public class MonetDB_IFLFilePlugin
extends AbstractPlugin
This class has methods to create GOBII intermediary files to be used when creating a GOBII monetdb dataset table. The GOBII IFL scripts require 3 files: a matrix of variants, a list of maker_ids, and a list of dnarun ids. The matrix of variants is created from the hmp.txt file at the same time the intermediary files for the postgres marker and dnarun related tables are created. (see MarkerDNARunFromHMP_IFLFilePlugin) Once the IFL scripts have been run to populate these postgres tables, the marker_id and dnarun_id values are created. This script pulls the id values from the postgres DB to create the final 2 intermediary files needed by the GOBII loadVariantMatrix.py script See this link for details: http://cbsugobii05.tc.cornell.edu:6084/display/TD/MonetDB+IFL The db config file should look like this: host=cbsudc01.tc.cornell.edu user= password= DB=gobii_maizeifltest (or other postgres db you want to query) The outputDir field should also contain the prefix for the file. Previously this was the dataset.name. But GOBII names their .h5 and monetdb table with DS_. We want to do the same to be consistent. THis will need to be queried from the db before running this plugin. If the dataset name is known, this is a simple query. AUgust2016 UPDATE: The list of markers in the marker_id, and dnarun_ids in dnarun_id file must be in proper order. They must be in the order the markers are stored in the monetdb table, ie in the order they are stored in the variant file. TO achieve this, the DB query orders the output by marker_idx (marker query) and dnarun_idx (dnarun query). These idx values were created sequentially when the marker and dnarun tables were created.
public MonetDB_IFLFilePlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public MonetDB_IFLFilePlugin()
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public java.lang.String dbConfigFile()
DB connection config file
public MonetDB_IFLFilePlugin dbConfigFile(java.lang.String value)
Set dbConfigFile. DB connection config file
value - dbConfigFilepublic java.lang.String datasetName()
Name of dataset whose marker and dnarun IDs are to be pulled
public MonetDB_IFLFilePlugin datasetName(java.lang.String value)
Set dataset name. Name of dataset whose marker and dnarun IDs are to be pulled
value - dataset namepublic java.lang.String outputDir()
Full path name of output directory, must end with a /
public MonetDB_IFLFilePlugin outputDir(java.lang.String value)
Set Path of output directory. Full path name of output directory, must end with a /
value - Path of output directory