
++++ b/src/gth/gthchain.h
+@@ -21,7 +21,7 @@
+ #include "core/array_api.h"
+ #include "core/file_api.h"
+ #include "core/range_api.h"
+-#include "extended/globalchaining.h"
++#include "extended/globalchaining_api.h"
+ #include "gth/jump_table.h"
+ #include "gth/stat.h"
+ 
+--- a/src/gth/jump_table.h
++++ b/src/gth/jump_table.h
+@@ -18,7 +18,7 @@
+ #define JUMP_TABLE_H
+ 
+ #include "core/range_api.h"
+-#include "extended/globalchaining.h"
++#include "extended/globalchaining_api.h"
+ 
+ typedef struct {
+   GtRange gen_range,
+--- a/src/gth/sa_collection.c
++++ b/src/gth/sa_collection.c
+@@ -16,7 +16,7 @@
+ */
+ 
+ #include "core/unused_api.h"
+-#include "extended/rbtree.h"
++#include "extended/rbtree_api.h"
+ #include "gth/sa_cmp.h"
+ #include "gth/sa_collection.h"
+ 
+--- a/src/gth/input.c
++++ b/src/gth/input.c
+@@ -19,11 +19,11 @@
+ #include <math.h>
+ #include "core/compat_api.h"
+ #include "core/fileutils_api.h"
+-#include "core/md5_seqid.h"
++#include "core/md5_seqid_api.h"
+ #include "core/safearith_api.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
+-#include "extended/regular_seqid.h"
++#include "extended/regular_seqid_api.h"
+ #include "gth/default.h"
+ #include "gth/desc_cache.h"
+ #include "gth/gthdef.h"
+--- a/src/gth/dp_scores_protein.c
++++ b/src/gth/dp_scores_protein.c
+@@ -15,8 +15,8 @@
+ */
+ 
+ #include "core/array2dim_api.h"
+-#include "core/array3dim.h"
+-#include "core/trans_table.h"
++#include "core/array3dim_api.h"
++#include "core/trans_table_api.h"
+ #include "core/unused_api.h"
+ #include "gth/align_common.h"
+ #include "gth/dp_scores_protein.h"
+--- a/src/gth/gthalignment.h
++++ b/src/gth/gthalignment.h
+@@ -20,9 +20,9 @@
+ #define GTHALIGNMENT_H
+ 
+ #include <stdio.h>
+-#include "core/arraydef.h"
++#include "core/arraydef_api.h"
+ #include "core/file_api.h"
+-#include "core/score_matrix.h"
++#include "core/score_matrix_api.h"
+ #include "gth/editoperation.h"
+ 
+ #define CONCRETEINTRONSYMBOL    '.'
+--- a/src/gth/bssm_param.c
++++ b/src/gth/bssm_param.c
+@@ -17,7 +17,7 @@
+ */
+ 
+ #include "lauxlib.h"
+-#include "core/bioseq.h"
++#include "core/bioseq_api.h"
+ #include "core/compat_api.h"
+ #include "core/fa_api.h"
+ #include "core/fileutils_api.h"
+--- a/src/gth/dp_param.c
++++ b/src/gth/dp_param.c
+@@ -16,7 +16,7 @@
+ */
+ 
+ #include <math.h>
+-#include "core/chardef.h"
++#include "core/chardef_api.h"
+ #include "core/ma_api.h"
+ #include "core/range_api.h"
+ #include "core/safearith_api.h"
+--- a/src/gth/dp_scores_protein.h
++++ b/src/gth/dp_scores_protein.h
+@@ -17,8 +17,8 @@
+ #ifndef DP_SCORES_PROTEIN_H
+ #define DP_SCORES_PROTEIN_H
+ 
+-#include "core/chardef.h"
+-#include "core/score_matrix.h"
++#include "core/chardef_api.h"
++#include "core/score_matrix_api.h"
+ #include "gth/bssm_param.h"
+ 
+ typedef struct {
+--- a/src/gth/gthalignment.c
++++ b/src/gth/gthalignment.c
+@@ -20,7 +20,7 @@
+ #include <stdlib.h>
+ #include <ctype.h>
+ #include <math.h>
+-#include "core/chardef.h"
++#include "core/chardef_api.h"
+ #include "core/codon_api.h"
+ #include "core/minmax_api.h"
+ #include "core/translator_api.h"
+--- a/src/gth/gthsplicesitescr.c
++++ b/src/gth/gthsplicesitescr.c
+@@ -15,7 +15,7 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/chardef.h"
++#include "core/chardef_api.h"
+ #include "core/minmax_api.h"
+ #include "core/unused_api.h"
+ #include "gth/gthsplicesitescr.h"
+--- a/src/gth/xml_final_sa_visitor.c
++++ b/src/gth/xml_final_sa_visitor.c
+@@ -15,7 +15,7 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/chardef.h"
++#include "core/chardef_api.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
+ #include "gth/indent.h"
+--- a/src/gth/seq_con.c
++++ b/src/gth/seq_con.c
+@@ -14,7 +14,7 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/class_alloc.h"
++#include "core/class_alloc_api.h"
+ #include "core/ma_api.h"
+ #include "core/unused_api.h"
+ #include "gth/seq_con_rep.h"
+--- a/src/gth/run_header.c
++++ b/src/gth/run_header.c
+@@ -15,7 +15,7 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/cstr_array.h"
++#include "core/cstr_array_api.h"
+ #include "gth/indent.h"
+ #include "gth/showbool.h"
+ #include "gth/time.h"
+--- a/src/gth/bssm_seq_processor.c
++++ b/src/gth/bssm_seq_processor.c
+@@ -21,13 +21,13 @@
+ #include "core/fasta_api.h"
+ #include "core/file_api.h"
+ #include "core/fileutils_api.h"
+-#include "core/output_file.h"
++#include "core/output_file_api.h"
+ #include "core/ma_api.h"
+-#include "core/mathsupport.h"
++#include "core/mathsupport_api.h"
+ #include "core/minmax_api.h"
+ #include "core/str_api.h"
+ #include "core/unused_api.h"
+-#include "core/xposix.h"
++#include "core/xposix_api.h"
+ #include "extended/reverse_api.h"
+ #include "gth/bssm_helper.h"
+ #include "gth/bssm_seq_processor.h"
+--- a/src/gth/md5_cache.c
++++ b/src/gth/md5_cache.c
+@@ -15,8 +15,8 @@
+ */
+ 
+ #include "core/ma_api.h"
+-#include "core/md5_tab.h"
+-#include "core/str_cache.h"
++#include "core/md5_tab_api.h"
++#include "core/str_cache_api.h"
+ #include "gth/gthdef.h"
+ #include "gth/md5_cache.h"
+ 
+--- a/src/gth/gthorf.c
++++ b/src/gth/gthorf.c
+@@ -16,8 +16,8 @@
+ */
+ 
+ #include "core/codon_api.h"
+-#include "core/orf.h"
+-#include "core/trans_table.h"
++#include "core/orf_api.h"
++#include "core/trans_table_api.h"
+ #include "core/unused_api.h"
+ #include "gth/gthorf.h"
+ #include "gth/gthstopcodon.h"
+--- a/src/gth/input.h
++++ b/src/gth/input.h
+@@ -18,10 +18,10 @@
+ #ifndef INPUT_H
+ #define INPUT_H
+ 
+-#include "core/array.h"
++#include "core/array_api.h"
+ #include "core/range_api.h"
+-#include "core/score_matrix.h"
+-#include "core/str_array.h"
++#include "core/score_matrix_api.h"
++#include "core/str_array_api.h"
+ #include "gth/duplicate_check.h"
+ #include "gth/gthoutput.h"
+ #include "gth/gthalphatype.h"
+--- a/src/gth/desc_cache.c
++++ b/src/gth/desc_cache.c
+@@ -15,7 +15,7 @@
+ */
+ 
+ #include "core/ma_api.h"
+-#include "core/str_cache.h"
++#include "core/str_cache_api.h"
+ #include "gth/desc_cache.h"
+ 
+ struct GthDescCache {
+--- a/src/gth/gt_gthbssmbuild.c
++++ b/src/gth/gt_gthbssmbuild.c
+@@ -37,7 +37,7 @@
+ */
+ 
+ #include "core/option_api.h"
+-#include "core/versionfunc.h"
++#include "core/versionfunc_api.h"
+ #include "gth/bssm_param.h"
+ #include "gth/gt_gthbssmbuild.h"
+ 
+--- a/src/gth/gt_gthbssmfileinfo.c
++++ b/src/gth/gt_gthbssmfileinfo.c
+@@ -16,7 +16,7 @@
+ */
+ 
+ #include "core/option_api.h"
+-#include "core/versionfunc.h"
++#include "core/versionfunc_api.h"
+ #include "gth/bssm_param.h"
+ #include "gth/gt_gthbssmfileinfo.h"
+ 
+--- a/src/gth/gt_gthbssmprint.c
++++ b/src/gth/gt_gthbssmprint.c
+@@ -27,7 +27,7 @@
+ */
+ 
+ #include "core/option_api.h"
+-#include "core/versionfunc.h"
++#include "core/versionfunc_api.h"
+ #include "gth/bssm_param.h"
+ #include "gth/gt_gthbssmprint.h"
+ 
+--- a/src/gth/gt_gthmkbssmfiles.c
++++ b/src/gth/gt_gthmkbssmfiles.c
+@@ -18,7 +18,7 @@
+ 
+ #include "core/compat_api.h"
+ #include "core/option_api.h"
+-#include "core/versionfunc.h"
++#include "core/versionfunc_api.h"
+ #include "gth/bssm_param.h"
+ #include "gth/gthspeciestab.h" /* XXX */
+ #include "gth/gt_gthmkbssmfiles.h"
+--- a/src/gth/ags.h
++++ b/src/gth/ags.h
+@@ -18,7 +18,7 @@
+ #ifndef AGS_H
+ #define AGS_H
+ 
+-#include "core/array.h"
++#include "core/array_api.h"
+ #include "core/error_api.h"
+ #include "gth/gthoutput.h"
+ #include "gth/bssm_param.h"
+--- a/src/gth/call_info.h
++++ b/src/gth/call_info.h
+@@ -18,7 +18,7 @@
+ #ifndef CALL_INFO_H
+ #define CALL_INFO_H
+ 
+-#include "core/array.h"
++#include "core/array_api.h"
+ #include "gth/gthoutput.h"
+ #include "gth/dp_options_core.h"
+ #include "gth/dp_options_est.h"
+--- a/src/gth/gthcluster.h
++++ b/src/gth/gthcluster.h
+@@ -18,7 +18,7 @@
+ #ifndef GTHCLUSTER_H
+ #define GTHCLUSTER_H
+ 
+-#include "core/array.h"
++#include "core/array_api.h"
+ #include "gth/pgl.h"
+ #include "gth/sa_collection.h"
+ 
+--- a/src/gth/gthsortags.h
++++ b/src/gth/gthsortags.h
+@@ -18,7 +18,7 @@
+ #ifndef GTHSORTAGS_H
+ #define GTHSORTAGS_H
+ 
+-#include "core/array.h"
++#include "core/array_api.h"
+ 
+ /* The following function sorts the AGSs of every PGL contained in <pgls>
+    according to the weighted mean of the average exon score and the average
+--- a/src/gth/pgl.h
++++ b/src/gth/pgl.h
+@@ -18,7 +18,7 @@
+ #ifndef PGL_H
+ #define PGL_H
+ 
+-#include "core/array.h"
++#include "core/array_api.h"
+ #include "core/error_api.h"
+ #include "extended/node_visitor_api.h"
+ #include "gth/sa.h"
+--- a/src/gth/sa.h
++++ b/src/gth/sa.h
+@@ -18,11 +18,11 @@
+ #ifndef SA_H
+ #define SA_H
+ 
+-#include "core/array.h"
++#include "core/array_api.h"
+ #include "core/error_api.h"
+ #include "core/file_api.h"
+ #include "core/str_api.h"
+-#include "core/strand.h"
++#include "core/strand_api.h"
+ #include "gth/backtrace_path.h"
+ #include "gth/bssm_param.h"
+ #include "gth/gthalphatype.h"
+--- a/src/gth/ags_build.h
++++ b/src/gth/ags_build.h
+@@ -18,7 +18,7 @@
+ #ifndef AGS_BUILD_H
+ #define AGS_BUILD_H
+ 
+-#include "core/bittab.h"
++#include "core/bittab_api.h"
+ #include "gth/ags.h"
+ #include "gth/pgl.h"
+ 
+--- a/src/gth/region_factory.c
++++ b/src/gth/region_factory.c
+@@ -15,11 +15,11 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/cstr_table.h"
++#include "core/cstr_table_api.h"
+ #include "core/basename_api.h"
+ #include "core/ma_api.h"
+ #include "core/hashmap_api.h"
+-#include "core/parseutils.h"
++#include "core/parseutils_api.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
+ #include "gth/region_factory.h"
+--- a/src/gth/gthtrans.c
++++ b/src/gth/gthtrans.c
+@@ -18,7 +18,7 @@
+ #include "core/codon_api.h"
+ #include "core/codon_iterator_simple_api.h"
+ #include "core/translator_api.h"
+-#include "core/trans_table.h"
++#include "core/trans_table_api.h"
+ #include "core/unused_api.h"
+ #include "gth/gthstopcodon.h"
+ #include "gth/indent.h"
+--- a/src/gth/similarity_filter.c
++++ b/src/gth/similarity_filter.c
+@@ -15,7 +15,7 @@
+   OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+ */
+ 
+-#include "core/trans_table.h"
++#include "core/trans_table_api.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
+ #include "core/warning_api.h"
+--- a/src/gth/bssm_train_visitor.h
++++ b/src/gth/bssm_train_visitor.h
+@@ -20,7 +20,7 @@
+ /* Implements the ``genome visitor'' interface. */
+ typedef struct GthBSSMTrainVisitor GthBSSMTrainVisitor;
+ 
+-#include "extended/node_visitor.h"
++#include "extended/node_visitor_api.h"
+ #include "extended/region_mapping_api.h"
+ #include "gth/bssm_seq_processor.h"
+ 

