PIP.Core
Class App

java.lang.Object
  PIP.Core.App

public class App
extends java.lang.Object

This is a simple helper class for the Application which stores things like connections to databases and properties

Field Summary

static java.util.logging.Logger

log

Constructor Summary

App()

Method Summary

static java.lang.String	ampsFile(java.lang.String al)
static java.lang.String	blastFile(java.lang.String a1)
static java.lang.String	clusterDir()
static java.lang.String	clusterDir(java.lang.String al)
static java.lang.String	clusterDirSimple()
static java.lang.String	dataFile(java.lang.String a1)
static void	deleteAllClusterDir()
static boolean	deleteDir(java.io.File dir)
static java.lang.String	getJobId()
static java.sql.Connection	getMSDConnection()
static java.util.Properties	getProperties()
static javax.jdo.PersistenceManager	getReadOnlyPersistanceManager()
static javax.jdo.PersistenceManager	getReadWritePersistanceManager()
static java.lang.String	getTaskId()
static void	mkTempCluster()
static java.lang.String	multiProtDir()
static java.lang.String	multiProtDir(java.lang.String al)
static java.lang.String	naccesFile(java.lang.String al)
static java.lang.String	orientationDir()
static java.lang.String	orientationDir(java.lang.String a1)
static java.lang.String	pdbFile(java.lang.String al)
static java.lang.String	residueSubsitutionFile(java.lang.String al)
static java.lang.String	scriptsDir()
static java.lang.String	scriptsDir(java.lang.String a1)
static java.lang.String	serialisedFile(java.lang.String al)
static java.lang.String	stampFile(java.lang.String al)
static java.lang.String	templateFile(java.lang.String a1)
static boolean	tryConnection()
static void	unhandledError(java.lang.Throwable e)
static java.lang.String	webDir()
static java.lang.String	webDir(java.lang.String a1)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log

public static java.util.logging.Logger log

Constructor Detail

App

public App()

Method Detail

getProperties

public static java.util.Properties getProperties()

getMSDConnection

public static java.sql.Connection getMSDConnection()
                                            throws java.lang.ClassNotFoundException,
                                                   java.sql.SQLException

Returns:

A connection to the MSD

Throws:

java.lang.ClassNotFoundException

java.sql.SQLException

getReadOnlyPersistanceManager

public static javax.jdo.PersistenceManager getReadOnlyPersistanceManager()

Returns:

a read only connection to SNAPPI-DB

tryConnection

public static boolean tryConnection()

getReadWritePersistanceManager

public static javax.jdo.PersistenceManager getReadWritePersistanceManager()

Returns:

a write connection to SNAPPI-DB

orientationDir

public static java.lang.String orientationDir(java.lang.String a1)

Parameters:

a1 - -

Returns:

orientationDir

public static java.lang.String orientationDir()

webDir

public static java.lang.String webDir(java.lang.String a1)

webDir

public static java.lang.String webDir()

scriptsDir

public static java.lang.String scriptsDir(java.lang.String a1)

scriptsDir

public static java.lang.String scriptsDir()

multiProtDir

public static java.lang.String multiProtDir()

multiProtDir

public static java.lang.String multiProtDir(java.lang.String al)

dataFile

public static java.lang.String dataFile(java.lang.String a1)

templateFile

public static java.lang.String templateFile(java.lang.String a1)

ampsFile

public static java.lang.String ampsFile(java.lang.String al)

residueSubsitutionFile

public static java.lang.String residueSubsitutionFile(java.lang.String al)

stampFile

public static java.lang.String stampFile(java.lang.String al)

blastFile

public static java.lang.String blastFile(java.lang.String a1)

pdbFile

public static java.lang.String pdbFile(java.lang.String al)

naccesFile

public static java.lang.String naccesFile(java.lang.String al)

serialisedFile

public static java.lang.String serialisedFile(java.lang.String al)

clusterDir

public static java.lang.String clusterDir()

clusterDirSimple

public static java.lang.String clusterDirSimple()

clusterDir

public static java.lang.String clusterDir(java.lang.String al)

mkTempCluster

public static void mkTempCluster()

getTaskId

public static java.lang.String getTaskId()

getJobId

public static java.lang.String getJobId()

unhandledError

public static void unhandledError(java.lang.Throwable e)

deleteAllClusterDir

public static void deleteAllClusterDir()

deleteDir

public static boolean deleteDir(java.io.File dir)