xcolor.c

经典生物信息学多序列比对工具clustalw

#include <stdio.h>
#include <stdarg.h>
#include <string.h>
#include <time.h>
#include <ctype.h>

#include <vibrant.h>

#include "clustalw.h"
#include "xmenu.h"

#define SIMPLE 1
#define COMPOUND 2

#define LEFTMARGIN 20
#define SEPARATION 2
#define CHARHEIGHT 10
#define CHARWIDTH 6
#define A4X 564
#define A4Y 800
#define A3X 832
#define A3Y 1159
#define USLETTERX 564
#define USLETTERY 750
#define SCOREY 3
#define HEADER 7
#define NOHEADER 0
#define MAXRESNO 6

#define MAXPARLEN 10
#define MAXPAR 100
 
static void print_ps_info(FILE *fd,int pagesize);
static void print_page_header(FILE *fd,int ps_rotation,int maxx,int maxy,
int page,int numpages,Boolean header,char *str_time,
char *ps_file,int ps_xtrans,int ps_ytrans,float ps_scale);
static void print_header_line(FILE *fd,panel_data name_data, panel_data seq_data,
int ix,int fr,int lr);
static void print_footer_line(FILE *fd,panel_data name_data, panel_data seq_data,
int ix,int fr,int lr);
static void print_quality_curve(FILE *fd,panel_data seq_data
,int fr,int lr,int score_height);
static void print_seq_line(FILE *fd,panel_data name_data, panel_data seq_data,
int row,int seq,int fr,int lr,int res_number);


typedef struct consensus_parameters
{
char consensus;
int cutoff;
int length;
char cutoff_list[20];
} consensus_para;
 
typedef struct color_parameters
{
int type;
char residue;
int color;
int length;
char cons_list[20];
} color_para;

static void init_color_lut(FILE *fd);
static int init_printer_lut(char *filename);
static char *init_consensus(panel_data data);
static int SaveColPara(char word[MAXPAR][MAXPARLEN],int num_words,int count);
static int SaveConPara(char word[MAXPAR][MAXPARLEN],int num_words,int count);
static int get_line(char *sinline,char word[MAXPAR][MAXPARLEN]);
static int residue_color(char res,char consensus);
static Boolean commentline(char *line);

#define DEF_NCOLORS 4
#define MAX_NCOLORS 8
#define DEFAULT_COLOR 0

typedef struct rgb_color {
	char name[20];
	float r,g,b;
} rgb_color;

rgb_color def_color_lut[MAX_NCOLORS]={
	"RED"          ,0.9, 0.1, 0.1,
	"BLUE"         ,0.1, 0.1, 0.7,
	"GREEN"        ,0.1, 0.9, 0.1,
	"ORANGE"       ,0.9, 0.6, 0.3,
	"CYAN"         ,0.1, 0.9, 0.9,
	"PINK"         ,0.9, 0.5, 0.5,
	"MAGENTA"      ,0.9, 0.1, 0.9,
	"YELLOW"       ,0.9, 0.9, 0.0,
};

char def_aacolor[MAX_NCOLORS][26]={"krh",
				"fwy",
				"ilmv",
				"gpst"};

char def_dnacolor[MAX_NCOLORS][26]={"a",
				"c",
				"tu",
				"g"};

extern char revision_level[];

extern int max_names;
 
extern int ncolors;
extern int ncolor_pars;
extern color color_lut[];
extern int inverted;
extern Boolean residue_exceptions;
extern Boolean segment_exceptions;
extern Boolean dnaflag;

int NumColParas;
int NumConParas;

color_para Col_Par[100];
consensus_para Con_Par[100];


void make_colormask(panel_data data)
{
	int i,j;

	for(i=0;i<data.nseqs;i++)
		for(j=0;j<data.ncols;j++)
			data.colormask[i][j] = DEFAULT_COLOR;

	if (ncolors > 1)
	{
        	data.consensus=init_consensus(data);

		for(i=0;i<data.nseqs;i++)
			for(j=0;j<data.ncols;j++)
				data.colormask[i][j] = residue_color(data.lines[i][j],data.consensus[j]);

	}
}

static void init_color_lut(FILE *fd)
{ 
	char sinline[1025];
	char *args[10];
	int i,numargs;
	Boolean found=FALSE;

	if (inverted==FALSE)
	{
        	strcpy(color_lut[0].name,"BLACK");
		color_lut[0].r=0.4;
		color_lut[0].g=0.4;
		color_lut[0].b=0.4;
		SelectColor(color_lut[0].r*255, color_lut[0].g*255, color_lut[0].b*255);
		color_lut[0].val=GetColor();
	}
	else
	{
        	strcpy(color_lut[0].name,"WHITE");
		color_lut[0].r=1.0;
		color_lut[0].g=1.0;
		color_lut[0].b=1.0;
		SelectColor(color_lut[0].r*255, color_lut[0].g*255, color_lut[0].b*255);
		color_lut[0].val=GetColor();
	}

	ncolors=1;
	if (fd != NULL)
	{
		for (;fgets(sinline,1024,fd)!=NULL;)
		{
			sinline[strlen(sinline)-1] = '\0';
			if (strcmp(sinline,"@rgbindex")==0) 
			{
				found = TRUE;
				break;
			}
		}
	}
	if (found == TRUE)
	{
		for (;fgets(sinline,1024,fd)!=NULL;)
		{
			if (commentline(sinline)) continue;
			if (sinline[0]=='@') break;
			numargs = getargs(sinline, args, 4);
			if (numargs != 4)
			{
				error("Problem in color rgb index - line %d\n",ncolors+1);
				break;
			}
			else
			{
				strcpy(color_lut[ncolors].name, args[0]);
				color_lut[ncolors].r=atof(args[1]);
				color_lut[ncolors].g=atof(args[2]);
				color_lut[ncolors].b=atof(args[3]);
				SelectColor(color_lut[ncolors].r*255, color_lut[ncolors].g*255, color_lut[ncolors].b*255);
				color_lut[ncolors].val=GetColor();
				ncolors++;
				if (ncolors>=MAXCOLORS) 
				{
					warning("Only using first %d colors in rgb index.",MAXCOLORS);
					break;
				}
			}
		}

	}

/* if we can't find a table, use the hard-coded colors */
        if (ncolors==1)
        {
		ncolors=MAX_NCOLORS+1;
		for(i=1;i<ncolors;i++)
		{
			strcpy(color_lut[i].name,def_color_lut[i-1].name);
			color_lut[i].r=def_color_lut[i-1].r;
			color_lut[i].g=def_color_lut[i-1].g;
			color_lut[i].b=def_color_lut[i-1].b;
			SelectColor(color_lut[i].r*255, color_lut[i].g*255, color_lut[i].b*255);
			color_lut[i].val=GetColor();
		}
	}

}

void init_color_parameters(char *par_file)
{

	int i,j,err;
	char sinline[1025];
	int maxparas = 50;
	char inword[MAXPAR][MAXPARLEN];
	int num_words;
	int in_consensus=FALSE,in_color=FALSE;
	int consensus_found=FALSE,color_found=FALSE;
	FILE *par_fd=NULL;

	if(par_file!=NULL)
		par_fd=fopen(par_file,"r");
	if(par_fd==NULL)
	{
                info("No color file found - using defaults");
		ncolor_pars=0;
	}

	init_color_lut(par_fd);
	if (par_fd != NULL) rewind(par_fd);
	if (ncolors==0) return;

	NumColParas=0;
	NumConParas=0;
	if (par_fd != NULL)
	{
		for(;fgets(sinline,1024,par_fd) != NULL;)
		{
			sinline[strlen(sinline)-1] = '\0';
			if (commentline(sinline)) continue;
			switch(sinline[0])
			{	
				case '\0':
					break;
				case '@':
					if (strcmp((char*)(sinline+1),"consensus")==0) 
					{
						in_consensus = TRUE;
						in_color = FALSE;
						consensus_found = TRUE;
					}
					else if (strcmp((char*)(sinline+1),"color")==0)
					{
						in_consensus = FALSE;
						in_color = TRUE;
						color_found = TRUE;
					}
					break;
				default:
					num_words = get_line(sinline,inword);
					if (in_consensus == TRUE) 
					{
						err = SaveConPara(inword,num_words,NumConParas);
						if (err == 0) NumConParas++;
					}
					else if (in_color == TRUE)
					{
						err = SaveColPara(inword,num_words,NumColParas);
						if (err == 0) NumColParas++;
					}
	
					if((NumColParas>maxparas) || (NumConParas>maxparas))
				     	error("Too many parameters in color file");
	
			}
		}
		if (color_found == FALSE)
		{
			error("@color not found in parameter file - using defaults\n");
			ncolor_pars=0;
		}
		fclose(par_fd);
	}
	ncolor_pars=NumColParas;

/* if no color parameters found, use the default aa groupings */
	if(ncolor_pars==0)
	{
		if (dnaflag)
		{
			for(i=0;i<DEF_NCOLORS;i++)
			{
				for(j=0;j<strlen(def_dnacolor[i]);j++)
				{
					Col_Par[ncolor_pars].type=SIMPLE;
					Col_Par[ncolor_pars].residue=def_dnacolor[i][j];
					Col_Par[ncolor_pars].color=i+1;
					ncolor_pars++;
				}
			}
		}
		else
		{
			for(i=0;i<DEF_NCOLORS;i++)
			{
				for(j=0;j<strlen(def_aacolor[i]);j++)
				{
					Col_Par[ncolor_pars].type=SIMPLE;
					Col_Par[ncolor_pars].residue=def_aacolor[i][j];
					Col_Par[ncolor_pars].color=i+1;
					ncolor_pars++;
				}
			}
		}
	}
	NumColParas=ncolor_pars;
}

char *find_file(char *def_file)
{
	char filename[FILENAMELEN];
	char *retname;
	FILE *fd;
	Boolean found=FALSE;
#ifdef UNIX
        char *path, *path1, *deb, *fin;
        sint lf, ltot;
        char *home;
#endif


        strcpy(filename,def_file);
        fd = fopen(filename,"r");
	if (fd != NULL)
		found=TRUE;
#ifdef UNIX
        if (found == FALSE)
        {
                home = getenv("HOME");
		if (home != NULL)
		{
                	sprintf(filename,"%s/%s",home,def_file);
                	fd = fopen(filename,"r");
			if (fd != NULL)
				found=TRUE;
		}
                if (found == FALSE)
                {
			path=getenv("PATH");/* get the list of path directories,
                        			separated by : */
			/* added for File System Standards  - Francois */
			path1=(char *)ckalloc((strlen(path)+64)*sizeof(char));
			strcpy(path1,path);
			strcat(path1,"/usr/share/clustalx:/usr/local/share/clustalx"); 

        		lf=(sint)strlen(def_file);
        		deb=path1;
        		do
                	{
                		fin=strchr(deb,':');
                		if(fin!=NULL)
                        	{
					strncpy(filename,deb,fin-deb);
					ltot=fin-deb;
				}
                		else
                        	{
					strcpy(filename,deb);
					ltot=(sint)strlen(filename);
				}
                		/* now one directory is in filename */
                		if( ltot + lf + 1 <= FILENAMELEN)
                        	{
                        		filename[ltot]='/';
                        		strcpy(filename+ltot+1,def_file); /* now dir is appended with filename */
                        		if( (fd = fopen(filename,"r") ) != NULL)
					{
						found=TRUE;
						break;
                        		}
                        	}
                		else found = FALSE;
                		deb=fin+1;
                	}
        		while (fin != NULL);
                }
        }
#endif
	if (found == TRUE)
	{
		fclose(fd);
		retname=(char *)ckalloc((strlen(filename)+1)*sizeof(char));
		strcpy(retname,filename);
	}
	else
		retname=NULL;
	return(retname);
}
 
static char *init_consensus(panel_data data)
{
	char *cons_data;
        int num_res,seq,res,par,cons_total,i;
        char residue;
 
	cons_data=(char *)ckalloc((data.ncols+1)*sizeof(char));

