org.openscience.nmrshiftdb
Class AdminPanel

java.lang.Object
  org.openscience.nmrshiftdb.AdminPanel

public class AdminPanel
extends java.lang.Object

This class handels some admin tasks

Author:

shk3

Constructor Summary

AdminPanel()

Method Summary

private static void	crossvalidateHose(java.lang.String[] args)
private static void	doInsert(AbInitioDataset aid, java.lang.String[] args) Insert a AbInitioDataset into the database.
private static void	executeAnalyzeSql(java.lang.String[] args) Analyzes the current sql logfile
private static void	executeBuildHose(java.lang.String[] args) Executes building of HOSECodes
private static void	executeCheckAssignments(java.lang.String[] args) Checks if shifts are assigned to other atom the spectrum type suggests
private static void	executeCheckDoubleMolecules(java.lang.String[] args) Executes checking of double molecules
private static void	executeCheckNCI(java.lang.String[] args) Executes ckecking vi NCI database
private static void	executeCheckShifts(java.lang.String[] args) Executes ckecking of shifts
private static void	executeCompareShifts(java.lang.String[] args) Executes comparing of shifts to cdk.
private static void	executeCreateInchis(java.lang.String[] args) Creates missing INChIs
private static void	executeCrosscheckHose(java.lang.String[] args) Executes an svm crossvalidation
private static void	executeCrossvalidate(java.lang.String[] args) Executes an svm crossvalidation
private static void	executeCrossvalidateWeka(java.lang.String[] args)
private static void	executeDeletePubchem(java.lang.String[] args)
private static void	executeMakeAromaticity(java.lang.String[] args) Executes making of aromaticities
private static void	executeMakeDescriptorsAll(java.lang.String[] args) Creates the proton descriptors
private static void	executeMakeDescriptorsNew(java.lang.String[] args) Creates the proton descriptors
private static void	executeMakePubchem(java.lang.String[] args) Creates a file for pubchem submit
private static void	executeMakeSmilesChiral(java.lang.String[] args) Executes making of chiral smiles
private static void	executeNCI(java.lang.String[] args) Inserts nci mapping from mapping files
private static void	executeReadACD(java.lang.String[] args) Executes reading of acd names file
private static void	executeReadAlk(java.lang.String[] args) Reads corina 3d coordinates
private static void	executeReadCorina(java.lang.String[] args) Reads corina 3d coordinates
private static void	executeReadDkfz(java.lang.String[] args) Executes reading dkfz files
private static void	executeReadGaussian(java.lang.String[] args) Executes reading Gaussain log files
private static void	executeReadMainz(java.lang.String[] args) Reads file from uni mainz.
private static void	executeReadMainzC(java.lang.String[] args) Reads file from uni mainz.(carbon)
private static void	executeReadWageningen(java.lang.String[] args) Reads file from uni mainz.
private static void	executeRebuildFingerprints(java.lang.String[] args) Several methods, use comments to activate
private static void	executeSynchronize(java.lang.String[] args) Executes synchronization
private static void	executeWriteCorina(java.lang.String[] args) Makes a file needed for corina coordinate generation
private static java.lang.String	getStartLayers(java.lang.String string)
static void	main(java.lang.String[] args) The main program for the AdminPanel class.
private static void	makeArff(java.lang.String[] args)
private static void	makeQA(java.lang.String[] args)
private static void	processData(java.util.Map map, java.lang.String[] args, java.util.Properties geraeteprops, NmrshiftdbUser user, java.util.Properties nmrprops, java.util.Properties jetspeedprops) Inserts a dkfz set into the db
private static void	readcasfromnci(java.lang.String[] args) Reads cas numbers from nci file
private static void	readcoumarines(java.lang.String[] args) Reads coumarine files
private static boolean	warn(java.lang.String text, java.io.BufferedReader br) Prints a warning and asks if to continue

Methods inherited from class java.lang.Object

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

Constructor Detail

AdminPanel

public AdminPanel()

Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

The main program for the AdminPanel class.

Parameters:

args - The directory whre the log files are and the src/java/ directory of nmrshiftdb distribution

Throws:

java.lang.Exception - Description of Exception

warn

private static boolean warn(java.lang.String text,
                            java.io.BufferedReader br)

Prints a warning and asks if to continue

Parameters:

text - The warning text

br - The buffered reader from System.in

Returns:

True=continue, false=break

executeMakePubchem

private static void executeMakePubchem(java.lang.String[] args)
                                throws java.lang.Exception

Creates a file for pubchem submit

Parameters:

args - The command line args

Throws:

java.lang.Exception - Description of Exception

executeSynchronize

private static void executeSynchronize(java.lang.String[] args)
                                throws java.lang.Exception

Executes synchronization

Parameters:

args - The command line args

Throws:

java.lang.Exception - Description of Exception

executeReadGaussian

private static void executeReadGaussian(java.lang.String[] args)
                                 throws java.lang.Exception

Executes reading Gaussain log files

Parameters:

args - The command line args

Throws:

java.lang.Exception

executeReadDkfz

private static void executeReadDkfz(java.lang.String[] args)
                             throws java.lang.Exception

Executes reading dkfz files

Parameters:

args - The command line args

Throws:

java.lang.Exception - Description of Exception

executeReadACD

private static void executeReadACD(java.lang.String[] args)
                            throws java.lang.Exception

Executes reading of acd names file

Parameters:

args - The command line args

Throws:

java.lang.Exception - Description of Exception

executeReadMainzC

private static void executeReadMainzC(java.lang.String[] args)
                               throws java.lang.Exception

Reads file from uni mainz.(carbon)

Parameters:

args - The command line args.

