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clustalw.h File Reference

#include "general.h"

Defines

#define MSDOS   1
#define MAXNAMES   30
#define MAXTITLES   60
#define FILENAMELEN   256
#define UNKNOWN   0
#define EMBLSWISS   1
#define PIR   2
#define PEARSON   3
#define GDE   4
#define CLUSTAL   5
#define MSF   6
#define RSF   7
#define USER   8
#define PHYLIP   9
#define NEXUS   10
#define FASTA   11
#define NONE   0
#define SECST   1
#define GMASK   2
#define PROFILE   0
#define SEQUENCE   1
#define BS_NODE_LABELS   2
#define BS_BRANCH_LABELS   1
#define PAGE_LEN   22
#define PAGEWIDTH   80
#define LINELENGTH   60
#define GCG_LINELENGTH   50
#define COMMANDSEP   '/'
#define DIRDELIM   '\\'
#define INT_SCALE_FACTOR   100
#define NUMRES   32
#define INPUT   0
#define ALIGNED   1
#define LEFT   1
#define RIGHT   2
#define NODE   0
#define LEAF   1
#define GAPCOL   32
#define LENCOL   33
#define MAXMAT   10

Typedefs

typedef node stree
 Part of the ClustalW package.
typedef nodetreeptr
 Part of the ClustalW package.

Functions

void aln_score (void)
void parse_params (Boolean)
void init_amenu (void)
void init_interface (void)
void main_menu (void)
FILE * open_output_file (char *, char *, char *, char *)
FILE * open_explicit_file (char *)
sint seq_input (Boolean)
Boolean open_alignment_output (char *)
void create_alignment_output (sint fseq, sint lseq)
void align (char *phylip_name)
void profile_align (char *p1_tree_name, char *p2_tree_name)
void make_tree (char *phylip_name)
void get_tree (char *phylip_name)
sint profile_input (void)
void new_sequence_align (char *phylip_name)
Boolean user_mat (char *, short *, short *)
Boolean user_mat_series (char *, short *, short *)
void get_help (char)
void clustal_out (FILE *, sint, sint, sint, sint)
void nbrf_out (FILE *, sint, sint, sint, sint)
void gcg_out (FILE *, sint, sint, sint, sint)
void phylip_out (FILE *, sint, sint, sint, sint)
void gde_out (FILE *, sint, sint, sint, sint)
void nexus_out (FILE *, sint, sint, sint, sint)
void fasta_out (FILE *, sint, sint, sint, sint)
void print_sec_struct_mask (int prf_length, char *mask, char *struct_mask)
void fix_gaps (void)
void calc_gap_coeff (char **alignment, sint *gaps, sint **profile, Boolean struct_penalties, char *gap_penalty_mask, sint first_seq, sint last_seq, sint prf_length, sint gapcoef, sint lencoef)
void calc_prf1 (sint **profile, char **alignment, sint *gaps, sint matrix[NUMRES][NUMRES], sint *seq_weight, sint prf_length, sint first_seq, sint last_seq)
void calc_prf2 (sint **profile, char **alignment, sint *seq_weight, sint prf_length, sint first_seq, sint last_seq)
void calc_seq_weights (sint first_seq, sint last_seq, sint *seq_weight)
void create_sets (sint first_seq, sint last_seq)
sint read_tree (char *treefile, sint first_seq, sint last_seq)
void clear_tree (treeptr p)
sint calc_similarities (sint nseqs)
int main (int argc, char **argv)
int SeqGCGCheckSum (char *seq, sint len)
sint malign (sint istart, char *phylip_name)
sint seqalign (sint istart, char *phylip_name)
sint palign1 (void)
float countid (sint s1, sint s2)
sint palign2 (char *p1_tree_name, char *p2_tree_name)
sint pairalign (sint istart, sint iend, sint jstart, sint jend)
lint prfalign (sint *group, sint *aligned)
unsigned long linrand (unsigned long r)
unsigned long addrand (unsigned long r)
void addrandinit (unsigned long s)
void init_matrix (void)
sint get_matrix (short *matptr, short *xref, sint matrix[NUMRES][NUMRES], Boolean neg_flag, sint scale)
sint read_user_matrix (char *filename, short *usermat, short *xref)
sint read_matrix_series (char *filename, short *usermat, short *xref)
int getargs (char *inline1, char *args[], int max)
void fill_chartab (void)
sint readseqs (sint first_seq)
void show_pair (sint istart, sint iend, sint jstart, sint jend)
void phylogenetic_tree (char *phylip_name, char *clustal_name, char *dist_name, char *nexus_name, char *pim_name)
void bootstrap_tree (char *phylip_name, char *clustal_name, char *nexus_name)
sint dna_distance_matrix (FILE *tree)
sint prot_distance_matrix (FILE *tree)
void guide_tree (FILE *tree, int first_seq, sint nseqs)
void calc_percidentity (FILE *pfile)
void alloc_aln (sint nseqs)
void realloc_aln (sint first_seq, sint nseqs)
void free_aln (sint nseqs)
void alloc_seq (sint seq_no, sint length)
void realloc_seq (sint seq_no, sint length)
void free_seq (sint seq_no)
void * ckalloc (size_t bytes)
void * ckrealloc (void *ptr, size_t bytes)
void * ckfree (void *ptr)
char prompt_for_yes_no (char *title, char *prompt)
void fatal (char *msg,...)
void error (char *msg,...)
void warning (char *msg,...)
void info (char *msg,...)
char * rtrim (char *str)
char * blank_to_ (char *str)
char * upstr (char *str)
char * lowstr (char *str)
void getstr (char *instr, char *outstr)
double getreal (char *instr, double minx, double maxx, double def)
int getint (char *instr, int minx, int maxx, int def)
void do_system (void)
Boolean linetype (char *line, char *code)
Boolean keyword (char *line, char *code)
Boolean blankline (char *line)
void get_path (char *str, char *path)

