|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--org.biojava.bio.symbol.AbstractSymbolList | +--org.biojava.bio.symbol.SimpleAlignment
A simple implementation of an Alignment.
This is a simple-stupid implementation that is made from a set of same-lengthed SymbolList objects each with an associated label. It does not handle differently lengthed sequences and doesn't contain any gap-editing concepts.
Inner classes inherited from class org.biojava.bio.symbol.SymbolList |
SymbolList.EmptySymbolList |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
EMPTY_LIST |
Constructor Summary | |
SimpleAlignment(java.util.Map labelToResList)
Generate an alignment from a list of SymbolLists. |
Method Summary | |
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
java.util.List |
getLabels()
The list of SymbolLists in the alignment. |
int |
length()
The number of symbols in this SymbolList. |
Alignment |
subAlignment(java.util.Set labels,
Location loc)
Make a view onto this alignment. |
Symbol |
symbolAt(int index)
Return the symbol at index, counting from 1. |
Symbol |
symbolAt(java.lang.Object label,
int column)
Retrieve a symbol by label and column. |
SymbolList |
symbolListForLabel(java.lang.Object label)
Retrieve a single row of the alignment by label. |
Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList |
iterator,
seqString,
subList,
subStr,
toList |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public SimpleAlignment(java.util.Map labelToResList) throws java.lang.IllegalArgumentException
The SymbolLists must all be of the same length.
labelToResList
- the label-to-symbol list mappingMethod Detail |
public int length()
public Alphabet getAlphabet()
Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.
public Symbol symbolAt(int index)
index
- the ofset into this SymbolListpublic java.util.List getLabels()
The index in the list is the same as the index in the alignment. Each SymbolList object will only be in the alignment once. However, a single underlying SymbolList may have more than one view within an alignment, each represented by a different GappedSymbolList.
public Symbol symbolAt(java.lang.Object label, int column)
label
- the SymbolList to retrieve fromcolumn
- the index of the column to retrievepublic Alignment subAlignment(java.util.Set labels, Location loc) throws java.util.NoSuchElementException
If labels is null, then each label will be kept. Otherwise, only those in labels will be kept. If loc is null, then the entire length of the alignment will be kept. If loc is not null, then only the columns within the location will be kept.
labels
- the Set of sequences to include by labelloc
- the Location to includepublic SymbolList symbolListForLabel(java.lang.Object label) throws java.util.NoSuchElementException
label
- the object from which to retrieve the symbol list
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |