!_TAG_FILE_FORMAT	2	/extended format; --format=1 will not append ;" to lines/
!_TAG_FILE_SORTED	1	/0=unsorted, 1=sorted, 2=foldcase/
!_TAG_PROGRAM_AUTHOR	Darren Hiebert	/dhiebert@users.sourceforge.net/
!_TAG_PROGRAM_NAME	Exuberant Ctags	//
!_TAG_PROGRAM_URL	http://ctags.sourceforge.net	/official site/
!_TAG_PROGRAM_VERSION	5.5.4	//
FLOATINFTY	kalignP.h	38;"	d
FLOAT_ZERO	kalignP_main.c	/^float FLOAT_ZERO = 1e-2;$/;"	v
INFTY	kalignP.h	37;"	d
MAX	kalignP_hirschberg.c	35;"	d	file:
MAX	kalignP_hirschberg_dna.c	36;"	d	file:
MAX	kalignP_hirschberg_large.c	35;"	d	file:
MAX3	kalignP_hirschberg.c	36;"	d	file:
MAX3	kalignP_hirschberg_dna.c	37;"	d	file:
MAX3	kalignP_hirschberg_large.c	36;"	d	file:
NODESIZE	kalignP.h	40;"	d
SEEK_END	kalignP_input.h	39;"	d
SEEK_START	kalignP_input.h	38;"	d
a	kalignP.h	/^	float a;   \/*aligned*\/$/;"	m	struct:states
a	kalignP_hirschberg_large.h	/^	float a;$/;"	m	struct:large_states
aa	kalignP.h	/^	int aa;$/;"	m	struct:parameters
add_gap_info_to_hirsch_path	kalignP_hirschberg.c	/^int* add_gap_info_to_hirsch_path(int* hirsch_path,int len_a,int len_b)\/*{{{*\/$/;"	f
add_label_simpletree	kalignP_tree.c	/^int add_label_simpletree(struct tree_node* p,int* nodes,int i)$/;"	f
add_unique_feature	kalignP_feature.c	/^struct feature* add_unique_feature(struct feature *n, struct feature *toadd)$/;"	f
add_unique_type	kalignP_feature.c	/^struct feature* add_unique_type(struct feature *n, struct feature *toadd)$/;"	f
advanced_backward_hirsch_pp_dyn	kalignP_advanced_gaps.c	/^struct states* advanced_backward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)$/;"	f
advanced_foward_hirsch_pp_dyn	kalignP_advanced_gaps.c	/^struct states* advanced_foward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)$/;"	f
advanced_hirsch_align_two_pp_vector	kalignP_advanced_gaps.c	/^int* advanced_hirsch_align_two_pp_vector(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])$/;"	f
advanced_hirsch_pp_dyn	kalignP_advanced_gaps.c	/^int* advanced_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path)$/;"	f
advanced_hirschberg_alignment	kalignP_advanced_gaps.c	/^int** advanced_hirschberg_alignment(struct alignment* aln,int* tree,float**submatrix, int** map,int window,float strength,float internal_gap_weight)$/;"	f
advanced_make_profile	kalignP_advanced_gaps.c	/^float* advanced_make_profile(float* prof, int* seq,int len,float** subm)$/;"	f
advanced_smooth_gaps	kalignP_advanced_gaps.c	/^void advanced_smooth_gaps(float* prof,int len,int window,float strength)$/;"	f
advanced_update	kalignP_advanced_gaps.c	/^float* advanced_update(const float* profa,const float* profb,float* newp,int* path,int sipa,int sipb,float internal_gap_weight)$/;"	f
alignment	kalignP.h	/^struct alignment{  \/*modified from 2010-09-29*\/$/;"	s
alignment_type	kalignP.h	/^	char* alignment_type;$/;"	m	struct:parameters
alignntree	kalignP_tree.c	/^struct ntree_data* alignntree(struct ntree_data* ntree_data,struct aln_tree_node* p)$/;"	f
aln	kalignP.h	/^	struct alignment* aln;$/;"	m	struct:ntree_data
aln_alloc	kalignP_mem.c	/^struct alignment* aln_alloc(struct alignment* aln)\/*{{{*\/ \/*modified from 2010-10-01*\/$/;"	f
aln_output	kalignP_output.c	/^void aln_output(struct alignment* aln,struct parameters* param)$/;"	f
aln_tree_node	kalignP.h	/^struct aln_tree_node{$/;"	s
alter_gaps	kalignP.h	/^	int alter_gaps;$/;"	m	struct:parameters
alter_range	kalignP.h	/^	float alter_range;$/;"	m	struct:parameters
alter_weight	kalignP.h	/^	int alter_weight;$/;"	m	struct:parameters
assign_gap_codes	kalignP_profile_alignment.c	/^int* assign_gap_codes(int* seq,int len)$/;"	f
b	kalignP.h	/^	struct states* b;$/;"	m	struct:hirsch_mem
b	kalignP_hirschberg_large.h	/^	struct large_states* b;$/;"	m	struct:hirsch_large_mem
backward_hirsch_dna_pp_dyn	kalignP_hirschberg_dna.c	/^struct states* backward_hirsch_dna_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)$/;"	f
backward_hirsch_dna_ps_dyn	kalignP_hirschberg_dna.c	/^struct states* backward_hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip)$/;"	f
backward_hirsch_dna_ss_dyn	kalignP_hirschberg_dna.c	/^struct states* backward_hirsch_dna_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm)$/;"	f
backward_hirsch_pp_dyn	kalignP_hirschberg.c	/^struct states* backward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)\/*{{{*\/$/;"	f
backward_hirsch_pp_dyn_new	kalignP_hirschberg.c	/^struct states* backward_hirsch_pp_dyn_new(const float* prof1,const float* prof2,struct hirsch_mem* hm)\/*{{{*\/$/;"	f
backward_hirsch_pp_dyn_new2	kalignP_hirschberg.c	/^struct states* backward_hirsch_pp_dyn_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm)\/*{{{*\/$/;"	f
backward_hirsch_pp_dyn_new2_0	kalignP_hirschberg.c	/^struct states* backward_hirsch_pp_dyn_new2_0(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm)\/*{{{*\/$/;"	f
backward_hirsch_ps_dyn	kalignP_hirschberg.c	/^struct states* backward_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip)\/*{{{*\/$/;"	f
backward_hirsch_ps_dyn_new	kalignP_hirschberg.c	/^struct states* backward_hirsch_ps_dyn_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int sip)\/*{{{*\/$/;"	f
backward_hirsch_ps_dyn_new0	kalignP_hirschberg.c	/^struct states* backward_hirsch_ps_dyn_new0(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int sip)\/*{{{*\/$/;"	f
