charite.christo.metannogen
Class Dataset2Reaction

java.lang.Object
  charite.christo.metannogen.Dataset2Reaction

All Implemented Interfaces:

ChRunnable

public class Dataset2Reaction
extends Object
implements ChRunnable

Field Summary

static boolean

debug

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

Dataset2Reaction(int highlightWhat)

Method Summary

static Set<String>[]	allLabelsOfDatasets()
static MReaction[]	dataset2unlocalizedReactions(Dataset d)
static Map<String,String>	findAttributes(byte[] T, int from, int to, Map<String,String> map, int recursion)
static Map<String,String>	findAttributes(String dolarSign, char equalsSign, byte[] T, int from, int toPos, Map<String,String> map0, int recursion)
static String[]	findTokensWithPrefix(String pfx, byte[] T, int from, int to)
static String[]	getEC_Classes(byte[] T)
static Map<String,ByteArray>	getMapNamedParagraphs()
static CharSequence	getMapNamedParagraphsErrors()
static MReaction[]	getReactions(Dataset d, Map<String,String> mapMetabolites, Map<String,String> mapCompartments, long mode)
Object	run(String id, Object arg)

Methods inherited from class java.lang.Object

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

Field Detail

debug

public static boolean debug

Constructor Detail

Dataset2Reaction

public Dataset2Reaction(int highlightWhat)

Method Detail

getReactions

public static MReaction[] getReactions(Dataset d,
                                       Map<String,String> mapMetabolites,
                                       Map<String,String> mapCompartments,
                                       long mode)

findAttributes

public static Map<String,String> findAttributes(byte[] T,
                                                int from,
                                                int to,
                                                Map<String,String> map,
                                                int recursion)

findTokensWithPrefix

public static String[] findTokensWithPrefix(String pfx,
                                            byte[] T,
                                            int from,
                                            int to)

findAttributes

public static Map<String,String> findAttributes(String dolarSign,
                                                char equalsSign,
                                                byte[] T,
                                                int from,
                                                int toPos,
                                                Map<String,String> map0,
                                                int recursion)

allLabelsOfDatasets

public static Set<String>[] allLabelsOfDatasets()

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable

getMapNamedParagraphs

public static Map<String,ByteArray> getMapNamedParagraphs()

getMapNamedParagraphsErrors

public static CharSequence getMapNamedParagraphsErrors()

dataset2unlocalizedReactions

public static MReaction[] dataset2unlocalizedReactions(Dataset d)

getEC_Classes

public static final String[] getEC_Classes(byte[] T)