lib/jointalign.c File Reference

#include "common.h"
#include "errabort.h"
#include "jointalign.h"

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Functions
void	htmlPrintJointAlignment (char *seq1, char *seq2, int columnNum, int start, int end, char *strand)
void	htmlPrintJointAlignmentLine (char *seq1, char *seq2, int start, int end)
boolean	ucaseMatch (char a, char b)
void	validateSeqs (char *seq1, char *seq2)
Variables
static char const	rcsid [] = "$Id: jointalign.c,v 1.11 2003/05/06 07:33:43 kate Exp $"

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Function Documentation

void htmlPrintJointAlignment	(	char *	seq1,
		char *	seq2,
		int	columnNum,
		int	start,
		int	end,
		char *	strand
	)

Definition at line 13 of file jointalign.c.

References htmlPrintJointAlignmentLine(), min, and validateSeqs().

{
int i;
validateSeqs( seq1, seq2 );

/*print the sequences with lines connecting identical residues
 *in columns of size columnNum*/
for( i=0; i<strlen(seq1); i += columnNum )
    htmlPrintJointAlignmentLine(seq1, seq2, i, min(i+columnNum, strlen(seq1)));

/*printf( "<tt><hr><br>%s<br>%s<br></tt>", seq1, seq2 );*/

}

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void htmlPrintJointAlignmentLine	(	char *	seq1,
		char *	seq2,
		int	start,
		int	end
	)

Definition at line 32 of file jointalign.c.

References ucaseMatch().

Referenced by htmlPrintJointAlignment().

{

int i;
printf("<tt>");
for( i=start; i<end; i++ )
    printf("%c",seq1[i]);
printf("<br>");
for( i=start; i<end; i++ )
    {
    if(ucaseMatch( seq1[i], seq2[i] ))
        printf("|");
    else
        printf("&nbsp;");
    }
printf("<br>");
for( i=start; i<end; i++ )
    printf("%c",seq2[i]);
printf("</tt>");
printf("<br><br>");
   

}

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boolean ucaseMatch	(	char	a,
		char	b
	)

Definition at line 58 of file jointalign.c.

References FALSE, and TRUE.

Referenced by htmlPrintJointAlignmentLine().

{
if( toupper( a ) == toupper( b ) )
    return( TRUE );
else 
    return( FALSE );
}

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void validateSeqs	(	char *	seq1,
		char *	seq2
	)

Definition at line 67 of file jointalign.c.

References errAbort().

Referenced by htmlPrintJointAlignment().

{
if( strlen(seq1) != strlen(seq2) )
    {
    printf("%s<br>%s<br>", seq1, seq2 );
    errAbort("The sequences are not properly aligned (different lengths)<br>\n"); 
    }
}

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Variable Documentation

char const rcsid[] = "$Id: jointalign.c,v 1.11 2003/05/06 07:33:43 kate Exp $" [static]

Definition at line 10 of file jointalign.c.

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