This constructor call will create a SlideMap object using the default parameter settings:
$sm = SlideMap->new( machine => "IAS", x_pin => 2, y_pin => 6, xspacing => 24, yspacing => 25);
The constructor will do all initialization, but will 'NOT' create a map in memory. That can be done as follows:
After the map has been created in memory, a reference to the map object is obtained by calling getMap. The map object is an array consisting of references to annonymous arrays holding array_row, array_col, plate_alias (or number), well number.
$map_ref = $sm->getMap;
Individual spots can be mapped back to their originating microtitre plate by supplying the row and column index of the spot to convert_spot:
($plate_num, $well, $plate_row, $plate_col) = $sm->convert_spot($array_row, $array_col);
Well is an integer representing the well position on a plate. Starting from well 1 (A1), this number increases across a row and then to the next row, so A12 in a 96-well plate is well 12 and B1 is well 13, etc. Plate_row is an 1-based integer that represents the row.
Likewise, the row and column indeces for a spot can be obtained from the plate_num and well used as source for the spot. NOTE: plate_num here refers to the position of the plate in the series of plates used for the printing, i.e. it is an plate ordinal.
($array_row, $array_col, $meta_row, $meta_col, $sub_row, $sub_col) = $sm->convert_well($plate_num, $well);
The meta_row and meta_col indeces refer to the row/col indeces of the pin that printed the spot in question. The sub_row and sub_col indeces refer to the indeces of the spot within a block. The array_row and array_col indeces are obvious.
SlideMap includes a convenience method to return the meta_row/col, and sub_row/col indeces for a pair of array_row, array_col indeces:
($_meta_row,$_meta_col,$_sub_row,$_sub_col) = $sm->get_meta($array_row, $array_col);
The following are get/set methods that can be used to customize a SlideMap object to accomodate array printers not supported at the time of release of SlideMap.pm.
All of the following 'set*' methods require re-initialization of the SlideMap object:
getMachine: returns the current machine setting:
$arrayer = $sm->getMachine;
setMachine: sets the machine type used for printing. Currently SlideMap supports 4 types of arrayers: 'IAS', 'MD', 'MD3', and 'Stanford'. To set the machine type:
setPrintHead: defines the numbers of pens in the print head, 'X' (plate_row) and 'Y' (plate_col):
getPrintHead: returns the numbers of pens in the print head:
($x_pin, $y_pin) = $sm->getPrintHead;
setBlockDimensions: set maximumn row and column indeces in blocks on the array, row first then column:
getBlockDimensions: returns block dimensions:
($x_spacing, $y_spacing) = $sm->getBlockDimensions;
setNoComplement: switches printing pattern in the 'X' dimension; this is in effect complementing (1 - x) in the 'X' dimension only. Valid values are 0 => complemented, and 1 => 'NOT' complemented:
$sm->setNoComplement([ 0 | 1 ]);
getNoComplement: returns the current value of the noComplement parameter:
$noComplement = $sm->getNoComplement;
setRepeatMode: number of repeated blocks in 'X' dimension. Valid values are 1 - 4:
$sm->setRepeatMode([ 1 | 2 | 3 | 4 ]);
getRepeatMode: returns the current value of the repeat parameter:
$repeat = $sm->getRepeatMode;
setFormat: microtitre plate format: valid values are 1 => 96-well, and 2=> 384-well:
$sm->setFormat([ 1 | 2 ]);
getFormat: returns the current value of the format parameter:
$plate_format = $sm->getFormat;
setPrintDirection: defines the order of printing used by the printer. Valid values are 0 => top->bottom, and 1 => left->right:
$sm->setPrintDirection([ 0 | 1 ]);
getPrintDirection: returns the current value of the print_dir parameter:
$direction = $sm->getPrintDirection;
setPlateOrder: define a list of plate labels (aliases) for the complete set of plates used for printing. The list should include all repeats of the plate:
$sm->setPlateOrder("[A,B,C,D,E,F,G ... | 1,2,3,4,5, ... ]");
getPlateOrder: returns a reference to an array containing the entire list of plate labels:
$plate_order_ref = $sm->getPlateOrder;
diagnostics: returns the full set of current values for the SlideMap parameters:
print_spots/print_wells: prints an entire set of row/col/plate/well values based on the current SlideMap parameters. if the optional parameter is set to 1 (true) then well numbers are printed as well numbers; if set to 0 or not set, then the well number is returned as row_col, i.e. A1, B12, etc. These methods are useful for diagnosing errors in the print pattern.
$sm->print_spots([ 1 | 0 ]); $sm->print_wells([ 1 | 0 ]);
The algorithms used to convert spots to wells and vise-versa are dynamically generated based on the type of arrayer (machine) supplied as a parameter to the constructor (or to setMachine). To view the algorithm currently being used, use either of the following methods:
Joseph A. White; firstname.lastname@example.org Version 1.2 Feb. 7, 2002