        for (res=0;res<data.ncols;res++)
        {
                cons_data[res] = '.';
                for (par=0;par<NumConParas;par++)
                {
                        cons_total = num_res = 0;
                        for (seq=0;seq<data.nseqs;seq++)
                        {
				residue=tolower(data.lines[seq][res]);
				if (isalpha(residue))
					num_res++;
                                for (i=0;i<Con_Par[par].length;i++)
                                        if (residue==tolower(Con_Par[par].cutoff_list[i]))
                                                cons_total++;
                        }
                        if (num_res != 0)
                                if (((cons_total*100)/num_res) >= Con_Par[par].cutoff)
                                        cons_data[res] = Con_Par[par].consensus;
                }
        }

	return(cons_data);
}

static int SaveColPara(char word[MAXPAR][MAXPARLEN],int num_words,int count)
{

	int i;

	if (num_words < 3)
	{
		error("Wrong format in color list");
		return(1);
	}

	if (word[1][0] != '=')
	{
		error("Wrong format in color list");
		return(2);
	}

	if (num_words == 3)
	{
		Col_Par[count].type = SIMPLE;
		Col_Par[count].residue = word[0][0];
		Col_Par[count].color = -1;
		for (i=0;i<ncolors;i++)
			if (strcmp(word[2],color_lut[i].name)==0) Col_Par[count].color = i;
		if (Col_Par[count].color == -1)
		{
			error("%s not found in rgb index - using %s",word[2],color_lut[0].name);
			Col_Par[count].color = 0;
		}
	}
	else
	{
		if (strcmp(word[3],"if")==0)
		{
			Col_Par[count].type = COMPOUND;
			Col_Par[count].residue = word[0][0];
			Col_Par[count].color = -1;
			for (i=0;i<ncolors;i++)
				if (strcmp(word[2],color_lut[i].name)==0) Col_Par[count].color = i;
			if (Col_Par[count].color == -1)
			{
				error("%s not found in rgb index - using %s",word[2],color_lut[0].name);
				Col_Par[count].color = 0;
			}
			Col_Par[count].length = num_words - 4;
			for (i=4;i<num_words;i++)
				Col_Par[count].cons_list[i-4] = word[i][0];
		}
		else
		{
			error("Wrong format in color list");
			return(3);
		}
	}

	return(0);
		
}


static int SaveConPara(char word[MAXPAR][MAXPARLEN],int num_words,int count)
{

	int i;

	if (num_words < 3)
	{
		error("Wrong format in consensus list");
		return(1);
	}

	if (word[1][0] != '=')
	{
		error("Wrong format in consensus list");
		return(2);
	}

	Con_Par[count].consensus = word[0][0];
	for (i=0;i<MAXPARLEN-1;i++)
	{
		if(word[2][i]=='%') word[2][i] = '\0';
	}
	Con_Par[count].cutoff = atoi(word[2]);
	Con_Par[count].length = num_words - 3;
	for (i=3;i<num_words;i++)
	{
		Con_Par[count].cutoff_list[i-3] = word[i][0];
	}

	return(0);
		
}

static int get_line(char *sinline,char word[MAXPAR][MAXPARLEN])
{
	int i=0, j, word_count=0, char_count=0;
	int in_word=FALSE;

	for(i=0;i<MAXPAR-1;i++)
		for(j=0;j<MAXPARLEN-1;j++)
			word[i][j]='\0';

	for (i=0;i<=strlen(sinline);i++)
	{
		switch (sinline[i])
		{
			case ' ':
			case '\t':
			case '\0':
			case ':':
				if (in_word)
				{
					word[word_count][char_count] = '\0';
					word_count++;
					char_count = 0;
					in_word = FALSE;
				}
				break;
			default:
				in_word = TRUE;
				word[word_count][char_count] = sinline[i];
				char_count++;
				break;
		}		

	}
	return(word_count);
}

static int residue_color(char res,char consensus)
{
	int i,j;

        for (i=0;i<NumColParas;i++)
        {
                if (tolower(res) == tolower(Col_Par[i].residue))
                {
                        switch (Col_Par[i].type)
                        {
                        case SIMPLE:
                                return(Col_Par[i].color);
                        case COMPOUND:
                                for (j=0;j<Col_Par[i].length;j++)
                                {
                                        if (consensus == Col_Par[i].cons_list[j]
)