| Calling Sequence
| PatEntry(a)
|
| Parameters
| | Name | Type | Description |
|
| a
| {integer,range,string,list(integer)} | PatEntry number(s) in the database DB |
| | or a string to be searched |
|
| Return Type
| PatEntry |
| Methods
| AC, Entry, ID, Match, print, Sequence, string, type |
| Synopsis
| When a Darwin database is read for the first time,
Darwin will automatically create a Patricia tree data structure
from the contents of the SEQ field for each entry.
This is accessed via a Pat index.
PatEntry is a data structure for entries to the Pat index for
the database DB. If the argument is an integer, a list of integers
or a range of integers, these are considered to be entries in the
Pat index of the database. If a string is given, it is assumed
to be a sequence, and the Pat index is searched for all the sequences
which contain the string exactly. The result is returned as a range,
even in the case that it is not found (an empty range) which is useful
as it points to the two closest neighbouring sequences in the database.
Searching for exact identity of peptides using PatEntry is very fast. |
| Examples
| > PatEntry(1);
PatEntry(1)
> PatEntry(1..5);
PatEntry(1..5)
> PatEntry('HHHHHHHH');
PatEntry(19663305..19663628)
> PatEntry('B');
PatEntry(4667614..4667613)
> PatEntry('C');
PatEntry(4667614..5600515)
> Sequence(PatEntry(CCCCCCCC));
CCCCCCCCCCCNFCCGKFKPPVNESHDQYSHLNRPDGNREGNDMPTHLGQPPRLEDVDLDDVNLGAGGAPVTSQPREQAG
GQPVFAMPPPSGAVGVNPFTGAPVAANENTSLNTTEQTTYTPDMVNQKY, CCCCCCCCCCNFCCGKFKPPVNESHDQYS
HLNRPDGNREGNDMPTHLGQPPRLEDVDLDDVNLGAGGAPVTSQPREQAGGQPVFAMPPPSGAVGVNPFTGAPVAANENT
SLNTTEQTTYTPDMVNQKY, CCCCCCCCCNFCCGKFKPPVNESHDQYSHLNRPDGNREGNDMPTHLGQPPRLEDVDLDD
VNLGAGGAPVTSQPREQAGGQPVFAMPPPSGAVGVNPFTGAPVAANENTSLNTTEQTTYTPDMVNQKY, CCCCCCCCLC
RDSCVSTWTKNSVANAVATNASSEVSIYSGSFLAILCTFSTGNLGEHRGADAVSLPLVSLFIVLA, CCCCCCCCNFCCG
KFKPPVNESHDQYSHLNRPDGNREGNDMPTHLGQPPRLEDVDLDDVNLGAGGAPVTSQPREQAGGQPVFAMPPPSGAVGV
NPFTGAPVAANENTSLNTTEQTTYTPDMVNQKY
|
| See also
| Entry, ID, Match, Sequence, string |