static void acdrelations_readtypefile
(AjPFile inf,
PKtype *T)
{
AjPStr line = NULL;
PKtypedat dattmp = NULL;
AjPList datlist = NULL;
if(!T)
ajFatal("Null arg error 1 in acdrelations_readtypefile");
if(!inf)
ajFatal("Null arg error 3 in acdrelations_readtypefile");
/* Allocate memory */
line = ajStrNew();
datlist = ajListNew();
/* Read data from file */
while(ajReadline(inf,&line))
{
/* Discard comment lines */
if(ajStrPrefixC(line,"#"))
continue;
/* Create object for holding line */
dattmp = ajKtypedatNew();
/* Tokenise line delimited by '|'
Parse first token (value of knowntype: attribute) */
ajStrAssignS(&dattmp->ktype, ajStrParseC(line, "|"));
ajStrRemoveSetC(&dattmp->ktype, "_");
ajStrRemoveWhite(&dattmp->ktype);
/* Parse second token (ACD datatype) */
ajStrAssignS(&dattmp->acdtype, ajStrParseC(NULL, "|"));
/* Parse third token (EDAM relations: value ) */
ajStrAssignS(&dattmp->edam, ajStrParseC(NULL, "|"));
/* Push line onto list */
ajListPushAppend(datlist, dattmp);
}
/* Write PKtype structure */
((*T)->n) = ajListToarray(datlist, (void***) &((*T)->dat));
/* Free memory */
ajStrDel(&line);
ajListFree(&datlist);
return;
}
AjPMatrixf ajMatrixfNewFile(const AjPStr filename)
{
AjPMatrixf ret = NULL;
AjPStr *orderstring = NULL;
AjPStr buffer = NULL;
AjPStr firststring = NULL;
AjPStr reststring = NULL;
const AjPStr tok = NULL;
ajint len = 0;
ajint i = 0;
ajint l = 0;
ajint k = 0;
ajint cols = 0;
ajint rows = 0;
const char *ptr = NULL;
AjPFile file = NULL;
AjBool first = ajTrue;
float **matrix = NULL;
float *templine = NULL;
float minval = -1.0;
AjPList rlabel_list = NULL;
AjPStr *rlabel_arr = NULL;
#ifndef WIN32
static const char *delimstr = " :\t\n";
#else
static const char *delimstr = " :\t\n\r";
#endif
rlabel_list = ajListNew();
firststring = ajStrNew();
reststring = ajStrNew();
file = ajDatafileNewInNameS(filename);
if(!file)
{
ajStrDel(&firststring);
ajStrDel(&reststring);
return NULL;
}
/* Read row labels */
while(ajReadline(file,&buffer))
{
ptr = ajStrGetPtr(buffer);
#ifndef WIN32
if(*ptr != '#' && *ptr != '\n')
#else
if(*ptr != '#' && *ptr != '\n' && *ptr != '\r')
#endif
{
if(first)
first = ajFalse;
else
{
ajFmtScanC(ptr, "%S", &firststring);
ajListPushAppend(rlabel_list, firststring);
firststring = ajStrNew();
}
}
}
first = ajTrue;
ajStrDel(&firststring);
rows = ajListToarray(rlabel_list, (void ***) &rlabel_arr);
ajFileSeek(file, 0, 0);
while(ajReadline(file,&buffer))
{
ajStrRemoveWhiteExcess(&buffer);
ptr = ajStrGetPtr(buffer);
if(*ptr && *ptr != '#')
{
if(first)
{
cols = ajStrParseCountC(buffer,delimstr);
AJCNEW0(orderstring, cols);
for(i=0; i<cols; i++)
orderstring[i] = ajStrNew();
tok = ajStrParseC(buffer, " :\t\n");
ajStrAssignS(&orderstring[l++], tok);
while((tok = ajStrParseC(NULL, " :\t\n")))
ajStrAssignS(&orderstring[l++], tok);
first = ajFalse;
ret = ajMatrixfNewAsym(orderstring, cols,
rlabel_arr, rows,
filename);
matrix = ret->Matrixf;
}
else
{
ajFmtScanC(ptr, "%S", &firststring);
