/* $Id: maputil.h,v 6.8 2001/06/26 16:42:59 vakatov Exp $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: $RCSfile: maputil.h,v $ * * Author: Jinghui Zhang * * Initial Version Creation Date: 03/21/97 * * $Revision: 6.8 $ * * File Description: * External include file for graphical alignments * * $Log: maputil.h,v $ * Revision 6.8 2001/06/26 16:42:59 vakatov * POINT --> BAND_POINT (to avoid conflicts with MS-Win standard headers) * * Revision 6.7 1998/07/22 00:02:37 zjing * move SortValNode from maputil to jzmisc * * Revision 6.6 1997/11/14 22:13:41 vakatov * [WIN32,DLL] Added NLM_EXTERN's * * Revision 6.5 1997/10/15 19:56:42 zjing * change get_align_annot_qual parameter * * Revision 6.4 1997/10/10 18:32:42 zjing * add support to collect OBJ_BIOSEQ_DELTA and functions to improve the alignment overview * * Revision 6.3 1997/10/06 14:42:39 zjing * functions for the overview of blast search results * * Revision 6.0 1997/08/25 18:06:37 madden * Revision changed to 6.0 * * Revision 5.9 1997/07/23 13:45:29 zjing * look up for the sequence index map * * $Revision: 6.8 $ * * File Description: * External include file for graphical alignments * * $Log: maputil.h,v $ * Revision 6.8 2001/06/26 16:42:59 vakatov * POINT --> BAND_POINT (to avoid conflicts with MS-Win standard headers) * * Revision 6.7 1998/07/22 00:02:37 zjing * move SortValNode from maputil to jzmisc * * Revision 6.6 1997/11/14 22:13:41 vakatov * [WIN32,DLL] Added NLM_EXTERN's * * Revision 6.5 1997/10/15 19:56:42 zjing * change get_align_annot_qual parameter * * Revision 6.4 1997/10/10 18:32:42 zjing * add support to collect OBJ_BIOSEQ_DELTA and functions to improve the alignment overview * * Revision 6.3 1997/10/06 14:42:39 zjing * functions for the overview of blast search results * * Revision 5.8 1997/06/19 18:38:23 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.7 1997/03/21 19:47:16 shavirin * Added NCBI header started logging and added protection for usage * it with C++ compiler * * * ========================================================================== */ #ifndef _MAPUTIL_ #define _MAPUTIL_ /****************************************************************************/ /* INCLUDES */ /****************************************************************************/ #include #include #include #include #include #include #include #include #include #include /*local include file*/ #include /****************************************************************************/ /* TYPEDEFS */ /****************************************************************************/ typedef struct genedata{ CharPtr symbol; Boolean landmark; /*is it a landmark gene?*/ Uint2 entityID; Uint2 itemID; Uint2 itemType; Uint2 subtype; Uint2 priority; Int4 x, y; /*the x, y coordinates on the picture*/ SeqLocPtr location; SeqFeatPtr sfp; ValNodePtr align_seg; struct genedata PNTR next; }GeneData, PNTR GeneDataPtr; typedef ValNodePtr EnzPtr; typedef struct enzdata{ CharPtr name; CharPtr pattern; Uint1 cut_pos; }EnzData, PNTR EnzDataPtr; typedef struct musksep{ /*Seq-entries from musk*/ SeqEntryPtr sep; Boolean is_bin; /*is it loaded from a binary file?*/ Char file_name[100]; /*the name for the ASN.1 Seq-entry file*/ Pointer dataptr; Uint2 datatype; } MuskSep, PNTR MuskSepPtr; /****************************************************************************/ /* FINCTION DEFINITIONS */ /****************************************************************************/ #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif NLM_EXTERN Int2 get_seg_num PROTO((SeqLocPtr slp)); NLM_EXTERN Int2 get_seglevels PROTO((BioseqPtr bsp)); NLM_EXTERN Int4Ptr get_priority_order PROTO((SeqEntryPtr sep, Int4Ptr num)); /**************************************************************** * * LoadLandMarkGene(sep) * get the landmark gene from the User-object in the descriptor * all the genes are linked to a ValNode and vnp->choice is set * to 1 to indicate it is a landmark gene * ******************************************************************/ NLM_EXTERN ValNodePtr LoadLandMarkGene PROTO((SeqEntryPtr sep)); /***************************************************************** * * if sfp is a Gene-ref and contains the gene in g_list, * return the string in g_list * else return NULL * *****************************************************************/ NLM_EXTERN Boolean check_landmark PROTO((SeqFeatPtr sfp, CharPtr mark)); /****************************************************************** * * load_gdata_marks(slp, gene_list, seglevels, sep, gdp) * Gather the current Seq-entry to create the corresponding list of * GeneDataPtr for the list of gene symbols * slp: the target Seq-local. can be set to NULL * gene_list: a list of query symbols * seglevels: levels of gather * sep: the Seq-entry * gdp: the header of GeneDataPtr * ********************************************************************/ NLM_EXTERN Boolean load_gdata_marks PROTO((SeqLocPtr slp, ValNodePtr gene_list, Int2 seglevels, SeqEntryPtr sep, GeneDataPtr PNTR pgdp)); NLM_EXTERN GeneDataPtr LinkGeneData PROTO((GeneDataPtr PNTR head, GeneDataPtr newgdp)); NLM_EXTERN GeneDataPtr GeneDataFree PROTO((GeneDataPtr head)); NLM_EXTERN GeneDataPtr make_gene_data PROTO((ValNodePtr gene_list)); NLM_EXTERN void RefreshGeneData PROTO((GeneDataPtr gdp)); /************************************************************************* * * return the best location of the gene from sep. * best is defined as the Bioseq with the highest searching prioirity * e_start, e_stop record the extremes of the all the presence of * the gene * *************************************************************************/ NLM_EXTERN SeqLocPtr get_location_for_query PROTO((SeqEntryPtr sep, CharPtr gene, Int4Ptr e_start, Int4Ptr e_stop)); /***************************************************************** * * Build a list of gene symbols to supply the Find Gene option in * the global view * ******************************************************************/ NLM_EXTERN ValNodePtr BuildGeneList PROTO((SeqEntryPtr sep)); /**************************************************** * * make_enzyme_list(file_name) * build a ValNodeList of EnzDataPtr from teh * input file * ****************************************************/ NLM_EXTERN EnzPtr make_enzyme_list PROTO((CharPtr file_name)); /************************************************** * * free_enzyme_list(enp) * Free a list of EnzDataPtr * **************************************************/ NLM_EXTERN EnzPtr free_enzyme_list PROTO((EnzPtr enp)); /********************************************************************** * * FreeEquivAlign(ealign_list) * Free a list of Seq-annot that is of type Seq-align * mostly, those are the externally loaded Seq-align for showing * the Equiv map * ***********************************************************************/ NLM_EXTERN ValNodePtr FreeEquivAlign PROTO((ValNodePtr ealign_list)); /******************************************************************* * * GetEquivAlignType(annot) * annot stores the alignments of markers mapped by more than * one groups. if return 1, the markers are the consistent markers * if return 2, the markers are inconsistent markers * if return 0, the alignment simply records the mapping to * the sequence map * if return -1, unknown status. Will be treated the same as 1 * *******************************************************************/ NLM_EXTERN Int2 GetEquivAlignType PROTO((SeqAnnotPtr annot)); /*********************************************************************** * * FreeMuskSep(sep_list) * Free the manually loaded Seq-entries * sep_list: a list of MuskSepPtr * ***********************************************************************/ NLM_EXTERN ValNodePtr FreeMuskSep PROTO((ValNodePtr sep_list)); /*##################################################################### # # functions related to BioseqDraw # # ######################################################################*/ /********************************************************************** * * get_Bioseq_type(bsp) * return the subclasses of Bioseq, such as the genetic or physical map * depending on its bsp->repr type and bsp->seq_ext type. * **********************************************************************/ #define PHYSICAL_MAP 1 #define GENETIC_MAP 2 #define RESTRICTION_MAP 3 #define CYTO_MAP 4 #define VIRTUAL_SEQ 5 #define SEG_SEQ 6 #define RAW_SEQ 7 NLM_EXTERN Uint1 get_Bioseq_type PROTO((BioseqPtr bsp)); /************************************************************************* * * MapLayout is an ORDERED list of MapPos, which contains the layout * for each map. It is used for determine the layout of map alignment * **************************************************************************/ typedef ValNode MapLayout, FAR *MapLayoutPtr; typedef struct mappos{ /*holding the positin of each map*/ SeqLocPtr slp; /*the range of the map on display*/ Int2 entityID; Int4 left, right; /*the left, right position on the graph*/ Int4 top, bottom; /*the top, bottom position on the graph*/ Int4 seq_top, seq_bottom; /*the top, bottom position of the sequence*/ }MapPos, PNTR MapPosPtr; NLM_EXTERN MapLayoutPtr MapLayoutFree PROTO ((MapLayoutPtr head)); #define MAX_DIM 100 /*the maximal dimension of a map alignment*/ typedef struct alignpos{ /*the position of each alignment mapped to the graph*/ Int4 left[MAX_DIM]; Int4 right[MAX_DIM]; Int4 top[MAX_DIM]; Int4 bottom[MAX_DIM]; }AlignPos, PNTR AlignPosPtr; /******************************************************************** * * SortAlignPosition(app, dim) * Sort out the order of a multiple alignment in the vertical * display mode. It is sorted to the descending order of * app->top. one app correspond to one aligned segment. It can * be of multiple dimensions * app: alignment position * dim: dimention of alignment * *********************************************************************/ NLM_EXTERN void SortAlignPosition PROTO((AlignPosPtr app, Int2 dim)); /*************************************************************************** * * getBioseqNumbering(bsp) * get the numbering object from Seq_descr. If no numbering, return NULL * ****************************************************************************/ NLM_EXTERN NumberingPtr getBioseqNumbering PROTO ((BioseqPtr bsp)); /********************************************************************** * * IS_NUM_GENE(gene_label): kludge function * determine if the gene_label is used as a map unit, such * as the case for C.elegans physical map * **********************************************************************/ NLM_EXTERN Boolean IS_NUM_GENE PROTO ((CharPtr gene_label)); /*********************************************************************** * * map_unit_label(): create a label for the map unit * if(np == NULL), use the actual position. use_kb =TRUE converts * to kilobase unit * ***********************************************************************/ NLM_EXTERN Boolean map_unit_label PROTO((Int4 pos, NumberingPtr np, CharPtr label, Boolean use_kb)); #define HUMAN_CYTO 1 #define FLY_CYTO 2 /**************************************************************** * * ck_cyto_type() a kludge to determine if the cytogenetic map * follows the band pattern of Fly or that of Human * ****************************************************************/ NLM_EXTERN Uint1 ck_cyto_type PROTO((SeqFeatPtr sfp)); /*band used for the Flybase*/ #define MISC_BND 0 /*band is unknown*/ #define BND 1 /*band*/ #define HET 2 /*heterochromatin*/ #define TEL 3 /*telemere*/ #define CEN 4 /*centromere*/ /*band used for Human chromosome*/ #define BAND_POINT 5 /*inclue the centromere and telemere*/ #define GIEMSA_POS 6 /*Giemsa positive*/ #define GIEMSA_NEG 7 /*Giemsa negative*/ #define ACRO_CENTRIC 8 /*Acrocentric*/ #define VARIABLE_REG 9 /*VariableReg*/ /********************************************************************** * * get_band_type(UserObjectPtr) * get the band type in a Cytogenetic map * ***********************************************************************/ NLM_EXTERN Uint1 get_band_type PROTO((UserObjectPtr uop)); /********************************************************************* * * get_band_name(uop) * parse the band name from a cytogenetic map * *********************************************************************/ NLM_EXTERN CharPtr get_band_name PROTO((UserObjectPtr uop)); /************************************************************************* * * is_label_match(obj_id, label) * return TRUE if obj_id->str matches with label * **************************************************************************/ NLM_EXTERN Boolean is_label_match PROTO((ObjectIdPtr obj_id, CharPtr label)); /*********************************************************************** * * a set of default parameters used in drawing and layout of the * sequence picture * ***********************************************************************/ #define LABEL_SPACE 12 /*for layout the mapdata*/ #define TICK_LEN 8 /*length of a tick mark*/ #define BAND_WIDTH 6 /*the width of the band of cytogenetic map*/ #ifdef WIN_MSWIN #define ENZ_WIDTH 14 /*the width of the enzyme for Windows*/ #else #define ENZ_WIDTH 10 #endif #define MAP_SPACE 30 /*the space separate the maps*/ #define LINE_SPACE 4 /*the space among clones if drawn as line*/ #define SIMPLE_LEN 100000 /*the min length for simple drawing*/ #ifdef WIN_MSWIN #define SEQ_WIDTH 14 /*the width of the enzyme for Windows*/ #else #define SEQ_WIDTH 10 #endif #define FEAT_WIDTH 5 NLM_EXTERN ValNodePtr free_slp_list PROTO((ValNodePtr slp_list)); NLM_EXTERN ValNodePtr get_equiv_align PROTO((SeqEntryPtr sep)); /*check to see if the alignment is designed to be displayed as the history*/ NLM_EXTERN Boolean is_annot_for_hist_alignment PROTO((SeqAnnotPtr annot)); /************************************************************************ * * is_map_segment(slp) * return TRUE if slp is a Seq-loc from a amp * return FALSE if it is not a map or the Bioseq is not loaded to * the memory yet * ************************************************************************/ NLM_EXTERN Boolean is_map_segment PROTO((SeqLocPtr slp)); /*************************************************************** * * figure_map_seqid(ext_loc) * a very unreliable way to figure out the if there is a * Seq-id for the map. It is dependent on the frequency of * the Seq-id in a segmented sequence * ****************************************************************/ NLM_EXTERN SeqIdPtr figure_map_seqid PROTO((SeqLocPtr ext_loc)); NLM_EXTERN Boolean make_Bioseq_list PROTO((SeqEntryPtr sep, ValNodePtr PNTR bsp_list, ValNodePtr PNTR equiv_align)); NLM_EXTERN Boolean start_new_stack PROTO((Int4 pre_pos, Int4 pos, Int4 scale, Int2Ptr label_width, Int2 c_width)); NLM_EXTERN Int4 calculate_ruler PROTO((Int4 scaleX)); #define GENE_MARK 0 #define CDS_MARK 1 /*********************************************************************** * * for each sequence in alignment stored in Seq-hist, if the aligned * sequence itself contains alignment, it is temporarily loaded as * a user-object in the descriptor of the bioseq. This function extract * the information from the descripor and store it as a list of gi's * plus the kludge offset value * ************************************************************************/ NLM_EXTERN ValNodePtr get_seqids_with_alignment PROTO((BioseqPtr mbsp)); /*********************************************************************** * * map the kludge offet factor for Unigene, RICE, MOUSE ,FlyBase, etc * ************************************************************************/ NLM_EXTERN Int4 get_kludge_factor PROTO((SeqIdPtr sip, Int4Ptr gi)); NLM_EXTERN Boolean BioseqHasLandMark PROTO((BioseqPtr bsp)); typedef struct repeat_region{ GatherRange gr; Char rep_name[20]; }RepeatRegion, PNTR RepeatRegionPtr; typedef struct align_region{ Char annotDB[21]; Uint1 displayOrder; GatherRange gr; /*extremes for the intervals*/ ValNodePtr intervals; /*the intervals. more than one if there are multiple alignments for the same sequence*/ Char seq_name[20]; FloatHi score; FloatHi p_val; FloatHi e_val; Int4 line; Int4 g_left, g_right, g_top, g_bottom; /*the rectangle that defines the alignment*/ Uint1 status; /*range from 0-4 for the lowest to the highest score*/ }AlignRegion, PNTR AlignRegionPtr; /*trying to parse the descriptor in Seq-annot for the alignment display*/ #define ANNOT_BLAST 1 /*it is annotation on the Blast search*/ #define ANNOT_CONSIST 2 /*annotates the consistency between a clone and the genome map. For Eric Green's map*/ #define ANNOT_FISH 3 /*it is the annotation on a FISH map */ NLM_EXTERN Uint1 get_align_annot_qual PROTO((SeqAnnotPtr annot, CharPtr annotDB, Int4 buf_size, Uint1Ptr annot_type)); /************************************************************************** * * collect_repeats_and_align(slp, rrp_list, arp_list, seglevels, sep) * * collect repeat features and alignment for global display * rrp_list: the list of the repeat features * arp_list: the list of the alignments * ***************************************************************************/ NLM_EXTERN Boolean collect_repeats_and_align PROTO((SeqLocPtr slp, ValNodePtr PNTR rrp_list, ValNodePtr PNTR arp_list, Int2 seglevels, SeqEntryPtr sep, Uint1Ptr align_has_status)); /************************************************************** * * get the alignment for the FISH map * for the Human Cytogenetic map, if there is a * Seq-annot stored as Hist-align and the intervals are * aligned to the FISH map, it will return the Seq-align * of the alignment to the FISH map * ***************************************************************/ NLM_EXTERN SeqAlignPtr get_FISH_align PROTO((BioseqPtr bsp)); /******************************************************* * * annot_is_user_defined(annot) * * determine if the Seq-annot contains the features * that were defined by the user. This is to * distinguish the local data from the public data * set * ********************************************************/ NLM_EXTERN Boolean annot_is_user_defined PROTO((SeqAnnotPtr annot)); /************************************************************* * * determine if the Bioseq in the SeqEntry contains * the UserObject for a Map Legend * **************************************************************/ NLM_EXTERN UserObjectPtr BioseqHasMapLegend PROTO((BioseqPtr bsp)); NLM_EXTERN Boolean SeqLocListHasLegend PROTO((ValNodePtr slp_list)); NLM_EXTERN Boolean IsSeqIndexMap PROTO((BioseqPtr bsp)); #define SEQINDEX_VAL 255 /*used to store as the choice in slp_list*/ /*functions related to the yac2band and viewctg*/ /*the YAC contig maps are either from Whitehead or from Eric Green's group*/ #define YAC_MIT 1 #define YAC_NHGRI 2 #define GENETIC_GENETHON 4 #define GENETIC_CHLC 8 /*find a list of the seqlocs on the contig that maps to the *current chromosome. For now, only the Whitehead map and the *Eric Green's map is considered. return a list of Seq-locs that *contains contigs within the region */ NLM_EXTERN Uint1 FindContigDB PROTO((SeqIdPtr sip)); /*return a list of Seq-locs which are the contigs mapped to * the current location on the genome * */ NLM_EXTERN ValNodePtr FindContigList PROTO((SeqLocPtr chr_slp)); NLM_EXTERN Boolean is_lod_score_annot PROTO((SeqAnnotPtr annot)); NLM_EXTERN Int2 GetLODScoreNumber PROTO((BioseqPtr bsp)); NLM_EXTERN CharPtr GetAnnotTitle PROTO((SeqAnnotPtr annot)); NLM_EXTERN Uint1 GetLODScoreBitValue PROTO((SeqFeatPtr sfp)); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif