liboxli-dev 2.1.2+dfsg-3 / usr / include / oxli / labelhash.hh

/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2013-2015, Michigan State University.
Copyright (C) 2015-2016, The Regents of the University of California.

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    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above
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      disclaimer in the documentation and/or other materials provided
      with the distribution.

    * Neither the name of the Michigan State University nor the names
      of its contributors may be used to endorse or promote products
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Contact: khmer-project@idyll.org
*/
#ifndef LABELHASH_HH
#define LABELHASH_HH

#include <stddef.h>
#include <stdint.h>
#include <map>
#include <string>
#include <utility>

#include "hashgraph.hh"
#include "oxli.hh"
#include "read_parsers.hh"

namespace oxli
{
    class Hashgraph;

    using read_parsers::ReadParser;
    namespace read_parsers
    {
        template<typename SeqIO> class ReadParser;
        class FastxReader;
    }

class LabelHash
{
protected:
    // Does the given tag already have the given label?
    bool _cmap_contains_label(const TagLabelMap& cmap,
                              const HashIntoType kmer,
                              const Label the_label)
    {
        std::pair<TagLabelMap::const_iterator, TagLabelMap::const_iterator> ret;
        ret = cmap.equal_range(kmer);
        for (TagLabelMap::const_iterator it=ret.first; it!=ret.second; ++it) {
            if (it->second == the_label) {
                return true;
            }
        }
        return false;
    }

    // Does the given label already have a tag associated with it?
    bool _cmap_contains_tag(const LabelTagMap& cmap,
                            Label& the_label,
                            HashIntoType& kmer)
    {
        std::pair<LabelTagMap::const_iterator, LabelTagMap::const_iterator> ret;
        ret = cmap.equal_range(the_label);
        for (LabelTagMap::const_iterator it=ret.first; it!=ret.second; ++it) {
            if(it->second == kmer) {
                return true;
            }
        }
        return false;
    }

    unsigned int _get_tag_labels(const HashIntoType tag,
                                 const TagLabelMap cmap,
                                 LabelSet& found_labels) const
    {
        unsigned int num_labels = 0;
        std::pair<TagLabelMap::const_iterator, TagLabelMap::const_iterator> ret;
        ret = cmap.equal_range(tag);
        for (TagLabelMap::const_iterator it=ret.first; it!=ret.second; ++it) {
            found_labels.insert(it->second);
            ++num_labels;
        }
        return num_labels;
    }

    unsigned int _get_tags_from_label(const Label& label,
                                      const LabelTagMap& cmap,
                                      TagSet& labeled_tags) const
    {
        unsigned int num_tags = 0;
        std::pair<LabelTagMap::const_iterator, LabelTagMap::const_iterator> ret;
        ret = cmap.equal_range(label);
        for (LabelTagMap::const_iterator it=ret.first; it!=ret.second; ++it) {
            labeled_tags.insert(it->second);
            ++num_tags;
        }
        return num_tags;
    }

    uint32_t _tag_labels_spin_lock;

public:
    oxli::Hashgraph * graph;

    explicit LabelHash(Hashgraph * ht) : graph(ht)
    {
        _tag_labels_spin_lock = 0;

    }

    ~LabelHash();

    TagLabelMap tag_labels;
    LabelTagMap label_tag;
    LabelSet all_labels;

    size_t n_labels() const
    {
        return all_labels.size();
    }

    template<typename SeqIO>
    void consume_seqfile_and_tag_with_labels(
        std::string const	  &filename,
        unsigned int	  &total_reads,
        unsigned long long  &n_consumed,
        CallbackFn	  callback	  = NULL,
        void *		  callback_data	  = NULL);

    template<typename SeqIO>
    void consume_seqfile_and_tag_with_labels(
        read_parsers::ReadParserPtr<SeqIO>& parser,
        unsigned int	    &total_reads,
        unsigned long long  &n_consumed,
        CallbackFn	    callback	    = NULL,
        void *		    callback_data   = NULL);

    template<typename SeqIO>
    void consume_partitioned_fasta_and_tag_with_labels(
        const std::string &filename,
        unsigned int &total_reads,
        unsigned long long &n_consumed,
        CallbackFn callback = NULL,
        void * callback_datac = NULL);

    void consume_sequence_and_tag_with_labels(const std::string& seq,
            unsigned long long& n_consumed,
            Label current_label,
            SeenSet * new_tags = 0);

    void get_tag_labels(const HashIntoType tag,
                        LabelSet& labels) const;
    void get_tags_from_label(const Label label,
                             TagSet& tags) const;

    void link_tag_and_label(const HashIntoType kmer, const Label label);

    unsigned int sweep_label_neighborhood(const std::string & seq,
                                          LabelSet& found_labels,
                                          unsigned int range,
                                          bool break_on_stoptags,
                                          bool stop_big_traversals);

    void traverse_labels_and_resolve(const SeenSet tagged_kmers,
                                     LabelSet& found_labels);

    void save_labels_and_tags(std::string);
    void load_labels_and_tags(std::string);

    void label_across_high_degree_nodes(const char * sequence,
                                        SeenSet& high_degree_nodes,
                                        const Label label);
};

} // namespace oxli

#define ACQUIRE_TAG_COLORS_SPIN_LOCK \
  while(!__sync_bool_compare_and_swap( &_tag_labels_spin_lock, 0, 1));

#define RELEASE_TAG_COLORS_SPIN_LOCK \
  __sync_bool_compare_and_swap( &_tag_labels_spin_lock, 1, 0);

#endif