SimpleAlignment (biojava-legacy 1.9.5 API)
-
-
Nested Class Summary
-
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
-
-
Field Summary
-
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
-
-
Constructor Summary
Constructors Constructor Description SimpleAlignment(Map<String,SymbolList> labelToResList)Generate an alignment from a list of SymbolLists.
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected voidfinalize()AlphabetgetAlphabet()The alphabet that this SymbolList is over.
List<String>getLabels()The list of SymbolLists in the alignment.
intgetScore()intlength()The number of symbols in this SymbolList.
voidsetScore(int score)AlignmentsubAlignment(Set<String> labels, Location loc)Make a view onto this alignment.
SymbolsymbolAt(int index)Return the symbol at index, counting from 1.
SymbolsymbolAt(String label, int column)Retrieve a symbol by label and column.
SymbolListsymbolListForLabel(String label)Retrieve a single row of the alignment by label.
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
-
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
-
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
-
-