/*#include "/us1/user/julie/dmalloc/malloc.h"*//*********************CLUSTALW.H*********************************************//****************************************************************************/   /*   Main header file for ClustalW.  Uncomment ONE of the following 4 lines   depending on which compiler you wish to use.   *//*#define VMS 1                 VAX or ALPHA VMS *//*#define MAC 1                 Think_C for Macintosh *//*#define MSDOS 1               Turbo C for PC's */#define UNIX 1                /*Ultrix/Decstation, Gnu C for                                 Sun, IRIX/SGI, OSF1/ALPHA *//***************************************************************************//***************************************************************************/#include "general.h"#define MAXNAMES		30	/* Max chars read for seq. names */#define MAXTITLES		60      /* Title length */#define FILENAMELEN 	256             /* Max. file name length */	#define UNKNOWN   0#define EMBLSWISS 1#define PIR 	  2#define PEARSON   3#define GDE    	  4#define CLUSTAL   5	/* DES */#define MSF       6 /* DES */#define RSF       7	/* JULIE */#define USER      8	/* DES */#define PHYLIP    9	/* DES */#define NEXUS    10/* DES */#define FASTA    11/* Ramu */#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   /* Number of lines of help sent to screen */#define PAGEWIDTH	80  /* maximum characters on output file page */#define LINELENGTH     	60  /* Output file line length */#define GCG_LINELENGTH 	50#ifdef VMS						/* Defaults for VAX VMS */#define COMMANDSEP '/'#define DIRDELIM ']'		/* Last character before file name in full file 							   specs */#define INT_SCALE_FACTOR 1000 /* Scaling factor to convert float to integer for profile scores */#elif MAC#define COMMANDSEP '/'#define DIRDELIM ':'#define INT_SCALE_FACTOR 100  /* Scaling factor to convert float to integer for profile scores */#elif MSDOS#define COMMANDSEP '/'#define DIRDELIM '\\'#define INT_SCALE_FACTOR 100  /* Scaling factor to convert float to integer for profile scores */#elif UNIX#define COMMANDSEP '-'#define DIRDELIM '/'#define INT_SCALE_FACTOR 1000 /* Scaling factor to convert float to integer for profile scores */#endif#define NUMRES 32		/* max size of comparison matrix */#define INPUT 0#define ALIGNED 1#define LEFT 1#define RIGHT 2#define NODE 0#define LEAF 1#define GAPCOL 32		/* position of gap open penalty in profile */#define LENCOL 33		/* position of gap extension penalty in profile */typedef struct node {		/* phylogenetic tree structure */        struct node *left;        struct node *right;        struct node *parent;        float dist;        sint  leaf;        int order;        char name[64];} stree, *treeptr;typedef struct {	char title[30];	char string[30];} MatMenuEntry;typedef struct {	int noptions;	MatMenuEntry opt[10];} MatMenu;#define MAXMAT 10typedef struct {	int llimit;		int ulimit;	short *matptr;	short *aa_xref;} SeriesMat;typedef struct {	int nmat;	SeriesMat mat[MAXMAT];} UserMatSeries;	/*   Prototypes*//* alnscore.c */void aln_score(void);/* interface.c */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);/* Align 2 alignments */void make_tree(char *phylip_name);void get_tree(char *phylip_name);sint profile_input(void);                        /* read a profile */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);/* calcgapcoeff.c */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);/* calcprf1.c */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);/* calcprf2.c */void calc_prf2(sint **profile, char **alignment, sint *seq_weight, sint prf_length,               sint first_seq, sint last_seq);/* calctree.c */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);/* clustalw.c */int main(int argc, char **argv);/* gcgcheck.c */int SeqGCGCheckSum(char *seq, sint len);/* malign.c */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);/* pairalign.c */sint pairalign(sint istart, sint iend, sint jstart, sint jend);/* prfalign.c */lint prfalign(sint *group, sint *aligned);/* random.c */unsigned long linrand(unsigned long r);unsigned long addrand(unsigned long r);void addrandinit(unsigned long s);/* readmat.c */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);/* sequence.c */void fill_chartab(void);sint readseqs(sint first_seq);/* showpair.c */void show_pair(sint istart, sint iend, sint jstart, sint jend);/* trees.c */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);/* util.c */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);