static Int4 FillCSANWithStru(PCSAN pcsanThis, PMMD pmmdThis, Int4 iLen)
{
Int4 iCount = 0;
CharPtr pcA;
PDNMG pdnmgThis = NULL;
PMGD pmgdThis = NULL;
if (!pcsanThis) return 0;
if (!pmmdThis) return 0;
if (!IsProtein(pmmdThis)) return 0;
if (!iLen) return 0;
pcsanThis->pcSeqAln = (CharPtr)MemNew((size_t) (1+ sizeof(char) * iLen));
pcA = pcsanThis->pcSeqAln;
pdnmgThis = pmmdThis->pdnmgHead;
iCount = 0;
while ((pdnmgThis != NULL) && (iCount < iLen))
{
iCount++;
pmgdThis = (PMGD) pdnmgThis->data.ptrvalue;
*pcA = (char) pmgdThis->pcIUPAC[0] ;
pcA++;
pdnmgThis = pdnmgThis->next;
}
while (iCount < iLen)
{
*pcA = '-';
pcA++;
iCount++;
}
pcsanThis->pcSeqAln[iLen] = '\0';
return iCount;
}
static Int4 FillCSANWithMask(PCSAN pcsanThis, PMMD pmmdThis, Int4 iLen)
{
Int4 iCount = 0;
CharPtr pcA;
PDNMG pdnmgThis = NULL;
PMGD pmgdThis = NULL;
Char cCode = ' ';
if (!pcsanThis) return 0;
if (!pmmdThis) return 0;
if (!IsProtein(pmmdThis)) return 0;
if (!iLen) return 0;
/* printf("Mask len=[%ld]{",(long) iLen);*/
pcsanThis->pcSeqAln = (CharPtr)MemNew((size_t) (1+ sizeof(char) * iLen));
pcA = pcsanThis->pcSeqAln;
pdnmgThis = pmmdThis->pdnmgHead;
iCount = 0;
while ((pdnmgThis != NULL) && (iCount < iLen))
{
iCount++;
pmgdThis = (PMGD) pdnmgThis->data.ptrvalue;
cCode = '.'; /* default loop character */
if (pmgdThis->bPDBSecStru & (Byte) SS_HELIX) /*author described */
cCode = 'a';
if (pmgdThis->bNCBISecStru & (Byte) SS_HELIX) /* VAST ss definition */
cCode = 'a';
if ((pmgdThis->bPDBSecStru & (Byte) SS_HELIX) && (pmgdThis->bNCBISecStru & (Byte) SS_HELIX))
cCode = 'A'; /* consensus !*/
if (pmgdThis->bPDBSecStru & (Byte) SS_STRAND) /* author described */
cCode = 'b';
if (pmgdThis->bNCBISecStru & (Byte) SS_STRAND) /* VAST ss definition */
cCode = 'b';
if ((pmgdThis->bPDBSecStru & (Byte) SS_STRAND) && (pmgdThis->bNCBISecStru & (Byte) SS_STRAND))
cCode = 'B'; /* consensus */
/* printf("%c", cCode); */
*pcA = cCode ;
pcA++;
pdnmgThis = pdnmgThis->next;
}
while (iCount < iLen) /* pad to the end if this is short */
{
*pcA = '-';
/* printf("%c", '-');*/
pcA++;
iCount++;
}
pcsanThis->pcSeqAln[iLen] = '\0';
/* printf("}\n"); */
return iCount;
}
bool CBioseq_Handle::IsAa(void) const
{
return IsProtein();
}