Package org.biojava.bio.alignment
Interface UnequalLengthAlignment
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- All Superinterfaces:
Alignment
,Changeable
,SymbolList
- All Known Implementing Classes:
AbstractULAlignment
,AbstractULAlignment.SubULAlignment
,FlexibleAlignment
public interface UnequalLengthAlignment extends Alignment
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
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Nested classes/interfaces inherited from interface org.biojava.bio.symbol.Alignment
Alignment.SymbolListIterator
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Field Summary
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Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.util.List
labelsAt(int column)
Returns a list labels, of all seqs that cover that columnjava.util.List
labelsInRange(Location loc)
Returns list of all the labels that intersect that rangeLocation
locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment-
Methods inherited from interface org.biojava.bio.symbol.Alignment
getLabels, subAlignment, symbolAt, symbolListForLabel, symbolListIterator
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Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList
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Method Detail
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locInAlignment
Location locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment
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labelsAt
java.util.List labelsAt(int column)
Returns a list labels, of all seqs that cover that column
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labelsInRange
java.util.List labelsInRange(Location loc)
Returns list of all the labels that intersect that range
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