/********************************************************************** * FILE: cisml.h * AUTHOR: Charles Grant * PROJECT: MEME * COPYRIGHT: 2007-2008, WSN * VERSION: $Revision: 1.1.1.1$ * DESCRIPTION: Print routines for the cisml format. * * "CisML: an XML-based format for sequence motif detection software." * Haverty and Weng. Bioinformatics. 20(11):1815-1817, 2004. * * http://bioinformatics.oxfordjournals.org/cgi/reprint/20/11/1815.pdf * http://zlab.bu.edu/~phaverty/SupplementalData/CisML/ * * In CisML, the parent-child relationships go like this: * * [ mulit-pattern -> ] pattern -> scanned-sequence -> matched-element * **********************************************************************/ #ifndef CISML_H #define CISML_H #include "utils.h" #include "xml-util.h" typedef struct cisml CISML_T; typedef struct cisml_match_it CISML_MATCH_IT_T; typedef struct multi_pattern MULTI_PATTERN_T; typedef struct multi_pattern_match MULTI_PATTERN_MATCH_T; typedef struct pattern PATTERN_T; typedef struct scanned_sequence SCANNED_SEQUENCE_T; typedef struct matched_element MATCHED_ELEMENT_T; /********************************************************************** allocate_cisml Constructor for the cisml data structure. Sets required fields to point to copies of the provided arguments. Other fields set to 0 or NULL. **********************************************************************/ CISML_T *allocate_cisml( const char *program_name, const char *pattern_file, const char *sequence_file ); /********************************************************************** free_cisml Destructor for the cisml data structure. **********************************************************************/ void free_cisml(CISML_T *cisml); /********************************************************************** get_cisml_program_name Gets the program_name member from a cisml object. **********************************************************************/ char *get_cisml_program_name(CISML_T *cisml); /********************************************************************** get_cisml_pattern_file Gets the pattern_file member from a cisml object. **********************************************************************/ char *get_cisml_pattern_file(CISML_T *cisml); /********************************************************************** get_cisml_sequence_file Gets the sequence_file member from a cisml object. **********************************************************************/ char *get_cisml_sequence_file(CISML_T *cisml); /********************************************************************** set_cisml_background_file Sets the background_file member in a cisml object. **********************************************************************/ void set_cisml_background_file(CISML_T *cisml, char *background_file); /********************************************************************** get_cisml_background_file Gets the background_file member from a cisml object. Return value may be NULL. **********************************************************************/ char *get_cisml_background_file(CISML_T *cisml); /********************************************************************** set_cisml_pattern_pvalue_cutoff Sets the pattern_pvalue_cutoff member in a cisml object. Defaults to 1.0 if not set. **********************************************************************/ void set_cisml_pattern_pvalue_cutoff( CISML_T *cisml, double pattern_pvalue_cutoff ); /********************************************************************** clear_cisml_pattern_pvalue_cutoff Sets the pattern_pvalue_cutoff member in a cisml object to null. **********************************************************************/ void clear_cisml_pattern_pvalue_cutoff(CISML_T *cisml); /********************************************************************** has_cisml_pattern_pvalue_cutoff Does a cisml object have a pattern_pvalue_cutoff? **********************************************************************/ BOOLEAN_T has_cisml_pattern_pvalue_cutoff(CISML_T *cisml); /********************************************************************** get_cisml_pattern_pvalue_cutoff Gets the pattern_pvalue_cutoff member from a cisml object. Defaults to 1.0 if the pattern p-value cutoff has not been set. **********************************************************************/ double get_cisml_pattern_pvalue_cutoff(CISML_T *cisml); /********************************************************************** set_cisml_sequence_pvalue_cutoff Sets the sequence_pvalue_cutoff member in a cisml object. **********************************************************************/ void set_cisml_sequence_pvalue_cutoff( CISML_T *cisml, double sequence_pvalue_cutoff ); /********************************************************************** clear_cisml_sequence_pvalue_cutoff Sets the sequence_pvalue_cutoff member in a cisml object to null. **********************************************************************/ void clear_cisml_sequence_pvalue_cutoff(CISML_T *cisml); /********************************************************************** has_cisml_sequence_pvalue_cutoff Does a cisml object have a sequence_pvalue_cutoff? **********************************************************************/ BOOLEAN_T has_cisml_sequence_pvalue_cutoff(CISML_T *cisml); /********************************************************************** get_cisml_sequence_pvalue_cutoff Gets the sequence_pvalue_cutoff member from a cisml object. Defaults to 1.0 if the sequence p-value cutoff has not been set. **********************************************************************/ double get_cisml_sequence_pvalue_cutoff(CISML_T *cisml); /********************************************************************** set_cisml_site_pvalue_cutoff Sets the site_pvalue_cutoff member in a cisml object. **********************************************************************/ void set_cisml_site_pvalue_cutoff(CISML_T *cisml, double site_pvalue_cutoff); /********************************************************************** clear_cisml_site_pvalue_cutoff Sets the site_pvalue_cutoff member in a cisml object to null. **********************************************************************/ void clear_cisml_site_pvalue_cutoff(CISML_T *cisml); /********************************************************************** has_cisml_site_pvalue_cutoff Does a cisml object have a