ambit2.reactions

Class ReactionDataBase

java.lang.Object

ambit2.reactions.ReactionDataBase

public class ReactionDataBase
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	DEFAULT_TXT_FILE_COLUMN_NAMES
List<String>	errors
List<GenericReaction>	excludedGenericReactions
List<GenericReaction>	genericReactions

Constructor Summary

Constructors

Constructor and Description
ReactionDataBase()
ReactionDataBase(List<String> smirksList)
ReactionDataBase(String fileName)
ReactionDataBase(String fileName, Map<String,Integer> columnIndices)
ReactionDataBase(String fileName, Map<String,Integer> columnIndices, int headerLines)

Method Summary

Modifier and Type	Method and Description
int	checkColumnIndices(Map<String,Integer> columnIndices)
void	configureGenericReactions(SMIRKSManager smrkMan)
void	excludeReactionsWithConfigErrors()
static Map<String,Integer>	getDefaultGenericReacitonTextFileColumnsIndices()
String	getErrorsAsString()
GenericReaction	getGenericReactionByID(int id)
void	loadReactionsFromJSON(File jsonFile, boolean FlagCleanDB)
void	loadReactionsFromTabDelimitedFile(File txtFile, boolean FlagCleanDB)
void	loadReactionsFromTabDelimitedFile(File txtFile, boolean FlagCleanDB, Map<String,Integer> columnIndices, int numHeaderLines)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_TXT_FILE_COLUMN_NAMES

public static final String[] DEFAULT_TXT_FILE_COLUMN_NAMES

genericReactions

public List<GenericReaction> genericReactions

excludedGenericReactions

public List<GenericReaction> excludedGenericReactions

errors

public List<String> errors

Constructor Detail

ReactionDataBase

public ReactionDataBase()

ReactionDataBase

public ReactionDataBase(String fileName)
                 throws Exception

Throws:

Exception

ReactionDataBase

public ReactionDataBase(String fileName,
                        Map<String,Integer> columnIndices)
                 throws Exception

Throws:

Exception

ReactionDataBase

public ReactionDataBase(String fileName,
                        Map<String,Integer> columnIndices,
                        int headerLines)
                 throws Exception

Throws:

Exception

ReactionDataBase

public ReactionDataBase(List<String> smirksList)

Method Detail

loadReactionsFromJSON

public void loadReactionsFromJSON(File jsonFile,
                                  boolean FlagCleanDB)
                           throws Exception

Throws:

Exception

loadReactionsFromTabDelimitedFile

public void loadReactionsFromTabDelimitedFile(File txtFile,
                                              boolean FlagCleanDB)
                                       throws Exception

Throws:

Exception

loadReactionsFromTabDelimitedFile

public void loadReactionsFromTabDelimitedFile(File txtFile,
                                              boolean FlagCleanDB,
                                              Map<String,Integer> columnIndices,
                                              int numHeaderLines)
                                       throws Exception

Throws:

Exception

checkColumnIndices

public int checkColumnIndices(Map<String,Integer> columnIndices)

Parameters:

columnIndices -

Returns:

the maximal needed column index or negative value if error is present

getDefaultGenericReacitonTextFileColumnsIndices

public static Map<String,Integer> getDefaultGenericReacitonTextFileColumnsIndices()

configureGenericReactions

public void configureGenericReactions(SMIRKSManager smrkMan)
                               throws Exception

Throws:

Exception

getGenericReactionByID

public GenericReaction getGenericReactionByID(int id)

getErrorsAsString

public String getErrorsAsString()

excludeReactionsWithConfigErrors

public void excludeReactionsWithConfigErrors()

toString

public String toString()

Overrides:

toString in class Object