backward_hirsch_ps_dyn_new1	kalignP_hirschberg.c	/^struct states* backward_hirsch_ps_dyn_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, int sip)\/*{{{*\/$/;"	f
backward_hirsch_ps_dyn_new2	kalignP_hirschberg.c	/^struct states* backward_hirsch_ps_dyn_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip)\/*{{{*\/$/;"	f
backward_hirsch_ss_dyn	kalignP_hirschberg.c	/^struct states* backward_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm)\/*{{{*\/$/;"	f
backward_hirsch_ss_dyn_new	kalignP_hirschberg.c	/^struct states* backward_hirsch_ss_dyn_new(float**subm,const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm)\/*{{{*\/$/;"	f
backward_large_hirsch_pp_dyn	kalignP_hirschberg_large.c	/^struct large_states* backward_large_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_large_mem* hm)$/;"	f
backward_large_hirsch_ps_dyn	kalignP_hirschberg_large.c	/^struct large_states* backward_large_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_large_mem* hm,int sip)$/;"	f
backward_large_hirsch_ss_dyn	kalignP_hirschberg_large.c	/^struct large_states* backward_large_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_large_mem* hm)$/;"	f
big_insert_hash	kalignP_misc.c	/^struct bignode* big_insert_hash(struct bignode *n,const unsigned int pos)$/;"	f
big_print_nodes	kalignP_misc.c	/^void big_print_nodes(struct bignode *n)$/;"	f
big_remove_nodes	kalignP_misc.c	/^void big_remove_nodes(struct bignode *n)$/;"	f
bignode	kalignP.h	/^struct bignode{$/;"	s
byg_count	kalignP_string_matching.c	/^int byg_count(char* pattern,char*text)\/*{{{*\/$/;"	f
byg_detect	kalignP_string_matching.c	/^int byg_detect(int* text,int n)\/*{{{*\/$/;"	f
byg_end	kalignP_string_matching.c	/^int byg_end(char* pattern,char*text)\/*{{{*\/$/;"	f
byg_start	kalignP_string_matching.c	/^int byg_start(char* pattern,char*text)\/*{{{*\/$/;"	f
check_identity	kalignP_string_matching.c	/^int check_identity(char* n,char*m)\/*{{{*\/$/;"	f
clustal_output	kalignP_output.c	/^void clustal_output(struct alignment* aln,char* outfile)$/;"	f
color	kalignP.h	/^	int color;$/;"	m	struct:feature
count_sequences_clustalw	kalignP_input.c	/^int count_sequences_clustalw(char* string)\/*{{{*\/$/;"	f
count_sequences_fasta	kalignP_input.c	/^int count_sequences_fasta(char* string)\/*{{{*\/$/;"	f
count_sequences_macsim	kalignP_input.c	/^int count_sequences_macsim(char* string)\/*{{{*\/$/;"	f
count_sequences_stockholm	kalignP_input.c	/^int count_sequences_stockholm(char* string)\/*{{{*\/$/;"	f
count_sequences_swissprot	kalignP_input.c	/^int count_sequences_swissprot(char* string)\/*{{{*\/$/;"	f
count_sequences_uniprot	kalignP_input.c	/^int count_sequences_uniprot(char* string)\/*{{{*\/$/;"	f
default_alignment	kalignP_alignment_types.c	/^int** default_alignment(struct alignment* aln,int* tree,float**submatrix, int** map)$/;"	f
detect_and_read_sequences	kalignP_input.c	/^struct alignment* detect_and_read_sequences(struct alignment* aln,struct parameters* param)\/*{{{*\/$/;"	f
detect_and_read_sequences_new	kalignP_input.c	/^struct alignment* detect_and_read_sequences_new(struct alignment* aln,struct parameters* param)\/*{{{*\/$/;"	f
diff_feature_score	kalignP.h	/^	float diff_feature_score;$/;"	m	struct:parameters
dim	kalignP_feature.c	/^static int dim;$/;"	v	file:
distance	kalignP.h	/^	char* distance;$/;"	m	struct:parameters
dna	kalignP.h	/^	int dna;$/;"	m	struct:parameters
dna_alignment	kalignP_hirschberg_dna.c	/^int** dna_alignment(struct alignment* aln,int* tree,float**submatrix, int** map,float strength)$/;"	f
dna_alignment_against_a	kalignP_hirschberg_dna.c	/^int** dna_alignment_against_a(struct alignment* aln,int* tree,float**submatrix, int** map,float strength)$/;"	f
dna_distance	kalignP_distance_calculation.c	/^float** dna_distance(struct alignment* si,float** dm,struct parameters* param, int nj)$/;"	f
dna_distance_calculation	kalignP_distance_calculation.c	/^float dna_distance_calculation(struct bignode* hash[],int* p,int seqlen,int diagonals,float mode)$/;"	f
dna_make_profile	kalignP_profile.c	/^float* dna_make_profile(float* prof, int* seq,int len,float** subm)\/*{{{*\/$/;"	f
dna_profile_distance	kalignP_profile_alignment.c	/^float** dna_profile_distance(struct alignment* aln,float** dm,struct parameters* param, int nj)$/;"	f
dna_set_gap_penalties	kalignP_profile.c	/^void dna_set_gap_penalties(float* prof,int len,int nsip,float strength,int nsip_c)\/*{{{*\/$/;"	f
dna_update	kalignP_profile.c	/^float* dna_update(const float* profa, const float* profb, float* newp,int* path,int sipa,int sipb)\/*{{{*\/$/;"	f
dna_update_only_a	kalignP_profile.c	/^float* dna_update_only_a(const float* profa, const float* profb, float* newp,int* path,int sipa,int sipb)\/*{{{*\/$/;"	f
done	kalignP.h	/^	int done;$/;"	m	struct:aln_tree_node
dp_matrix	kalignP.h	/^struct dp_matrix{$/;"	s
dp_matrix_alloc	kalignP_mem.c	/^struct dp_matrix* dp_matrix_alloc(struct dp_matrix *dp,int x,int y)$/;"	f
dp_matrix_free	kalignP_mem.c	/^void dp_matrix_free(struct dp_matrix *dp)$/;"	f
dp_matrix_realloc	kalignP_mem.c	/^struct dp_matrix* dp_matrix_realloc(struct dp_matrix *dp,int x,int y)$/;"	f
edge	kalignP.h	/^ 	int edge;$/;"	m	struct:tree_node
end	kalignP.h	/^	int end;$/;"	m	struct:feature
end	kalignP.h	/^	int* end;$/;"	m	struct:names
enda	kalignP.h	/^	int enda;$/;"	m	struct:hirsch_mem
enda	kalignP_hirschberg_large.h	/^	int enda;$/;"	m	struct:hirsch_large_mem
endb	kalignP.h	/^	int endb;$/;"	m	struct:hirsch_mem
endb	kalignP_hirschberg_large.h	/^	int endb;$/;"	m	struct:hirsch_large_mem
entrophy	kalignP_conservation.c	/^void entrophy(int* prof,int len)$/;"	f
f	kalignP.h	/^	struct feature *f;$/;"	m	struct:utype_ufeat
f	kalignP.h	/^	struct states* f;$/;"	m	struct:hirsch_mem
f	kalignP_hirschberg_large.h	/^	struct large_states* f;$/;"	m	struct:hirsch_large_mem
f_only_pp_dyn	kalignP_dp.c	/^int* f_only_pp_dyn(int* path, struct dp_matrix *dp,const float* fprof1,const float* fprof2,const int len_a,const int len_b,int fdim,int stride)$/;"	f
fasta_output	kalignP_output.c	/^void fasta_output(struct alignment* aln,char* outfile)$/;"	f
feature	kalignP.h	/^struct feature{$/;"	s
feature_backward_hirsch_pp_dyn	kalignP_feature.c	/^struct states* feature_backward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)$/;"	f
feature_foward_hirsch_pp_dyn	kalignP_feature.c	/^struct states* feature_foward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)$/;"	f
feature_hirsch_align_two_pp_vector	kalignP_feature.c	/^int* feature_hirsch_align_two_pp_vector(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path, float input_states[],int old_cor[])$/;"	f
feature_hirsch_pp_dyn	kalignP_feature.c	/^int* feature_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path)$/;"	f
feature_hirschberg_alignment	kalignP_feature.c	/^int** feature_hirschberg_alignment(struct alignment* aln,int* tree,float**submatrix, int** map,struct feature_matrix* fm)$/;"	f
feature_hirschberg_update	kalignP_feature.c	/^float* feature_hirschberg_update(const float* profa,const float* profb,float* newp,int* path,int sipa,int sipb)$/;"	f
feature_matrix	kalignP.h	/^struct feature_matrix{$/;"	s
feature_mode	kalignP.h	/^	char* feature_mode;$/;"	m	struct:parameters
feature_type	kalignP.h	/^	char* feature_type;$/;"	m	struct:parameters
feature_update	kalignP_profile.c	/^float*  feature_update(const float* profa, const float* profb,float* newp,int* path,int stride)\/*{{{*\/$/;"	f
find_best_topology	kalignP_tree.c	/^struct ntree_data* find_best_topology(struct ntree_data* ntree_data,int* leaves,int* nodes)$/;"	f
format	kalignP.h	/^	char* format;$/;"	m	struct:parameters
foward_hirsch_dna_pp_dyn	kalignP_hirschberg_dna.c	/^struct states* foward_hirsch_dna_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)$/;"	f
foward_hirsch_dna_ps_dyn	kalignP_hirschberg_dna.c	/^struct states* foward_hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip)$/;"	f
foward_hirsch_dna_ss_dyn	kalignP_hirschberg_dna.c	/^struct states* foward_hirsch_dna_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm)$/;"	f
foward_hirsch_pp_dyn	kalignP_hirschberg.c	/^struct states* foward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)\/*{{{*\/$/;"	f
foward_hirsch_pp_dyn_new	kalignP_hirschberg.c	/^struct states* foward_hirsch_pp_dyn_new(const float* prof1,const float* prof2,struct hirsch_mem* hm)\/*{{{*\/$/;"	f
foward_hirsch_pp_dyn_new2	kalignP_hirschberg.c	/^struct states* foward_hirsch_pp_dyn_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm)\/*{{{*\/$/;"	f
foward_hirsch_pp_dyn_new2_0	kalignP_hirschberg.c	/^struct states* foward_hirsch_pp_dyn_new2_0(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm)\/*{{{*\/$/;"	f
foward_hirsch_ps_dyn	kalignP_hirschberg.c	/^struct states* foward_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip)\/*{{{*\/$/;"	f
foward_hirsch_ps_dyn_new	kalignP_hirschberg.c	/^struct states* foward_hirsch_ps_dyn_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm,int sip)\/*{{{*\/$/;"	f
foward_hirsch_ps_dyn_new0	kalignP_hirschberg.c	/^struct states* foward_hirsch_ps_dyn_new0(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm,int sip)\/*{{{*\/$/;"	f
foward_hirsch_ps_dyn_new1	kalignP_hirschberg.c	/^struct states* foward_hirsch_ps_dyn_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm,unsigned int* nResArray1, int sip)\/*{{{*\/$/;"	f
foward_hirsch_ps_dyn_new2	kalignP_hirschberg.c	/^struct states* foward_hirsch_ps_dyn_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip)\/*{{{*\/$/;"	f
foward_hirsch_ss_dyn	kalignP_hirschberg.c	/^struct states* foward_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm)\/*{{{*\/$/;"	f
foward_hirsch_ss_dyn_new	kalignP_hirschberg.c	/^struct states* foward_hirsch_ss_dyn_new(float**subm,const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm)\/*{{{*\/$/;"	f
foward_large_hirsch_pp_dyn	kalignP_hirschberg_large.c	/^struct large_states* foward_large_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_large_mem* hm)$/;"	f
foward_large_hirsch_ps_dyn	kalignP_hirschberg_large.c	/^struct large_states* foward_large_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_large_mem* hm,int sip)$/;"	f
foward_large_hirsch_ss_dyn	kalignP_hirschberg_large.c	/^struct large_states* foward_large_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_large_mem* hm)$/;"	f
fpp_dyn	kalignP_dp.c	/^int* fpp_dyn(int* path, struct dp_matrix *dp,const float* prof1,const float* prof2,const float* fprof1,const float* fprof2,const int len_a,const int len_b,int fdim,int stride)$/;"	f
free_aln	kalignP_mem.c	/^void free_aln(struct alignment* aln)\/*{{{*\/ \/*modified from 2010-10-01*\/$/;"	f
free_feature_matrix	kalignP_mem.c	/^void free_feature_matrix(struct feature_matrix* fm)$/;"	f
free_ft	kalignP_mem.c	/^void free_ft(struct feature* n)$/;"	f
free_param	kalignP_mem.c	/^void free_param(struct parameters* param)$/;"	f