debian/patches/series

 debian-gt-libs.patch
 gt-path-fix.patch
+headers-api.patch

doc/gthmanual/Makefile

@@ -13,8 +13,7 @@ ISPELLALL=author.ispell\
           speciestable.ispell
 
 all: ispellall\
-     gthmanual.pdf\
-     gthlicense.pdf
+     gthmanual.pdf
 
 ${GTHMANUALTMP}.tex: gthmanual.tex execcommand.pl
 	#findemptyoutfiles.sh

doc/gthmanual/gthlicense.tex

-\documentclass[12pt]{article}
-\usepackage{times,url,a4wide,xspace}
-\parindent0pt
-\parskip5pt
-
-\newcommand{\Software}[0]{\emph{GenomeThreader}\xspace}
-\newcommand{\Licensorname}[0]{\emph{Gordon Gremme, Universit\"at Hamburg}\xspace}
-\newcommand{\Thepaper}[0]{web-site: \par\url{http://www.genomethreader.org}\xspace}
-\newcommand{\Email}[0]{\texttt{\small gordon@gremme.org}\xspace}
-\newcommand{\Persontocontact}[0]{Gordon Gremme\xspace}
-\newcommand{\Noncommercial}[0]{\\{\normalsize for non-commerical users}}
-
-\newcommand{\Licensor}[0]{\textsc{Licensor}\xspace}
-\newcommand{\Licensee}[0]{\textsc{Licensee}\xspace}
-\newcommand{\Agreement}[0]{\textsc{Agreement}\xspace}
-\newcommand{\Sites}[0]{\textsc{Sites}\xspace}
-\newcommand{\Fillline}[0]{\rule{10cm}{1pt}}
-\newcommand{\Paragraph}[2]{\item \textbf{#1:} #2}
-
-\title{\Software License Agreement\Noncommercial}
-\author{\vspace*{-1cm}}
-\date{\vspace*{-1cm}\today}
-\begin{document}
-\maketitle
-
-This document is the license agreement for the \Software Software Package.
-There is no distribution fee for \Software for non commercial research
-institutions. Commercial research institutions who want to use \Software
-should directly contact \Persontocontact via Email at
-\begin{center}
-\Email
-\end{center}
-
-\Licensorname (\Licensor), as sole holder of all the proprietary rights to 
-\Software grants to the licensee as defined in paragraph \ref{DefSites}
-(\Licensee) a perpetual, non-exclusive, non-assignable, personal 
-license to use the proprietary \Software software, subject to 
-the conditions set forth below.
-
-\begin{enumerate}
-
-\Paragraph{Restricted License}{Use of \Software, or any part 
-thereof, or any software derived in whole or in part therefrom, is 
-restricted to use by \Licensee only, and is limited to the following 
-uses unless \Licensor agrees otherwise by prior written agreement.
-}
-
-\begin{itemize}
-\item
-\Licensee is authorized to use \Software on all computers 
-at the separate geographic locations itemized in paragraph \ref{DefSites} below 
-(the \Sites) and at no other locations. The \Sites must include all 
-locations from which remote (telephone or network) access will be 
-made.
-\item
-\Licensee may not copy \Software, or any part thereof in 
-any form, except for backup or archiving purposes, and for the 
-purpose of distributing it to computers at the given \Sites. \Licensee 
-agrees not to remove or destroy any proprietary markings or 
-confidential legends placed upon or contained within \Software 
-and any related materials.
-\item
-\Licensee may not sell, rent, sublicense, or otherwise distribute 
-in any manner whatsoever \Software, or any part thereof, or 
-any software derived in whole or in part therefrom, without the prior 
-written approval of \Licensor.
-\end{itemize}
-
-\Paragraph{Title}{The \Agreement grants \Licensee no title or right of 
-ownership in \Software, and no property rights in any 
-copyrighted materials delivered hereunder.
-}
-
-\Paragraph{Non-Disclosure}{\Licensee agrees to receive and keep 
-\Software in confidence and not to disclose it to any third 
-party without the express written consent of \Licensor.
-}
-
-\Paragraph{Proper Credit and Recognition}{Appropriate credits consist 
-of including in any documentation and publications about research 
-using \Software a reference to the following \Thepaper
-}
-
-\Paragraph{Disclaimer of Warranty}{\Licensor provides \Software 
-on an \textbf{as is} basis. \Licensor does not warrant its validity of 
-performance, efficiency, or suitability, nor does \Licensor warrant 
-that \Software is free from errors. All warranties, 
-including without limitation, any warranty or merchantability or 
-fitness for a particular purpose, are hereby excluded.
-}
-
-\Paragraph{Lack of Maintenance Services}{\Licensee understands and 
-agrees that \Licensor (or any other person or entity with proprietary 
-rights in the software licensed hereunder) is under no obligation to 
-provide either maintenance services, update services, notices of 
-latent defects, or correction of defects for \Software. 
-\Licensor nevertheless reserves the right to update, modify, or 
-discontinue this software at any time.
-}
-
-\Paragraph{Limitation of Liability, Indemnification}{Even if advised 
-of the possibility of such damages, under no circumstances shall 
-\Licensor (or any other person or entity with proprietary rights in 
-the software licensed hereunder) be liable to \Licensee or any third 
-party for direct, indirect, or consequential damages of any 
-character, including, without limitation, loss of profits, loss of 
-use, loss of good will, or computer failure or malfunction, 
-regardless of the nature of the claim or action, whether in 
-negligence or other tort, breach of contract, product liability, or 
-otherwise. \Licensee agrees to indemnify \Licensor (or any other person 
-or entity with proprietary rights in the software licensed hereunder) 
-for any and all liability it may incur to third parties resulting 
-from \Licensee's use of 
-\Software.
-%\Software, subject to the limits of Florida law.
-
-}
-
-\Paragraph{Applicable Law}{This \Agreement is deemed to be made under, 
-and shall be governed by the laws of the Federal Republic of Germany. 
-Both parties consent to jurisdiction in the Federal Republic of Germany.
-German law applies to this \Agreement without giving effect to its 
-conflict of laws (IPR) provisions. 
-}
-
-\Paragraph{Binding Effect Agreement}{This \Agreement shall be binding 
-upon and inure to the benefit of the heirs, successors and assigns of 
-\Licensee, but \Licensee may not assign this \Agreement or any of its 
-rights or obligations hereunder without the prior written approval of 
-\Licensor.
-}
-
-\Paragraph{Entire Agreement}{This \Agreement represents the complete 
-and exclusive statement of the agreements between the parties 
-relating to the licensing of \Software, and supersedes all 
-prior and simultaneous agreements and representations between them 
-relating to such licensing. This \Agreement may not be modified except 
-with the written approval of the \Licensor.
-}
-
-\newpage
-
-\Paragraph{Definition of Sites}{
-The separate geographical locations 
-referred to as \Sites are listed below:
-
-\begin{center}
-\begin{tabular}{ll}
-1.&\Fillline\\[5mm]
-2.&\Fillline\\[5mm]
-3.&\Fillline
-\end{tabular}
-\end{center}
-}
-\label{DefSites}
-
-\Paragraph{Mailing Address}{A signed copy of this license \Agreement
-shall be mailed or sent as a FAX by \Licensee to \Licensor at the 
-following address:
-
-\begin{tabular}{@{}l}
-\Persontocontact\\
-Zentrum f\"ur Bioinformatik\\
-Universit\"at Hamburg\\
-Bundesstrasse 43\\
-20146 Hamburg\\
-Germany\\
-FAX: +49 40 42838 7312
-\end{tabular}
-
-An Email describing how to download \Software shall be send by \Licensor to 
-\Licensee to the following Email address:
-
-\begin{center}
-\begin{tabular}{lc}
-Electronic Mail:&\Fillline\\[5mm]
-Name:&\Fillline
-\end{tabular}
-\end{center}
-
-In previous cases, we had problems with our FAX machine or could not
-decipher the E-mail address of the \Licensor.
-To verify that we have received the FAX properly, you may want send a 
-short E-mail to \Email stating that you have send the FAX. 
-Once we have received the signed agreement we will process it a soon as 
-possible. 
-}
-
-\Paragraph{Execution and Delivery}{By its execution and delivery of 
-this \Agreement, \Licensee covenants and agrees to be bound by the 
-above stated terms and conditions, and warrants and represents that 
-the person or persons signing this Licensing \Agreement is authorized 
-to bind and commit \Licensee to this \Agreement.
-}
-
-\end{enumerate}
-
-\begin{center}
-\begin{tabular}{lc}
-Research Institution:&\Fillline\\[5mm]
-Address:&\Fillline\\[5mm]
-Signature:&\Fillline\\[5mm]
-Name and Title:&\Fillline\\[5mm]
-Date:&\Fillline
-\end{tabular}
-\end{center}
-
-\end{document}

gthdata/README

 This directory contains the binary distribution of GenomeThreader (gth).
-All rights reserved. Do not distribute.
 
 It contains the following directories
 

src/align_dna.c

-#include "core/tooldriver.h"
+#include "core/tooldriver_api.h"
 #include "libgenomethreader/gt_align_dna.h"
 #include "libgenomethreader/gthversionfunc.h"
 

src/gth.c

 #include "gth_config.h"
-#include "core/tooldriver.h"
+#include "core/tooldriver_api.h"
 #include "gth/gt_gth.h"
 #include "libgenomethreader/gthpre.h"
 #include "libgenomethreader/gthversionfunc.h"

src/gth/ags.c

+/*
+  Copyright (c) 2004-2009 Gordon Gremme <gordon@gremme.org>
+  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg
+
+  Permission to use, copy, modify, and distribute this software for any
+  purpose with or without fee is hereby granted, provided that the above
+  copyright notice and this permission notice appear in all copies.
+
+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+*/
+
+#include "gth/ags.h"
+
+struct GthAGSObject {
+  const GthPGL *pgl;
+};
+
+GthAGS* gth_ags_new(const GthPGL *pgl)
+{
+  GthAGS *ags;
+  gt_assert(pgl);
+
+  ags = gt_malloc(sizeof *ags);
+  ags->agso = gt_malloc(sizeof *ags->agso);
+  ags->agso->pgl = pgl;
+
+  ags->gen_id = NULL;
+
+  ags->exons = gt_array_new(sizeof (GthExonAGS));
+  ags->splicesiteprobs = gt_array_new(sizeof (GthSpliceSiteProb));
+  ags->alignments = gt_array_new(sizeof (GthSA*));
+
+  ags->numofstoredsaclusters = 0;
+  ags->overallscore = GTH_UNDEF_GTHDBL;
+
+  return ags;
+}
+
+void gth_ags_delete(GthAGS *ags)
+{
+  if (!ags) return;
+  gt_str_delete(ags->gen_id);
+  gt_array_delete(ags->exons);
+  gt_array_delete(ags->splicesiteprobs);
+  gt_array_delete(ags->alignments);
+  gt_free(ags->agso);
+  gt_free(ags);
+}
+
+bool gth_ags_is_forward(const GthAGS *ags)
+{
+  gt_assert(ags);
+  return gth_pgl_is_forward(ags->agso->pgl);
+}
+
+GtUword gth_ags_filenum(const GthAGS *ags)
+{
+  gt_assert(ags);
+  return gth_pgl_filenum(ags->agso->pgl);
+}
+
+GtUword gth_ags_total_length(const GthAGS *ags)
+{
+  gt_assert(ags);
+  return gth_pgl_total_length(ags->agso->pgl);
+}
+
+GtUword gth_ags_genomic_offset(const GthAGS *ags)
+{
+  gt_assert(ags);
+  return gth_pgl_genomic_offset(ags->agso->pgl);
+}
+
+GtStr* gth_ags_get_gen_id(const GthAGS *ags)
+{
+  gt_assert(ags && ags->gen_id);
+  return ags->gen_id;
+}
+
+GthExonAGS* gth_ags_get_exon(const GthAGS *ags, GtUword exon)
+{
+  gt_assert(ags && ags->exons);
+  gt_assert(exon < gt_array_size(ags->exons));
+  return gt_array_get(ags->exons, exon);
+}
+
+GtUword gth_ags_num_of_exons(const GthAGS *ags)
+{
+  gt_assert(ags && ags->exons);
+  return gt_array_size(ags->exons);
+}
+
+GtStrand gth_ags_genomic_strand(const GthAGS *ags)
+{
+  gt_assert(ags);
+  return gth_ags_is_forward(ags) ? GT_STRAND_FORWARD : GT_STRAND_REVERSE;
+}
+
+static GtUword gth_ags_left_intron_border(const GthAGS *ags,
+                                            GtUword intron)
+{
+  GthExonAGS *exon;
+  gt_assert(ags);
+  exon = gth_ags_get_exon(ags, intron);
+  return SHOWGENPOSAGS(exon->range.end + 1);
+}
+
+static GtUword gth_ags_right_intron_border(const GthAGS *ags,
+                                             GtUword intron)
+{
+  GthExonAGS *exon;
+  gt_assert(ags);
+  exon = gth_ags_get_exon(ags, intron + 1);
+  return SHOWGENPOSAGS(exon->range.start - 1);
+}
+
+GtRange gth_ags_donor_site_range(const GthAGS *ags, GtUword intron)
+{
+  GtRange range;
+  gt_assert(ags);
+  range.start = gth_ags_left_intron_border(ags, intron);
+  range.end = range.start + 1;
+  return range;
+}
+
+GtRange gth_ags_acceptor_site_range(const GthAGS *ags, GtUword intron)
+{
+  GtRange range;
+  gt_assert(ags);
+  range.end = gth_ags_right_intron_border(ags, intron);
+  range.start = range.end - 1;
+  return range;
+}
+
+double gth_ags_donor_site_prob(const GthAGS *ags, GtUword intron)
+{
+  gt_assert(ags);
+  return ((GthSpliceSiteProb*) gt_array_get(ags->splicesiteprobs, intron))
+         ->donorsiteprob;
+}
+
+double gth_ags_acceptor_site_prob(const GthAGS *ags, GtUword intron)
+{
+  gt_assert(ags);
+  return ((GthSpliceSiteProb*) gt_array_get(ags->splicesiteprobs, intron))
+         ->acceptorsiteprob;
+}

