typename RangeT::size_type List< RangeT, TraitsT, ContainerT >::insert(const RangeT& value)
{
if ( value.end() > Traits::limit() )
{
qDebug( qPrintable(QString("ListError - insert - size: %1 - limit: %2 - sum: %3 - Range - begin: %4 - end: %5")
.arg(size()).arg(Traits::limit()).arg(Traits::length_sum()).arg(value.begin()).arg(value.end())) );
return 0;
}
if ( value.size() == 0 ) return 0;
iterator_pair sequence( merge_range( value ) );
return sequence.first != sequence.second
? Traits::merge_and_replace( m_set, sequence, value )
: Traits::simple_merge( m_set, sequence.first, value );
}
typename RangeT::size_type List< RangeT, TraitsT, ContainerT >::insert(const RangeT& value)
{
if ( value.end() > limit() )
{
// throw ListException( value, limit() );
CString msg;
msg.Format( _T( "ListError - insert - size: %u - limit: %I64u - sum: %I64u - " )
_T( "Range - begin: %I64u - end: %I64u" ),
size(), limit(), Traits::length_sum(), value.begin(), value.end() );
theApp.Message( MSG_ERROR, msg );
return 0;
}
if ( value.size() == 0 ) return 0;
iterator_pair sequence( merge_range( value ) );
return sequence.first != sequence.second
? Traits::merge_and_replace( m_set, sequence, value )
: Traits::simple_merge( m_set, sequence.first, value );
}
bool cluster::searchANDmodify(paired_end* currentPE, long *overlap_start, long *overlap_end)
{
bool overlap = false;
bool overlap_tag_start, overlap_tag_end;
long tmp1, tmp2, tmp3, tmp4;
tmp1 = end1_range_low;
tmp2 = end1_range_high;
tmp3 = end2_range_low;
tmp4 = end2_range_high;
*overlap_start = 0;
*overlap_end = 0;
range *nextrange, *nextPErange;
if (strcmp(currentPE->chromosome_start, chromosome_1) == 0 && strcmp(currentPE->strand_start, strand_start) == 0)
{
if (strcmp(currentPE->chromosome_end, chromosome_2) == 0 && strcmp(currentPE->strand_end, strand_end) == 0)
{
//check start point
nextrange = endpoint1;
overlap_tag_start = false;
overlap_tag_end = false;
while (nextrange != NULL)
{
nextPErange = currentPE->start;
while (nextPErange != NULL)
{
if (nextPErange->start <= nextrange->end + deviation_end && nextPErange->end >= nextrange->start - deviation_end)
{
overlap_tag_start = true;
if (nextPErange->start >= nextrange->start)
{
if (nextPErange->end >= nextrange->end)
{
*overlap_start += nextrange->end - nextPErange->start + 1;
}
else
{
*overlap_start += nextPErange->end - nextPErange->start + 1;
}
}
else if (nextPErange->end >= nextrange->end)
{
*overlap_start += nextrange->end - nextrange->start + 1;
}
else
{
*overlap_start += nextPErange->end - nextrange->start + 1;
}
if (nextPErange->start < tmp1)
{
tmp1 = nextPErange->start;
}
if (nextPErange->end > tmp2)
{
tmp2 = nextPErange->end;
}
}
nextPErange = nextPErange->next;
}
nextrange = nextrange->next;
}
//check end point
nextrange = endpoint2;
while (nextrange != NULL)
{
nextPErange = currentPE->end;
while (nextPErange != NULL)
{
if (nextPErange->start <= nextrange->end + deviation_end && nextPErange->end >= nextrange->start - deviation_end)
{
overlap_tag_end = true;
if (nextPErange->start >= nextrange->start)
{
if (nextPErange->end >= nextrange->end)
{
*overlap_end += nextrange->end - nextPErange->start + 1;
}
else
{
*overlap_end += nextPErange->end - nextPErange->start + 1;
}
}
else if (nextPErange->end >= nextrange->end)
{
*overlap_end += nextrange->end - nextrange->start + 1;
}
else
{
*overlap_end += nextPErange->end - nextrange->start + 1;
}
if (nextPErange->start < tmp3)
{
tmp3 = nextPErange->start;
}
if (nextPErange->end > tmp4)
{
tmp4 = nextPErange->end;
}
}
nextPErange = nextPErange->next;
}
nextrange = nextrange->next;
}
//check whether overlap or not
if (overlap_tag_start == true && overlap_tag_end == true)
{
overlap = true;
end1_range_low = tmp1;
end1_range_high = tmp2;
end2_range_low = tmp3;
end2_range_high = tmp4;
merge_range(currentPE);
}
}
}
else if (strcmp(currentPE->chromosome_start, chromosome_2) == 0 && strcmp(currentPE->strand_start, strand_end) == 0)
{
if (strcmp(currentPE->chromosome_end, chromosome_1) == 0 && strcmp(currentPE->strand_end, strand_start) == 0)
{
//check start point
nextrange = endpoint2;
overlap_tag_start = false;
overlap_tag_end = false;
while (nextrange != NULL)
{
nextPErange = currentPE->start;
while (nextPErange != NULL)
{
if (nextPErange->start <= nextrange->end + deviation_end && nextPErange->end >= nextrange->start - deviation_end)
{
overlap_tag_start = true;
if (nextPErange->start >= nextrange->start)
{
if (nextPErange->end >= nextrange->end)
{
*overlap_start += nextrange->end - nextPErange->start + 1;
}
else
{
*overlap_start += nextPErange->end - nextPErange->start + 1;
}
}
else if (nextPErange->end >= nextrange->end)
{
*overlap_start += nextrange->end - nextrange->start + 1;
}
else
{
*overlap_start += nextPErange->end - nextrange->start + 1;
}
if (nextPErange->start < tmp3)
{
tmp3 = nextPErange->start;
}
if (nextPErange->end > tmp4)
{
tmp4 = nextPErange->end;
}
}
nextPErange = nextPErange->next;
}
nextrange = nextrange->next;
}
//check end point
nextrange = endpoint1;
while (nextrange != NULL)
{
nextPErange = currentPE->end;
while (nextPErange != NULL)
{
if (nextPErange->start <= nextrange->end + deviation_end && nextPErange->end >= nextrange->start - deviation_end)
{
overlap_tag_end = true;
if (nextPErange->start >= nextrange->start)
{
if (nextPErange->end >= nextrange->end)
{
*overlap_end += nextrange->end - nextPErange->start + 1;
}
else
{
*overlap_end += nextPErange->end - nextPErange->start + 1;
}
}
else if (nextPErange->end >= nextrange->end)
{
*overlap_end += nextrange->end - nextrange->start + 1;
}
else
{
*overlap_end += nextPErange->end - nextrange->start + 1;
}
if (nextPErange->start < tmp1)
{
tmp1 = nextPErange->start;
}
if (nextPErange->end > tmp2)
{
tmp2 = nextPErange->end;
}
}
nextPErange = nextPErange->next;
}
nextrange = nextrange->next;
}
//check whether overlap or not
if (overlap_tag_start = true && overlap_tag_end == true)
{
overlap = true;
end1_range_low = tmp1;
end1_range_high = tmp2;
end2_range_low = tmp3;
end2_range_high = tmp4;
merge_range(currentPE);
}
}
}
return overlap;
}
int pdfmerge_main(int argc, char **argv)
{
pdf_write_options opts = { 0 };
char *output = "out.pdf";
char *infile_src;
int c;
while ((c = fz_getopt(argc, argv, "adlszo:")) != -1)
{
switch (c)
{
case 'o': output = fz_optarg; break;
case 'a': opts.do_ascii ++; break;
case 'd': opts.do_expand ^= PDF_EXPAND_ALL; break;
case 'l': opts.do_linear ++; break;
case 's': opts.do_clean ++; break;
case 'z': opts.do_deflate ++; break;
default: usage(); break;
}
}
if (fz_optind == argc)
usage();
ctx = fz_new_context(NULL, NULL, FZ_STORE_UNLIMITED);
if (!ctx)
{
fprintf(stderr, "Cannot initialise context\n");
exit(1);
}
fz_try(ctx)
{
doc_des = pdf_create_document(ctx);
}
fz_catch(ctx)
{
fprintf(stderr, "Failed to allocate destination document file %s\n", output);
exit(1);
}
/* Step through the source files */
while (fz_optind < argc)
{
fz_try(ctx)
{
infile_src = argv[fz_optind++];
pdf_drop_document(ctx, doc_src);
doc_src = pdf_open_document(ctx, infile_src);
if (fz_optind == argc || !isrange(argv[fz_optind]))
merge_range("1-");
else
merge_range(argv[fz_optind++]);
}
fz_catch(ctx)
{
fprintf(stderr, "Failed merging document %s\n", infile_src);
exit(1);
}
}
fz_try(ctx)
{
pdf_save_document(ctx, doc_des, output, &opts);
}
fz_always(ctx)
{
pdf_drop_document(ctx, doc_des);
pdf_drop_document(ctx, doc_src);
}
fz_catch(ctx)
{
fprintf(stderr, "Error encountered during file save.\n");
exit(1);
}
fz_flush_warnings(ctx);
fz_drop_context(ctx);
return 0;
}
int pdfmerge_main(int argc, char **argv)
{
pdf_write_options opts = { 0 };
char *output = "out.pdf";
char *flags = "";
char *input;
int c;
while ((c = fz_getopt(argc, argv, "o:O:")) != -1)
{
switch (c)
{
case 'o': output = fz_optarg; break;
case 'O': flags = fz_optarg; break;
default: usage(); break;
}
}
if (fz_optind == argc)
usage();
ctx = fz_new_context(NULL, NULL, FZ_STORE_UNLIMITED);
if (!ctx)
{
fprintf(stderr, "error: Cannot initialize MuPDF context.\n");
exit(1);
}
pdf_parse_write_options(ctx, &opts, flags);
fz_try(ctx)
{
doc_des = pdf_create_document(ctx);
}
fz_catch(ctx)
{
fprintf(stderr, "error: Cannot create destination document.\n");
exit(1);
}
/* Step through the source files */
while (fz_optind < argc)
{
input = argv[fz_optind++];
fz_try(ctx)
{
pdf_drop_document(ctx, doc_src);
doc_src = pdf_open_document(ctx, input);
if (fz_optind == argc || !fz_is_page_range(ctx, argv[fz_optind]))
merge_range("1-N");
else
merge_range(argv[fz_optind++]);
}
fz_catch(ctx)
{
fprintf(stderr, "error: Cannot merge document '%s'.\n", input);
exit(1);
}
}
fz_try(ctx)
{
pdf_save_document(ctx, doc_des, output, &opts);
}
fz_always(ctx)
{
pdf_drop_document(ctx, doc_des);
pdf_drop_document(ctx, doc_src);
}
fz_catch(ctx)
{
fprintf(stderr, "error: Cannot save output file: '%s'.\n", output);
exit(1);
}
fz_flush_warnings(ctx);
fz_drop_context(ctx);
return 0;
}
