org.biojava.bio.alignment
Interface UnequalLengthAlignment
- All Superinterfaces:
- Alignment, Changeable, SymbolList
- All Known Implementing Classes:
- AbstractULAlignment, AbstractULAlignment.SubULAlignment
- 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
Method Summary |
java.util.List |
labelsAt(int column)
Returns a list labels, of all seqs that cover that column |
java.util.List |
labelsInRange(Location loc)
Returns list of all the labels that intersect that range |
Location |
locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment |
locInAlignment
public Location locInAlignment(java.lang.Object label)
- The location of an individual SymbolList relative to overall Alignment
labelsAt
public java.util.List labelsAt(int column)
- Returns a list labels, of all seqs that cover that column
labelsInRange
public java.util.List labelsInRange(Location loc)
- Returns list of all the labels that intersect that range