src/gth/ags.h

+/*
+  Copyright (c) 2003-2009 Gordon Gremme <gordon@gremme.org>
+  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg
+
+  Permission to use, copy, modify, and distribute this software for any
+  purpose with or without fee is hereby granted, provided that the above
+  copyright notice and this permission notice appear in all copies.
+
+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+*/
+
+#ifndef AGS_H
+#define AGS_H
+
+#include "core/array.h"
+#include "core/error_api.h"
+#include "gth/gthoutput.h"
+#include "gth/bssm_param.h"
+#include "gth/pgl.h"
+#include "gth/sa.h"
+
+#define SHOWGENPOSAGS(P)\
+        SHOWGENPOS(gth_ags_is_forward(ags), gth_ags_total_length(ags),\
+                   gth_ags_genomic_offset(ags), P)
+
+typedef struct {
+  GtRange range; /* the borders of the exon in the genomic sequence */
+  GthDbl score;
+} GthExonAGS;
+
+typedef struct {
+  GthFlt donorsiteprob,
+         acceptorsiteprob;
+} GthSpliceSiteProb;
+
+typedef struct GthAGSObject GthAGSObject;
+
+/* the alternative gene structure (AGS) class */
+typedef struct GthAGS {
+  GtStr *gen_id;                 /* the id of the genomic sequence this two
+                                    values could also be included in the PGL
+                                    structure, but including them here is better
+                                    for the stand alone version of the assemble
+                                    program */
+  GtArray *exons,                /* contains the actual structure of the AGS and
+                                    the exonscores */
+          *splicesiteprobs,      /* contains the splice site probabilities */
+          *alignments;           /* pointer to the generating spliced alignments
+                                    I.e., the alignments which constitute this
+                                    alternative gene structure. */
+  GtUword numofstoredsaclusters; /* number of stored SA clusters */
+                                 /* (needed in assembly phase) */
+  GthDbl overallscore; /* overall score used for sorting of AGSs */
+
+  GthAGSObject *agso;
+} GthAGS;
+
+GthAGS*       gth_ags_new(const GthPGL*);
+void          gth_ags_delete(GthAGS*);
+bool          gth_ags_is_forward(const GthAGS*);
+GtUword gth_ags_filenum(const GthAGS*);
+GtUword gth_ags_total_length(const GthAGS*);
+GtUword gth_ags_genomic_offset(const GthAGS*);
+GtStr*        gth_ags_get_gen_id(const GthAGS*);
+GthExonAGS*   gth_ags_get_exon(const GthAGS *ags, GtUword exon);
+GtUword gth_ags_num_of_exons(const GthAGS *ags);
+GtStrand      gth_ags_genomic_strand(const GthAGS*);
+GtRange       gth_ags_donor_site_range(const GthAGS*, GtUword intron);
+GtRange       gth_ags_acceptor_site_range(const GthAGS*, GtUword intron);
+double        gth_ags_donor_site_prob(const GthAGS*, GtUword intron);
+double        gth_ags_acceptor_site_prob(const GthAGS*, GtUword intron);
+
+#endif

src/gth/ags_build.c

+/*
+  Copyright (c) 2003-2011 Gordon Gremme <gordon@gremme.org>
+  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg
+
+  Permission to use, copy, modify, and distribute this software for any
+  purpose with or without fee is hereby granted, provided that the above
+  copyright notice and this permission notice appear in all copies.
+
+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+*/
+
+#include "gth/ags_build.h"
+
+typedef struct {
+  GthDbl exonscore;        /* the score of this exonnode */
+  GtUword lengthofscoringexon; /* the length of the exon where the
+                                        exonscore came from */
+} Exonscoreinfo;
+
+typedef struct {
+  /* begin of core */
+  GtRange range;               /* the range of the exonnode */
+  bool leftmergeable,          /* true if the left border is mergeable */
+       rightmergeable;         /* true if the right border is mergeable */
+  Introninfo *successorintron; /* points to the successor intron of this exon,
+                                  if defined. points to NULL, otherwise. */
+  /* end of core */
+
+  GtArray *exonscores;   /* all exon scores of all exons, where this node
+                            resulted from */
+} Exonnode;
+
+#define SAVE_EXONSCORE_ALLOWED_DIFFERENCE       30
+
+typedef enum
+{
+  MERGEABLE_LEFTSIDE_A_BEFORE_B = 0,
+  MERGEABLE_LEFTSIDE_A_EQUALS_B,
+  MERGEABLE_LEFTSIDE_A_AFTER_B,
+  NON_MERGEABLE_LEFTSIDE,
+} Leftsidestatus;
+
+typedef enum
+{
+  MERGEABLE_RIGHTSIDE_A_BEFORE_B = 0,
+  MERGEABLE_RIGHTSIDE_A_EQUALS_B,
+  MERGEABLE_RIGHTSIDE_A_AFTER_B,
+  NON_MERGEABLE_RIGHTSIDE,
+} Rightsidestatus;
+
+/*
+  The following function returns the core of an Exonnode.
+  That is, the node without the pointers to the successors of this node.
+  The input is the spliced alignment \textit{sa}, and the index <exonindex>
+  of the exon to be processed.
+*/
+
+Exonnode getcoreExonnodefromSA(GthSA *sa, GtUword exonindex)
+{
+  Exonnode node;
+  Exonscoreinfo scoreinfo;
+
+  /* alignment contains at least one exon */
+  gt_assert(gth_sa_num_of_exons(sa));
+  /* number of exons minus 1 equals number of introns */
+  gt_assert(gth_sa_num_of_exons(sa) - 1 ==
+         gth_sa_num_of_introns(sa));
+  /* exonindex is valid */
+  gt_assert(exonindex < gth_sa_num_of_exons(sa));
+
+  node.exonscores = gt_array_new(sizeof (Exonscoreinfo));
+
+  node.range.start = gth_sa_get_exon(sa, exonindex)->leftgenomicexonborder;
+  node.range.end = gth_sa_get_exon(sa, exonindex)->rightgenomicexonborder;
+
+  if (exonindex == 0) /* this is the first exon */
+    node.leftmergeable = true;
+  else
+    node.leftmergeable = false;
+
+  if (exonindex == gth_sa_num_of_exons(sa) - 1) {
+    /* this is the last exon */
+    node.rightmergeable = true;
+  }
+  else
+    node.rightmergeable = false;
+
+  /* save successor intron */
+  if (exonindex < gth_sa_num_of_exons(sa) - 1) {
+    /* exon has successor intron */
+    node.successorintron = gth_sa_get_intron(sa, exonindex);
+  }
+  else {
+    /* exon has no successor intron */
+    node.successorintron = NULL;
+  }
+
+  /* save exonscore */
+  scoreinfo.exonscore = gth_sa_get_exon(sa, exonindex)->exonscore;
+  scoreinfo.lengthofscoringexon = node.range.end - node.range.start + 1;
+
+  gt_array_add(node.exonscores, scoreinfo);
+
+  return node;
+}
+
+static void freecoreExonnode(Exonnode *node)
+{
+  if (!node) return;
+  gt_array_delete(node->exonscores);
+}
+
+static Leftsidestatus getleftsidestatus(Exonnode *nodeA, Exonnode *nodeB)
+{
+  /* -------...
+      ]-----... */
+  if (nodeA->range.start < nodeB->range.start && nodeB->leftmergeable)
+    return MERGEABLE_LEFTSIDE_A_BEFORE_B;
+
+  /* -------...
+     -------... */
+  if (nodeA->range.start == nodeB->range.start)
+    return MERGEABLE_LEFTSIDE_A_EQUALS_B;
+
+  /*  ]-----...
+     -------... */
+  if (nodeA->range.start > nodeB->range.start && nodeA->leftmergeable)
+    return MERGEABLE_LEFTSIDE_A_AFTER_B;
+
+  return NON_MERGEABLE_LEFTSIDE;
+}
+
+#ifndef NDEBUG
+static bool leftsideismergeable(Exonnode *nodeA, Exonnode *nodeB)
+{
+  switch (getleftsidestatus(nodeA, nodeB))
+  {
+    case MERGEABLE_LEFTSIDE_A_BEFORE_B:
+    case MERGEABLE_LEFTSIDE_A_EQUALS_B:
+    case MERGEABLE_LEFTSIDE_A_AFTER_B:
+      return true;
+    case NON_MERGEABLE_LEFTSIDE:
+      return false;
+    default:
+      gt_assert(0);
+      return false;
+  }
+}
+#endif
+
+static Rightsidestatus getrightsidestatus(Exonnode *nodeA, Exonnode *nodeB)
+{
+  /* ...-----[
+     ...------- */
+  if (nodeA->range.end < nodeB->range.end && nodeA->rightmergeable)
+    return MERGEABLE_RIGHTSIDE_A_BEFORE_B;
+
+  /* ...-------
+     ...------- */
+  if (nodeA->range.end == nodeB->range.end)
+    return MERGEABLE_RIGHTSIDE_A_EQUALS_B;
+
+  /* ...-------
+     ...-----[  */
+  if (nodeA->range.end > nodeB->range.end && nodeB->rightmergeable)
+    return MERGEABLE_RIGHTSIDE_A_AFTER_B;
+
+  return NON_MERGEABLE_RIGHTSIDE;
+}
+
+#ifndef NDEBUG
+static bool rightsideismergeable(Exonnode *nodeA, Exonnode *nodeB)
+{
+  switch (getrightsidestatus(nodeA, nodeB)) {
+    case MERGEABLE_RIGHTSIDE_A_BEFORE_B:
+    case MERGEABLE_RIGHTSIDE_A_EQUALS_B:
+    case MERGEABLE_RIGHTSIDE_A_AFTER_B:
+      return true;
+    case NON_MERGEABLE_RIGHTSIDE:
+      return false;
+    default:
+      gt_assert(0);
+      return false;
+  }
+}
+#endif
+
+#ifndef NDEBUG
+static bool nodesaremergeable(Exonnode *nodeA, Exonnode *nodeB)
+{
+  if (gt_range_overlap(&nodeA->range, &nodeB->range) &&
+      leftsideismergeable(nodeA, nodeB) &&
+      rightsideismergeable(nodeA, nodeB)) {
+    return true;
+  }
+  return false;
+}
+#endif
+
+static void mergeleftside(Exonnode *nodeA, Exonnode *nodeB)
+{
+  switch (getleftsidestatus(nodeA, nodeB)) {
+    case MERGEABLE_LEFTSIDE_A_BEFORE_B:
+      /* -------...
+          ]-----...
+         nothing to do */
+      break;
+    case MERGEABLE_LEFTSIDE_A_EQUALS_B:
+      /* -------...
+         -------... */
+      if (!nodeA->leftmergeable || !nodeB->leftmergeable)
+        nodeA->leftmergeable = false;
+      break;
+    case MERGEABLE_LEFTSIDE_A_AFTER_B:
+      /*  ]-----...
