textbender.d.transfer
Class Transfer

java.lang.Object
  Transfer

@ThreadSafe
public class Transfer
extends Object

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

isTransferMutant

public 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.

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.

Parameters:

gene - whose sequence to inspect for mutation

g - gene meta-data ('g') element, of gene

gList - list of all gene meta-data ('g') elements in the document

mutantAbstractor - to use

domLS - DOM implementation to use

parser - parser to use

b - string builder to use, overwriting its existing content

Returns:

true if abstract form of sequence differs from that of all immediate transfer ancestors, or if there are no such ancestors

See Also:

d/transfer/note.xht#Maintenance-of-Ancestry-Records

recordAsTransferSource

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

Records a gene as a transfer source. This entails 1) overwriting the target gene's transfer source sequence 'tSS' attribute; and 2) recording the source sequence as the immediate ancestor of the target, with all prior ancestry contained within it.

Parameters:

sourceGene - to record as the transfer source sequence

sourceGG - the 'g' list ('gg') element of the source document

sourceGList - list of all gene meta-data ('g') elements in source document

targetG - gene meta-data ('g') element, of targt gene

nodeTransformSource - to use, via its setNode()

eSS - identity transformer to use, as a string serializer for creating embedded sequence copy

eSSWriter - eSS string writer

eSSResult - result, pre-set to eSSWriter

b - string builder to use, overwriting its existing content

Throws:

TransformerException