org.biojava.bio.alignment
Class AbstractULAlignment
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbolList
org.biojava.bio.alignment.AbstractULAlignment
- All Implemented Interfaces:
- UnequalLengthAlignment, Alignment, SymbolList, Changeable
- Direct Known Subclasses:
- FlexibleAlignment
public abstract class AbstractULAlignment
- extends AbstractSymbolList
- implements UnequalLengthAlignment
Method Summary |
protected void |
debug(java.lang.String s)
|
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 |
java.lang.Object |
leftMost()
leftMost and rightMost return labels. |
java.util.SortedSet |
orderedLables(java.util.Comparator comp)
|
java.lang.Object |
rightMost()
|
Alignment |
subAlignment(java.util.Set labels,
int min,
int max)
Retreives a subAlignment |
Alignment |
subAlignment(java.util.Set labels,
Location loc)
Retrieves a subalignment specified by the location. |
Symbol |
symbolAt(int index)
this will return the ambiguity symbol associated with all symbols in that column |
java.util.Iterator |
symbolListIterator()
Creates an Iterator over the SymbolLists in the alignment. |
Methods inherited from class java.lang.Object |
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
alphabet
protected Alphabet alphabet
AbstractULAlignment
public AbstractULAlignment()
symbolAt
public Symbol symbolAt(int index)
- this will return the ambiguity symbol associated with all symbols in that column
- Specified by:
symbolAt
in interface SymbolList
- Parameters:
index
- the offset into this SymbolList
- Returns:
- the Symbol at that index
labelsAt
public java.util.List labelsAt(int column)
- Description copied from interface:
UnequalLengthAlignment
- Returns a list labels, of all seqs that cover that column
- Specified by:
labelsAt
in interface UnequalLengthAlignment
labelsInRange
public java.util.List labelsInRange(Location loc)
- Description copied from interface:
UnequalLengthAlignment
- Returns list of all the labels that intersect that range
- Specified by:
labelsInRange
in interface UnequalLengthAlignment
symbolListIterator
public java.util.Iterator symbolListIterator()
- Description copied from interface:
Alignment
- Creates an Iterator over the SymbolLists in the alignment. This should be
similar to iterating over the labels and then fetching each SymbolList, but
the order is not guaranteed to be the same.
- Specified by:
symbolListIterator
in interface Alignment
- Returns:
- an Iterator
debug
protected void debug(java.lang.String s)
leftMost
public java.lang.Object leftMost()
- leftMost and rightMost return labels. If there are more than one
that start at the same location it returns the longest, if they are
the same length it returns the first one it found;
rightMost
public java.lang.Object rightMost()
subAlignment
public Alignment subAlignment(java.util.Set labels,
Location loc)
throws java.lang.IndexOutOfBoundsException
- Retrieves a subalignment specified by the location.
WARNING: It is assumed that the location is contiguous. If
the location is non-contiguous it may be preferable to use a block iterator
to retrieve each sub location independently.
- Specified by:
subAlignment
in interface Alignment
- Parameters:
labels
- the Set of sequences to include by labelloc
- the Location to include
- Returns:
- a sub Alignment
- Throws:
java.lang.IndexOutOfBoundsException
- See Also:
subAlignment(Set labels, int min, int max)
subAlignment
public Alignment subAlignment(java.util.Set labels,
int min,
int max)
throws java.util.NoSuchElementException
- Retreives a subAlignment
- Parameters:
labels
- the labels of the SymbolLists
to be in the Alignmentmin
- the left most coordinatemax
- the right most coordinate
- Returns:
- an Alignment
- Throws:
java.util.NoSuchElementException
- if one of the values in labels
is not in the parent alignment
orderedLables
public java.util.SortedSet orderedLables(java.util.Comparator comp)