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/***************************************************************************
* utilpars.c:
* -- all common routines for main programs in this directory
*
* $Log: utilpars.c,v $
* Revision 6.3 2006/01/31 22:31:49 kans
* added O for pyrrolysine and J for leu or ile ambiguity
*
* Revision 6.2 2001/12/06 17:00:41 kans
* TextSave takes size_t, not Int2, otherwise titin protein tries to allocate negative number
*
* Revision 6.1 2000/10/26 16:45:23 kans
* ValidAminoAcid also checks single letter abbreviation
*
* Revision 6.0 1997/08/25 18:08:16 madden
* Revision changed to 6.0
*
* Revision 5.1 1997/06/19 18:39:44 vakatov
* [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization
*
* Revision 5.0 1996/05/28 13:23:23 ostell
* Set to revision 5.0
*
* Revision 4.1 1995/11/17 21:28:35 kans
* asn2ff now uses gather (Tatiana)
*
* Revision 1.4 1995/06/08 14:31:50 tatiana
* change TERM to '*' in ParFlat_AA_array
*
* Revision 1.3 1995/05/15 21:46:05 ostell
* added Log line
*
*
* 10-12-93
****************************************************************************/
#include "utilpars.h"
/*-----------------
*
* The following associative array is to be used only
* until the method for accessing the seqcode tables
* is finalized.
* -Karl 2/10/94
The tables now are:
{ symbol "A", name "Alanine" },
{ symbol "B" , name "Asp or Asn" },
{ symbol "C", name "Cysteine" },
{ symbol "D", name "Aspartic Acid" },
{ symbol "E", name "Glutamic Acid" },
{ symbol "F", name "Phenylalanine" },
{ symbol "G", name "Glycine" },
{ symbol "H", name "Histidine" } ,
{ symbol "I", name "Isoleucine" },
{ symbol "", name "" },
{ symbol "K", name "Lysine" },
{ symbol "L", name "Leucine" },
{ symbol "M", name "Methionine" },
{ symbol "N", name "Asparagine" } ,
{ symbol "", name "" },
{ symbol "P", name "Proline" },
{ symbol "Q", name "Glutamine"},
{ symbol "R", name "Arginine"},
{ symbol "S", name "Serine"},
{ symbol "T", name "Threoine"},
{ symbol "", name ""},
{ symbol "V", name "Valine"},
{ symbol "W", name "Tryptophan" },
{ symbol "X", name "Undetermined or atypical"},
{ symbol "Y", name "Tyrosine"},
{ symbol "Z", name "Glu or Gln" }
code iupacaa3 ,
num 25 , -- continuous 0-23
one-letter FALSE , -- all 3 letter codes
table {
{ symbol "Ter", name "Termination" } ,
{ symbol "Ala", name "Alanine" },
{ symbol "Asx" , name "Asp or Asn" },
{ symbol "Cys", name "Cysteine" },
{ symbol "Asp", name "Aspartic Acid" },
{ symbol "Glu", name "Glutamic Acid" },
{ symbol "Phe", name "Phenylalanine" },
{ symbol "Gly", name "Glycine" },
{ symbol "His", name "Histidine" } ,
{ symbol "Ile", name "Isoleucine" },
{ symbol "Lys", name "Lysine" },
{ symbol "Leu", name "Leucine" },
{ symbol "Met", name "Methionine" },
{ symbol "Asn", name "Asparagine" } ,
{ symbol "Pro", name "Proline" },
{ symbol "Gln", name "Glutamine"},
{ symbol "Arg", name "Arginine"},
{ symbol "Ser", name "Serine"},
{ symbol "Thr", name "Threoine"},
{ symbol "Sec", name "Selenocysteine"},
{ symbol "Val", name "Valine"},
{ symbol "Trp", name "Tryptophan" },
{ symbol " X ", name "Undetermined or atypical"},
{ symbol "Tyr", name "Tyrosine"},
{ symbol "Glx", name "Glu or Gln" }
*---------------*/
typedef struct struct_AA1_toAA3 {
CharPtr aa3;
Uint1 aa1;
