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#ifdef _cplusplus
extern "C" {
#endif
#include "compmat.h"
/* Function: simple_CompProb(match,rnd)
*
* Descrip: Makes a simple CompProb matrix
*
*
* Arg: match [UNKN ] Undocumented argument [Probability]
* Arg: rnd [UNKN ] Undocumented argument [Probability]
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
# line 50 "compmat.dy"
CompProb * simple_CompProb(Probability match,Probability rnd)
{
CompProb * p;
Probability rem;
int i,j;
p = CompProb_alloc();
rem = (1.0-match)/20;
for(i=0;i<26;i++) {
for(j=i;j<26;j++) {
if( i == j ) {
p->comp[i][j] = match/rnd;
} else {
p->comp[i][j] = rem/rnd;
p->comp[j][i] = rem/rnd;
}
}
}
return p;
}
/* Function: fold_column_RandomModel_CompProb(cp,rm)
*
* Descrip: Folds a random model in over the columns
*
*
* Arg: cp [UNKN ] Undocumented argument [CompProb *]
* Arg: rm [UNKN ] Undocumented argument [RandomModel *]
*
*/
# line 76 "compmat.dy"
void fold_column_RandomModel_CompProb(CompProb * cp,RandomModel * rm)
{
int i,j;
for(i=0;i<26;i++) {
for(j=0;j<26;j++) {
if( rm->aminoacid[j] < 0.00000000000001 ) {
continue;
}
cp->comp[i][j] = cp->comp[i][j] / rm->aminoacid[j];
}
}
}
/* Function: simple_aa_CompProb(match,set,rnd)
*
* Descrip: Makes a simple CompProb with simple aa rules
*
*
* Arg: match [UNKN ] Undocumented argument [Probability]
* Arg: set [UNKN ] Undocumented argument [Probability]
* Arg: rnd [UNKN ] Undocumented argument [Probability]
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
# line 94 "compmat.dy"
CompProb * simple_aa_CompProb(Probability match,Probability set,Probability rnd)
{
CompProb * p;
Probability rem;
int i,j,k;
char * aa_set[] = { "FYW","LIV","RK","DE" };
p = CompProb_alloc();
rem = (1.0-match)/20;
for(i=0;i<26;i++) {
for(j=i;j<26;j++) {
if( i == j ) {
p->comp[i][j] = match/rnd;
} else {
for( k = 0;k<4;k++) {
if( strchr(aa_set[k],'A'+i) != NULL && strchr(aa_set[k],'A'+j) != NULL ) {
p->comp[i][j] = set/rnd;
p->comp[j][i] = set/rnd;
fprintf(stderr,"Setting %c,%c to %.2f\n",'A'+i,'A'+j,set/rnd);
} else {
p->comp[i][j] = rem/rnd;
p->comp[j][i] = rem/rnd;
}
}
}
}
}
return p;
}
/* Function: CompMat_from_CompProb(cp)
*
* Descrip: Maps a CompProb to a CompMat going through
* Probability2Score
*
*
* Arg: cp [UNKN ] Undocumented argument [CompProb *]
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
# line 130 "compmat.dy"
CompMat * CompMat_from_CompProb(CompProb * cp)
{
int i,j;
CompMat * cm;
cm = CompMat_alloc();
for(i=0;i<26;i++) {
for(j=0;j<26;j++) {
cm->comp[i][j] = Probability2Score(cp->comp[i][j]);
}
}
return cm;
}
/* Function: CompProb_from_halfbit(cm)
*
* Descrip: Maps a halfbit matrix to a prob matrix by rebasing
* etc.
*
* *Really* not sensible!
*
*
* Arg: cm [UNKN ] Undocumented argument [CompMat *]
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
# line 153 "compmat.dy"
CompProb * CompProb_from_halfbit(CompMat * cm)
{
CompProb * out;
int i,j;
out = CompProb_alloc();
for(i=0;i<26;i++)
for(j=0;j<26;j++)
out->comp[i][j] = halfbit2Probability(cm->comp[i][j]);
return out;
}
/* Function: CompMat_from_halfbit(cm)
*
* Descrip: flips a halfbit based matrix (eg, blosum62) into a score
* based matrix just by rebasing the log etc.
*
* Not a sensible function ...
*
*
*
* Arg: cm [UNKN ] Undocumented argument [CompMat *]
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
# line 173 "compmat.dy"
CompMat * CompMat_from_halfbit(CompMat * cm)
{
CompMat * out;
int i,j;
out = CompMat_alloc();
for(i=0;i<26;i++)
for(j=0;j<26;j++)
out->comp[i][j] = Probability2Score(halfbit2Probability(cm->comp[i][j]));
return out;
}
/* Function: factor_CompMat(cm,factor)
*
* Descrip: multiples all the scores by the amount
*
*
* Arg: cm [UNKN ] compmat object [CompMat *]
* Arg: factor [UNKN ] amount to multiple by [int]
*
*/
# line 193 "compmat.dy"
void factor_CompMat(CompMat * cm,int factor)
{
int i,j;
for(i=0;i<26;i++)
for(j=0;j<26;j++)
cm->comp[i][j] *= factor;
}
/* Function: fail_safe_CompMat_access(cm,aa1,aa2)
*
* Descrip: gives the fail form of the macro CompMat_AAMATCH which
* checks that aa1 and a2 are sensible and that cm is not NULL.
*
*
* Arg: cm [UNKN ] compmat object [CompMat *]
* Arg: aa1 [UNKN ] first amino acid [int]
* Arg: aa2 [UNKN ] second amino acid [int]
*
* Return [UNKN ] Undocumented return value [Score]
*
*/
# line 212 "compmat.dy"
Score fail_safe_CompMat_access(CompMat * cm,int aa1,int aa2)
{
if( cm == NULL) {
warn("Attempting to access NULL CompMat.");
return 0;
}
if( aa1 < 0 || aa1 >= 26 || aa2 < 0 || aa2 > 26) {
warn("Attempting to access CompMat with aminoacid numbers %d:%d (they must be bound between 0:26, returning 0 here",aa1,aa2);
return 0;
}
else return cm->comp[aa1][aa2];
}
/* Function: write_Blast_CompMat(cm,ofp)
*
* Descrip: writes a protien CompMat with a standard
* alphabet.
*
*
* Arg: cm [UNKN ] CompMat object [CompMat *]
* Arg: ofp [UNKN ] file to output [FILE *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
# line 234 "compmat.dy"
boolean write_Blast_CompMat(CompMat * cm,FILE * ofp)
{
return write_Blast_CompMat_alphabet(cm,"ARNDCQEGHILKMFPSTWYVBZX",ofp);
}
/* Function: bad_CompMat_alphabet(al)
*
* Descrip: checks that this string is ok for BLAST alphabet mappings.
*
*
* Arg: al [UNKN ] Undocumented argument [char *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
# line 243 "compmat.dy"
boolean bad_CompMat_alphabet(char * al)
{
char * runner;
for(runner=al;*runner;runner++)
if( !isalpha((int)*runner) && toupper((int)*runner) != *runner ) {
warn("Attempting to use [%s] as a CompMat alphabet: needs all upper case, no spaced letters",al);
return TRUE;
}
return FALSE;
}
/* Function: write_Blast_CompMat_alphabet(cm,alphabet,ofp)
*
* Descrip: actualy writes out the Blast CFormat. The alphabet is
* what order you want the amino acids. If you want the
* standard format use /write_Blast_CompMat
*
*
* Arg: cm [UNKN ] comp mat object [CompMat *]
* Arg: alphabet [UNKN ] string for alphabet to be used [char *]
* Arg: ofp [UNKN ] fileoutput [FILE *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
# line 264 "compmat.dy"
boolean write_Blast_CompMat_alphabet(CompMat * cm,char * alphabet,FILE * ofp)
{
char * runner;
char * run2;
int minnumbers[26];
int len;
int i;
int min;
if( bad_CompMat_alphabet(alphabet) == TRUE )
return FALSE; /* warning already issued */
fprintf(ofp,"# File made by *Wise CompMat library module\n");
fprintf(ofp,"# Comparison matrix in BLAST format\n");
fprintf(ofp,"# Usually matrices are given in half-bit units\n");
fprintf(ofp,"# First line is alphabet, the * column is the lowest score\n");
fprintf(ofp,"# File Created [%s]\n",now_string());
fprintf(ofp,"# Matrix name [%s]\n",cm->name == NULL ? "No Name" : cm->name);
/*** print out alphabet wit correct spacing ***/
fprintf(ofp," %c",alphabet[0]);
for(runner=alphabet+1;*runner;runner++)
fprintf(ofp," %c",*runner);
fprintf(ofp," *\n");
/*** print out each row: remember the minimum number for printing later **/
for(runner=alphabet,len=0;*runner;runner++) {
min = cm->comp[*runner-'A'][0];
fprintf(ofp,"%- d",cm->comp[*runner-'A'][0]);
for(run2=alphabet+1;*run2;run2++) {
fprintf(ofp," %- d",cm->comp[*runner-'A'][*run2-'A']);
if( cm->comp[*runner-'A'][*run2-'A'] < min )
min = cm->comp[*runner-'A'][*run2-'A'];
}
minnumbers[len++] = min;
fprintf(ofp," % d\n",min);
}
/*** final row... * ***/
fprintf(ofp,"% d",minnumbers[0]);
for(i=1;i<len;i++)
fprintf(ofp," % d",minnumbers[i]);
fprintf(ofp," 1\n");
/*** finished! ***/
return TRUE;
}
/* Function: read_Blast_file_CompMat(filename)
*
* Descrip: Opens file, reads matrix, closes file.
* calls /read_Blast_CompMat for the actual format
* reading. Uses /openfile to open the file,
* so will open from config files.
*
*
* Arg: filename [UNKN ] Undocumented argument [char *]
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
# line 324 "compmat.dy"
CompMat * read_Blast_file_CompMat(char * filename)
{
CompMat * out;
FILE * ifp;
ifp = openfile(filename,"r");
if( ifp == NULL ) {
warn("Could not open %s as a filename for read Blast matrix",filename);
return NULL;
}
out = read_Blast_CompMat(ifp);
if( out != NULL ) {
out->name = stringalloc(filename);
}
fclose(ifp);
return out;
}
/* Function: read_Blast_CompMat(ifp)
*
* Descrip: reads a BLAST format matrix and
* allocates a new ComMat structure.
*
*
* Arg: ifp [UNKN ] Undocumented argument [FILE *]
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
# line 350 "compmat.dy"
CompMat * read_Blast_CompMat(FILE * ifp)
{
char buffer[MAXLINE];
int alphabet[MAXLINE];
char * runner;
int len;
int linenum;
int row;
CompMat * out;
/***
Skip over # lines...
