Sequence *free_constraint_list (Constraint_list *CL)
{
Sequence *S;
int a, b;
Constraint_list *pCL;
/*Prepare the selective freeing of the CL data structure:
If the CL has been obtained from copy, every pointer that is identical to the parent CL (CL->pCL)
will not be saved.
*/
if ( !CL)return NULL;
else S=CL->S;
if ( CL->copy_mode==SOFT_COPY && !CL->pCL)
{vfree(CL); return S;}
else if ( CL->copy_mode==SOFT_COPY)
{
pCL=CL->pCL;
CL->residue_index=NULL;
if ( CL->M ==pCL->M )CL->M=NULL;
if (CL->start_index ==pCL->start_index )CL->start_index=NULL;
if (CL->end_index ==pCL->end_index )CL->end_index=NULL;
if ( CL->fp ==pCL->fp )CL->fp=NULL;
if ( CL->matrices_list ==pCL->matrices_list )CL->matrices_list=NULL;
if ( CL->STRUC_LIST ==pCL->STRUC_LIST )CL->STRUC_LIST=NULL;
if ( CL->W ==pCL->W )CL->W=NULL;
if ( CL->DM ==pCL->DM )CL->DM=NULL;
if ( CL->ktupDM ==pCL->ktupDM )CL->ktupDM=NULL;
if ( CL->translation ==pCL->translation )CL->translation=NULL;
if ( CL->moca ==pCL->moca )CL->moca=NULL;
if ( CL->Prot_Blast ==pCL->Prot_Blast )CL->Prot_Blast=NULL;
if ( CL->DNA_Blast ==pCL->DNA_Blast )CL->DNA_Blast=NULL;
if ( CL->Pdb_Blast ==pCL->Pdb_Blast )CL->Pdb_Blast=NULL;
if ( CL->seq_for_quadruplet ==pCL->seq_for_quadruplet )CL->seq_for_quadruplet=NULL;
if ( CL->TC ==pCL->TC )CL->TC=NULL;
}
/*End of selective freeing of the CL data structure*/
if ( CL->residue_index)free_arrayN(CL->residue_index, 3);
if ( CL->M)free_int (CL->M, -1);
if ( CL->fp)vfclose (CL->fp);
if ( CL->matrices_list)free_char(CL->matrices_list,-1);
if ( CL->start_index)free_int ( CL->start_index,-1);
if ( CL->end_index)free_int ( CL->end_index,-1);
if ( CL->STRUC_LIST)free_sequence ( CL->STRUC_LIST, (CL->STRUC_LIST)->nseq);
if ( CL->W)free_weights (CL->W);
CL->DM=free_distance_matrix (CL->DM);
CL->ktupDM=free_distance_matrix (CL->ktupDM);
if ( CL->translation)vfree(CL->translation);
if ( CL->moca)free_moca (CL->moca);
if ( CL->Prot_Blast)free_blast_param ( CL->Prot_Blast);
if ( CL->DNA_Blast) free_blast_param ( CL->DNA_Blast);
if ( CL->Pdb_Blast) free_blast_param ( CL->Pdb_Blast);
if ( CL->TC) free_TC_param ( CL->TC);
if (CL->seq_for_quadruplet)vfree (CL->seq_for_quadruplet);
vfree(CL);
return S;
}
int 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 = vrna_alloc(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 = vrna_alloc(sizeof(char)*54);
strcpy(mask,
"%ABCDEFGHIJKLMNOPQRSTUVWabcdefghijklmnopqrstuvwxyz");
if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
break;
case 'u' :
mask = vrna_alloc(sizeof(char)*28);
strcpy(mask,"~ABCDEFGHIJKLMNOPQRSTUVW");
break;
case 'l' :
mask = vrna_alloc(sizeof(char)*28);
strcpy(mask,"~abcdefghijklmnopqrstuvwxyz");
break;
case 'c' :
mask = vrna_alloc(sizeof(char)*12);
strcpy(mask,"~1234567890");
break;
case 'n' :
mask = vrna_alloc(sizeof(char)*64);
strcpy (mask,
"%ABCDEFGHIJKLMNOPQRSTUVWabcdefghijklmnopqrstuvwxyz1234567890");
if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
break;
case 'R' : /* RNA */
mask = vrna_alloc(sizeof(char)*10);
strcpy(mask,"%GCAUgcau");
if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
break;
case 'D' : /* DNA */
mask = vrna_alloc(sizeof(char)*10);
strcpy (mask,"%GCATgcat");
if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
break;
case 'A' : /* AMINOACIDS */
mask = vrna_alloc(sizeof(char)*42);
strcpy(mask,"%ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy");
if(argv[i][3]=='+') mask[0] = '~'; /* make case sensitive */
break;
case 'S' : /* SECONDARY STRUCTURES */
mask = vrna_alloc(sizeof(char)*6);
strcpy(mask,"~().^");
break;
case '%' : /* ARBITRARY ALPHABETS */
l = strlen(argv[i]);
if(argv[i][l] == '+'){
mask = vrna_alloc(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 = vrna_alloc(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 = vrna_alloc(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) vrna_message_error("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:
vrna_message_error("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;
}