pattern_pvalue_cutoff? **********************************************************************/ BOOLEAN_T has_cisml_site_pvalue_cutoff(CISML_T *cisml); /********************************************************************** get_cisml_site_pvalue_cutoff Gets the site_pvalue_cutoff member from a cisml object. Defaults to 1.0 if the site p-value cutoff has not been set. **********************************************************************/ double get_cisml_site_pvalue_cutoff(CISML_T *cisml); /********************************************************************** set_cisml_site_qvalue_cutoff Sets the site_qvalue_cutoff member in a cisml object. **********************************************************************/ void set_cisml_site_qvalue_cutoff(CISML_T *cisml, double site_qvalue_cutoff); /********************************************************************** clear_cisml_site_qvalue_cutoff Sets the site_qvalue_cutoff member in a cisml object to null. **********************************************************************/ void clear_cisml_site_qvalue_cutoff(CISML_T *cisml); /********************************************************************** has_cisml_site_qvalue_cutoff Does a cisml object have a site_qvalue_cutoff? **********************************************************************/ BOOLEAN_T has_cisml_site_qvalue_cutoff(CISML_T *cisml); /********************************************************************** get_cisml_site_qvalue_cutoff Gets the site_qvalue_cutoff member from a cisml object. Defaults to 1.0 if the site q-value cutoff has not been set. **********************************************************************/ double get_cisml_site_qvalue_cutoff(CISML_T *cisml); /********************************************************************** set_cisml_sequence_filter Sets the sequence_filter member in a cisml object. **********************************************************************/ void set_cisml_sequence_filter(CISML_T *cisml, char *sequence_filter); /********************************************************************** get_cisml_sequence_filter Gets the sequence_filter member from a cisml object. May return NULL. **********************************************************************/ char *get_cisml_sequence_filter(CISML_T *cisml); /********************************************************************** get_cisml_num_multi_patterns Gets the number of multi-patterns from a cisml object. **********************************************************************/ int get_cisml_num_multi_patterns(CISML_T *cisml); /********************************************************************** get_cisml_multi_patterns Gets the array of pointers to multi_patterns from a cisml object. May return NULL. **********************************************************************/ MULTI_PATTERN_T **get_cisml_multi_patterns(CISML_T *cisml); /********************************************************************** get_cisml_num_patterns Gets the number of patterns from a cisml object. **********************************************************************/ int get_cisml_num_patterns(CISML_T *cisml); /********************************************************************** get_cisml_patterns Gets the array of pointers to patterns from a cisml object. **********************************************************************/ PATTERN_T **get_cisml_patterns(CISML_T *cisml); /********************************************************************** get_cisml_num_stored_matches Gets the number of stored matches for all patterns in a cisml object. **********************************************************************/ int get_cisml_num_stored_matches(CISML_T *cisml); /********************************************************************** add_cisml_multi_pattern Adds a pattern to the array of pointers to patterns in a cisml object. **********************************************************************/ void add_cisml_multi_pattern(CISML_T *cisml, MULTI_PATTERN_T* multi_pattern); /********************************************************************** add_cisml_pattern Adds a pattern to the array of pointers to patterns in a cisml object. **********************************************************************/ void add_cisml_pattern(CISML_T *cisml, PATTERN_T* pattern); /********************************************************************** allocate_cisml_match_iterator Constructor for an iterator used to traverse all matched elements in in a cisml object. It stores the current index into the array of matched elements for each of the patterns in the CisML object. **********************************************************************/ CISML_MATCH_IT_T *allocate_cisml_match_iterator(CISML_T *cisml); /********************************************************************** free_cisml_match_iterator Destructor for the CisML match iterator. **********************************************************************/ void free_cisml_match_iterator(CISML_MATCH_IT_T *it); /********************************************************************** cisml_match_iterator_next Returns the next matched element from the CisML object. Matches are returned in order of ascending p-value. ***********************************************************************/ MATCHED_ELEMENT_T *cisml_match_iterator_next(CISML_MATCH_IT_T *it); /********************************************************************** allocate_multi_pattern Constructor for the cisml multi_pattern data structure. **********************************************************************/ MULTI_PATTERN_T *allocate_multi_pattern(); /********************************************************************** free_multi_pattern Destructor for the cisml multi_pattern data structure. **********************************************************************/ void free_multi_pattern(MULTI_PATTERN_T *multi_pattern); /********************************************************************** set_multi_pattern_score Sets the score member in a cisml pattern object. **********************************************************************/ void set_multi_pattern_score(MULTI_PATTERN_T *multi_pattern, double score); /********************************************************************** has_multi_pattern_score Does a multi_pattern object have a score? **********************************************************************/ BOOLEAN_T has_multi_pattern_score(MULTI_PATTERN_T *multi_pattern); /********************************************************************** clear_multi_pattern_score Sets the score member in a cisml multi_pattern object to null. **********************************************************************/ void clear_multi_pattern_score(MULTI_PATTERN_T *multi_pattern); /********************************************************************** get_multi_pattern_score Gets the score member from a cisml multi_pattern object. **********************************************************************/ double get_multi_pattern_score(MULTI_PATTERN_T *multi_pattern); /********************************************************************** set_multi_pattern_pvalue Sets the pvalue member in a cisml pattern object. **********************************************************************/ void set_multi_pattern_pvalue(MULTI_PATTERN_T *multi_pattern, double pvalue); /********************************************************************** has_multi_pattern_pvalue Does a multi_pattern object have a pvalue? **********************************************************************/ BOOLEAN_T has_multi_pattern_pvalue(MULTI_PATTERN_T *multi_pattern); /********************************************************************** clear_multi_pattern_pvalue Sets the pvalue member in a cisml multi_pattern object to null. **********************************************************************/ void clear_multi_pattern_pvalue(MULTI_PATTERN_T *multi_pattern); /********************************************************************** get_multi_pattern_pvalue Gets the pvalue member from a cisml multi_pattern object. **********************************************************************/ double get_multi_pattern_pvalue(MULTI_PATTERN_T *multi_pattern); /********************************************************************** get_multi_pattern_num_patterns Gets the number of patterns from a cisml multi_pattern object. **********************************************************************/ int get_multi_pattern_num_patterns(MULTI_PATTERN_T *multi_pattern); /********************************************************************** get_multi_pattern_match Sets the match member in a cisml multi-pattern object. **********************************************************************/ MULTI_PATTERN_MATCH_T *get_multi_pattern_match( MULTI_PATTERN_T *multi_pattern ); /********************************************************************** set_multi_pattern_match Sets the pvalue member in a cisml pattern object. **********************************************************************/ void set_multi_pattern_match( MULTI_PATTERN_T *multi_pattern, MULTI_PATTERN_MATCH_T *match ); /********************************************************************** get_multi_pattern_patterns Gets the array of pointers to patterns from a cisml object. **********************************************************************/ PATTERN_T **get_multi_pattern_patterns(MULTI_PATTERN_T *multi_pattern); /********************************************************************** add_multi_pattern_pattern Adds a pattern to the array of pointers to patterns in a multi_pattern object. **********************************************************************/ void add_multi_pattern_pattern( MULTI_PATTERN_T *multi_pattern, PATTERN_T* pattern ); /************************************************************************* * Calculate the q-values from the p-values of the multi-patterns *************************************************************************/ void multi_pattern_calculate_qvalues( int num_multi_pattern, MULTI_PATTERN_T **multi_patterns, ARRAY_T *sampled_pvalues ); /********************************************************************** allocate_multi_pattern_match Constructor for the cisml multi_pattern_match data structure. **********************************************************************/ MULTI_PATTERN_MATCH_T *allocate_multi_pattern_match( char *seq_name, char *seq, int start, int stop, double pvalue ); /********************************************************************** free_multi_pattern_match Destructor for the cisml multi_pattern_match data structure. **********************************************************************/ void free_multi_pattern_match(MULTI_PATTERN_MATCH_T *match); /********************************************************************** set_multi_pattern_match_evalue Sets the evalue member in a cisml multi_pattern_match object. **********************************************************************/ void set_multi_pattern_match_evalue(MULTI_PATTERN_MATCH_T *match, double evalue); /********************************************************************** get_multi_pattern_match_pvalue Gets the pvalue member from a cisml multi_pattern_match object. **********************************************************************/ double get_multi_pattern_match_pvalue(MULTI_PATTERN_MATCH_T* match); /********************************************************************** set_multi_pattern_match_qvalue Sets the qvalue member in a cisml multi_pattern_match object. **********************************************************************/ void set_multi_pattern_match_qvalue(MULTI_PATTERN_MATCH_T *match, double qvalue); /********************************************************************** get_multi_pattern_match_qvalue Gets the qvalue member from a cisml multi_pattern_match object. **********************************************************************/ double get_multi_pattern_match_qvalue(MULTI_PATTERN_MATCH_T* match); /********************************************************************** allocate_pattern Constructor for the cisml pattern data structure. Sets required fields to point to copies of the provided arguments. Other fields set to NULL. **********************************************************************/ PATTERN_T *allocate_pattern(char *accession, char *name); /********************************************************************** free_pattern Destructor for the cisml pattern data structure. **********************************************************************/ void free_pattern(PATTERN_T *pattern); /********************************************************************** add_pattern_elements_to_scanned_seq Updates each scanned sequence belonging to pattern with the matched_elements assocaited with that