read first line: is alphabet ie
A R T G .... *
***/
while( fgets(buffer,MAXLINE,ifp) != NULL)
if( buffer[0] != '#')
break;
/** loop over line, getting letters: warn if longer than one, or not a letter **/
for(len=0,runner=strtok(buffer,spacestr);runner != NULL;runner=strtok(NULL,spacestr)) {
if( *runner == '*' )
break; /* end column */
if( !isalpha((int)*runner) || strlen(runner) > 1 ) {
warn("In read Blast comp mat, probably an error: trying to interpret [%s] as an amino acid",runner);
return NULL;
}
alphabet[len++] = toupper((int)*runner) -'A';
}
out = blank_CompMat();
linenum = 0;
/** get len lines, each line, get len numbers and put them away **/
while( fgets(buffer,MAXLINE,ifp) != NULL ) {
if( linenum >= len )
break;
for(runner=strtok(buffer,spacestr),row = 0;runner != NULL && row < len;runner=strtok(NULL,spacestr),row++) {
if( is_integer_string(runner,&out->comp[alphabet[linenum]][alphabet[row]]) == FALSE ) {
warn("In read Blast comp mat, probably an error: trying to interpret [%s] as a number ... continuing",runner);
}
}
linenum++;
}
return out;
}
/* Function: read_Blast_file_CompProb(filename)
*
* Descrip: Reads a BLAST format comp prob from file
*
*
* Arg: filename [UNKN ] Undocumented argument [char *]
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
# line 413 "compmat.dy"
CompProb * read_Blast_file_CompProb(char * filename)
{
FILE * ifp;
CompProb * out;
ifp = openfile(filename,"r");
if( ifp == NULL ) {
warn("Could not open %s for compprob",filename);
return NULL;
}
out = read_Blast_CompProb(ifp);
fclose(ifp);
return out;
}
/* Function: read_Blast_CompProb(ifp)
*
* Descrip: reads a BLAST format matrix and
* allocates a new CompProb structure.
*
*
* Arg: ifp [READ ] file input [FILE *]
*
* Return [UNKN ] newly allocated CompProb [CompProb *]
*
*/
# line 440 "compmat.dy"
CompProb * read_Blast_CompProb(FILE * ifp)
{
char buffer[MAXLINE];
int alphabet[MAXLINE];
char * runner;
int len;
int linenum;
int row;
CompProb * out;
/***
Skip over # lines...
read first line: is alphabet ie
A R T G .... *
***/
while( fgets(buffer,MAXLINE,ifp) != NULL)
if( buffer[0] != '#')
break;
/** loop over line, getting letters: warn if longer than one, or not a letter **/
for(len=0,runner=strtok(buffer,spacestr);runner != NULL;runner=strtok(NULL,spacestr)) {
if( *runner == '*' )
break; /* end column */
if( !isalpha((int)*runner) || strlen(runner) > 1 ) {
warn("In read Blast comp mat, probably an error: trying to interpret [%s] as an amino acid",runner);
return NULL;
}
alphabet[len++] = toupper((int)*runner) -'A';
}
out = blank_CompProb();
linenum = 0;
/** get len lines, each line, get len numbers and put them away **/
while( fgets(buffer,MAXLINE,ifp) != NULL ) {
if( strstartcmp(buffer,"//") == 0 )
break;
if( linenum >= len )
break;
for(runner=strtok(buffer,spacestr),row = 0;runner != NULL && row < len;runner=strtok(NULL,spacestr),row++) {
if( is_double_string(runner,&out->comp[alphabet[linenum]][alphabet[row]]) == FALSE ) {
warn("In read Blast comp prob, probably an error: trying to interpret [%s] as a number ... continuing",runner);
}
}
linenum++;
}
return out;
}
/* Function: blank_CompMat(void)
*
* Descrip: makes a 0,0 matrix
*
*
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
# line 503 "compmat.dy"
CompMat * blank_CompMat(void)
{
register int i;
register int j;
CompMat * out;
out = CompMat_alloc();
if( out == NULL)
return NULL;
for(i=0;i<26;i++)
for(j=0;j<26;j++)
out->comp[i][j] = 0;
return out;
}
/* Function: blank_CompProb(void)
*
* Descrip: makes a 1.0 prob matrix
*
*
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
# line 524 "compmat.dy"
CompProb * blank_CompProb(void)
{
register int i;
register int j;
CompProb * out;
out = CompProb_alloc();
if( out == NULL)
return NULL;
for(i=0;i<26;i++)
for(j=0;j<26;j++)
out->comp[i][j] = 1.0;
return out;
}
# line 594 "compmat.c"
/* Function: hard_link_CompProb(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [CompProb *]
