umms.core.alignment.AlignmentPair Class Reference

Inheritance diagram for umms.core.alignment.AlignmentPair:

Collaboration diagram for umms.core.alignment.AlignmentPair:

Public Member Functions
void	add (SAMRecord record)
boolean	isComplete ()
Collection< SAMRecord >	makePairs ()
boolean	hasEntries ()
boolean	valuesAreEmpty ()

Detailed Description

Represents a paired alignment in all detail, with possbily multiple mappings through the genome. An alignment pair is meant to be built iteratively as mappings of an insert are found. Once all pieces are assembled, it can do useful things.

Author

mgarber

Member Function Documentation

void umms.core.alignment.AlignmentPair.add

(

SAMRecord

record

)

boolean umms.core.alignment.AlignmentPair.hasEntries

(

)

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boolean umms.core.alignment.AlignmentPair.isComplete

(

)

Collection<SAMRecord> umms.core.alignment.AlignmentPair.makePairs

(

)

boolean umms.core.alignment.AlignmentPair.valuesAreEmpty

(

)

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The documentation for this class was generated from the following file:

• java/umms/core/alignment/AlignmentPair.java