FlexibleAlignment (biojava-legacy 1.9.5 API)
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Nested Class Summary
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Nested classes/interfaces inherited from class org.biojava.bio.alignment.AbstractULAlignment
AbstractULAlignment.LeftRightLocationComparator<T>, 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 LocationalignmentRangeprotected Map<Object,AlignmentElement>dataprotected List<String>labelOrder-
Fields inherited from class org.biojava.bio.alignment.AbstractULAlignment
alphabet
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Fields inherited from interface org.biojava.bio.alignment.ARAlignment
ADD_LABEL, REMOVE_LABEL
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Fields inherited from interface org.biojava.bio.alignment.EditableAlignment
GAPS, LOCATION
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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 FlexibleAlignment(List<AlignmentElement> seqList)construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). since more than one sequence in an alignment could have the same name this works as long as the labels are different objects even though they may hold the same name.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description voidaddSequence(AlignmentElement ae)add a new a alignment usings a location to the reference sequence.
protected booleanallGaps(SymbolList seq, int start, int end)make sure that all Symbols in this range are gaps
voidedit(Object label, Edit edit)edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
protected AlignmentElementgetAE(Object label)AlphabetgetAlphabet()The alphabet that this SymbolList is over.
List<String>getLabels()getLabels will return a list of labels in left to right order
List<Object>getLabelsAt(int column)protected intgreater(int x, int y)intlength()The number of symbols in this SymbolList.
protected intlesser(int x, int y)LocationlocInAlignment(Object label)The location of an individual SymbolList relative to overall Alignment
protected LocationlocInSeq(Object label, Location viewLoc)protected intposInSeq(Object label, int column)get the position in the sequence corresponding to the postion within the alignment
voidremoveGaps(GappedSymbolList seq, int start, int length)because there is a bug in GappedSymbolList
voidremoveSequence(Object label)protected voidresetRange()check that begining is at 1 otherwise shift everything over
protected voidshift(Object label, int offset)moves the whole sequence
protected voidshiftAll(int offset)voidshiftAtAlignmentLoc(Object label, Location loc, int offset)loc in this case is the Alignment Location
voidshiftAtSequenceLoc(Object label, Location loc, int offset)loc in this case is the SymbolList Location
SymbolsymbolAt(String label, int column)This gets the symbol for an individual sequence at position in the overall alignment If the sequence is not aligned at that location it returns null
SymbolListsymbolListForLabel(String label)Retrieve a single row of the alignment by label.
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Methods inherited from class org.biojava.bio.alignment.AbstractULAlignment
debug, labelsAt, labelsInRange, leftMost, orderedLables, rightMost, subAlignment, subAlignment, symbolAt, symbolListIterator
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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
subAlignment, symbolListIterator
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Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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