free_real_tree	kalignP_mem.c	/^void free_real_tree(struct aln_tree_node* p)$/;"	f
free_utf	kalignP_mem.c	/^void free_utf(struct utype_ufeat* utf)$/;"	f
freesimpletree	kalignP_mem.c	/^void freesimpletree(struct tree_node* p)$/;"	f
ft	kalignP.h	/^	struct feature** ft;$/;"	m	struct:alignment
ga	kalignP.h	/^	float ga;  \/*gap in sequence a *\/ $/;"	m	struct:states
ga	kalignP_hirschberg_large.h	/^	float ga;$/;"	m	struct:large_states
gap_inc	kalignP.h	/^	float gap_inc;$/;"	m	struct:parameters
gb	kalignP.h	/^	float gb;  \/*gap in sequence b*\/ $/;"	m	struct:states
gb	kalignP_hirschberg_large.h	/^	float gb;$/;"	m	struct:large_states
get_distance_from_pairwise_alignment	kalignP_distance_calculation.c	/^float get_distance_from_pairwise_alignment(int* path,int* seq1,int* seq2)$/;"	f
get_feature_matrix	kalignP_feature.c	/^struct feature_matrix* get_feature_matrix(struct feature_matrix* fm, struct alignment* aln,struct parameters* param)$/;"	f
get_input_into_string	kalignP_input.c	/^char* get_input_into_string(char* string,char* infile)\/*{{{*\/$/;"	f
get_meaningful_names	kalignP_output.c	/^struct names* get_meaningful_names(struct alignment* aln,int id)$/;"	f
get_unique_features	kalignP_feature.c	/^struct utype_ufeat* get_unique_features(struct alignment* aln,struct utype_ufeat* utf)$/;"	f
gpe	kalignP.h	/^	float gpe;$/;"	m	struct:parameters
gpe	kalignP.h	/^    float **gpe;  \/*position specific gapextension array, added 2010-09-29*\/ $/;"	m	struct:alignment
gpe	kalignP_main.c	/^float gpe = (float)0.0;$/;"	v
gpe_pos	kalignP_feature.c	/^static int gpe_pos;$/;"	v	file:
gpo	kalignP.h	/^	float gpo;$/;"	m	struct:parameters
gpo	kalignP.h	/^    float **gpo; \/*position specific gapopen array, added 2010-09-29*\/$/;"	m	struct:alignment
gpo	kalignP_main.c	/^float gpo = (float)0.0;$/;"	v
gpo_pos	kalignP_feature.c	/^static int gpo_pos;$/;"	v	file:
help_flag	kalignP.h	/^	int help_flag;$/;"	m	struct:parameters
hirsch_align_two_dna_pp_vector	kalignP_hirschberg_dna.c	/^int* hirsch_align_two_dna_pp_vector(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path, float input_states[],int old_cor[])$/;"	f
hirsch_align_two_dna_ps_vector	kalignP_hirschberg_dna.c	/^int* hirsch_align_two_dna_ps_vector(const float* prof1,const int* seq2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip)$/;"	f
hirsch_align_two_dna_ss_vector	kalignP_hirschberg_dna.c	/^int* hirsch_align_two_dna_ss_vector(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])$/;"	f
hirsch_align_two_pp_vector	kalignP_hirschberg.c	/^int* hirsch_align_two_pp_vector(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])\/*{{{*\/$/;"	f
hirsch_align_two_pp_vector_new	kalignP_hirschberg.c	/^int* hirsch_align_two_pp_vector_new(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])\/*{{{*\/$/;"	f
hirsch_align_two_pp_vector_new2	kalignP_hirschberg.c	/^int* hirsch_align_two_pp_vector_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])\/*{{{*\/$/;"	f
hirsch_align_two_pp_vector_new2_0	kalignP_hirschberg.c	/^int* hirsch_align_two_pp_vector_new2_0(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])\/*{{{*\/$/;"	f
hirsch_align_two_ps_vector	kalignP_hirschberg.c	/^int* hirsch_align_two_ps_vector(const float* prof1,const int* seq2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip)\/*{{{*\/$/;"	f
hirsch_align_two_ps_vector_new	kalignP_hirschberg.c	/^int* hirsch_align_two_ps_vector_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip)\/*{{{*\/$/;"	f
hirsch_align_two_ps_vector_new0	kalignP_hirschberg.c	/^int* hirsch_align_two_ps_vector_new0(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip)\/*{{{*\/$/;"	f
hirsch_align_two_ps_vector_new1	kalignP_hirschberg.c	/^int* hirsch_align_two_ps_vector_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],unsigned int* nResArray1, int sip)\/*{{{*\/$/;"	f
hirsch_align_two_ps_vector_new2	kalignP_hirschberg.c	/^int* hirsch_align_two_ps_vector_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],unsigned int* nResArray1, float* weightArray1, int sip)\/*{{{*\/$/;"	f
hirsch_align_two_ss_vector	kalignP_hirschberg.c	/^int* hirsch_align_two_ss_vector(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])\/*{{{*\/$/;"	f
hirsch_align_two_ss_vector_new	kalignP_hirschberg.c	/^int* hirsch_align_two_ss_vector_new(float**subm,const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[] )\/*{{{*\/$/;"	f
hirsch_dna_pp_dyn	kalignP_hirschberg_dna.c	/^int* hirsch_dna_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path)$/;"	f
hirsch_dna_ps_dyn	kalignP_hirschberg_dna.c	/^int* hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path,int sip)$/;"	f
hirsch_dna_ss_dyn	kalignP_hirschberg_dna.c	/^int* hirsch_dna_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path)$/;"	f
hirsch_large_align_two_pp_vector	kalignP_hirschberg_large.c	/^int* hirsch_large_align_two_pp_vector(const float* prof1,const float* prof2,struct hirsch_large_mem* hm,int* hirsch_path,float input_states[],int old_cor[])$/;"	f
hirsch_large_align_two_ps_vector	kalignP_hirschberg_large.c	/^int* hirsch_large_align_two_ps_vector(const float* prof1,const int* seq2,struct hirsch_large_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip)$/;"	f
hirsch_large_align_two_ss_vector	kalignP_hirschberg_large.c	/^int* hirsch_large_align_two_ss_vector(float**subm,const int* seq1,const int* seq2,struct hirsch_large_mem* hm,int* hirsch_path,float input_states[],int old_cor[])$/;"	f
