|
'STRAP:multiple sequence alignments ' | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object charite.christo.metannogen.Metannogen
public class Metannogen
HELP
Field Summary | |
---|---|
static int |
PORT
|
Fields inherited from interface charite.christo.interfaces.ChRunnable |
---|
APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE |
Constructor Summary | |
---|---|
Metannogen()
|
Method Summary | |
---|---|
static Map<String,String> |
getDictionaryCompartments()
See command line parameter -dictionaryOfSpecies |
static Map<String,String> |
getDictionarySpecies()
See command line parameter -dictionaryOfCompartments |
static ReactionCollection |
getNetwork(String id)
Returns the networks with the ID for example "KEGG". |
static ReactionCollection[] |
getNetworks()
Returns an array of all networks. |
static ReactionCollection |
getNetworkTranslated(ReactionCollection networkOrig)
Translates a given network with the dictionaries for species and compartments. |
static Reaction[] |
getReactionsOfFocusedDataset()
For validation after input of datasets |
static void |
main(String... argv)
|
static MReactionCollection |
newReactionCollectionDatasets(long filter_options)
Generates a new network object from all datasets. |
static boolean |
reactionIdShouldBeExported(String id)
|
Object |
run(String id,
Object arg)
|
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final int PORT
Constructor Detail |
---|
public Metannogen()
Method Detail |
---|
public static void main(String... argv)
public static ReactionCollection[] getNetworks()
public static ReactionCollection getNetwork(String id)
public static MReactionCollection newReactionCollectionDatasets(long filter_options)
filter_options
- zero or a bit mask from Reaction.FILTER_REJECTED_DATASETS and Reaction.FILTER_NOT_EXCLUDEDpublic static ReactionCollection getNetworkTranslated(ReactionCollection networkOrig)
public static Map<String,String> getDictionaryCompartments()
public static Map<String,String> getDictionarySpecies()
public static Reaction[] getReactionsOfFocusedDataset()
public Object run(String id, Object arg)
run
in interface ChRunnable
public static boolean reactionIdShouldBeExported(String id)
|
'STRAP:multiple sequence alignments ' | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |