static wbool outputMatch( char *where, size_t read, wbool disp )
{
wbool done;
char *endrec;
int i;
done = FALSE;
if( where >= &Buff[read] ) {
done = TRUE; // this is the string we added to buffer! we're done buffer
} else if( disp ) {
if( PrtFn ) {
if( FOut != NULL ) {
fprintf( FOut, FOutFmt, FName );
fprintf( FOut, "\n" );
}
if( PrtFiles && !PrtAll ) {
printFileName();
}
PrtFn = FALSE;
}
MatchCount++;
TotalMatchCount++;
if( PrtMatch ) {
i = Context + 1;
for( ;; ) { // scan back to beginning of the record
if( where == Buff ) break;
if( *where == '\n' ) {
if( --i == 0 ) {
++where;
break;
}
}
--where;
}
endrec = where;
i = Context * 2 + 1;
while( --i >= 0 ) {
do { // find the end of record
++endrec;
} while( *endrec != '\n' && endrec != (Buff + read + 1) );
}
if( PrtLines ) {
printf( "%.5u: ", Recs );
if( Context ) printf( "\r\n" );
}
dumpMatch( where, endrec - where + 1 );
}
if( QuitFirst || OnePerFile ) {
done = TRUE;
ExitStatus = 1;
}
}
return( done );
}
void findRepeats(SeqStructPtr seqP)
{
int curPos;
Boolean anyMatchThisSeq, matchAtThisPos;
MatchStruct match;
memset( (char *)&match, 0, sizeof(MatchStruct) ); /* clear match struct */
anyMatchThisSeq = False; /* avoid dumping description more than once. */
/* loop on all positions in the sequence. note that a match
will advance curPos past all matching chars to the first
unmatched char. */
while ( match.curPos <= seqP->seqLen)
{
/* now loop on all the different lengths of repeats we're
looking for (i.e. di, tri, tetra nucleotides. if we
find a match at a shorter repeat length, forego testing
for longer lengths. */
match.testLen = MIN_UNIT_LENGTH;
matchAtThisPos = False;
while ((match.testLen <= MAX_UNIT_LENGTH) && (!matchAtThisPos))
{
/* initialize the state of the match */
match.curScore = 0; /* no points yet */
match.testCtr = 0; /* no chars tested yet */
match.testPos = match.curPos + match.testLen;
match.insertions = 0;
match.deletions = 0;
match.missense = 0;
/* there are some things we don't want to test for (IGNORE - ignoring single repeat) */
if (! ignoreSeq(seqP,&match))
matchAtThisPos = testForNRepeat(seqP, &match);
else
matchAtThisPos = False;
if (! matchAtThisPos) match.testLen++;
}
if (matchAtThisPos)
{
dumpMatch(seqP,&match,anyMatchThisSeq);
anyMatchThisSeq |= matchAtThisPos;
match.curPos = match.testPos;
}
else
match.curPos++; /* no, so advance to next base. */
}
}
