1Bio::Search::Hit::BlastUHsietr(3C)ontributed Perl DocumeBnitoa:t:iSoenarch::Hit::BlastHit(3)
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6 Bio::Search::Hit::BlastHit - Blast-specific subclass of
7 Bio::Search::Hit::GenericHit
8
10 use Bio::Search::Hit::BlastHit;
11 my $hit = Bio::Search::Hit::BlastHit->new(-algorithm => 'blastp');
12 # See Bio::Search::Hit::GenericHit for information about working with
14 Hits.
15 # TODO: Describe how to configure a SearchIO stream so that it
17 generates # GenericHit objects.
18
20 This object is a subclass of Bio::Search::Hit::GenericHit and provides
21 some operations that facilitate working with BLAST and PSI-BLAST Hits.
22 For general information about working with Hits, see
24 Bio::Search::Hit::GenericHit.
25
27 Mailing Lists
28 User feedback is an integral part of the evolution of this and other
29 Bioperl modules. Send your comments and suggestions preferably to the
30 Bioperl mailing list. Your participation is much appreciated.
31 bioperl-l@bioperl.org - General discussion
33 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
34 Support
36 Please direct usage questions or support issues to the mailing list:
37 bioperl-l@bioperl.org
39 rather than to the module maintainer directly. Many experienced and
41 reponsive experts will be able look at the problem and quickly address
42 it. Please include a thorough description of the problem with code and
43 data examples if at all possible.
44 Reporting Bugs
46 Report bugs to the Bioperl bug tracking system to help us keep track of
47 the bugs and their resolution. Bug reports can be submitted via the
48 web:
49 http://bugzilla.open-bio.org/
51
53 Email jason@bioperl.org Email sac@bioperl.org
54
56 The rest of the documentation details each of the object methods.
57 Internal methods are usually preceded with a _
58 new
60 Title : new
61 Usage : my $obj = Bio::Search::Hit::GenericHit->new();
62 Function: Builds a new Bio::Search::Hit::GenericHit object
63 Returns : Bio::Search::Hit::GenericHit
64 Args : See Bio::Search::Hit::GenericHit() for other args.
65 Here are the BLAST-specific args that can be used when
66 creating BlastHit objects:
67 -iteration => integer for the PSI-Blast iteration number
68 -found_again => boolean, true if hit appears in a
69 "previously found" section of a PSI-Blast report.
70 iteration
72 Usage : $hit->iteration( $iteration_num );
73 Purpose : Gets the iteration number in which the Hit was found.
74 Example : $iteration_num = $sbjct->iteration();
75 Returns : Integer greater than or equal to 1
76 Non-PSI-BLAST reports will report iteration as 1, but this number
77 is only meaningful for PSI-BLAST reports.
78 Argument : iteration_num (optional, used when setting only)
79 Throws : none
80 See Also : found_again()
82 found_again
84 Title : found_again
85 Usage : $hit->found_again;
86 $hit->found_again(1);
87 Purpose : Gets a boolean indicator whether or not the hit has
88 been found in a previous iteration.
89 This is only applicable to PSI-BLAST reports.
90 This method indicates if the hit was reported in the
92 "Sequences used in model and found again" section of the
93 PSI-BLAST report or if it was reported in the
94 "Sequences not found previously or not previously below threshold"
95 section of the PSI-BLAST report. Only for hits in iteration > 1.
96 Example : if( $hit->found_again()) { ... };
98 Returns : Boolean, true (1) if the hit has been found in a
99 previous PSI-BLAST iteration.
100 Returns false (0 or undef) for hits that have not occurred in a
101 previous PSI-BLAST iteration.
102 Argument : Boolean (1 or 0). Only used for setting.
103 Throws : none
104 See Also : iteration()
106perl v5.12.0 2010-04-29 Bio::Search::Hit::BlastHit(3)