hirsch_large_mem	kalignP_hirschberg_large.h	/^struct hirsch_large_mem{$/;"	s
hirsch_large_mem_alloc	kalignP_hirschberg_large.c	/^struct hirsch_large_mem* hirsch_large_mem_alloc(struct hirsch_large_mem* hm,int x)$/;"	f
hirsch_large_mem_free	kalignP_hirschberg_large.c	/^void hirsch_large_mem_free(struct hirsch_large_mem* hm)$/;"	f
hirsch_large_mem_realloc	kalignP_hirschberg_large.c	/^struct hirsch_large_mem* hirsch_large_mem_realloc(struct hirsch_large_mem* hm,int x)$/;"	f
hirsch_large_pp_dyn	kalignP_hirschberg_large.c	/^int* hirsch_large_pp_dyn(const float* prof1,const float* prof2,struct hirsch_large_mem* hm, int* hirsch_path)$/;"	f
hirsch_large_ps_dyn	kalignP_hirschberg_large.c	/^int* hirsch_large_ps_dyn(const float* prof1,const int* seq2,struct hirsch_large_mem* hm, int* hirsch_path,int sip)$/;"	f
hirsch_large_ss_dyn	kalignP_hirschberg_large.c	/^int* hirsch_large_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_large_mem* hm, int* hirsch_path)$/;"	f
hirsch_mem	kalignP.h	/^struct hirsch_mem{$/;"	s
hirsch_mem_alloc	kalignP_mem.c	/^struct hirsch_mem* hirsch_mem_alloc(struct hirsch_mem* hm,int x)$/;"	f
hirsch_mem_free	kalignP_mem.c	/^void hirsch_mem_free(struct hirsch_mem* hm)$/;"	f
hirsch_mem_realloc	kalignP_mem.c	/^struct hirsch_mem* hirsch_mem_realloc(struct hirsch_mem* hm,int x)$/;"	f
hirsch_pp_dyn	kalignP_hirschberg.c	/^int* hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path)\/*{{{*\/$/;"	f
hirsch_pp_dyn_new	kalignP_hirschberg.c	/^int* hirsch_pp_dyn_new(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path)\/*{{{*\/$/;"	f
hirsch_pp_dyn_new2	kalignP_hirschberg.c	/^int* hirsch_pp_dyn_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm, int* hirsch_path)\/*{{{*\/$/;"	f
hirsch_ps_dyn	kalignP_hirschberg.c	/^int* hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path,int sip)\/*{{{*\/$/;"	f
hirsch_ps_dyn_new	kalignP_hirschberg.c	/^int* hirsch_ps_dyn_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm, int* hirsch_path,int sip)\/*{{{*\/$/;"	f
hirsch_ps_dyn_new1	kalignP_hirschberg.c	/^int* hirsch_ps_dyn_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm, int* hirsch_path,unsigned int* nResArray1,  int sip)\/*{{{*\/$/;"	f
hirsch_ps_dyn_new2	kalignP_hirschberg.c	/^int* hirsch_ps_dyn_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm, int* hirsch_path,unsigned int* nResArray1, float* weightArray1, int sip)\/*{{{*\/$/;"	f
hirsch_ss_dyn	kalignP_hirschberg.c	/^int* hirsch_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path)\/*{{{*\/$/;"	f
hirsch_ss_dyn_new	kalignP_hirschberg.c	/^int* hirsch_ss_dyn_new(float**subm, const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm, int* hirsch_path)\/*{{{*\/$/;"	f
hirschberg_alignment	kalignP_hirschberg.c	/^int** hirschberg_alignment(struct alignment* aln,int* tree,float**submatrix, int** map,int window,float strength)\/*{{{*\/$/;"	f
hirschberg_alignment_against_a	kalignP_hirschberg.c	/^int** hirschberg_alignment_against_a(struct alignment* aln,int* tree,float**submatrix, int** map,int window,float strength)\/*{{{*\/$/;"	f
hirschberg_large_alignment	kalignP_hirschberg_large.c	/^int** hirschberg_large_alignment(struct alignment* aln,int* tree,float**submatrix, int** map,int window,float strength)$/;"	f
hirschberg_profile_alignment	kalignP_profile_alignment.c	/^int** hirschberg_profile_alignment(struct alignment* aln,int* tree,float**submatrix, int** map)$/;"	f
id	kalignP.h	/^	int id;$/;"	m	struct:parameters
increase_gaps	kalignP_profile.c	/^void increase_gaps(float* prof,int len,int window,float strength)\/*{{{*\/$/;"	f
infile	kalignP.h	/^	char **infile;$/;"	m	struct:parameters
input	kalignP.h	/^	char *input;$/;"	m	struct:parameters
insert	kalignP_misc.c	/^struct node* insert(struct node *n, int pos)$/;"	f
insert_hash	kalignP_misc.c	/^struct node* insert_hash(struct node *n, int pos)$/;"	f
interface	kalignP_interface.c	/^struct parameters* interface(struct parameters* param,int argc,char **argv)$/;"	f
internal_gap_weight	kalignP.h	/^	float internal_gap_weight;$/;"	m	struct:parameters
internal_lables	kalignP.h	/^	int* internal_lables;$/;"	m	struct:aln_tree_node
is_member	kalignP_profile_alignment.c	/^int is_member(struct alignment* aln,int test)$/;"	f
label	kalignP.h	/^ 	int label;$/;"	m	struct:tree_node
large_states	kalignP_hirschberg_large.h	/^struct large_states{$/;"	s
large_update	kalignP_hirschberg_large.c	/^float* large_update(float* profa,float* profb,float* newp,int* path,int sipa,int sipb)$/;"	f
left	kalignP.h	/^	struct tree_node* left;$/;"	m	struct:tree_node
len	kalignP.h	/^	int len;$/;"	m	struct:aln_tree_node
len	kalignP.h	/^	int* len; $/;"	m	struct:names
len_a	kalignP.h	/^	int len_a;$/;"	m	struct:hirsch_mem
len_a	kalignP_hirschberg_large.h	/^	int len_a;$/;"	m	struct:hirsch_large_mem
len_b	kalignP.h	/^	int len_b;$/;"	m	struct:hirsch_mem
len_b	kalignP_hirschberg_large.h	/^	int len_b;$/;"	m	struct:hirsch_large_mem
links	kalignP.h	/^	struct aln_tree_node** links;$/;"	m	struct:aln_tree_node
local_gpe	kalignP_hirschberg_large.c	/^float local_gpe;$/;"	v
local_gpo	kalignP_hirschberg_large.c	/^float local_gpo;$/;"	v
local_numprofiles	kalignP_profile_alignment.h	/^int local_numprofiles;$/;"	v
local_numseq	kalignP_profile_alignment.h	/^int local_numseq;$/;"	v
local_tgpe	kalignP_hirschberg_large.c	/^float local_tgpe;$/;"	v
