include/objtools/align_format/align_format_util.hpp File Reference

#include <cgi/cgictx.hpp>
#include <corelib/ncbistre.hpp>
#include <corelib/ncbireg.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/blastdb/Blast_def_line_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <objtools/align_format/format_flags.hpp>
#include <util/math/matrix.hpp>

Include dependency graph for align_format_util.hpp:

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Classes

class  CAlignFormatUtil
 This class contains misc functions for displaying BLAST results. More...
struct  CAlignFormatUtil::SBlastError
 Error info structure. More...
struct  CAlignFormatUtil::SDbInfo
 Blast database info. More...

Defines

#define DIM(static_array)   (sizeof(static_array)/sizeof(*static_array))
 Calculates the dimensions of a static array.

Typedefs

typedef map< string, string > TUrlMap
 Type definition for a map of tags - URLs.

Enumerations

enum  { ePMatrixSize = 23 }
 protein matrix define More...

Functions

static TUrlMap k_UrlMap ((const TUrlMap::value_type *)&k_all_url_pairs[0],(const TUrlMap::value_type *) k_all_url_pairs+(sizeof(k_all_url_pairs)/sizeof(*k_all_url_pairs)))
 create map source of all static URL's using previously defined pairs

Variables

static const string kClassInfo = "class=\"info\""
 class info
const string kEntrezUrl
 entrez
const string kTraceUrl
 trace db
const string kGenomeButton
 genome button
const string kUnigeneUrl
 unigene
const string kStructureUrl
 structure
const string kStructure_Overview
 structure overview
const string kGeoUrl
 Geo.
const string kGeneUrl
 Gene.
const string kBioAssayProtURL
 Bioassay for proteins.
const string kBioAssayNucURL
 Bioassay for nucleotides.
const string kMapviwerUrl
 mapviewer linkout
const string kEntrezSubseqUrl
 Sub-sequence.
const string kBl2seqUrl
 Bl2seq.
const string k_GetSeqSubmitForm []
const string k_GetSeqSelectForm
const string k_GetTreeViewForm
const string kGeneInfoUrl
const string kGetTreeViewCgi = "http://www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi"
const string kEntrezQueryCgi = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
const string kTraceCgi = "http://www.ncbi.nlm.nih.gov/Traces/trace.cgi"
const string kMapSearchCgi = "http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi"
const string kCBlastCgi = "http://www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi"
const string kEntrezViewerCgi = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"
const string kBl2SeqWBlastCgi = "http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi"
const string kEntrezSitesCgi = "http://www.ncbi.nlm.nih.gov/sites/entrez"
static pair< string, string > k_all_url_pairs []
 list all static url patterns
const int k_NumAsciiChar = 128
 Number of ASCII characters for populating matrix columns.
const char k_PSymbol []
 Residues.

Define Documentation

#define DIM (  static_array   )     (sizeof(static_array)/sizeof(*static_array))
 

Calculates the dimensions of a static array.

Definition at line 230 of file align_format_util.hpp.

Typedef Documentation

typedef map<string, string> TUrlMap
 

Type definition for a map of tags - URLs.

Definition at line 234 of file align_format_util.hpp.

Enumeration Type Documentation

anonymous enum
 

protein matrix define

Enumerator:
ePMatrixSize 

Definition at line 243 of file align_format_util.hpp.

Function Documentation

static TUrlMap k_UrlMap (  (const TUrlMap::value_type *)&  k_all_url_pairs[0],
(const TUrlMap::value_type *) k_all_url_pairs+(sizeof(k_all_url_pairs)/sizeof(*k_all_url_pairs)) 
)  [static]
 

create map source of all static URL's using previously defined pairs

Referenced by CAlignFormatUtil::GetURLDefault().

Variable Documentation

pair<string,string> k_all_url_pairs[] [static]
 

Initial value:

{
  pair <string,string>  ("ENTREZ",  kEntrezUrl ),
  pair <string,string>  ("UNIGEN",  kUnigeneUrl),  
  pair <string,string>  ("GEO",    kGeoUrl),
  pair <string,string>  ("GENE",  kGeneUrl),
  pair <string,string>  ("GENE_INFO",  kGeneInfoUrl),
  pair <string,string>  ("BIOASSAY_PROT",  kBioAssayProtURL),
  pair <string,string>  ("BIOASSAY_NUC",  kBioAssayNucURL),
  pair <string,string>  ("ENTREZ_SUBSEQ",  kEntrezSubseqUrl),
  pair <string,string>  ("TRACE",  kTraceUrl),
  pair <string,string>  ("GENOME_BTN",  kGenomeButton),
  pair <string,string>  ("STRUCTURE_URL",  kStructureUrl),
  pair <string,string>  ("STRUCTURE_OVW",  kStructure_Overview),
  pair <string,string>  ("MAPVIEWER",  kMapviwerUrl),
  pair <string,string>  ("BL2SEQ",  kBl2seqUrl),
  pair <string,string>  ("GETSEQ_SUB_FRM_0",  k_GetSeqSubmitForm[0]),
  pair <string,string>  ("GETSEQ_SUB_FRM_1",  k_GetSeqSubmitForm[1]),
  pair <string,string>  ("GETSEQ_SEL_FRM",  k_GetSeqSelectForm),
  pair <string,string>  ("TREEVIEW_FRM",  k_GetTreeViewForm),
  
  pair <string,string>  ("TREEVIEW_CGI",  kGetTreeViewCgi),
  pair <string,string>  ("ENTREZ_QUERY_CGI",  kEntrezQueryCgi),
  pair <string,string>  ("ENTREZ_VIEWER_CGI",  kEntrezViewerCgi),
  pair <string,string>  ("TRACE_CGI",  kTraceCgi),
  pair <string,string>  ("MAP_SEARCH_CGI",  kMapSearchCgi),
  pair <string,string>  ("CBLAST_CGI",  kCBlastCgi),
  pair <string,string>  ("BL2SEQ_WBLAST_CGI",  kBl2SeqWBlastCgi),
  pair <string,string>  ("ENTREZ_SITES_CGI",  kEntrezSitesCgi)
}
list all static url patterns

Definition at line 198 of file align_format_util.hpp.

const string k_GetSeqSelectForm
 

Initial value:

 "<FORM><input \
type=\"button\" value=\"Select all\" onClick=\"handleCheckAll('select', \
'getSeqAlignment%d', 'getSeqGi')\"></form></td><td><FORM><input \
type=\"button\" value=\"Deselect all\" onClick=\"handleCheckAll('deselect', \
'getSeqAlignment%d', 'getSeqGi')\"></form>"

Definition at line 160 of file align_format_util.hpp.

const string k_GetSeqSubmitForm[]
 

Initial value:

 {"<FORM  method=\"post\" \
action=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?SUBMIT=y\" \
name=\"%s%d\"><input type=button value=\"Get selected sequences\" \
onClick=\"finalSubmit(%d, 'getSeqAlignment%d', 'getSeqGi', '%s%d', %d)\"><input \
type=\"hidden\" name=\"db\" value=\"\"><input type=\"hidden\" name=\"term\" \
value=\"\"><input type=\"hidden\" name=\"doptcmdl\" value=\"docsum\"><input \
type=\"hidden\" name=\"cmd\" value=\"search\"></form>",
                                     
                                     "<FORM  method=\"POST\" \
action=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi\" \
name=\"%s%d\"><input type=button value=\"Get selected sequences\" \
onClick=\"finalSubmit(%d, 'getSeqAlignment%d', 'getSeqGi', '%s%d', %d)\"><input \
type=\"hidden\" name=\"val\" value=\"\"><input \
type=\"hidden\" name=\"cmd\" value=\"retrieve\"></form>"
}

Definition at line 142 of file align_format_util.hpp.

const string k_GetTreeViewForm
 

Initial value:

  "<FORM  method=\"post\" \
action=\"http://www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi?request=page&rid=%s&queryID=%s&distmode=on\" \
name=\"tree%s%d\" target=\"trv%s\"> \
<input type=button value=\"Distance tree of results\" onClick=\"extractCheckedSeq('getSeqAlignment%d', 'getSeqGi', 'tree%s%d')\"> \
<input type=\"hidden\" name=\"sequenceSet\" value=\"\"><input type=\"hidden\" name=\"screenWidth\" value=\"\"></form>"

Definition at line 167 of file align_format_util.hpp.

const int k_NumAsciiChar = 128
 

Number of ASCII characters for populating matrix columns.

Definition at line 248 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetAsciiProteinMatrix(), and CDisplaySeqalign::~CDisplaySeqalign().

const char k_PSymbol[]
 

Residues.

Definition at line 95 of file align_format_util.cpp.

Referenced by CAlignFormatUtil::GetAsciiProteinMatrix().

const string kBioAssayNucURL
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.gov/entrez\
?db=pcassay&term=%d[RNATargetGI]&RID=%s&log$=pcassay%s&blast_rank=%d\"><img border=0 height=16 width=16 \
src=\"images/Bioassay.gif\" alt=\"PubChem BioAssay Info\"></a>"
Bioassay for nucleotides.

Definition at line 118 of file align_format_util.hpp.

const string kBioAssayProtURL
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.gov/entrez\
?db=pcassay&term=%d[PigGI]&RID=%s&log$=pcassay%s&blast_rank=%d\"><img border=0 height=16 width=16 \
src=\"images/Bioassay.gif\" alt=\"PubChem BioAssay Info\"></a>"
Bioassay for proteins.

Definition at line 112 of file align_format_util.hpp.

const string kBl2seqUrl
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.gov/\
blast/bl2seq/wblast2.cgi?PROGRAM=tblastx&WORD=3&RID=%s&ONE=%s&TWO=%s\">Get \
TBLASTX alignments</a>"
Bl2seq.

Definition at line 136 of file align_format_util.hpp.

const string kBl2SeqWBlastCgi = "http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi"
 

Definition at line 190 of file align_format_util.hpp.

const string kCBlastCgi = "http://www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi"
 

Definition at line 186 of file align_format_util.hpp.

const string kClassInfo = "class=\"info\"" [static]
 

class info

Definition at line 58 of file align_format_util.hpp.

const string kEntrezQueryCgi = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
 

Definition at line 180 of file align_format_util.hpp.

const string kEntrezSitesCgi = "http://www.ncbi.nlm.nih.gov/sites/entrez"
 

Definition at line 192 of file align_format_util.hpp.

const string kEntrezSubseqUrl
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.\
gov/entrez/viewer.fcgi?val=%d&db=%s&from=%d&to=%d&view=gbwithparts&RID=%s\">"
Sub-sequence.

Definition at line 131 of file align_format_util.hpp.

const string kEntrezUrl
 

Initial value:

 "<a %shref=\"http://www.ncbi.nlm.nih.gov/entre\
z/query.fcgi?cmd=Retrieve&db=%s&list_uids=%d&dopt=%s&RID=%s&log$=%s%s&blast_rank=%d\" %s>"
entrez

Definition at line 62 of file align_format_util.hpp.

const string kEntrezViewerCgi = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"
 

Definition at line 188 of file align_format_util.hpp.

const string kGeneInfoUrl
 

Initial value:

"http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=%d&RID=%s&log$=geneexplicit%s&blast_rank=%d"

Definition at line 174 of file align_format_util.hpp.

const string kGeneUrl
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/\
query.fcgi?db=gene&cmd=search&term=%d[%s]&RID=%s&log$=gene%s&blast_rank=%d\"><img border=0 height=16 width=16 \
src=\"images/G.gif\" alt=\"Gene info\"></a>"
Gene.

Definition at line 106 of file align_format_util.hpp.

const string kGenomeButton
 

Initial value:

 "<table border=0 width=600 cellpadding=8>\
<tr valign=\"top\"><td><a href=\
\"http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=%d&RID=%s&CLIENT=\
%s&QUERY_NUMBER=%d\"><img border=0 src=\"html/GenomeView.gif\"></a></td>\
<td>Show positions of the BLAST hits in the %s genome \
using the Entrez Genomes MapViewer</td></tr></table><p>"
genome button

Definition at line 72 of file align_format_util.hpp.

const string kGeoUrl
 

Initial value:

  "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/\
query.fcgi?db=geo&term=%d[gi]&RID=%s&log$=geo%s&blast_rank=%d\"><img border=0 height=16 width=16 src=\
\"images/E.gif\" alt=\"Geo\"></a>"
Geo.

Definition at line 100 of file align_format_util.hpp.

const string kGetTreeViewCgi = "http://www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi"
 

Definition at line 178 of file align_format_util.hpp.

const string kMapSearchCgi = "http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi"
 

Definition at line 184 of file align_format_util.hpp.

const string kMapviwerUrl
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?direct=on&gbgi=%d&THE_BLAST_RID=%s&log$=map%s&blast_rank=%d\"><img border=0 height=16 width=16 \
src=\"images/M.gif\" alt=\"Genome view with mapviewer\"></a>"
mapviewer linkout

Definition at line 126 of file align_format_util.hpp.

const string kStructure_Overview
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.\
gov/Structure/cblast/cblast.cgi?blast_RID=%s&blast_rep_gi=%d&hit=%d&blast_CD_\
RID=%s&blast_view=%s&hsp=0&taxname=%s&client=blast\">Related Structures</a>"
structure overview

Definition at line 94 of file align_format_util.hpp.

Referenced by CShowBlastDefline::DisplayBlastDefline(), and CShowBlastDefline::DisplayBlastDeflineTable().

const string kStructureUrl
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.gov/St\
ructure/cblast/cblast.cgi?blast_RID=%s&blast_rep_gi=%d&hit=%d&blast_CD_RID=%s\
&blast_view=%s&hsp=0&taxname=%s&client=blast&log$=structure%s&blast_rank=%d\"><img border=0 height=16 width=\
16 src=\"http://www.ncbi.nlm.nih.gov/Structure/cblast/str_link.gif\" alt=\"Re\
lated structures\"></a>"
structure

Definition at line 87 of file align_format_util.hpp.

const string kTraceCgi = "http://www.ncbi.nlm.nih.gov/Traces/trace.cgi"
 

Definition at line 182 of file align_format_util.hpp.

const string kTraceUrl
 

Initial value:

 "<a %shref=\"http://www.ncbi.nlm.nih.gov/Traces\
/trace.cgi?cmd=retrieve&dopt=fasta&val=%s&RID=%s\">"
trace db

Definition at line 67 of file align_format_util.hpp.

const string kUnigeneUrl
 

Initial value:

 "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?\
db=%s&cmd=Display&dopt=%s_unigene&from_uid=%d&RID=%s&log$=unigene%s&blast_rank=%d\"><img border=0 h\
eight=16 width=16 src=\"images/U.gif\" alt=\"UniGene info\"></a>"
unigene

Definition at line 81 of file align_format_util.hpp.

Generated on Wed Dec 9 07:22:03 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Wed Dec 09 08:18:27 2009 by modify_doxy.py rev. 173732