--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include "distance_matrix.h"
+#include "statgeom.h"
+#include "split.h"
+#include "cluster.h"
+#include "treeplot.h"
+#include "utils.h"
+
+
+#define PUBLIC
+#define PRIVATE static
+
+PRIVATE char scale1[] = "....,....1....,....2....,....3....,....4";
+PRIVATE char scale2[] = "....,....5....,....6....,....7....,....8";
+
+PRIVATE void usage(void);
+
+main(int argc, char *argv[])
+{
+ int n,i,j,l;
+ int intty;
+ int outtty;
+ char *mask, junk[20];
+ char **s;
+ char **ss[4];
+ float *B;
+ float **dm;
+ Split *S;
+ Union *U;
+ char DistAlgorithm='H';
+ int nn[4];
+ short Do_Split=0, Do_Wards=0, Do_Stg=1, Do_4_Stg=0, Do_Nj=0, Do_Mat=0;
+ float per_digit, per_gap;
+
+ mask = space(sizeof(char)*54);
+ strcpy (mask,"%ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz");
+ for (i=1; i<argc; i++) {
+ if (argv[i][0]=='-') {
+ switch ( argv[i][1] ) {
+ case 'X':
+ if (argv[i][2]=='\0') { Do_Stg = 1 ; break; }
+ Do_Split = 0;
+ Do_Wards = 0;
+ Do_Stg = 0;
+ Do_Nj = 0;
+ for(j=2;j<strlen(argv[i]);j++) {
+ switch(argv[i][j]) {
+ case 's' : Do_Split = 1;
+ break;
+ case 'w' : Do_Wards = 1;
+ break;
+ case 'b' : Do_Stg = 1;
+ break;
+ case 'n' : Do_Nj = 1;
+ break;
+ case 'm' : Do_Mat = 1;
+ break;
+ default :
+ usage();
+ }
+ }
+ break;
+ case 'Q':
+ Do_4_Stg = 1;
+ break;
+ case 'M':
+ if(mask) { free(mask); mask = NULL; }
+ switch (argv[i][2] ) {
+ case '\0' :
+ usage();
+ break;
+ case 'a' :
+ mask = space(sizeof(char)*54);
+ strcpy(mask,
+ "%ABCDEFGHIJKLMNOPQRSTUVWabcdefghijklmnopqrstuvwxyz");
+ if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
+ break;
+ case 'u' :
+ mask = space(sizeof(char)*28);
+ strcpy(mask,"~ABCDEFGHIJKLMNOPQRSTUVW");
+ break;
+ case 'l' :
+ mask = space(sizeof(char)*28);
+ strcpy(mask,"~abcdefghijklmnopqrstuvwxyz");
+ break;
+ case 'c' :
+ mask = space(sizeof(char)*12);
+ strcpy(mask,"~1234567890");
+ break;
+ case 'n' :
+ mask = space(sizeof(char)*64);
+ strcpy (mask,
+ "%ABCDEFGHIJKLMNOPQRSTUVWabcdefghijklmnopqrstuvwxyz1234567890");
+ if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
+ break;
+ case 'R' : /* RNA */
+ mask = space(sizeof(char)*10);
+ strcpy(mask,"%GCAUgcau");
+ if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
+ break;
+ case 'D' : /* DNA */
+ mask = space(sizeof(char)*10);
+ strcpy (mask,"%GCATgcat");
+ if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
+ break;
+ case 'A' : /* AMINOACIDS */
+ mask = space(sizeof(char)*42);
+ strcpy(mask,"%ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy");
+ if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
+ break;
+ case 'S' : /* SECONDARY STRUCTURES */
+ mask = space(sizeof(char)*6);
+ strcpy(mask,"~().^");
+ break;
+ case '%' : /* ARBITRARY ALPHABETS */
+ l = strlen(argv[i]);
+ if(argv[i][l] == '+'){
+ mask = space(sizeof(char)*(l-2));
+ mask[0] = '~';
+ for(j=1;j<=l-4;j++) mask[j] = argv[i][j+2];
+ mask[l-3]='\0';
+ }
+ if(argv[i][l] == '!'){
+ mask = space(sizeof(char)*(l-2));
+ mask[0] = '!';
+ for(j=1;j<=l-4;j++) mask[j] = argv[i][j+2];
+ mask[l-3]='\0';
+ }
+ else {
+ mask = space(sizeof(char)*(l-1));
+ mask[0] = '%';
+ for(j=1;j<=l-3;j++) mask[j] = argv[i][j+2];
+ mask[l-2]='\0';
+ }
+ break;
+ default :
+ usage();
+ }
+ break;
+ case 'D' : /* choose algorithm */
+ switch(argv[i][2]) {
+ case '\0' :
+ usage();
+ break;
+ case 'H' :
+ DistAlgorithm = 'H';
+ break;
+ case 'A' :
+ DistAlgorithm = 'A';
+ if(argv[i][3]==',') {
+ per_digit=-1.;
+ sscanf(argv[i],"%[^,],%g",junk,&per_digit);
+ if(per_digit<0.) usage();
+ per_gap = per_digit;
+ Set_StrEdit_GapCosts(per_digit,per_gap);
+ }
+ break;
+ case 'G' :
+ DistAlgorithm = 'G';
+ if(argv[i][3]==',') {
+ per_digit=-1.;
+ per_gap =-1.;
+ sscanf(argv[i]+4,"%f,%f",&per_digit,&per_gap);
+ if((per_digit<0.)||(per_gap<0)) usage();
+ Set_StrEdit_GapCosts(per_digit,per_gap);
+ }
+ break;
+ default:
+ usage();
+ }
+ break;
+ case 'd' : /* choose distance matrix */
+ switch(argv[i][2]) {
+ case 'D' : /* Dayhoff Distances */
+ case 'A' : /* Aminoacid Distance (Hofacker & Borstnik) */
+ case 'B' : /* RY distances for nucleotides */
+ case 'H' : /* Hogeweg's Distance for Secondary Structures */
+ case 'S' : /* Simple Distance (superfluous option) */
+ Set_StrEdit_CostMatrix(argv[i][2]);
+ break;
+ default :
+ usage();
+ }
+ break;
+ default :
+ usage();
+ }
+ }
+ }
+
+ /* END PARSING OF COMMAND LINE */
+
+ intty = isatty(fileno(stdin));
+ outtty= isatty(fileno(stdout));
+
+ if(intty){
+ if(outtty) {
+ printf("Input sequences; @ to mark end of input\n");
+ printf("%s%s\n", scale1, scale2);
+ }
+ else {
+ fprintf(stderr,"Input sequences; @ to mark end of input\n");
+ fprintf(stderr,"%s%s\n", scale1, scale2);
+ }
+ }
+
+ while ((s=read_sequence_list(&n,mask))!=NULL) {
+ dm = NULL;
+ if(Do_4_Stg) {
+ ss[0] = s;
+ nn[0] = n;
+ for(i=1;i<4;i++) {
+ ss[i] = read_sequence_list(&n,mask);
+ if(ss[i]==NULL) nrerror("read_sequences: wrong or insufficient data.");
+ nn[i] = n;
+ }
+ printf_taxa_list();
+ B = statgeom4(ss,nn);
+ printf_stg(B);
+ SimplifiedBox(B,"box.ps"); /* This is preliminary !!! */
+ free(B);
+
+ for(i=0;i<4;i++){
+ for(j=0;j<nn[i];j++) free(ss[i][j]);
+ free(ss[i]);
+ }
+ /* free(ss); */ /* attempt to free a non-heap object */
+ }
+ else {
+ printf_taxa_list();
+ if(Do_Stg) {
+ B = statgeom(s,n);
+ if (B) {
+ printf_stg(B);
+ SimplifiedBox(B,"box.ps");
+ free(B);
+ }
+ }
+ if((Do_Split)||(Do_Wards)||(Do_Nj)||(Do_Mat)) {
+ switch(DistAlgorithm) {
+ case 'H' :
+ dm = Hamming_Distance_Matrix(s,n);
+ printf("> %s\n","H (Hamming Distance)");
+ break;
+ case 'A' :
+ dm = StrEdit_SimpleDistMatrix(s,n);
+ printf("> %s\n","A (Needleman-Wunsch Distance)");
+ break;
+ case 'G' :
+ dm = StrEdit_GotohDistMatrix(s,n);
+ printf("> %s\n","G (Gotoh Distance)");
+ break;
+ default:
+ nrerror("This can't happen.");
+ }
+ }
+ if(Do_Split) {
+ S = split_decomposition(dm);
+ sort_Split(S);
+ print_Split(S);
+ free_Split(S);
+ }
+ if(Do_Wards) {
+ U = wards_cluster(dm);
+ printf_phylogeny(U,"W");
+ PSplot_phylogeny(U,"wards.ps","Ward's Method");
+ free(U);
+ }
+ if(Do_Nj) {
+ U = neighbour_joining(dm);
+ printf_phylogeny(U,"Nj");
+ PSplot_phylogeny(U,"nj.ps","Neighbor Joining");
+ free(U);
+ }
+ if(Do_Mat) printf_distance_matrix(dm);
+ }
+
+ if (dm!=NULL) free_distance_matrix(dm);
+ for(i=0;i<n;i++) free(s[i]);
+ free(s);
+ }
+ return 0;
+}
+
+/* -----------------------------------------------------------------------*/
+
+PRIVATE void usage(void)
+{
+ nrerror("usage: AnalyseSeqs [-X[bswnm]] [-Q] [-M{mask}] \n"
+ " [-D{H|A[,cost]|G[,cost1,cost2]}] [-d{D|B|H|S}]");
+}
git://source.jalview.org / jabaws.git / blobdiff