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
CompProb * hard_link_CompProb(CompProb * obj)
{
if( obj == NULL ) {
warn("Trying to hard link to a CompProb object: passed a NULL object");
return NULL;
}
obj->dynamite_hard_link++;
return obj;
}
/* Function: CompProb_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
CompProb * CompProb_alloc(void)
{
CompProb * out; /* out is exported at end of function */
/* call ckalloc and see if NULL */
if((out=(CompProb *) ckalloc (sizeof(CompProb))) == NULL) {
warn("CompProb_alloc failed ");
return NULL; /* calling function should respond! */
}
out->dynamite_hard_link = 1;
#ifdef PTHREAD
pthread_mutex_init(&(out->dynamite_mutex),NULL);
#endif
/* comp[26][26] is an array: no default possible */
out->name = NULL;
return out;
}
/* Function: free_CompProb(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [CompProb *]
*
* Return [UNKN ] Undocumented return value [CompProb *]
*
*/
CompProb * free_CompProb(CompProb * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a CompProb obj. Should be trappable");
return NULL;
}
#ifdef PTHREAD
assert(pthread_mutex_lock(&(obj->dynamite_mutex)) == 0);
#endif
if( obj->dynamite_hard_link > 1) {
return_early = 1;
obj->dynamite_hard_link--;
}
#ifdef PTHREAD
assert(pthread_mutex_unlock(&(obj->dynamite_mutex)) == 0);
#endif
if( return_early == 1)
return NULL;
if( obj->name != NULL)
ckfree(obj->name);
ckfree(obj);
return NULL;
}
/* Function: hard_link_CompMat(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [CompMat *]
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
CompMat * hard_link_CompMat(CompMat * obj)
{
if( obj == NULL ) {
warn("Trying to hard link to a CompMat object: passed a NULL object");
return NULL;
}
obj->dynamite_hard_link++;
return obj;
}
/* Function: CompMat_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
CompMat * CompMat_alloc(void)
{
CompMat * out; /* out is exported at end of function */
/* call ckalloc and see if NULL */
if((out=(CompMat *) ckalloc (sizeof(CompMat))) == NULL) {
warn("CompMat_alloc failed ");
return NULL; /* calling function should respond! */
}
out->dynamite_hard_link = 1;
#ifdef PTHREAD
pthread_mutex_init(&(out->dynamite_mutex),NULL);
#endif
/* comp[26][26] is an array: no default possible */
out->name = NULL;
return out;
}
/* Function: free_CompMat(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [CompMat *]
*
* Return [UNKN ] Undocumented return value [CompMat *]
*
*/
CompMat * free_CompMat(CompMat * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a CompMat obj. Should be trappable");
return NULL;
}
#ifdef PTHREAD
assert(pthread_mutex_lock(&(obj->dynamite_mutex)) == 0);
#endif
if( obj->dynamite_hard_link > 1) {
return_early = 1;
obj->dynamite_hard_link--;
}
#ifdef PTHREAD
assert(pthread_mutex_unlock(&(obj->dynamite_mutex)) == 0);
#endif
if( return_early == 1)
return NULL;
if( obj->name != NULL)
ckfree(obj->name);
ckfree(obj);
return NULL;
}
/* Function: replace_name_CompMat(obj,name)
*
* Descrip: Replace member variable name
* For use principly by API functions
*
*
* Arg: obj [UNKN ] Object holding the variable [CompMat *]
* Arg: name [OWNER] New value of the variable [char *]
*
* Return [SOFT ] member variable name [boolean]
*
*/
boolean replace_name_CompMat(CompMat * obj,char * name)
{
if( obj == NULL) {
warn("In replacement function name for object CompMat, got a NULL object");
return FALSE;
}
obj->name = name;
return TRUE;
}
/* Function: access_name_CompMat(obj)
*
* Descrip: Access member variable name
* For use principly by API functions
*
*
* Arg: obj [UNKN ] Object holding the variable [CompMat *]
*
* Return [SOFT ] member variable name [char *]
*
*/
char * access_name_CompMat(CompMat * obj)
{
if( obj == NULL) {
warn("In accessor function name for object CompMat, got a NULL object");
return NULL;
}
return obj->name;
}
#ifdef _cplusplus
}
#endif
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