Throws:

java.lang.Exception - Database problems.

executeReadMainz

private static void executeReadMainz(java.lang.String[] args)
                              throws java.lang.Exception

Reads file from uni mainz.

Parameters:

args - The command line args.

Throws:

java.lang.Exception - Database problems.

executeCreateInchis

private static void executeCreateInchis(java.lang.String[] args)
                                 throws java.lang.Exception

Creates missing INChIs

Parameters:

args - The command line args.

Throws:

java.lang.Exception - Databse problems.

executeRebuildFingerprints

private static void executeRebuildFingerprints(java.lang.String[] args)
                                        throws java.lang.Exception

Several methods, use comments to activate

Parameters:

args - The command line args.

Throws:

java.lang.Exception - Databse problems.

processData

private static void processData(java.util.Map map,
                                java.lang.String[] args,
                                java.util.Properties geraeteprops,
                                NmrshiftdbUser user,
                                java.util.Properties nmrprops,
                                java.util.Properties jetspeedprops)
                         throws java.lang.Exception

Inserts a dkfz set into the db

Parameters:

map - The data as a hashmap

args - The command line args

geraeteprops - Description of Parameter

user - Description of Parameter

nmrprops - Description of Parameter

jetspeedprops - Description of Parameter

Throws:

java.lang.Exception - Databse problems

executeWriteCorina

private static void executeWriteCorina(java.lang.String[] args)
                                throws java.lang.Exception

Makes a file needed for corina coordinate generation

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeNCI

private static void executeNCI(java.lang.String[] args)
                        throws java.lang.Exception

Inserts nci mapping from mapping files

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeDeletePubchem

private static void executeDeletePubchem(java.lang.String[] args)
                                  throws java.lang.Exception

Throws:

java.lang.Exception

executeReadCorina

private static void executeReadCorina(java.lang.String[] args)
                               throws java.lang.Exception

Reads corina 3d coordinates

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeReadAlk

private static void executeReadAlk(java.lang.String[] args)
                            throws java.lang.Exception

Reads corina 3d coordinates

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeMakeDescriptorsAll

private static void executeMakeDescriptorsAll(java.lang.String[] args)
                                       throws java.lang.Exception

Creates the proton descriptors

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeMakeDescriptorsNew

private static void executeMakeDescriptorsNew(java.lang.String[] args)
                                       throws java.lang.Exception

Creates the proton descriptors

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeCrosscheckHose

private static void executeCrosscheckHose(java.lang.String[] args)
                                   throws java.lang.Exception

Executes an svm crossvalidation

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeCrossvalidate

private static void executeCrossvalidate(java.lang.String[] args)
                                  throws java.lang.Exception

Executes an svm crossvalidation

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeAnalyzeSql

private static void executeAnalyzeSql(java.lang.String[] args)
                               throws java.lang.Exception

Analyzes the current sql logfile

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

readcasfromnci

private static void readcasfromnci(java.lang.String[] args)
                            throws java.lang.Exception

Reads cas numbers from nci file

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeMakeAromaticity

private static void executeMakeAromaticity(java.lang.String[] args)
                                    throws java.lang.Exception

Executes making of aromaticities

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeMakeSmilesChiral

private static void executeMakeSmilesChiral(java.lang.String[] args)
                                     throws java.lang.Exception

Executes making of chiral smiles

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeBuildHose

private static void executeBuildHose(java.lang.String[] args)
                              throws java.lang.Exception

Executes building of HOSECodes

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeCheckDoubleMolecules

private static void executeCheckDoubleMolecules(java.lang.String[] args)
                                         throws java.lang.Exception

Executes checking of double molecules

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeCompareShifts

private static void executeCompareShifts(java.lang.String[] args)
                                  throws java.lang.Exception

Executes comparing of shifts to cdk.

Parameters:

args - The command line args.

Throws:

java.lang.Exception - Databse problems.

executeCheckAssignments

private static void executeCheckAssignments(java.lang.String[] args)
                                     throws java.lang.Exception

Checks if shifts are assigned to other atom the spectrum type suggests

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeCheckNCI

private static void executeCheckNCI(java.lang.String[] args)
                             throws java.lang.Exception

Executes ckecking vi NCI database

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

executeCheckShifts

private static void executeCheckShifts(java.lang.String[] args)
                                throws java.lang.Exception

Executes ckecking of shifts

Parameters:

args - The command line args

Throws:

java.lang.Exception - Databse problems

doInsert

private static void doInsert(AbInitioDataset aid,
                             java.lang.String[] args)
                      throws java.lang.Exception

Insert a AbInitioDataset into the database.

Parameters:

aid - The AbInitioDataset

args - The command-line arguments

Throws:

java.lang.Exception - Database problems

executeCrossvalidateWeka

private static void executeCrossvalidateWeka(java.lang.String[] args)
                                      throws java.lang.Exception

Throws:

java.lang.Exception

crossvalidateHose

private static void crossvalidateHose(java.lang.String[] args)

makeQA

private static void makeQA(java.lang.String[] args)

readcoumarines

private static void readcoumarines(java.lang.String[] args)
                            throws java.lang.Exception

Reads coumarine files

Parameters:

args - The command line args.

Throws:

java.lang.Exception - Database problems.

makeArff

private static void makeArff(java.lang.String[] args)

executeReadWageningen

private static void executeReadWageningen(java.lang.String[] args)
                                   throws java.lang.Exception

Reads file from uni mainz.

Parameters:

args - The command line args.

Throws:

java.lang.Exception - Database problems.

getStartLayers

private static java.lang.String getStartLayers(java.lang.String string)