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static char const rcsid[] = "$Id: splutil.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $";
/* splutil.c
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* ===========================================================================
*
* File Name: splutil.c
*
* Author: Sarah Wheelan
*
* $Revision: 6.7 $
*
* Contents: splice site matrices and associated utilites
*
* ==========================================================================
*
* $Log: splutil.c,v $
* Revision 6.7 2003/05/30 17:25:38 coulouri
* add rcsid
*
* Revision 6.6 2000/04/22 15:56:04 wheelan
* changed is_donor to take a FloatHiPtr instead of returning a FloatHi
*
* Revision 6.5 1998/09/24 12:46:17 wheelan
* put in log and revision stuff
*
*
*
*/
#include <ncbi.h>
#include <sequtil.h>
#include <sqnutils.h>
#include <splutil.h>
/**********
#include <salutil.h>
#include <bandalgn.h>
#include <blast.h>
**********/
extern void is_donor (CharPtr str, Int4 len, FloatHiPtr score)
{
FloatHi one[4]={0.35, 0.35, 0.19, 0.11};
FloatHi two[4]={0.59, 0.13, 0.14, 0.14};
FloatHi three[4]={0.08, 0.02, 0.82, 0.08};
FloatHi four[4]={0.01, 0.01, 1.00, 0.01};
FloatHi five[4]={0.01, 0.01, 0.01, 1.00};
FloatHi six[4]={0.51, 0.03, 0.43, 0.03};
FloatHi seven[4]={0.71, 0.08, 0.12, 0.09};
FloatHi eight[4]={0.06, 0.05, 0.84, 0.05};
FloatHi nine[4]={0.15, 0.16, 0.17, 0.52};
FloatHi score1;
Int4 i;
Int4 PNTR num=NULL;
if (score == NULL)
return;
if ((num = MemNew((len+2)*sizeof(Int4)))==NULL) {
/* memory error */
return;
}
for (i = 0; i <= len; i++){
if (str[i]=='A')
num[i] = 0;
if (str[i]=='C')
num[i] = 1;
if (str[i]=='G')
num[i] = 2;
if (str[i]=='T')
num[i] = 3;
}
score1 = one[num[0]];
score1 *= two[num[1]];
score1 *= three[num[2]];
score1 *= four[num[3]];
score1 *= five[num[4]];
score1 *= six[num[5]];
score1 *= seven[num[6]];
score1 *= eight[num[7]];
score1 *= nine[num[8]];
MemFree(num);
num=NULL;
*score = score1;
return;
}
extern Int4 getSplicePos (CharPtr str, Int4 overlaplength)
{
Int4 offset = -1;
Int4 xcursor = 0;
Int4 c;
FloatHi topscore = 0.00,score;
Char tmpstr[9];
if (str == NULL)
return 0;
while (xcursor <= overlaplength)
{
for (c = 0; c < 9; c++)
{
tmpstr[c] = str[xcursor+c];
}
is_donor(tmpstr, 8, &score);
if (score > topscore)
{
topscore = score;
offset = xcursor;
}
xcursor += 1;
}
if (topscore > 0 && offset >=0)
return offset;
return 0;
}
extern FloatHi is_acceptor (CharPtr str, Int4 len)
{
FloatHi aone[4]={0.06, 0.44, 0.05, 0.44};
FloatHi atwo[4]={0.08, 0.37, 0.05, 0.49};
FloatHi athree[4]={0.27, 0.28, 0.22, 0.23};
FloatHi afour[4]={0.04, 0.74, 0.001, 0.22};
FloatHi afive[4]={1.00, 0.01, 0.01, 0.01};
FloatHi asix[4]={0.01, 0.01, 0.99, 0.01};
FloatHi aseven[4]={0.25, 0.16, 0.50, 0.09};
FloatHi ascore;
Int4 i;
Int4 PNTR num;
if ((num = MemNew(len*sizeof(Int4)))==NULL) {
/* memory error */
return(0);
}
for (i = 0; i <= len; i++){
if (str[i]=='A')
num[i] = 0;
if (str[i]=='C')
num[i] = 1;
if (str[i]=='G')
num[i] = 2;
if (str[i]=='T')
num[i] = 3;
}
ascore = aone[num[len-6]];
ascore *= atwo[num[len-5]];
ascore *= athree[num[len-4]];
ascore *= afour[num[len-3]];
ascore *= afive[num[len-2]];
ascore *= asix[num[len-1]];
ascore *= aseven[num[len]];
MemFree(num);
num=NULL;
return ascore;
}
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