} ParFlat_AA1_to_AA3;
ParFlat_AA1_to_AA3
ParFlat_AA_array[ParFlat_TOTAL_AA] = {
"Ala", 'A',
"Asx", 'B',
"Cys", 'C',
"Asp", 'D',
"Glu", 'E',
"Phe", 'F',
"Gly", 'G',
"His", 'H',
"Ile", 'I',
"Xle", 'J', /* was - notice no 'J', breaks naive meaning of index -Karl */
"Lys", 'K',
"Leu", 'L',
"Met", 'M',
"Asn", 'N',
"Pyl", 'O', /* was - no 'O' */
"Pro", 'P',
"Gln", 'Q',
"Arg", 'R',
"Ser", 'S',
"Thr", 'T',
"Val", 'V',
"Trp", 'W',
"Sec", 'U', /* was - not in iupacaa */
"Xxx", 'X',
"Tyr", 'Y',
"Glx", 'Z',
"TERM", '*', /* not in iupacaa */ /*changed by Tatiana 06.07.95?`*/
"OTHER", 'X'};
/*--------------------- TextSave() -------------------------*/
/*****************************************************************************
* TextSave(text, len)
* -- allocates a null terminated string and copies len characters into
* it starting at text.
* -- returns a pointer to the allocated string. If len is 0 returns NULL
*
* 3-26-93
*****************************************************************************/
NLM_EXTERN CharPtr TextSave(CharPtr text, size_t len)
{
CharPtr str = NULL;
if ((text == NULL) || (len == 0))
return str;
str = MemNew((size_t)(len + 1));
MemCopy(str, text, (size_t)len);
return (str);
} /* TextSave */
/*------------------------- DelTailBlank() ---------------------------*/
/***************************************************************************
* DelTailBlank:
* -- return a string without tail blanks
* 10-12-93
***************************************************************************/
NLM_EXTERN void DelTailBlank(CharPtr str)
{
Int4 size;
size = StringLen(str);
while (size > 0 && str[size-1] == ' ') {
str[size-1] = '\0';
size--;
}
} /* DelTailBlank */
/*-------------------- MatchArrayStringIcase() ----------------------------*/
/***************************************************************************
* MatchArrayStringIcase:
* -- return array position of the "str" (ignored case) in the array_string
* -- return -1 if no match
* 10-12-93
***************************************************************************/
NLM_EXTERN Int2 MatchArrayStringIcase(CharPtr array_string[], Int2 totalstr, CharPtr text)
{
Int2 i;
for (i = 0; i < totalstr && text != NULL; i++)
if (StringICmp(text, array_string[i]) == 0)
return (i);
return (-1);
} /* MatchArrayStringIcase */
/*-------------------------- ValidAminoAcid() ------------------------*/
/***************************************************************************
* ValidAminoAcid:
* -- return a sequential code for the amino acid if "aa" is a valid
* amino acid; otherwise return 255, unknown
* -- using NCBIstdaa, IUPAC3aa
* 7-8-93
* for now, use iupacaa and return 'X' if no match found
* -Karl 2/10/94
***************************************************************************/
NLM_EXTERN Uint1 ValidAminoAcid(CharPtr aa)
{
Int2 i;
if (aa == NULL) (Uint1) 'X';
for (i = 0; i < ParFlat_TOTAL_AA && aa != NULL; i++)
if (StringICmp(aa, ParFlat_AA_array[i].aa3) == 0) {
return (ParFlat_AA_array[i].aa1);
}
if (aa [1] != '\0') return (Uint1) 'X';
for (i = 0; i < ParFlat_TOTAL_AA && aa != NULL; i++)
if (aa [0] == ParFlat_AA_array[i].aa1) {
return (ParFlat_AA_array[i].aa1);
}
return (Uint1) 'X';
} /* ValidAminoAcid */
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