/* JISON 19/7/4
k = ajSeqcvtGetCodeK(ret->Cvt,
ajStrGetCharFirst(firststring)); */
k = ajSeqcvtGetCodeS(ret->Cvt, firststring);
len = MAJSTRGETLEN(firststring);
ajStrAssignSubC(&reststring, ptr, len, -1);
/*
** Must discard the first string (label) and use
** reststring otherwise ajArrFloatLine would fail (it
** cannot convert a string to a float)
**
** Use cols,1,cols in below because although 2nd and
** subsequent lines have one more string in them (the
** residue label in the 1st column) we've discarded that
** from the string that's passed
*/
templine = ajArrFloatLine(reststring,delimstr,1,cols);
for(i=0; i<cols; i++)
{
if(templine[i] < minval)
minval = templine[i];
/* JISON 19/7/4
matrix[k][ajSeqcvtGetCodeK(ret->Cvt,
ajStrGetCharFirst(orderstring[i]))]
= templine[i]; */
matrix[k][ajSeqcvtGetCodeAsymS(ret->Cvt,
orderstring[i])]
= templine[i];
}
AJFREE(templine);
}
}
}
ajDebug("fill rest with minimum value %d\n", minval);
ajFileClose(&file);
ajStrDel(&buffer);
for(i=0; i<cols; i++)
ajStrDel(&orderstring[i]);
AJFREE(orderstring);
ajDebug("read matrix file %S\n", filename);
ajStrDel(&firststring);
ajStrDel(&reststring);
for(i=0; i<rows; i++)
ajStrDel(&rlabel_arr[i]);
AJFREE(rlabel_arr);
ajListFree(&rlabel_list);
return ret;
}
AjPMatrix ajMatrixNewFile(const AjPStr filename)
{
AjPMatrix ret = NULL;
AjPStr buffer = NULL;
const AjPStr tok = NULL;
AjPStr firststring = NULL;
AjPStr *orderstring = NULL;
AjPFile file = NULL;
AjBool first = ajTrue;
const char *ptr = NULL;
ajint **matrix = NULL;
ajint minval = -1;
ajint i = 0;
ajint l = 0;
ajint k = 0;
ajint cols = 0;
ajint rows = 0;
ajint *templine = NULL;
AjPList rlabel_list = NULL;
AjPStr *rlabel_arr = NULL;
#ifndef WIN32
static const char *delimstr = " :\t\n";
#else
static const char *delimstr = " :\t\n\r";
#endif
rlabel_list = ajListNew();
firststring = ajStrNew();
file = ajDatafileNewInNameS(filename);
if(!file)
{
ajStrDel(&firststring);
ajListFree(&rlabel_list);
return NULL;
}
/* Read row labels */
while(ajReadline(file,&buffer))
{
ptr = ajStrGetPtr(buffer);
#ifndef WIN32
if(*ptr != '#' && *ptr != '\n')
#else
if(*ptr != '#' && *ptr != '\n' && *ptr != '\r')
#endif
{
if(first)
first = ajFalse;
else
{
ajFmtScanC(ptr, "%S", &firststring);
ajListPushAppend(rlabel_list, firststring);
firststring = ajStrNew();
}
}
}
first = ajTrue;
ajStrDel(&firststring);
rows = ajListToarray(rlabel_list, (void ***) &rlabel_arr);
ajFileSeek(file, 0, 0);
while(ajReadline(file,&buffer))
{
ajStrRemoveWhiteExcess(&buffer);
ptr = ajStrGetPtr(buffer);
if(*ptr && *ptr != '#')
{
if(first)
{
cols = ajStrParseCountC(buffer,delimstr);
AJCNEW0(orderstring, cols);
for(i=0; i<cols; i++)
orderstring[i] = ajStrNew();
tok = ajStrParseC(buffer, " :\t\n");
ajStrAssignS(&orderstring[l++], tok);
while((tok = ajStrParseC(NULL, " :\t\n")))
ajStrAssignS(&orderstring[l++], tok);
first = ajFalse;
ret = ajMatrixNewAsym(orderstring, cols,
rlabel_arr, rows,
filename);
matrix = ret->Matrix;
