// TMEV Preferences
//
// Warning: The lines preceeded by "//" are comments, and are ignored by the 
//  TIGR MultiExperimentViewer when reading your preferences. The lines that 
//  do not start with "//" are the values read by the program, and care should 
//  be taken to present these values in the correct format. Make sure that there 
//  is a TAB between the preference name and the value.
//
// Listed below are the user preferences, and the syntax/options for each one:
//
// Input Preference - How you prefer to enter data into TIGR MultiExperimentViewer
//
//  Database - Loads slides from database as default and connects to database.
//  File - Loads slides from flatfiles as default, but also connects to database.
//  Only File - Loads slides from flatfiles only. No database connection.

Input Preference	Only File

// Database Server Name - Sets the path to the database. This is not necessary if 
//  'Input Preference' is set to 'Only File'.
//
//  For sybase, use the following string:
//
//     jdbc:sybase:Tds:<yourhost>:<yourport>
//
//  For oracle, use the following string:
//
//    jdbc:oracle:thin:<yourhost>:<yourport>
//
//  Replace <yourhost> with the name of your database server and
//   <yourport> with the port that it listens to.

Database Server Name	jdbc:sybase:Tds:server:2025

// Database Names - Sets the list of databases to choose arrays from. All 
//  stored procedures must be accessible from all of the available databases 
//  on this list. The database names should be separated by a colon ':'. 
//  This is not necessary if 'Input Preference' is set to 'Only File'.

Database Names	arraydb

// Element Info - Sets the number of row and column pairs and the number of
//  intensities per element, separated by a colon ':'. For example, 3:2 would 
//  indicate each element having three pairs of row and column values, such as 
//  (row, column meta_row, meta_column, sub_row, sub_column), and two intensities, 
//  such as (Cy3, Cy5). The input file must have the row and column pairs listed 
//  at the beginning of the line, followed by intensities and then any additional 
//  fields (see below for details). This preference must be of the form #:# and 
//  is mandatory.

Element Info	3:2

// Headers - Sets the number of non-element row and column headers in the input file, 
//  separated by a colon ':'. For example, 2:4 would indicate the first two rows 
//  and first four columns of every input file are considered headers.

Headers	0:0

// Unique ID - Sets the number of the column that represents the unique identifiers 
//  for each element. This column should not contain duplicate values, and every 
//  element should have a value in this column.

Unique ID	9

// Spot Name - Set the number of the column that represents the name of each 
//  element. These are usually descriptive and human decipherable strings. These 
//  values do not need to be unique.

Spot Name	14

// Additional Fields - Indicates the names of additional data fields 
//  (after row, column, cy3, cy5) to be stored and displayed. The field names 
//  should be separated by a colon ':'. If you have additional fields you want to 
//  have the TIGR MultiExperimentViewer process, each line of your input from the 
//  flat file or row returned from the database must have a number of additional 
//  columns equal to the number of additional fields. Each field name must be unique.
//  For more information, see the TIGR MultiExperimentViewer documentation.

Additional Fields	Clone Name:GB#:TC#:Putative:Cluster:Com Name