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nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator > Member List

This is the complete list of members for nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >, including all inherited members.

aligner() const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
aligner_type typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
AlignmentStream(aligner_type _aligner, const uint32 _count, const pattern_set_type _patterns, const qualities_set_type _quals, const text_set_type _texts, sink_iterator _sinks, const uint32 _max_pattern_length, const uint32 _max_text_length)nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
init_context(const uint32 i, context_type *context) const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
input_pattern_string typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
input_text_string typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
load_strings(const uint32 i, const uint32 window_begin, const uint32 window_end, const context_type *context, strings_type *strings) const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
m_alignernvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
m_countnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
m_max_pattern_lengthnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
m_max_text_lengthnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
m_patternsnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
m_qualsnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
m_sinksnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
m_textsnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
max_pattern_length() const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
max_text_length() const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
output(const uint32 i, const context_type *context) const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
pattern_length(const uint32 i, context_type *context) const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
pattern_prefetcher_type typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
pattern_string typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
quals_string typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
sink_type typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
size() const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
text_length(const uint32 i, context_type *context) const nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >inline
text_prefetcher_type typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >
text_string typedefnvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >