/usr/include/ncbi/pobutil.h is in libncbi6-dev 6.1.20110713-3ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 | #ifndef _POBUTIL_
#define _POBUTIL_
#include <seqport.h>
#include <simutil.h>
#include <jzmisc.h>
#include <tofasta.h>
#include <dust.h>
#define LINE 40
#define REPEAT_BREAK_LEN 10000
#define REPEAT_OVERLAP_LEN 100
#define RUN_SIM_1 1
#define RUN_SIM_2 2
#define RUN_SIM_3 3
#define RUN_BANDALGN 8
#define FILE_IO 0
#define STD_IO 1
/****************************************************************
*
* SortDenseDiagByLocation()
* Sort the DenseDiag from Blastn and Blastp to ascending order
* of the locations
*
*****************************************************************/
void SortAlignByLocation PROTO((SeqAnnotPtr blast_sap));
SeqAnnotPtr sim_for_blast PROTO((SeqAnnotPtr blast_sap, SeqIdPtr query_id, Int4 which_sim));
/*****************************************************************
*
* clean_empty_seqalign(): clean up Seq-align that has no
* data
*
*****************************************************************/
SeqAlignPtr clean_empty_seqalign PROTO((SeqAlignPtr PNTR head));
/**********************************************************************
*
* functions related to the filtering of the repeat sequence
* such as ALUs in primates
*
***********************************************************************/
ValNodePtr make_repeat_lib PROTO((CharPtr file_name, ValNodePtr PNTR slp_list, Boolean io_type));
void free_alu_list PROTO((ValNodePtr alu_sep_list, ValNodePtr alu_slp_list));
/*****************************************************
*
* filter_repeats_for_bigloc(slp, max_len, min_overlap)
* break the slp into smaller pieces and merge the results
*
* slp: the big Seq-loc
* max_len: the maximum allowed length for search
* if -1, set to default
* min_overlap: the minimum length for search
* if -1, set to the default
*
*******************************************************/
ValNodePtr filter_repeats_for_bigloc PROTO((SeqLocPtr slp, Int4 max_len, Int4 min_overlap, ValNodePtr alu_slp_list));
SeqLocPtr filter_repeats PROTO((SeqLocPtr slp, ValNodePtr alu_slp_list, ValNodePtr PNTR ends_list));
void SaveRepeats PROTO((BioseqPtr bsp, ValNodePtr ends_list));
void load_dust_bsp PROTO((BioseqPtr dust_bsp, SeqLocPtr dustloc));
/*******************************************************************
*
* look for the repeat feature in sep and mask the residue in
* dust_bsp
*
*******************************************************************/
void mask_with_repeat_feature PROTO((BioseqPtr bsp, SeqEntryPtr sep, BioseqPtr dust_bsp));
/*******************************************************************
*
* misc functions
*
*******************************************************************/
void get_output_name PROTO((CharPtr name, CharPtr buf));
void write_asn_output PROTO((CharPtr name, BioseqPtr bsp, SeqAnnotPtr annot, Int4 option, Boolean io_type));
Boolean save_SeqAnnot PROTO((SeqAnnotPtr annot, CharPtr name, Boolean io_type));
void prt_FASTA_file PROTO((BioseqPtr bsp, SeqLocPtr dustloc, Boolean io_type));
/**************************************************************
*
* functions related to the pre and post process of the
* blast results
*
***************************************************************/
void restore_blast_id PROTO((SeqAnnotPtr sap, SeqIdPtr sip));
void link_blast_sap PROTO((SeqAnnotPtr PNTR blast_sap, SeqAnnotPtr new));
SeqLocPtr break_blast_job PROTO((SeqLocPtr slp, SeqIdPtr sip, Int4 max_len, Int4 overlap_len));
void clean_all_internal_repeats PROTO((SeqAlignPtr PNTR head));
/*******************************************************************
*
* merge_blast_result(head, new)
* when the input query is too big, it is broken into several
* overlapping Seq-loc to be sent to blast. The results can be
* merged if two Dense-diags are actually represent one HSP
*
********************************************************************/
SeqAnnotPtr merge_blast_result PROTO((SeqAnnotPtr PNTR head, SeqAnnotPtr new));
/***************************************************************
*
* functions related to the filtering of the organism
*
***************************************************************/
/********************************************************************
*
* get_organism(bsp)
* filter the taxname from the organism field in Bioseq
*
********************************************************************/
CharPtr get_organism PROTO((BioseqPtr bsp));
/****************************************************************
*
* sim2_for_blast(blast_sap, query_id)
* run sim2 with the Seq-annot from blast
*
****************************************************************/
SeqAnnotPtr sim2_for_blast PROTO((SeqAnnotPtr blast_sap, SeqIdPtr query_id));
void filter_blast_query PROTO((SeqAnnotPtr blast_sap, BioseqPtr query));
/******************************************************************
*
* functions related to dust
*
******************************************************************/
BioseqPtr make_dust_bsp PROTO((BioseqPtr bsp, Int4 start, Int4 stop, SeqLocPtr dustloc));
/***********************************************************
*
* Function for finding human repeat features
*
************************************************************/
Boolean LIBCALL FindHumanRepeats (BioseqPtr bsp, Boolean show_prog_mon);
/*****************************************************************
*
* AluFeat
* DeskTop function for creating human repeat features
*
*****************************************************************/
Int2 LIBCALLBACK AluFeat (Pointer data);
#define REGISTER_ALUFEAT ObjMgrProcLoadEx(OMPROC_FILTER,"Find Human Repeats","AluFeat",OBJ_BIOSEQ,2,OBJ_BIOSEQ,2,NULL,AluFeat,PROC_PRIORITY_DEFAULT,"Analysis")
/*****************************************************************
*
* convert alignment to a faked feature
*
*****************************************************************/
Boolean load_align_to_interval PROTO((SeqAnnotPtr align_annot, Int4 min_gap_len, BioseqPtr bsp));
Int4 get_score_value PROTO((ScorePtr sp));
#endif
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