// ----------------------------------------
// ---------- mussa_class.hh -----------
// ----------------------------------------
+#include <QObject>
+#include <QString>
+
#include <boost/filesystem/path.hpp>
+#include <boost/shared_ptr.hpp>
#include <list>
#include <string>
#include <istream>
#include "alg/annotation_colors.hpp"
+#include "alg/mussa_callback.hpp"
#include "alg/nway_paths.hpp"
#include "alg/sequence.hpp"
std::string int_to_str(int an_int);
-class Mussa
+class Mussa;
+//! provide a simple name to point to our Mussa shared_ptr
+typedef boost::shared_ptr<Mussa> MussaRef;
+
+class Mussa : public QObject
{
- friend class ConnWindow;
- public:
+ Q_OBJECT
+
+signals:
+ //! call whatever signaling system we want
+ void progress(const QString& description, int cur, int max);
+ //! triggered when our state changes between unsaved(true) and saved(false)
+ void isModified(bool);
+
+public:
+ typedef std::set<Sequence> motif_set;
enum analysis_modes { TransitiveNway, RadialNway, EntropyNway,
RecursiveNway };
Mussa();
Mussa(const Mussa &);
- void save();
+ //! dynamically construct a new Mussa object and return a reference to it
+ static MussaRef init();
+
+ //! save all of mussa
+ void save(boost::filesystem::path save_path="");
//! save the nway comparison
void save_muway(boost::filesystem::path save_path);
//! load a saved analysis directory
void load(boost::filesystem::path ana_path);
+ // ! return path to the where the analysis is stored
+ boost::filesystem::path get_analysis_path() const;
+ //! set analysis path
+ void set_analysis_path(boost::filesystem::path);
//! clear parameters and initialize data lists
void clear();
//! set parameters from a file - 'mupa' ~ mussa parameters
+ void load_mupa_file(std::string para_file_path);
void load_mupa_file(boost::filesystem::path para_file_path);
+ //! load mussa parameters from a stream, specifing output location
+ void load_mupa_stream(
+ std::istream & para_file,
+ boost::filesystem::path& file_path_base
+ );
+
// set parameters individually (eg from user input into gui classes)
//! set analysis name
void set_name(std::string a_name);
//! return name for this analysis
- std::string get_name();
+ std::string get_name() const;
+ //! return a reasonable window title for this analysis
+ /*! this returns the "variable" portion for a title
+ */
+ std::string get_title() const;
//! return number of sequences in this analyzis
/*! this returns either the_seqs.size() or seq_files.size()
* (silly delayed loading of sequence data)
*/
int size() const;
+
//! set number of bases for this window size
void set_window(int a_window);
//! get number of bases for the sliding window
int get_window() const;
- //! set number of bases that must match for a window to be saved
+ //! set number of bases that must match for a window to be saved
+ //! if threshold > soft_threshold this also sets soft_threshold
void set_threshold(int a_threshold);
//! get number of bases that must match for a window to be saved
int get_threshold() const;
- void set_soft_thres(int sft_thres);
- int get_soft_thres() const;
+ //! sets the threshold used for computing the nway paths
+ //! must be in range [threshold..window size]
+ void set_soft_threshold(int sft_thres);
+ int get_soft_threshold() const;
void set_analysis_mode(enum analysis_modes new_ana_mode);
enum analysis_modes get_analysis_mode() const;
//! return a string name for an analysis mode
std::string get_analysis_mode_name() const;
+ //! set our current dirty state
+ void set_dirty(bool);
+ //! return if we have unsaved changes
+ bool is_dirty() const;
+ //! is there anything loaded into this analysis?
+ bool empty() const;
//! return the refined paths found by the nway analysis.
const NwayPaths& paths() const;
+ //! given selected_paths, and view_paths, compute per base pair matches
+ //template <class IteratorT>
+ void createLocalAlignment(std::list<ConservedPath>::iterator begin,
+ std::list<ConservedPath>::iterator end,
+ std::list<ConservedPath::path_type>& result,
+ std::list<std::vector<bool> >& reversed);
+
//! run seqcomp and the nway filtering algorithm.
/*!analyze will run seqcomp and then the nway algorithm
* on whatever sequences have been loaded into this mussa instance.
- * w & t are for command line override functionality, set to 0 to ignore
* \throws mussa_analysis_error
*/
- void analyze(int w=0, int t=0,
- enum analysis_modes ana_mode=TransitiveNway,
- double ent_thres=0.0);
+ void analyze();
/*! Run the nway filtering algorithm,
* this might be used when changing the soft threshhold?
*/
void nway();
//! appends a string sequence to the list of the_seqs
- void add_a_seq(std::string a_seq);
+ // void append_sequence(std::string a_seq);
+ //! appends a sequence to the list of the_seqs (makes copy)
+ void append_sequence(const Sequence& a_seq);
+ //! append a sequence to the list of seqs (shared)
+ void append_sequence(boost::shared_ptr<Sequence> a_seq);
+
//! Load a sequence from a fasta file and any annotations
/*! \param[in] seq_file the full path to the fasta file
* \param[in] annot_file the full path to an annotation file,
* use 0 start from the beginning.
* \param[in] sub_seq_end ending slice index to select a subsequence
* use 0 to go to the end.
+ * \param[in] name sequence name, only used if not null
*/
void load_sequence(boost::filesystem::path seq_file,
boost::filesystem::path annot_file,
- int fasta_index, int sub_seq_start=0, int sub_seq_end=0);
+ int fasta_index, int sub_seq_start=0, int sub_seq_end=0,
+ std::string *name=0);
//! allow examining the sequences we have loaded
- const std::vector<Sequence>& sequences() const;
+ typedef std::vector<boost::shared_ptr<Sequence> > vector_sequence_type;
+ const vector_sequence_type& sequences() const;
// deprecated - support bridge for python version of mussa
// these save & load from the old file format
void save_old();
void load_old(char * load_file_path, int s_num);
- // manage motif lists
- //! add vector of motifs and colors to our motif collection
- /*! this depends on sets and color maps being unique
+ // manage motif lists
+ //! add a motif it wont be applied until update_sequences_motif is called
+ void add_motif(const Sequence& motifs, const Color& colors);
+ //! add vector of motifs and colors to our motif collection
+ /*! this will automatically call update_sequences_motif
+ * this depends on sets and color maps being unique
* (aka if you add the same item more than once it doesn't
- * increase the size of the data structure
+ * increase the size of the data structure)
*/
- void add_motifs(const std::vector<std::string>& motifs,
+ void set_motifs(const std::vector<Sequence>& motifs,
const std::vector<Color>& colors);
- //! load motifs from an ifstream
/*! The file should look something like
* <sequence> <red> <green> <blue>
* where sequence is a string of IUPAC symbols
* and red,green,blue are a white space separated list of floats
* in the range [0.0, 1.0]
*/
- void load_motifs(std::istream &);
//! load a list of motifs from a file named filename
void load_motifs(boost::filesystem::path filename);
+ //! load motifs from an ifstream
+ /*! \sa Mussa::load_motifs(boost::filesystem::path)
+ */
+ void load_motifs(std::istream &);
+ //! save motif list to the specified filename
+ void save_motifs(boost::filesystem::path filename);
+ //! save motif list to an ostream
+ void save_motifs(std::ostream &);
//! return our motifs;
- const std::set<std::string>& motifs() const;
+ const motif_set& motifs() const;
//! return color mapper
- AnnotationColors& colorMapper();
+ boost::shared_ptr<AnnotationColors> colorMapper();
private:
//! push motifs to our attached sequences
int window;
//! how many base pairs need to match order to record a window as conserved
int threshold;
+ //! stores current filter used by GUI to change the connections shown
int soft_thres;
//! which nway comparison algorithm to use.
enum analysis_modes ana_mode;
bool thres_append;
//! sequence data
- std::vector<Sequence> the_seqs;
+ vector_sequence_type the_seqs;
//! the seqcomp data
std::vector<std::vector<FLPs> > all_comps;
//! N-way data, ie the mussa results
NwayPaths the_paths;
//! motif list
- std::set<std::string> motif_sequences;
+ motif_set motif_sequences;
//! color manager
- AnnotationColors color_mapper;
+ boost::shared_ptr<AnnotationColors> color_mapper;
+ //! path to our analysis
+ boost::filesystem::path analysis_path;
+ //! flag indicating if we have unsaved changes
+ bool dirty;
// Private methods
- //! loads sequence and annotations from fasta and annotation file
+ //! runs all the seqcomps needed to support the nway comparison
void seqcomp();
};
projects / mussa.git / blobdiff