lsn	kalignP.h	/^	unsigned int* lsn; \/*length of annotation lines*\/$/;"	m	struct:alignment
m	kalignP.h	/^	float** m;$/;"	m	struct:feature_matrix
macsim_output	kalignP_output.c	/^void macsim_output(struct alignment* aln,char* outfile,char* infile)$/;"	f
main	kalignP_main.c	/^int main(int argc,char **argv)$/;"	f
make_dna	kalignP_misc.c	/^struct alignment* make_dna(struct alignment* aln)$/;"	f
make_feature_profile	kalignP_profile.c	/^float* make_feature_profile(float* prof,struct feature* f,int len,struct feature_matrix* fm)\/*{{{*\/$/;"	f
make_large_profile	kalignP_hirschberg_large.c	/^float* make_large_profile(float* prof, int* seq,int len,float** subm)$/;"	f
make_profile	kalignP_profile.c	/^float* make_profile(float* prof, int* seq,int len, float** subm)\/*{{{*\/$/;"	f
make_profile2	kalignP_profile.c	/^float* make_profile2(float* prof, int* seq,int len,float** subm)\/*{{{*\/$/;"	f
make_profile_from_alignment	kalignP_profile_alignment.c	/^float* make_profile_from_alignment(float* prof, int num,struct alignment* aln,float** subm)$/;"	f
make_profile_new	kalignP_profile.c	/^float* make_profile_new(float* prof, int* seq, float *gpoArray, float* gpeArray, float *tgpeArray, int len, float** subm)\/*{{{*\/$/;"	f
make_seq	kalignP_misc.c	/^struct alignment* make_seq(struct alignment* aln,int a,int b,int* path)$/;"	f
make_unified_profile	kalignP_feature.c	/^float* make_unified_profile(float* prof,struct alignment* aln, int num,float** subm,struct feature_matrix* fm)$/;"	f
make_wu_profile	kalignP_profile.c	/^float* make_wu_profile(float* prof,float* wu,int len)\/*{{{*\/$/;"	f
map	kalignP.h	/^	int** map;$/;"	m	struct:ntree_data
mdim	kalignP.h	/^	int mdim;$/;"	m	struct:feature_matrix
mirror_hirsch_path	kalignP_hirschberg.c	/^int* mirror_hirsch_path(int* hirsch_path,int len_a,int len_b)\/*{{{*\/$/;"	f
mirror_path	kalignP_misc.c	/^int* mirror_path(int* path)$/;"	f
msf_output	kalignP_output.c	/^void msf_output(struct alignment* aln,char* outfile)$/;"	f
nRes	kalignP.h	/^	unsigned int** nRes;   \/*number of residues at each position of a sequence or consensus sequence*\/$/;"	m	struct:alignment
name	kalignP.h	/^	char* name;$/;"	m	struct:sequence_info
names	kalignP.h	/^struct names{$/;"	s
names_alloc	kalignP_mem.c	/^struct names* names_alloc(struct names* n)$/;"	f
names_free	kalignP_mem.c	/^void names_free(struct names* n)$/;"	f
next	kalignP.h	/^	struct bignode *next;$/;"	m	struct:bignode
next	kalignP.h	/^	struct feature *next;$/;"	m	struct:feature
next	kalignP.h	/^	struct node *next;$/;"	m	struct:node
next	kalignP.h	/^	struct sequence_info* next;$/;"	m	struct:sequence_info
nj	kalignP_tree.c	/^int* nj(float **dm,int* tree)$/;"	f
nj	kalignP_upgma.c	/^int* nj(float **dm,int* tree)$/;"	f
node	kalignP.h	/^struct node{$/;"	s
note	kalignP.h	/^	char* note;$/;"	m	struct:feature
nsip	kalignP.h	/^	unsigned int* nsip;  \/*number of sequences involved in the consensus*\/$/;"	m	struct:alignment
ntree	kalignP.h	/^	int ntree;$/;"	m	struct:ntree_data
ntree	kalignP.h	/^	int ntree;$/;"	m	struct:parameters
ntree_alignment	kalignP_alignment_types.c	/^struct ntree_data* ntree_alignment(struct ntree_data* ntree_data)$/;"	f
ntree_data	kalignP.h	/^struct ntree_data{$/;"	s
ntree_sub_alignment	kalignP_alignment_types.c	/^struct ntree_data* ntree_sub_alignment(struct ntree_data* ntree_data,int* tree,int num)$/;"	f
ntreeify	kalignP_tree.c	/^void ntreeify(struct aln_tree_node* p,int ntree)$/;"	f
num	kalignP.h	/^	int num;$/;"	m	struct:aln_tree_node
num	kalignP.h	/^	unsigned int num;$/;"	m	struct:bignode
numprofiles	kalignP_main.c	/^unsigned int numprofiles = 0;  \/*numprofiles = numseq << 1 - 1*\/$/;"	v
numseq	kalignP_main.c	/^unsigned int numseq = 0;$/;"	v
outfile	kalignP.h	/^	char *outfile;$/;"	m	struct:parameters
output	kalignP_output.c	/^void output(struct alignment* aln,struct parameters* param)$/;"	f
parameter_message	kalignP_interface.c	/^void parameter_message(struct parameters* param)$/;"	f
parameters	kalignP.h	/^struct parameters{$/;"	s
path	kalignP.h	/^	int* path;$/;"	m	struct:aln_tree_node
pos	kalignP.h	/^	unsigned int pos[NODESIZE];$/;"	m	struct:bignode
pos	kalignP.h	/^        int pos;$/;"	m	struct:node
pp_dyn	kalignP_dp.c	/^int* pp_dyn(int* path, struct dp_matrix *dp,const float* prof1,const float* prof2,const int len_a,const int len_b)$/;"	f
print_newick_tree	kalignP_misc.c	/^void print_newick_tree(struct aln_tree_node* p,struct alignment* aln,FILE *fout)$/;"	f
print_phyloxml_tree	kalignP_misc.c	/^void print_phyloxml_tree(struct aln_tree_node* p,struct alignment* aln,FILE *fout)$/;"	f
print_simple_phylip_tree	kalignP_tree.c	/^void print_simple_phylip_tree(struct aln_tree_node* p)$/;"	f
print_svg_tree	kalignP.h	/^	char* print_svg_tree;$/;"	m	struct:parameters
print_tree	kalignP.h	/^	char* print_tree;$/;"	m	struct:parameters
print_tree	kalignP_misc.c	/^void print_tree(struct aln_tree_node* p,struct alignment* aln,char* outfile)$/;"	f
printsimpleTree	kalignP_tree.c	/^void printsimpleTree(struct tree_node* p)$/;"	f
printtree	kalignP_tree.c	/^void printtree(struct aln_tree_node* p)$/;"	f
profile	kalignP.h	/^	float** profile;$/;"	m	struct:ntree_data
profile	kalignP.h	/^	int* profile;$/;"	m	struct:aln_tree_node
profile_alignment_main	kalignP_profile_alignment.c	/^void profile_alignment_main(struct alignment* aln,struct parameters* param,float** submatrix)$/;"	f
protein_pairwise_alignment_distance	kalignP_distance_calculation.c	/^float** protein_pairwise_alignment_distance(struct alignment* aln,float** dm,struct parameters* param,float**subm, int nj)$/;"	f
protein_profile_wu_distance	kalignP_profile_alignment.c	/^float** protein_profile_wu_distance(struct alignment* aln,float** dm,struct parameters* param, int nj)$/;"	f
protein_wu_distance	kalignP_distance_calculation.c	/^float** protein_wu_distance(struct alignment* si,float** dm,struct parameters* param, int nj)$/;"	f
protein_wu_distance2	kalignP_distance_calculation.c	/^float** protein_wu_distance2(struct alignment* aln,float** dm,struct parameters* param)$/;"	f
protein_wu_distance_calculation	kalignP_distance_calculation.c	/^float protein_wu_distance_calculation(struct bignode* hash[],const int* seq,const int seqlen,const int diagonals,const float mode) \/*diagonals = length1 + length2*\/$/;"	f
protein_wu_distance_calculation2	kalignP_distance_calculation.c	/^float protein_wu_distance_calculation2(struct node* hash[],int* seq,int seqlen,int diagonals,int mode)$/;"	f
protein_wu_distance_calculation3	kalignP_distance_calculation.c	/^float protein_wu_distance_calculation3(struct node* hash[],int* seq,int seqlen,int diagonals,int mode)$/;"	f
protein_wu_sw	kalignP_distance_calculation.c	/^struct alignment* protein_wu_sw(struct node* hash[],struct alignment* aln,int a,int b)$/;"	f
ps_dyn	kalignP_dp.c	/^int* ps_dyn(int* path, struct dp_matrix *dp,const float* prof1,const int* seq2,const int len_a,const int len_b,int sip)$/;"	f
q_sort	kalignP_misc.c	/^void q_sort(struct alignment* aln, int left, int right)$/;"	f
quickSort	kalignP_misc.c	/^void quickSort(struct alignment* aln, int array_size)$/;"	f
quiet	kalignP.h	/^	int quiet;$/;"	m	struct:parameters
read_alignment	kalignP_input.c	/^struct alignment* read_alignment(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_alignment_clustal	kalignP_input.c	/^struct alignment* read_alignment_clustal(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_alignment_from_swissprot	kalignP_input.c	/^struct alignment* read_alignment_from_swissprot(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_alignment_macsim_xml	kalignP_input.c	/^struct alignment* read_alignment_macsim_xml(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_alignment_stockholm	kalignP_input.c	/^struct alignment* read_alignment_stockholm(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_alignment_uniprot_xml	kalignP_input.c	/^struct alignment* read_alignment_uniprot_xml(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_ft	kalignP_input.c	/^struct feature* read_ft(struct feature* ft,char* p)\/*{{{*\/$/;"	f
read_matrix	kalignP_misc.c	/^float** read_matrix(float** subm,struct parameters* param)$/;"	f
read_sequences	kalignP_input.c	/^struct alignment* read_sequences(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_sequences_clustal	kalignP_input.c	/^struct alignment* read_sequences_clustal(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_sequences_from_swissprot	kalignP_input.c	/^struct alignment* read_sequences_from_swissprot(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_sequences_macsim_xml	kalignP_input.c	/^struct alignment* read_sequences_macsim_xml(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_sequences_new	kalignP_input.c	/^struct alignment* read_sequences_new(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_sequences_stockholm	kalignP_input.c	/^struct alignment* read_sequences_stockholm(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
read_sequences_uniprot_xml	kalignP_input.c	/^struct alignment* read_sequences_uniprot_xml(struct alignment* aln,char* string)\/*{{{*\/$/;"	f
readsimpletree	kalignP_tree.c	/^int* readsimpletree(struct tree_node* p,int* tree)$/;"	f
readtree	kalignP_misc.c	/^int* readtree(struct aln_tree_node* p,int* tree)$/;"	f
real_nj	kalignP_tree.c	/^struct aln_tree_node* real_nj(float **dm,int ntree)$/;"	f
real_upgma	kalignP_tree.c	/^struct aln_tree_node* real_upgma(float **dm,int ntree)$/;"	f
real_upgma	kalignP_upgma.c	/^struct aln_tree_node* real_upgma(float **dm)$/;"	f
realtree	kalignP.h	/^	struct aln_tree_node* realtree;$/;"	m	struct:ntree_data
reformat	kalignP.h	/^	int reformat;$/;"	m	struct:parameters
remove_nodes	kalignP_misc.c	/^void remove_nodes(struct node *n)$/;"	f
right	kalignP.h	/^	struct tree_node*right;$/;"	m	struct:tree_node
s	kalignP.h	/^	int** s;      \/*sequences in digit mapped by aacode*\/$/;"	m	struct:alignment
s	kalignP.h	/^	struct states* s;$/;"	m	struct:dp_matrix
same_feature_score	kalignP.h	/^	float same_feature_score;$/;"	m	struct:parameters
secret	kalignP.h	/^	float secret;$/;"	m	struct:parameters
seq	kalignP.h	/^	char**seq;    \/*sequences in text*\/$/;"	m	struct:alignment
seq	kalignP.h	/^	int* seq;$/;"	m	struct:aln_tree_node
sequence_info	kalignP.h	/^struct sequence_info{$/;"	s
set_gap_penalties	kalignP_profile.c	/^void set_gap_penalties(float* prof,int len,int nsip,float strength,int nsip_c)\/*{{{*\/$/;"	f
set_gap_penalties2	kalignP_profile.c	/^void set_gap_penalties2(float* prof,int len,int nsip,int window,float strength)\/*{{{*\/$/;"	f
set_gap_penalties_new	kalignP_profile.c	/^void set_gap_penalties_new(float* prof,int len,int nsip,float strength,int nsip_c, float* weightArray)\/*{{{*\/$/;"	f
set_large_gap_penalties	kalignP_hirschberg_large.c	/^void set_large_gap_penalties(float* prof,int len,int nsip)$/;"	f
set_unified_gap_penalties	kalignP_feature.c	/^void set_unified_gap_penalties(float* prof,int len,int nsip)$/;"	f
si	kalignP.h	/^	struct sequence_info** si;$/;"	m	struct:alignment
simple_backward_hirsch_pp_dyn	kalignP_simple_gaps.c	/^struct states* simple_backward_hirsch_pp_dyn(const int* prof1,const int* prof2,struct hirsch_mem* hm)$/;"	f
simple_foward_hirsch_pp_dyn	kalignP_simple_gaps.c	/^struct states* simple_foward_hirsch_pp_dyn(const int* prof1,const int* prof2,struct hirsch_mem* hm)$/;"	f
simple_hirsch_align_two_pp_vector	kalignP_simple_gaps.c	/^int* simple_hirsch_align_two_pp_vector(const int* prof1,const int* prof2,struct hirsch_mem* hm,int* hirsch_path,int input_states[],int old_cor[])$/;"	f
simple_hirsch_pp_dyn	kalignP_simple_gaps.c	/^int* simple_hirsch_pp_dyn(const int* prof1,const int* prof2,struct hirsch_mem* hm, int* hirsch_path)$/;"	f
simple_hirschberg_alignment	kalignP_simple_gaps.c	/^int** simple_hirschberg_alignment(struct alignment* aln,int* tree,int**submatrix, int** map)$/;"	f
simple_make_profile	kalignP_simple_gaps.c	/^int* simple_make_profile(int* prof, int* seq,int len,int** subm)$/;"	f
simple_update	kalignP_simple_gaps.c	/^int* simple_update(int* profa,int* profb,int* newp,int* path)$/;"	f
simpleinsert	kalignP_tree.c	/^struct tree_node* simpleinsert(struct tree_node* p,int target, int new_edge,int leaf_label)$/;"	f
sip	kalignP.h	/^	unsigned int** sip;   \/*index to the original sequences that are involved in the consensus*\/$/;"	m	struct:alignment
size	kalignP.h	/^	int size;$/;"	m	struct:hirsch_mem
size	kalignP_hirschberg_large.h	/^	int size;$/;"	m	struct:hirsch_large_mem
sl	kalignP.h	/^	unsigned int* sl;  \/*length of the sequence*\/$/;"	m	struct:alignment
smooth_gaps	kalignP_profile.c	/^void smooth_gaps(float* prof,int len,int window,float strength)\/*{{{*\/$/;"	f
smooth_window	kalignP.h	/^	int smooth_window;$/;"	m	struct:parameters
sn	kalignP.h	/^	char** sn;    \/*annotation lines*\/$/;"	m	struct:alignment
sort	kalignP.h	/^	char* sort;$/;"	m	struct:parameters
sort_in_relation	kalignP_misc.c	/^struct alignment* sort_in_relation(struct alignment* aln,char* sort)$/;"	f
sort_sequences	kalignP_misc.c	/^struct alignment* sort_sequences(struct alignment* aln,int* tree,char* sort)$/;"	f
ss_dyn	kalignP_dp.c	/^int* ss_dyn(float**subm,int* path, struct dp_matrix *dp,const int* seq1,const int* seq2,const int len_a,const int len_b)$/;"	f
start	kalignP.h	/^	int start;$/;"	m	struct:feature
start	kalignP.h	/^	int* start;$/;"	m	struct:names
starta	kalignP.h	/^	int starta;$/;"	m	struct:hirsch_mem
starta	kalignP_hirschberg_large.h	/^	int starta;$/;"	m	struct:hirsch_large_mem
startb	kalignP.h	/^	int startb;$/;"	m	struct:hirsch_mem
startb	kalignP_hirschberg_large.h	/^	int startb;$/;"	m	struct:hirsch_large_mem
states	kalignP.h	/^struct states{$/;"	s
stats	kalignP_stats.c	/^void stats(struct alignment* aln)$/;"	f
stride	kalignP.h	/^	int stride;$/;"	m	struct:feature_matrix
stride	kalignP_feature.c	/^static int stride;$/;"	v	file:
sub_matrix	kalignP.h	/^	char* sub_matrix;$/;"	m	struct:parameters
submatrix	kalignP.h	/^	float**submatrix;$/;"	m	struct:ntree_data
t	kalignP.h	/^	struct feature *t;$/;"	m	struct:utype_ufeat
tb	kalignP.h	/^	char** tb;$/;"	m	struct:dp_matrix
tb_mem	kalignP.h	/^	void* tb_mem;$/;"	m	struct:dp_matrix
tgpe	kalignP.h	/^	float tgpe;$/;"	m	struct:parameters
tgpe	kalignP.h	/^    float **tgpe;\/*position specific terminal gapextension array, added 2010-09-29*\/ $/;"	m	struct:alignment
tgpe	kalignP_main.c	/^float tgpe = (float)0.0;$/;"	v
tgpe_pos	kalignP_feature.c	/^static int tgpe_pos;$/;"	v	file:
ticker	kalignP_tree.c	/^int* ticker(int* milometer,int elements)$/;"	f
tmalloc	kalignP.h	45;"	d
traverse_ft	kalignP_feature.c	/^struct utype_ufeat* traverse_ft(struct utype_ufeat* utf,struct feature* n)$/;"	f
tree	kalignP.h	/^	char* tree;$/;"	m	struct:parameters
tree	kalignP.h	/^	int* tree;$/;"	m	struct:ntree_data
tree_node	kalignP.h	/^struct tree_node{$/;"	s
type	kalignP.h	/^	char* type;$/;"	m	struct:feature
update	kalignP_profile.c	/^float* update(const float* profa, const float* profb,float* newp,int* path,int sipa,int sipb)\/*{{{*\/$/;"	f
update2	kalignP_profile.c	/^float* update2(const float* profa, const float* profb,float* newp,int* path,int sipa,int sipb,float internal_gap_weight)\/*{{{*\/\/*{{{*\/$/;"	f
update_gaps	kalignP_misc.c	/^void update_gaps(int old_len,int*gis,int new_len,int *newgaps)$/;"	f
update_new	kalignP_profile.c	/^float* update_new(const float* profa, const float* profb,float* newp,int* path,int sipa,int sipb)\/*{{{*\/$/;"	f
update_new2	kalignP_profile.c	/^float* update_new2(float **profile,int* path,struct alignment *aln, int a, int b, int idxc)\/*{{{*\/$/;"	f
update_only_a	kalignP_profile.c	/^float* update_only_a(const float* profa, const float* profb,float* newp,int* path,int sipa,int sipb)\/*{{{*\/$/;"	f
upgma	kalignP_tree.c	/^int* upgma(float **dm,int* tree)$/;"	f
upgma	kalignP_upgma.c	/^int* upgma(float **dm,int* tree)$/;"	f
usage	kalignP_input.h	/^static char  usage[] = "\\n\\$/;"	v
utype_ufeat	kalignP.h	/^struct utype_ufeat{$/;"	s
value	kalignP.h	/^	char* value;$/;"	m	struct:sequence_info
x	kalignP.h	/^	float x;$/;"	m	struct:states
x	kalignP.h	/^	int x;$/;"	m	struct:dp_matrix
x	kalignP_hirschberg_large.h	/^	float x;$/;"	m	struct:large_states
y	kalignP.h	/^	int y;$/;"	m	struct:dp_matrix
zlevel	kalignP.h	/^	float zlevel;$/;"	m	struct:parameters