}
else
{
ajFmtScanC(ptr, "%S", &firststring);
/* JISON 19/7/4
k = ajSeqcvtGetCodeK(ret->Cvt, ajStrGetCharFirst(firststring)); */
k = ajSeqcvtGetCodeS(ret->Cvt, firststring);
/*
** cols+1 is used below because 2nd and subsequent lines have
** one more string in them (the residue label)
*/
templine = ajArrIntLine(buffer,delimstr,2,cols+1);
for(i=0; i<cols; i++)
{
if(templine[i] < minval)
minval = templine[i];
/* JISON 19/7/4
matrix[k][ajSeqcvtGetCodeK(ret->Cvt,
ajStrGetCharFirst(orderstring[i]))]
= templine[i]; */
matrix[k][ajSeqcvtGetCodeAsymS(ret->Cvt,
orderstring[i])]
= templine[i];
}
AJFREE(templine);
}
}
}
ajDebug("fill rest with minimum value %d\n", minval);
ajFileClose(&file);
ajStrDel(&buffer);
for(i=0; i<cols; i++)
ajStrDel(&orderstring[i]);
AJFREE(orderstring);
ajDebug("read matrix file %S\n", filename);
ajStrDel(&firststring);
for(i=0; i<rows; i++)
ajStrDel(&rlabel_arr[i]);
AJFREE(rlabel_arr);
ajListFree(&rlabel_list);
return ret;
}
static void acdrelations_readdatfile
(AjPFile inf,
PEdam *P)
{
AjPStr line = NULL;
const AjPStr tok = NULL;
const AjPStr subtok = NULL;
AjPStr strtmp = NULL;
AjPList strlist = NULL;
AjPStr acdtype = NULL;
AjPStr relations = NULL;
PEdamdat dattmp = NULL;
AjPList datlist = NULL;
if(!P)
ajFatal("Null arg error 1 in acdrelations_readdatfile");
if(!inf)
ajFatal("Null arg error 3 in acdrelations_readdatfile");
/* Allocate memory */
line = ajStrNew();
acdtype = ajStrNew();
relations = ajStrNew();
datlist = ajListNew();
/* Read data from file */
while(ajReadline(inf,&line))
{
/* Discard comment lines */
if(ajStrPrefixC(line,"#"))
continue;
/* Tokenise line, delimited by '|'.
Parse first token (ACD datatype ) */
ajStrAssignS(&acdtype, ajStrParseC(line, "|"));
/* Parse second token (EDAM relations: value ) */
ajStrAssignS(&relations, ajStrParseC(NULL, "|"));
/* Parse third token (attribute:value strings block) */
tok = ajStrParseC(NULL, "|");
/* Create new string list */
strlist = ajListstrNew();
/* Tokenise third token itself into tokens delimited by ' ' (space)
Parse tokens (individual attribute:value strings)*/
if((subtok=ajStrParseC(tok, ";")))
{
strtmp = ajStrNew();
ajStrAssignS(&strtmp, subtok);
ajStrRemoveWhite(&strtmp);
ajListstrPushAppend(strlist, strtmp);
while((subtok=ajStrParseC(NULL, ";")))
{
strtmp = ajStrNew();
ajStrAssignS(&strtmp, subtok);
ajStrRemoveWhite(&strtmp);
ajListstrPushAppend(strlist, strtmp);
}
}
/* Write PEdamdat structure & push onto list */
dattmp = ajEdamdatNew();
ajStrRemoveWhite(&acdtype);
ajStrAssignS(&dattmp->acdtype, acdtype);
ajStrAssignS(&dattmp->edam, relations);
dattmp->n = ajListstrToarray(strlist, &dattmp->acdattr);
ajListPushAppend(datlist, dattmp);
/* Clear nodes (but not strings) from string list */
ajListstrFree(&strlist);
}
/* Write PEdam structure */
((*P)->n) = ajListToarray(datlist, (void***) &((*P)->dat));
/* Free memory */
ajStrDel(&line);
ajStrDel(&acdtype);
ajStrDel(&relations);
ajListFree(&datlist);
return;
}
