Database Routines

dbconnect

description: return database handle for specified database name
input: database name
output: database handle
example: my $dbh = dbconnect('comboscr');

get_bac_filter_panel_pattern

description: return a bac's filter, panel and pattern
input: (dbh, filter name, bac name)
output: ($filter, $panel, $pattern)
example: my ($filter, $panel, $pattern) = &get_bac_filter_panel_pattern($dbh, 'Nipponbare-PU', '053G06');

get_pools

Description: Retrieves from the database the pools and their sorted order.
Input: Database handle.
Output: 1) An array of the order for pools as defined by SQL.; 2) A hash with the pool id as the key and the pool description as the value
Examples: get_pools($dbh,\@order,\%labels);

get_pool_sets

Description: Retrieves from the database the pool sets and their sorted order.
Input: Database handle.
Output: 1) An array of the order of the pool sets as defined by SQL.; 2) A hash with the pool_set id as the key and the description as the value
Examples: get_pool_sets($dbh,\@order,\%labels);

overgo_name_to_prc

description: return plate, row and col values for an overgo name
input: (dbh, overgo name)
output: plate, row and col
example: my ($plate, $row, $col) = overgo_name_to_prc($dbh, '1jp1234567');

overgo_filter

description: given a list of overgos, return valid overgos
input: %input - keys: dbh, overgos, cutoff; overgos can be formatted as either contig/position or plate/row/col; cutoff is optional (default = 30bp, can also specify a cutoff of 'none' to return everything)
output: @valid_overgos
example: my %input = (dbh => $dbh, overgos => ['1jp1234567', '27A07', '8jp7654321'], cutoff => 28);; or; my %input = (dbh => $dbh, overgos => ['1jp1234567']);; or; my %input = (dbh => $dbh, overgos => [@overgos]);; my @valid_overgos = overgo_filter(%input);

Web Routines

project_referer

description: returns the project type (rice or soybean) based on the HTTP_REFERER cgi env. var.
input: $ENV{HTTP_REFERER}
output: rice or soybean (undef if the referer cannot be determined)
example: my $project = project_referer($ENV{HTTP_REFERER});

table_head0

description: print <table border=``0'' cellspacing=``2'' cellpadding=``2''>
input: none

table_head1

description: print <table border=``1'' cellspacing=``2'' cellpadding=``2''>
input: none

print_overgo_query_html

Description

Prints out the HTML needed to query the user in regards to what overgo they wish to choose.

Input

1) Database handle.

2) CGI handle.

3) If to use HTML tables. 0 = no, 1 = yes, 2 = yes & leave table open (often because the calling program wishes to add other information to the table; a two column table is created)

4..8) Five variables on which sections to display. 0 = no display, 1 = display normal, 2 = display with wildcard. It is up to the calling program to handle the wildcard.

The sections are: 4) Contig-position ... a unified field for the user to put this information 5) Contig, position ... two fields for data entry 6) Plate, row, column ... three fields for data entry 7) Pool 8) Pool set

The routine should be enclosed within a form otherwise the user will not be able to choose the drop down menus properly.

Output

Just prints to stdout.

The user's selection can be obtained via a cgi_handle->query('xxx') where 'xxx' is:

  conpos

  contig
  position

  plate
  row
  column

  pool

  poolset

For the 5 sections respectively. It is up to the calling program to handle the wildcards if there are any.

Examples

(A) Using tables & leave table open, displaying 2nd, 4th, and 5th sections. The 2nd wildcarded.

overgo_query_html($dbh,$q,2,0,2,0,1,1);

(B) Not using tables, displaying only the 3rd section without wildcards

overgo_query_html($dbh,$q,0,0,0,1,0,0);