net.maizegenetics.analysis.gobii

Class GOBIIDbUtils

net.maizegenetics.analysis.gobii.GOBIIDbUtils

public class GOBIIDbUtils

These methods were largely borrowed from Jeff's privatemaizegenetics GenomeAnnosDB.java, then modified as needed for GOBII postgres access. Currently, this file is ONLY connecting to postgres, not monetd. if plugins are created that need to connect to monetdb, a new connectToDB() method for monetdb must be created, or the existing one will need to be changed to indicate the database type for connection. For connecting to a monetdb instance, see example in privatemaizegenetics.lynn.MonetdbFileProcessing.MonetDBQtoPosList.connectToDBOrDie

Method Detail

connectToDB

public static java.sql.Connection connectToDB(java.lang.String configFile)

connectToDatabaseOrDie

public static java.sql.Connection connectToDatabaseOrDie(java.lang.String dbName,
                                                         java.util.Properties props)

readNextLine

public static java.lang.String[] readNextLine(java.io.BufferedReader reader,
                                              java.lang.String inFile)

postgreSQLCopyFromReader

public static void postgreSQLCopyFromReader(java.sql.Connection conn,
                                            java.lang.String table,
                                            java.io.BufferedReader reader)

executePostgreSQLQuery

public static java.sql.ResultSet executePostgreSQLQuery(java.sql.Statement st,
                                                        java.lang.String query,
                                                        boolean echoQuery)

populateTableFromFile

public static void populateTableFromFile(java.sql.Connection conn,
                                         java.lang.String table,
                                         java.lang.String sourceFile,
                                         boolean header)

createPostgreSQLStatement

public static java.sql.Statement createPostgreSQLStatement(java.sql.Connection conn)

printPostgreSQLResultSet

public static void printPostgreSQLResultSet(java.sql.ResultSet rs)

printPostgreSQLResultSet

public static void printPostgreSQLResultSet(java.sql.ResultSet rs,
                                            int stride)

printPostgreSQLResultSetToFile

public static void printPostgreSQLResultSetToFile(java.sql.ResultSet rs,
                                                  java.lang.String outFile)