Define Documentation

#define ALIGNED   1
 

#define BS_BRANCH_LABELS   1
 

#define BS_NODE_LABELS   2
 

#define CLUSTAL   5
 

#define COMMANDSEP   '/'
 

#define DIRDELIM   '\\'
 

#define EMBLSWISS   1
 

#define FASTA   11
 

#define FILENAMELEN   256
 

#define GAPCOL   32
 

#define GCG_LINELENGTH   50
 

#define GDE   4
 

#define GMASK   2
 

#define INPUT   0
 

#define INT_SCALE_FACTOR   100
 

#define LEAF   1
 

#define LEFT   1
 

#define LENCOL   33
 

#define LINELENGTH   60
 

#define MAXMAT   10
 

#define MAXNAMES   30
 

#define MAXTITLES   60
 

#define MSDOS   1
 

#define MSF   6
 

#define NEXUS   10
 

#define NODE   0
 

#define NONE   0
 

#define NUMRES   32
 

#define PAGE_LEN   22
 

#define PAGEWIDTH   80
 

#define PEARSON   3
 

#define PHYLIP   9
 

#define PIR   2
 

#define PROFILE   0
 

#define RIGHT   2
 

#define RSF   7
 

#define SECST   1
 

#define SEQUENCE   1
 

#define UNKNOWN   0
 

#define USER   8
 


Typedef Documentation

typedef struct node stree
 

Part of the ClustalW package.

typedef struct node * treeptr
 

Part of the ClustalW package.


Function Documentation

unsigned long addrand unsigned long  r  ) 
 

void addrandinit unsigned long  s  ) 
 

void align char *  phylip_name  ) 
 

void alloc_aln sint  nseqs  ) 
 

void alloc_seq sint  seq_no,
sint  length
 

void aln_score void   ) 
 

char* blank_to_ char *  str  ) 
 

Boolean blankline char *  line  ) 
 

void bootstrap_tree char *  phylip_name,
char *  clustal_name,
char *  nexus_name
 

void calc_gap_coeff char **  alignment,
sint *  gaps,
sint **  profile,
Boolean  struct_penalties,
char *  gap_penalty_mask,
sint  first_seq,
sint  last_seq,
sint  prf_length,
sint  gapcoef,
sint  lencoef
 

void calc_percidentity FILE *  pfile  ) 
 

void calc_prf1 sint **  profile,
char **  alignment,
sint *  gaps,
sint  matrix[NUMRES][NUMRES],
sint *  seq_weight,
sint  prf_length,
sint  first_seq,
sint  last_seq
 

void calc_prf2 sint **  profile,
char **  alignment,
sint *  seq_weight,
sint  prf_length,
sint  first_seq,
sint  last_seq
 

void calc_seq_weights sint  first_seq,
sint  last_seq,
sint *  seq_weight
 

sint calc_similarities sint  nseqs  ) 
 

void* ckalloc size_t  bytes  ) 
 

void* ckfree void *  ptr  ) 
 

void* ckrealloc void *  ptr,
size_t  bytes
 

void clear_tree treeptr  p  ) 
 

void clustal_out FILE *  ,
sint  ,
sint  ,
sint  ,
sint 
 

float countid sint  s1,
sint  s2
 

void create_alignment_output sint  fseq,
sint  lseq
 

void create_sets sint  first_seq,
sint  last_seq
 

sint dna_distance_matrix FILE *  tree  ) 
 

void do_system void   ) 
 

void error char *  msg,
  ...
 

