Package org.biojava.bio.alignment
Class AbstractULAlignment
- java.lang.Object
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- org.biojava.utils.AbstractChangeable
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- org.biojava.bio.symbol.AbstractSymbolList
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- org.biojava.bio.alignment.AbstractULAlignment
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- All Implemented Interfaces:
Alignment
,UnequalLengthAlignment
,SymbolList
,Changeable
- Direct Known Subclasses:
FlexibleAlignment
public abstract class AbstractULAlignment extends AbstractSymbolList implements UnequalLengthAlignment
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
AbstractULAlignment.LeftRightLocationComparator<T>
Orders by location left to right.class
AbstractULAlignment.SubULAlignment
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Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
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Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment
Alignment.SymbolListIterator
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Field Summary
Fields Modifier and Type Field Description protected Alphabet
alphabet
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Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Constructor Summary
Constructors Constructor Description AbstractULAlignment()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
debug(java.lang.String s)
java.util.List<java.lang.String>
labelsAt(int column)
Returns a list labels, of all seqs that cover that columnjava.util.List<java.lang.String>
labelsInRange(Location loc)
Returns list of all the labels that intersect that rangejava.lang.Object
leftMost()
leftMost and rightMost return labels.java.util.SortedSet<java.lang.String>
orderedLables(java.util.Comparator<java.lang.String> comp)
java.lang.Object
rightMost()
Alignment
subAlignment(java.util.Set<java.lang.String> labels, int min, int max)
Retreives a subAlignmentAlignment
subAlignment(java.util.Set<java.lang.String> 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 columnjava.util.Iterator<SymbolList>
symbolListIterator()
Creates an Iterator over the SymbolLists in the alignment.-
Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString
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Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.biojava.bio.alignment.Alignment
getLabels, symbolAt, symbolListForLabel
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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, toList
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Methods inherited from interface org.biojava.bio.alignment.UnequalLengthAlignment
locInAlignment
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Constructor Detail
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AbstractULAlignment
public AbstractULAlignment()
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Method Detail
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symbolAt
public Symbol symbolAt(int index)
this will return the ambiguity symbol associated with all symbols in that column- Specified by:
symbolAt
in interfaceSymbolList
- Parameters:
index
- the offset into this SymbolList- Returns:
- the Symbol at that index
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labelsAt
public java.util.List<java.lang.String> labelsAt(int column)
Description copied from interface:UnequalLengthAlignment
Returns a list labels, of all seqs that cover that column- Specified by:
labelsAt
in interfaceUnequalLengthAlignment
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labelsInRange
public java.util.List<java.lang.String> labelsInRange(Location loc)
Description copied from interface:UnequalLengthAlignment
Returns list of all the labels that intersect that range- Specified by:
labelsInRange
in interfaceUnequalLengthAlignment
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symbolListIterator
public java.util.Iterator<SymbolList> 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 interfaceAlignment
- Returns:
- an Iterator
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debug
protected void debug(java.lang.String s)
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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;
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rightMost
public java.lang.Object rightMost()
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subAlignment
public Alignment subAlignment(java.util.Set<java.lang.String> 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 interfaceAlignment
- 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)
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subAlignment
public Alignment subAlignment(java.util.Set<java.lang.String> labels, int min, int max) throws java.util.NoSuchElementException
Retreives a subAlignment- Parameters:
labels
- the labels of theSymbolLists
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 inlabels
is not in the parent alignment
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orderedLables
public java.util.SortedSet<java.lang.String> orderedLables(java.util.Comparator<java.lang.String> comp)
- Parameters:
comp
-- Returns:
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