sequence. **********************************************************************/ void add_pattern_elements_to_scanned_seq(PATTERN_T *pattern); /********************************************************************** add_pattern_matched_element Adds a pointer to a matched element to the heap of pointers to matched_elements in a cisml pattern object. Before adding to the heap, check the pvalue for the element. if it's greater the pvalues we've already thrown away, we refuse to add it. Also, check max_stored_matches. If we've hit the limit, purge the heap of the least significian matched elements. Set to FALSE the Boolean that indicates that set of matched elements is complete. **********************************************************************/ BOOLEAN_T add_pattern_matched_element( PATTERN_T *pattern, MATCHED_ELEMENT_T *element ); /********************************************************************** set_pattern_max_stored_matches Sets the maximum number of matched elements that will be stored in a cisml pattern object. This requires creating a new element heap using the new maximum number of elements, copying the elements from the existing heap, freeing the existing heap, and pointing the pattern to the new heap. It fails if the new max is smaller than the current max_stored_matches. Returns TRUE if successful, FALSE otherwise. **********************************************************************/ BOOLEAN_T set_pattern_max_stored_matches(PATTERN_T *pattern, int max); /********************************************************************** set_pattern_max_pvalue_retained Sets the maximum p-value of the matched elements retained by the pattern. **********************************************************************/ void set_pattern_max_pvalue_retained(PATTERN_T *pattern, double max_pvalue); /********************************************************************** get_pattern_max_stored_matches Gets the maximum number of elements that will be stored in a cisml pattern object. **********************************************************************/ int get_pattern_max_stored_matches(PATTERN_T *pattern); /********************************************************************** get_pattern_num_stored_matches Gets the maximum number of elements that will be stored in a cisml pattern object. **********************************************************************/ int get_pattern_num_stored_matches(PATTERN_T *pattern); /********************************************************************** get_pattern_is_complete Returns a flag indicating whether or not all matched elements have been added to the pattern. If flag is true, the element heap is no longer available and all matched elements are stored in an array of matched element pointers, sorted by p-value. **********************************************************************/ BOOLEAN_T get_pattern_is_complete(PATTERN_T *pattern); /********************************************************************** set_pattern_is_complete Sets the flag indicating that all matched elements have been added to the pattern to true. Moves all matched elments out of the element heap into an array of matched element pointers, sorted by p-value. No further elements can be added to the pattern once this function has been called. **********************************************************************/ void set_pattern_is_complete(PATTERN_T *pattern); /********************************************************************** get_pattern_max_pvalue_retained Returns the maximum p-value of the matched elements retained by the pattern. **********************************************************************/ double get_pattern_max_pvalue_retained(PATTERN_T *pattern); /********************************************************************** get_pattern_name Gets the name member from a cisml pattern object. **********************************************************************/ char *get_pattern_name(PATTERN_T* pattern); /********************************************************************** get_pattern_accession Gets the accession member from a cisml pattern object. **********************************************************************/ char *get_pattern_accession(PATTERN_T* pattern); /********************************************************************** set_pattern_pvalue Sets the pvalue member in a cisml pattern object. **********************************************************************/ void set_pattern_pvalue(PATTERN_T *pattern, double pvalue); /********************************************************************** clean_pattern_pvalue Sets the pvalue member in a cisml pattern object to null. **********************************************************************/ void clear_pattern_pvalue(PATTERN_T *pattern); /********************************************************************** has_pattern_pvalue Does a pattern object have a pvalue? **********************************************************************/ BOOLEAN_T has_pattern_pvalue(PATTERN_T *pattern); /********************************************************************** get_pattern_pvalue Gets the pvalue member from a cisml pattern object. **********************************************************************/ double get_pattern_pvalue(PATTERN_T* pattern); /********************************************************************** has_pattern_qvalues Does the matched-elements for the pattern have qvalues available? **********************************************************************/ BOOLEAN_T has_pattern_qvalues(PATTERN_T *pattern); /********************************************************************** set_pattern_score Sets the score member in a cisml pattern object. **********************************************************************/ void set_pattern_score(PATTERN_T *pattern, double score); /********************************************************************** clear_pattern_score Sets the score member in a cisml pattern object to null. **********************************************************************/ void clear_pattern_pvalue(PATTERN_T *pattern); /********************************************************************** has_pattern_score Does a pattern object have a score? **********************************************************************/ BOOLEAN_T has_pattern_score(PATTERN_T *pattern); /********************************************************************** get_pattern_score Gets the score member from a cisml pattern object. **********************************************************************/ double get_pattern_score(PATTERN_T* pattern); /********************************************************************** set_pattern_db Sets the db member in a cisml pattern object. **********************************************************************/ void set_pattern_db(PATTERN_T *pattern, char *db); /********************************************************************** get_pattern_db Gets the db member from a cisml pattern object. May return NULL. **********************************************************************/ char *get_pattern_db(PATTERN_T* pattern); /********************************************************************** set_pattern_lsid Sets the lsid member in a cisml pattern object. **********************************************************************/ void set_pattern_lsid(PATTERN_T *pattern, char *lsid); /********************************************************************** get_pattern_lsid Gets the lsid member from a cisml pattern object. May return NULL. **********************************************************************/ char *get_pattern_lsid(PATTERN_T* pattern); /********************************************************************** get_pattern_num_scanned_sequences Gets the number of scanned_sequence objects in a cisml pattern object. **********************************************************************/ int get_pattern_num_scanned_sequences(PATTERN_T *pattern); /********************************************************************** get_pattern_num_scanned_positions Gets the number of sites scanned with a cisml pattern object. **********************************************************************/ long get_pattern_num_scanned_positions(PATTERN_T *pattern); /********************************************************************** get_pattern_num_stored_matches Gets the total number of matched element objects stored in a cisml pattern object. **********************************************************************/ int get_pattern_num_stored_matches(PATTERN_T *pattern); /********************************************************************** get_pattern_stored_matches Gets the array of matched element objects stored in a cisml pattern object. **********************************************************************/ MATCHED_ELEMENT_T **get_pattern_stored_matches(PATTERN_T *pattern); /********************************************************************** get_pattern_matched_elements Gets the array of matched_element objects contained in a cisml pattern object. **********************************************************************/ MATCHED_ELEMENT_T **get_pattern_matched_elements(PATTERN_T *pattern); /************************************************************************* * Calculate the q-values for each matched-element in this pattern * from the p-values. *************************************************************************/ void pattern_calculate_qvalues( PATTERN_T *pattern, ARRAY_T *sampled_pvalues ); /********************************************************************** get_pattern_scanned_sequences Gets the array of pointers to scanned_sequence objects in a cisml pattern object. May return NULL. **********************************************************************/ SCANNED_SEQUENCE_T **get_pattern_scanned_sequences(PATTERN_T *pattern); /********************************************************************** allocate_scanned_sequence Constructor for the cisml scanned_sequence data structure. Sets required fields to point to copies of the provided arguments. Other fields set to NULL. **********************************************************************/ SCANNED_SEQUENCE_T *allocate_scanned_sequence( char *accession, char *name, PATTERN_T *parent ); /********************************************************************** free_scanned_sequence Destructor for the cisml scanned_sequence data structure. **********************************************************************/ void free_scanned_sequence(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** free_scanned_sequence_from_matched_elements Removes the matches from a scanned sequences only **********************************************************************/ void free_scanned_sequence_from_matched_elements( SCANNED_SEQUENCE_T *scanned_sequence ); /********************************************************************** get_scanned_sequence_parent Get a pointer to the pattern pointing to this scanned_sequence object. **********************************************************************/ PATTERN_T *get_scanned_sequence_parent( SCANNED_SEQUENCE_T *scanned_sequence ); /********************************************************************** get_scanned_sequence_name Gets the program_name member from a cisml scanned_sequence object. **********************************************************************/ char *get_scanned_sequence_name(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** get_scanned_sequence_accession Gets the accession member from a cisml scanned_sequence object. **********************************************************************/ char *get_scanned_sequence_accession(SCANNED_SEQUENCE_T* scanned_sequence); /********************************************************************** set_scanned_sequence_pvalue Sets the pvalue member in a cisml scanned_sequence object. **********************************************************************/ void set_scanned_sequence_pvalue( SCANNED_SEQUENCE_T *scanned_sequence, double pvalue ); /********************************************************************** clear_scanned_sequence_pvalue Sets the pvalue member in a cisml scanned_sequence object to null. **********************************************************************/ void clear_scanned_sequence_pvalue(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** has_scanned_sequence_pvalue Does a scanned_sequence object have a pvalue? **********************************************************************/ BOOLEAN_T has_scanned_sequence_pvalue(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** get_scanned_sequence_pvalue Gets the pvalue member from a cisml scanned_sequence object. **********************************************************************/ double get_scanned_sequence_pvalue(SCANNED_SEQUENCE_T* scanned_sequence); /********************************************************************** set_scanned_sequence_score Sets the score member in a cisml scanned_sequence object. **********************************************************************/ void set_scanned_sequence_score( SCANNED_SEQUENCE_T *scanned_sequence, double score ); /********************************************************************** clear_scanned_sequence_score Sets the score member in a cisml scanned_sequence object to null. **********************************************************************/ void clear_scanned_sequence_score(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** has_scanned_sequence_score Does a scanned_sequence object have a score? **********************************************************************/ BOOLEAN_T has_scanned_sequence_score(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** get_scanned_sequence_score Gets the score member from a cisml scanned_sequence object. **********************************************************************/ double get_scanned_sequence_score(SCANNED_SEQUENCE_T* scanned_sequence); /********************************************************************** set_scanned_sequence_length Sets the length member in a cisml scanned_sequence object. **********************************************************************/ void set_scanned_sequence_length( SCANNED_SEQUENCE_T *scanned_sequence, int length ); /********************************************************************** clear_scanned_sequence_length Sets the length member in a cisml scanned_sequence object to null. **********************************************************************/ void clear_scanned_sequence_length(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** has_scanned_sequence_length Does a scanned_sequence object have a length? **********************************************************************/ BOOLEAN_T has_scanned_sequence_length(SCANNED_SEQUENCE_T *scanned_sequence); /********************************************************************** get_scanned_sequence_length Gets the length member from a cisml scanned_sequence object. **********************************************************************/ int get_scanned_sequence_length(SCANNED_SEQUENCE_T* scanned_sequence); /********************************************************************** set_scanned_sequence_db Sets the db member in a cisml scanned_sequence object. **********************************************************************/ void set_scanned_sequence_db(SCANNED_SEQUENCE_T *scanned_sequence, char *db); /********************************************************************** get_scanned_sequence_db Gets the db member from a cisml scanned_sequence object. May return NULL. **********************************************************************/ char *get_scanned_sequence_db(SCANNED_SEQUENCE_T* scanned_sequence); /********************************************************************** set_scanned_sequence_lsid Sets the lsid member in a cisml scanned_sequence object. **********************************************************************/ void set_scanned_sequence_lsid( SCANNED_SEQUENCE_T *scanned_sequence, char *lsid ); /********************************************************************** get_scanned_sequence_lsid Gets the lsid member from a cisml scanned_sequence object. May return NULL. **********************************************************************/ char *get_scanned_sequence_lsid(SCANNED_SEQUENCE_T* scanned_sequence); /********************************************************************** add_scanned_sequence_matched_element Adds a matched element to the array of matched elements in the scanned sequence. **********************************************************************/ void add_scanned_sequence_matched_element( SCANNED_SEQUENCE_T *sequence, MATCHED_ELEMENT_T *element ); /********************************************************************** add_scanned_sequence_scanned_position Increments the count of scanned elements in a scanned_sequence. **********************************************************************/ void add_scanned_sequence_scanned_position(SCANNED_SEQUENCE_T *sequence); /********************************************************************** get_scanned_sequence_num_matched_elements Gets the number of matched_element objects in a cisml scanned_sequence object. **********************************************************************/ int get_scanned_sequence_num_matched_elements(SCANNED_SEQUENCE_T *sequence); /********************************************************************** get_scanned_sequence_num_scanned_positions Gets the number of positions in the scanned_sequence where we have scanned for a matched_element. **********************************************************************/ long get_scanned_sequence_num_scanned_positions(SCANNED_SEQUENCE_T *sequence); /********************************************************************** get_scanned_sequence_num_matched_elements Gets the number of matched_element objects in a cisml scanned_sequence object. **********************************************************************/ int get_scanned_sequence_num_matched_elements(SCANNED_SEQUENCE_T *sequence); /********************************************************************** get_scanned_sequence_num_scanned_positions Gets the number of positions in the scanned_sequence where we have scanned for a matched_element. **********************************************************************/ long get_scanned_sequence_num_scanned_positions(SCANNED_SEQUENCE_T *sequence); /********************************************************************** get_scanned_sequences_elements Gets the array of pointers to matched_element objects in a cisml scanned_sequence object. May return NULL. **********************************************************************/ MATCHED_ELEMENT_T **get_scanned_sequence_matched_elements( SCANNED_SEQUENCE_T *sequence ); /********************************************************************** get_scanned_sequences_matched_elements Gets the array of pointers to matched_element objects in a cisml scanned_sequence object. May return NULL. **********************************************************************/ MATCHED_ELEMENT_T **get_scanned_sequence_matched_elements( SCANNED_SEQUENCE_T *sequence ); /********************************************************************** allocate_matched_element Constructor for the cisml matched_element data structure. Sets required fields to the provided arguments. Other fields set to NULL. **********************************************************************/ MATCHED_ELEMENT_T *allocate_matched_element( int start, int stop, SCANNED_SEQUENCE_T *parent ); /********************************************************************** allocate_matched_element_without_inversion Alternative Constructor for the cisml matched_element data structure. Sets required fields to the provided arguments. Other fields set to NULL. JH: I had to add this because the existing constructor inverts the DNA sequence if the start site is greater than the stop site. I could not simply copy an existing matched element's content and feed it to the constructor without the content being changed. For the record I think this is a poor way to design a constructor. **********************************************************************/ MATCHED_ELEMENT_T *allocate_matched_element_without_inversion( int start, int stop, const char *seq, SCANNED_SEQUENCE_T *parent ); /********************************************************************** allocate_matched_element_with_score Constructor for the cisml matched_element data structure. Sets required fields to the provided arguments. Sets score and pvalue. Other fields set to NULL. **********************************************************************/ MATCHED_ELEMENT_T *allocate_matched_element_with_score( int start, int stop, double score, double pvalue, SCANNED_SEQUENCE_T *parent ); /********************************************************************** free_matched_element Destructor for the cisml matched_element data structure. **********************************************************************/ void free_matched_element(MATCHED_ELEMENT_T *element); /********************************************************************** get_matched_element_start Gets the start member from a cisml matched_element object. **********************************************************************/ int get_matched_element_start(MATCHED_ELEMENT_T* matched_element); /********************************************************************** set_matched_element_start Sets the start member from a cisml matched_element object. **********************************************************************/ void set_matched_element_start(MATCHED_ELEMENT_T* matched_element, int newstart); /********************************************************************** get_matched_element_stop Gets the stop member from a cisml matched_element object. **********************************************************************/ int get_matched_element_stop(MATCHED_ELEMENT_T* matched_element); /********************************************************************** set_matched_element_stop sets the stop member from a cisml matched_element object. **********************************************************************/ void set_matched_element_stop(MATCHED_ELEMENT_T* element, int newstop); /********************************************************************** set_matched_element_score Sets the score member in a cisml matched_element object. **********************************************************************/ void set_matched_element_score( MATCHED_ELEMENT_T *element, double score ); /********************************************************************** has_matched_element_score Does a matched_element object have a score? **********************************************************************/ BOOLEAN_T has_matched_element_score(MATCHED_ELEMENT_T *element); /********************************************************************** get_matched_element_score Gets the score member from a cisml matched_element object. **********************************************************************/ double get_matched_element_score(MATCHED_ELEMENT_T* element); /********************************************************************** set_matched_element_pvalue Sets the pvalue member in a cisml matched_element object. **********************************************************************/ void set_matched_element_pvalue( MATCHED_ELEMENT_T *element, double pvalue ); /********************************************************************** has_matched_element_pvalue Does a matched_element object have a pvalue? **********************************************************************/ BOOLEAN_T has_matched_element_pvalue(MATCHED_ELEMENT_T *element); /********************************************************************** get_matched_element_pvalue Gets the pvalue member from a cisml matched_element object. **********************************************************************/ double get_matched_element_pvalue(MATCHED_ELEMENT_T* element); /********************************************************************** has_matched_element_qvalue Does a matched_element object have a qvalue? **********************************************************************/ BOOLEAN_T has_matched_element_qvalue(MATCHED_ELEMENT_T *element); /********************************************************************** get_matched_element_qvalue Gets the qvalue member from a cisml matched_element object. **********************************************************************/ double get_matched_element_qvalue(MATCHED_ELEMENT_T* element); /********************************************************************** set_matched_element_clusterid Sets the clusterid member in a cisml matched_element object. **********************************************************************/ void set_matched_element_clusterid( MATCHED_ELEMENT_T *element, char *clusterid ); /********************************************************************** get_matched_element_clusterid Gets the clusterid member from a cisml matched_element object. May return NULL. **********************************************************************/ char *get_matched_element_clusterid(MATCHED_ELEMENT_T* element); /********************************************************************** get_matched_element_sequence Gets the sequence member from a cisml matched_element object. Caller should not free the string. May return