Package org.biojava.bio.alignment
Interface UnequalLengthAlignment
- All Superinterfaces:
Alignment
,Changeable
,SymbolList
- All Known Implementing Classes:
AbstractULAlignment
,AbstractULAlignment.SubULAlignment
,FlexibleAlignment
UnequalLengthAlignment has the following behavior. Two or more SymbolLists may align in such a way that their ends do not overlap.
example 1 aaaaaatttcttt 2 tttgtttggggggc
length returns ??
symbolAt(1,1) returns 20
symbolAt(2,1) returns null -- NOT an exception
symbolAt(2,99) throws NoSuchElementException
leftMost returns 1
rightMost returns 2
locInAlignment (1) returns (1,13)
locInAlignment (2) returns (7,20)
alignmentRange() returns (7,13)
- Author:
- David Waring
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment
Alignment.SymbolListIterator
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Field Summary
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Method Summary
Modifier and TypeMethodDescriptionlabelsAt
(int column) Returns a list labels, of all seqs that cover that columnlabelsInRange
(Location loc) Returns list of all the labels that intersect that rangelocInAlignment
(Object label) The location of an individual SymbolList relative to overall AlignmentMethods inherited from interface org.biojava.bio.alignment.Alignment
getLabels, subAlignment, symbolAt, symbolListForLabel, symbolListIterator
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList
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Method Details
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locInAlignment
The location of an individual SymbolList relative to overall Alignment -
labelsAt
Returns a list labels, of all seqs that cover that column -
labelsInRange
Returns list of all the labels that intersect that range
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