void fasta_out FILE *  ,
sint  ,
sint  ,
sint  ,
sint 
 

void fatal char *  msg,
  ...
 

void fill_chartab void   ) 
 

void fix_gaps void   ) 
 

void free_aln sint  nseqs  ) 
 

void free_seq sint  seq_no  ) 
 

void gcg_out FILE *  ,
sint  ,
sint  ,
sint  ,
sint 
 

void gde_out FILE *  ,
sint  ,
sint  ,
sint  ,
sint 
 

void get_help char   ) 
 

sint get_matrix short *  matptr,
short *  xref,
sint  matrix[NUMRES][NUMRES],
Boolean  neg_flag,
sint  scale
 

void get_path char *  str,
char *  path
 

void get_tree char *  phylip_name  ) 
 

int getargs char *  inline1,
char *  args[],
int  max
 

int getint char *  instr,
int  minx,
int  maxx,
int  def
 

double getreal char *  instr,
double  minx,
double  maxx,
double  def
 

void getstr char *  instr,
char *  outstr
 

void guide_tree FILE *  tree,
int  first_seq,
sint  nseqs
 

void info char *  msg,
  ...
 

void init_amenu void   ) 
 

void init_interface void   ) 
 

void init_matrix void   ) 
 

Boolean keyword char *  line,
char *  code
 

Boolean linetype char *  line,
char *  code
 

unsigned long linrand unsigned long  r  ) 
 

char* lowstr char *  str  ) 
 

int main int  argc,
char **  argv
 

void main_menu void   ) 
 

void make_tree char *  phylip_name  ) 
 

sint malign sint  istart,
char *  phylip_name
 

void nbrf_out FILE *  ,
sint  ,
sint  ,
sint  ,
sint 
 

void new_sequence_align char *  phylip_name  ) 
 

void nexus_out FILE *  ,
sint  ,
sint  ,
sint  ,
sint 
 

Boolean open_alignment_output char *   ) 
 

FILE* open_explicit_file char *   ) 
 

FILE* open_output_file char *  ,
char *  ,
char *  ,
char * 
 

sint pairalign sint  istart,
sint  iend,
sint  jstart,
sint  jend
 

sint palign1 void   ) 
 

sint palign2 char *  p1_tree_name,
char *  p2_tree_name
 

void parse_params Boolean   ) 
 

void phylip_out FILE *  ,
sint  ,
sint  ,
sint  ,
sint 
 

void phylogenetic_tree char *  phylip_name,
char *  clustal_name,
char *  dist_name,
char *  nexus_name,
char *  pim_name
 

lint prfalign sint *  group,
sint *  aligned
 

void print_sec_struct_mask int  prf_length,
char *  mask,
char *  struct_mask
 

void profile_align char *  p1_tree_name,
char *  p2_tree_name
 

sint profile_input void   ) 
 

char prompt_for_yes_no char *  title,
char *  prompt
 

sint prot_distance_matrix FILE *  tree  ) 
 

sint read_matrix_series char *  filename,
short *  usermat,
short *  xref
 

sint read_tree char *  treefile,
sint  first_seq,
sint  last_seq
 

sint read_user_matrix char *  filename,
short *  usermat,
short *  xref
 

sint readseqs sint  first_seq  ) 
 

void realloc_aln sint  first_seq,
sint  nseqs
 

void realloc_seq sint  seq_no,
sint  length
 

char* rtrim char *  str  ) 
 

sint seq_input Boolean   ) 
 

sint seqalign sint  istart,
char *  phylip_name
 

int SeqGCGCheckSum char *  seq,
sint  len
 

void show_pair sint  istart,
sint  iend,
sint  jstart,
sint  jend
 

char* upstr char *  str  ) 
 

Boolean user_mat char *  ,
short *  ,
short * 
 

Boolean user_mat_series char *  ,
short *  ,
short * 
 

void warning char *  msg,
  ...
 


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