NULL. **********************************************************************/ const char *get_matched_element_sequence(MATCHED_ELEMENT_T* element); /********************************************************************** set_matched_element_strand Sets the strand member in a cisml matched_element object. **********************************************************************/ void set_matched_element_strand(MATCHED_ELEMENT_T* element, char strand); /********************************************************************** get_matched_element_strand Gets the strand member in a cisml matched_element object. **********************************************************************/ char get_matched_element_strand(MATCHED_ELEMENT_T* element); /********************************************************************** get_matched_element_scanned_seq Returns the parent_scanned_sequence member in a matched_element object. **********************************************************************/ SCANNED_SEQUENCE_T *get_matched_element_scanned_seq(MATCHED_ELEMENT_T* element); /********************************************************************** set_matched_element_sequence Sets the sequence member in a cisml matched_element object. **********************************************************************/ void set_matched_element_sequence(MATCHED_ELEMENT_T* element, char *seq); /************************************************************************* * sort_matched_elements * * Sort an array of pointers to matched-elements sites by pvalue * or by sequence name and position. * * JH - I opened this up to make it accessible outside of the CISML code * because I needed the matched elements sorted for the BLS implementation *************************************************************************/ void sort_matched_elements( BOOLEAN_T sort_by_pvalue, int num_elements, MATCHED_ELEMENT_T **elements ); /********************************************************************** print_cisml_start Print the opening section of the CisML XML **********************************************************************/ void print_cisml_start( FILE* out, char *program_name, BOOLEAN_T print_header, const char *stylesheet, BOOLEAN_T print_namespace ); /********************************************************************** print_cisml_end Print the closing section of the CisML XML **********************************************************************/ void print_cisml_end(FILE* out); /********************************************************************** print_cisml_parmeters Print parameters element for CisML **********************************************************************/ void print_cisml_parameters(FILE *out, CISML_T *cisml); /********************************************************************** print_cisml Print the cisml data structure as CisML XML **********************************************************************/ void print_cisml( FILE* out, /* The target file IN */ CISML_T *cisml, /* The cisml data structure to save IN */ BOOLEAN_T print_header, /* FLAG indicates if the header should be printed IN */ const char *stylesheet, /* the stylesheet file IN */ BOOLEAN_T print_namespace /* FLAG indicates if the namespace should be printed IN */ ); /********************************************************************** print_cisml_start_pattern Print the starting tag for a CisML pattern **********************************************************************/ void print_cisml_start_pattern( CISML_T *cisml, FILE *out, PATTERN_T *pattern ); /********************************************************************** print_cisml_end_pattern Print the ending tag for a CisML pattern **********************************************************************/ void print_cisml_end_pattern(FILE *out); /********************************************************************** print_cisml_scanned_sequences() Print the XML for of a CisML scanned sequence element. **********************************************************************/ void print_cisml_scanned_sequences( CISML_T *cisml, FILE *out, int num_seqs, SCANNED_SEQUENCE_T **sequences ); /********************************************************************** print_cisml_scanned_sequence_start() Print the starting XML tag for a CisML scanned sequence element. **********************************************************************/ void print_cisml_scanned_sequence_start( CISML_T *cisml, FILE *out, SCANNED_SEQUENCE_T *seq ); /********************************************************************** print_cisml_scanned_sequence_end() Print the ending XML tag for a CisML scanned sequence element. **********************************************************************/ void print_cisml_scanned_sequence_end(FILE *out); /********************************************************************** * This function saves CisML results as a set of files in a * directory. The file names are provided by the input parameters: * cisml is a pointer to the ciml structure to be printed. * ouput_dirname will be the name of the output directory * xml_filename will be the CisML output * html_filename will be the name of the HTML output * text_filename will be the name of the plain text output * gff_filename will be the name of the GFF output * allow_clobber will determine whether or not existing files will * be overwritten. * print_namespace will determine whether or not the standard name * space will be written *********************************************************************/ bool print_full_results( CISML_T *cisml, char *output_dirname, char *xml_filename, char *html_filename, char *text_filename, char *gff_filename, BOOLEAN_T allow_clobber, BOOLEAN_T print_namespace ); /********************************************************************** * This function saves the CisML results as a set of files in a * directory. The files include: * fimo.xml which uses the CisML schema * fimo.txt which uses plain text with tab-delimited columns * fimo.gff which uses the gff file format. *********************************************************************/ bool print_cisml_as_text(CISML_T *cisml); /********************************************************************** read_cisml Reads in a CisML XML file and create the cisml_t data structure **********************************************************************/ CISML_T* read_cisml(const char* cisml_filename); #endif