Package 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:
Alignment
,UnequalLengthAlignment
,SymbolList
,Changeable
- Direct Known Subclasses:
FlexibleAlignment
public abstract class AbstractULAlignment
extends AbstractSymbolList
implements UnequalLengthAlignment
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionclass
Orders by location left to right.class
Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment
Alignment.SymbolListIterator
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Field Summary
FieldsFields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
labelsAt
(int column) Returns a list labels, of all seqs that cover that columnlabelsInRange
(Location loc) Returns list of all the labels that intersect that rangeleftMost()
leftMost and rightMost return labels.orderedLables
(Comparator<String> comp) subAlignment
(Set<String> labels, int min, int max) Retreives a subAlignmentsubAlignment
(Set<String> labels, Location loc) Retrieves a subalignment specified by the location.symbolAt
(int index) this will return the ambiguity symbol associated with all symbols in that columnCreates 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
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.biojava.bio.alignment.Alignment
getLabels, symbolAt, symbolListForLabel
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, toList
Methods inherited from interface org.biojava.bio.alignment.UnequalLengthAlignment
locInAlignment
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Field Details
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alphabet
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Constructor Details
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AbstractULAlignment
public AbstractULAlignment()
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Method Details
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symbolAt
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
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
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
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
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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
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subAlignment
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:
IndexOutOfBoundsException
- See Also:
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subAlignment
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:
NoSuchElementException
- if one of the values inlabels
is not in the parent alignment
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orderedLables
- Parameters:
comp
-- Returns:
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