|
![]() |
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectTransfer
@ThreadSafe public class Transfer
Utilities for conducting recombinant transfers.
Method Summary | |
---|---|
static boolean |
isTransferMutant(Element gene,
Element g,
List<Element> gList,
MutantAbstractor mutantAbstractor,
DOMImplementationLS domLS,
LSParser parser,
StringBuilder b)
Returns true if the gene's sequence has changed enough that the mutation should be recorded in transfer ancestry. |
static void |
recordAsTransferSource(Element sourceGene,
Element sourceGG,
List<Element> sourceGList,
Element targetG,
DOMSource nodeTransformSource,
Transformer eSS,
StringWriter eSSWriter,
StreamResult eSSResult,
StringBuilder b)
Records a gene as a transfer source. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
---|
public static boolean isTransferMutant(Element gene, Element g, List<Element> gList, MutantAbstractor mutantAbstractor, DOMImplementationLS domLS, LSParser parser, StringBuilder b)
Errors/doubts will fall on the side of mutation. Worst outcome is, caller will add redundant info to ancestry, which later tracers can prune away.
gene
- whose sequence to inspect for mutationg
- gene meta-data ('g') element, of genegList
- list of all gene meta-data ('g') elements in the documentmutantAbstractor
- to usedomLS
- DOM implementation to useparser
- parser to useb
- string builder to use, overwriting its existing content
public static void recordAsTransferSource(Element sourceGene, Element sourceGG, List<Element> sourceGList, Element targetG, DOMSource nodeTransformSource, Transformer eSS, StringWriter eSSWriter, StreamResult eSSResult, StringBuilder b) throws TransformerException
sourceGene
- to record as the transfer source sequencesourceGG
- the 'g' list ('gg') element of the source documentsourceGList
- list of all gene meta-data ('g') elements
in source documenttargetG
- gene meta-data ('g') element, of targt genenodeTransformSource
- to use, via its setNode()eSS
- identity transformer to use, as a string serializer
for creating embedded sequence copyeSSWriter
- eSS string writereSSResult
- result, pre-set to eSSWriterb
- string builder to use, overwriting its existing content
TransformerException
|
![]() |
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |