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public interface UnequalLengthAlignment
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)
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.symbol.Alignment |
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Alignment.SymbolListIterator |
Field Summary |
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Fields inherited from interface org.biojava.bio.symbol.Alignment |
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CONTENT |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
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EDIT, EMPTY_LIST |
Method Summary | |
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List |
labelsAt(int column)
Returns a list labels, of all seqs that cover that column |
List |
labelsInRange(Location loc)
Returns list of all the labels that intersect that range |
Location |
locInAlignment(Object label)
The location of an individual SymbolList relative to overall Alignment |
Methods inherited from interface org.biojava.bio.symbol.Alignment |
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getLabels, subAlignment, symbolAt, symbolListForLabel, symbolListIterator |
Methods inherited from interface org.biojava.bio.symbol.SymbolList |
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edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Method Detail |
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Location locInAlignment(Object label)
List labelsAt(int column)
List labelsInRange(Location loc)
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