+         -------... */
+      nodeA->range.start   = nodeB->range.start;
+      nodeA->leftmergeable = nodeB->leftmergeable;
+      break;
+    case NON_MERGEABLE_LEFTSIDE:
+    default: gt_assert(0);
+  }
+}
+
+static void mergerightside(Exonnode *nodeA, Exonnode *nodeB)
+{
+  switch (getrightsidestatus(nodeA, nodeB)) {
+    case MERGEABLE_RIGHTSIDE_A_BEFORE_B:
+      /* ...-----[
+         ...------- */
+      nodeA->range.end      = nodeB->range.end;
+      nodeA->rightmergeable = nodeB->rightmergeable;
+      break;
+    case MERGEABLE_RIGHTSIDE_A_EQUALS_B:
+      /* ...-------
+         ...------- */
+      if (!nodeA->rightmergeable || !nodeB->rightmergeable)
+        nodeA->rightmergeable = false;
+      break;
+    case MERGEABLE_RIGHTSIDE_A_AFTER_B:
+     /* ...-------
+        ...-----[
+        nothing to do */
+     break;
+    case NON_MERGEABLE_RIGHTSIDE:
+    default: gt_assert(0);
+  }
+}
+
+/*
+  The following function merges the exon nodes <nodeA> and
+  <nodeB>. That is, <nodeA> is modified to the merged node and
+  <nodeB> stays the same.
+*/
+
+static void mergenodes(Exonnode *nodeA, Exonnode *nodeB)
+{
+  GtUword i;
+
+  gt_assert(nodesaremergeable(nodeA, nodeB));
+
+  /* merge nodes */
+  mergeleftside(nodeA, nodeB);
+  mergerightside(nodeA, nodeB);
+
+  /* merge successor introns */
+  if (nodeA->successorintron == NULL && nodeB->successorintron != NULL) {
+    /* save successor intron of node B in node A */
+    nodeA->successorintron = nodeB->successorintron;
+  }
+  /* in the cases that (nodeA==NULL && nodeB==NULL) and that
+     (nodeA!=NULL && nodeB==NULL) nothing has to be done */
+
+  /* merge the exonscores */
+  for (i = 0; i < gt_array_size(nodeB->exonscores); i++) {
+    gt_array_add(nodeA->exonscores,
+              *(Exonscoreinfo*) gt_array_get(nodeB->exonscores, i));
+  }
+}
+
+static GthDbl computeexonscore(Exonnode *node)
+{
+  GtUword i, maxlength = 0;
+  GthDbl maxscore = DBL_MIN;
+  Exonscoreinfo *exonscoreinfo;
+
+  /* compute maximal length */
+  for (i = 0; i < gt_array_size(node->exonscores); i++) {
+    exonscoreinfo = gt_array_get(node->exonscores, i);
+    if (exonscoreinfo->lengthofscoringexon > maxlength)
+      maxlength = exonscoreinfo->lengthofscoringexon;
+  }
+
+  /* save exonscore */
+  for (i = 0; i < gt_array_size(node->exonscores); i++) {
+    exonscoreinfo = gt_array_get(node->exonscores, i);
+    if ((exonscoreinfo->lengthofscoringexon
+        + SAVE_EXONSCORE_ALLOWED_DIFFERENCE >= maxlength) &&
+        (exonscoreinfo->exonscore > maxscore)) {
+      maxscore = exonscoreinfo->exonscore;
+    }
+  }
+
+  return maxscore;
+}
+
+static void addSAtoAGS(GthAGS *ags, GthSACluster *sacluster, GtArray *nodes)
+{
+  GtUword i, currentnode = 0, currentexon = 0,
+                numofexons = gth_sa_num_of_exons(sacluster->representative);
+  Exonnode node;
+
+  /* genomic strands equal */
+  gt_assert(gth_ags_is_forward(ags) ==
+            gth_sa_gen_strand_forward(sacluster->representative));
+
+  /* set genomic id */
+  if (!ags->gen_id)
+    ags->gen_id = gt_str_ref(gth_sa_gen_id_str(sacluster->representative));
+#ifndef NDEBUG
+  else {
+    /* genomic ids equal */
+    gt_assert(!gt_str_cmp(ags->gen_id,
+                          gth_sa_gen_id_str(sacluster->representative)));
+  }
+#endif
+
+  /* save SA pointers */
+  gt_array_add(ags->alignments, sacluster->representative);
+  for (i = 0; i < gt_array_size(sacluster->members); i++) {
+    gt_array_add(ags->alignments, *(GthSA**)
+                               gt_array_get(sacluster->members, i));
+  }
+  ags->numofstoredsaclusters++;
+
+  while (currentexon < numofexons) {
+    node = getcoreExonnodefromSA(sacluster->representative, currentexon);
+
+    if (currentnode < gt_array_size(nodes)) {
+      /* compare current node with current exon */
+      if (!gt_range_overlap(&node.range,
+                            &((Exonnode*) gt_array_get(nodes, currentnode))
+                             ->range)) {
+        /* the current exon does not overlap with the current node,
+           visit next node */
+        currentnode++;
+      }
+      else {
+        /* left borders are equal, merge exon and node */
+        mergenodes(gt_array_get(nodes, currentnode), &node);
+        currentnode++;
+        currentexon++;
+      }
+      freecoreExonnode(&node);
+    }
+    else {
+      /* save this node */
+      gt_array_add(nodes, node);
+      currentnode++;
+      currentexon++;
+    }
+  }
+}
+
+void gth_build_AGS_from_assembly(GthAGS *ags, GtBittab *assembly,
+                                 GtArray *saclusters)
+{
+  GtUword i;
+  GtArray *nodes;
+  GthExonAGS exonAGS;
+  GthSpliceSiteProb splicesiteprob;
+  Exonnode *exonnode;
+
+  nodes = gt_array_new(sizeof (Exonnode));
+
+  /* compute AGS, the exons are stored es Exonnodes, which are saved later
+     (see below) */
+  for (i = 0; i < gt_array_size(saclusters); i++) {
+    if (gt_bittab_bit_is_set(assembly, i))
+      addSAtoAGS(ags, *(GthSACluster**) gt_array_get(saclusters, i), nodes);
+  }
+
+  /* save exons */
+  for (i = 0; i < gt_array_size(nodes); i++) {
+    exonnode = gt_array_get(nodes, i);
+    exonAGS.range = exonnode->range;
+    exonAGS.score = computeexonscore(exonnode);
+    gt_array_add(ags->exons, exonAGS);
+  }
+
+  /* at least one exon node exists */
+  gt_assert(gt_array_size(nodes));
+  /* save the splice site probabilites (stored in the intron infos) */
+  for (i = 0; i < gt_array_size(nodes) - 1; i++) {
+    exonnode = gt_array_get(nodes, i);
+    splicesiteprob.donorsiteprob    = exonnode->successorintron
+                                      ->donorsiteprobability;
+    splicesiteprob.acceptorsiteprob = exonnode->successorintron
+                                      ->acceptorsiteprobability;
+    gt_array_add(ags->splicesiteprobs, splicesiteprob);
+  }
+  /* last successor intron info points to null */
+  gt_assert(((Exonnode*) gt_array_get_last(nodes))->successorintron == NULL);
+
+  /* free space for nodes */
+  for (i = 0; i < gt_array_size(nodes); i++) {
+    exonnode = gt_array_get(nodes, i);
+    freecoreExonnode(exonnode);
+  }
+  gt_array_delete(nodes);
+}

src/gth/ags_build.h

+/*
+  Copyright (c) 2003-2011 Gordon Gremme <gordon@gremme.org>
+  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg
+
+  Permission to use, copy, modify, and distribute this software for any
+  purpose with or without fee is hereby granted, provided that the above
+  copyright notice and this permission notice appear in all copies.
+
+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+*/
+
+#ifndef AGS_BUILD_H
+#define AGS_BUILD_H
+
+#include "core/bittab.h"
+#include "gth/ags.h"
+#include "gth/pgl.h"
+
+void gth_build_AGS_from_assembly(GthAGS*, GtBittab *assembly,
+                                 GtArray *saclusters);
+
+#endif

src/gth/align_common.h

+/*
+  Copyright (c) 2003-2009 Gordon Gremme <gordon@gremme.org>
+  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg
+
+  Permission to use, copy, modify, and distribute this software for any
+  purpose with or without fee is hereby granted, provided that the above
+  copyright notice and this permission notice appear in all copies.
+
+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+*/
+
+#ifndef ALIGN_COMMON_H
+#define ALIGN_COMMON_H
+
+/* This modules contains the common functions which are used in the dna and the
+   protein DP. */
+
+#include "gth/bssm_param.h"
+#include "gth/dp_param.h"
+#include "gth/stat.h"
+
+#define SCORE(T,N,M)       dpm->core.score[T][N][M]
+#define GTH_MINUSINFINITY  ((GthFlt) -99999.0)
+#define DASH               (SEPARATOR-3)
+#define UNSET              (SEPARATOR-4)
+
+/*
+  The following updates maxvalue if it is smaller than value.
+  The variable <retrace> is defined accordingly.
+*/
+
+#define UPDATEMAX(C)\
+        if (maxvalue < value)\
+        {\
+          maxvalue = value;\
+          retrace = (GthPath) C;\
+        }
+
+typedef unsigned char GthPath;
+
+#endif

src/gth/align_dna.h

+/*
+  Copyright (c) 2003-2010 Gordon Gremme <gordon@gremme.org>
+  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg
+
+  Permission to use, copy, modify, and distribute this software for any
+  purpose with or without fee is hereby granted, provided that the above
+  copyright notice and this permission notice appear in all copies.
+
+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+*/
+
+#ifndef ALIGN_DNA_H
+#define ALIGN_DNA_H
+
+#include "gth/align_common.h"
+#include "gth/dp_options_core.h"
+#include "gth/dp_options_est.h"
+#include "gth/dp_options_postpro.h"
+#include "gth/path_matrix.h"
+#include "gth/sa.h"
+
+#define DASH_DASH_WEIGHT        0.0
+
+/* XXX: precompute this for performance reasons (part of core DP) */
+#define ADDOUTPUTWEIGHT(VAR,N,M)\
+        if ((N) < (gen_alphabet_mapsize-1))\
+        {\
+          if ((M) < (gen_alphabet_mapsize-1))\
+          {\
+            if ((N)==(M))\
+            {\
+              VAR += dp_options_est->identityweight;\
+            }\
+            else\
+            {\
+              VAR += dp_options_est->mismatchweight;\
+            }\
+          }\
+          else if ((M) == DASH)\
+          {\
+            VAR += dp_options_est->deletionweight;\
+          }\
+          else\
+          {\
+            VAR += dp_options_est->undetcharweight;\
+          }\
+        }\
+        else if ((N) == DASH)\
+        {\
+          if ((M) == DASH)\
+          {\
+            /* N=M=DASH: can happen in gthcomputescores() */\
+            VAR += DASH_DASH_WEIGHT;\
+          }\
+          else\
+          {\
+            VAR += dp_options_est->deletionweight;\
+          }\
+        }\
+        else\
+        {\
+          if ((M) == DASH)\
+          {\
+            VAR += dp_options_est->deletionweight;\
+          }\
+          else\
+          {\
+            VAR += dp_options_est->undetcharweight;\
+          }\
+        }
+
+typedef struct GthDPMatrix GthDPMatrix;
+
+typedef void (*GthDNACompletePathMatrixJT)(GthDPMatrix *dpm,
+                                           const unsigned char *gen_seq_tran,
+                                           const unsigned char *ref_seq_tran,
+                                           GtUword genomic_offset,
+                                           GtAlphabet *gen_alphabet,
+                                           GthDPParam *dp_param,
+                                           GthDPOptionsEST *dp_options_est,
+                                           GthDPOptionsCore *dp_options_core,
+                                           GthJumpTable *jumpt_table,
+                                           GtArray *gen_ranges,
+                                           GtUword ref_dp_length,
+                                           GtUword ref_offset,
+                                           GthPathMatrix **pm);
+#define ADDOUTPUTWEIGHTIDENTITY(VAR,N)\
+        if ((N) < (gen_alphabet_mapsize-1))\
+        {\
+          VAR += dp_options_est->identityweight;\
+        }\
+        else if ((N) == DASH)\
+        {\
+          VAR += DASH_DASH_WEIGHT;\
+        }\
+        else\
+        {\
+          VAR += dp_options_est->undetcharweight;\
+        }
+
+/* The following function implements the Spliced Alignment of Genomic DNA with
+   cDNA, as described by Usuka, Zhu and Brendel. */
+int gth_align_dna(GthSA*,
+                  GtArray *gen_ranges,
+                  const unsigned char *gen_seq_tran,
+                  const unsigned char *gen_seq_orig,
+                  const unsigned char *ref_seq_tran,
+                  const unsigned char *ref_seq_orig,
+                  GtUword ref_dp_length,
+                  GtAlphabet *gen_alphabet,
+                  GtAlphabet *ref_alphabet,
+                  bool introncutout,
+                  GtUword autoicmaxmatrixsize,
+                  bool showeops,
+                  bool comments,
+                  bool gs2out,
+                  const GtRange *gen_seq_bounds,
+                  GthSpliceSiteModel *splice_site_model,
+                  GthDPOptionsCore *dp_options_core,
+                  GthDPOptionsEST *dp_options_est,
+                  GthDPOptionsPostpro *dp_options_postpro,
+                  GthDNACompletePathMatrixJT complete_path_matrix_jt,
+                  GthJumpTable *jump_table,
+                  GtUword ref_offset,
+                  GthStat*,
+                  GtFile*);
+
+/* can return NULL */
+GthSA* gth_align_dna_simple(GthInput *input,
+                            const GtRange *gen_range,
+                            GtUword gen_file_num,
+                            GtUword gen_seq_num,
+                            bool gen_strand_forward,
+                            GtUword ref_file_num,
+                            GtUword ref_seq_num,
+                            GthSpliceSiteModel *splice_site_model);
+
+void gth_show_backtrace_matrix(GthPath **path,
+                               GtUword gen_dp_length,
+                               GtUword ref_dp_length,
+                               const GtRange *btmatrixgenrange,
+                               const GtRange *btmatrixrefrange);
+
+#endif

src/gth/align_dna_imp.h

+/*
+  Copyright (c) 2003-2010 Gordon Gremme <gordon@gremme.org>
+  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg
+
+  Permission to use, copy, modify, and distribute this software for any
+  purpose with or without fee is hereby granted, provided that the above
+  copyright notice and this permission notice appear in all copies.
+
+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+*/
+
+#ifndef ALIGN_DNA_IMP_H
+#define ALIGN_DNA_IMP_H
+
+#include "gth/align_dna.h"
+
+#define DNA_NUMOFSCORETABLES  2
+
+/*
+  Here comes the dirty bitvector stuff to quarter the backtrace matrix.
+  In this case the Retrace type defined above is only used in the lower E_STATE.
+*/
+
+#define LOWER_E_STATE_MASK      0x7     /* |0000|0111| */
+#define LOWER_I_STATE_MASK      0x8     /* |0000|1000| */
+#define UPPER_E_STATE_MASK      0x70    /* |0111|0000| */
+#define UPPER_I_STATE_MASK      0x80    /* |1000|0000| */
+
+#define UPPER_E_N               (DNA_E_N << 4)
+#define UPPER_E_M               (DNA_E_M << 4)
+
+#define I_STATE_E_N             (DNA_E_N << 3)
+#define I_STATE_I_N             (DNA_I_N << 3)
+
+#define UPPER_I_STATE_I_N       (I_STATE_I_N << 4)
+
+/* these definitions refer to the state index for the two N x M score matrices
+*/
+typedef enum {
+  DNA_E_STATE = 0,
+  DNA_I_STATE,
+  DNA_NUMOFSTATES
+} DnaStates;
+
+/*
+  These definitions are used to retrace the optimal path in align_dna.c.
+  E, I refer to the original state, N, M, and NM refer to which index
+  should be decremented.
+
+  IMPORTANT: Definition has to be consistent with dna_retracenames in
+  align_dna.c.
+*/
+typedef enum {
+  DNA_I_N = 0, /* deletion     |01|0^14
+                  or intron    |01|length */
+  DNA_E_N,     /* deletion     |01|0^14
+                  or intron    |01|length */
+  DNA_E_NM,    /* match        |00|length
+                  or mismatch  |11|0^14   */
+  DNA_I_NM,    /* match        |00|length
+                  or mismatch  |11|0^14   */
+  DNA_E_M,     /* insertion    |10|0^14   */
+  DNA_I_M,     /* insertion    |10|0^14   */
+  DNA_NUMOFRETRACE
+} DnaRetrace;
+
+/* the following structure bundles all tables involved in the dynamic
+   programming for cDNAs/ESTs */
+struct GthDPMatrix {
+  GthFlt *score[DNA_NUMOFSTATES][DNA_NUMOFSCORETABLES]; /* table to store the
+                                                           score of a path */
+  GthPath **path;                   /* backtrace table of size
+                                        gen_dp_length * ref_dp_length */
+  GthPath **path_jt;
+  GtUword *intronstart[DNA_NUMOFSCORETABLES],
+                *exonstart[DNA_NUMOFSCORETABLES],
+                gen_dp_length,
+                ref_dp_length;
+};
+
+#endif