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java.lang.Object | +--org.biojava.bio.dp.SimpleStatePath
A no-frills implementation of StatePath.
Inner classes inherited from class org.biojava.bio.symbol.SymbolList |
SymbolList.EmptySymbolList |
Fields inherited from interface org.biojava.bio.dp.StatePath |
SCORES,
SEQUENCE,
STATES |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
EMPTY_LIST |
Constructor Summary | |
SimpleStatePath(double score,
SymbolList sequence,
SymbolList states,
SymbolList scores)
|
Method Summary | |
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
java.util.List |
getLabels()
The list of SymbolLists in the alignment. |
double |
getScore()
Return the overall score for this state-path and it's emissions. |
java.util.Iterator |
iterator()
An Iterator over all Symbols in this SymbolList. |
int |
length()
The number of symbols in this SymbolList. |
java.lang.String |
seqString()
Stringify this symbol list. |
Alignment |
subAlignment(java.util.Set labels,
Location loc)
Make a view onto this alignment. |
SymbolList |
subList(int start,
int end)
Return a new SymbolList for the symbols start to end inclusive. |
java.lang.String |
subStr(int start,
int end)
Return a region of this symbol list as a String. |
Symbol |
symbolAt(int col)
Return the symbol at index, counting from 1. |
Symbol |
symbolAt(java.lang.Object label,
int col)
Retrieve a symbol by label and column. |
SymbolList |
symbolListForLabel(java.lang.Object label)
Retrieve a single row of the alignment by label. |
java.util.List |
toList()
Returns a List of symbols. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores) throws java.lang.IllegalArgumentException
Method Detail |
public double getScore()
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 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 int length()
public 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 Symbol symbolAt(int col) throws java.lang.IndexOutOfBoundsException
index
- the ofset into this SymbolListpublic Symbol symbolAt(java.lang.Object label, int col) throws java.lang.IndexOutOfBoundsException, java.util.NoSuchElementException
label
- the SymbolList to retrieve fromcolumn
- the index of the column to retrievepublic SymbolList symbolListForLabel(java.lang.Object label) throws java.util.NoSuchElementException
label
- the object from which to retrieve the symbol listpublic java.util.Iterator iterator()
This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
public SymbolList subList(int start, int end)
The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolListpublic java.util.List toList()
This is an immutable list of symbols. Do not edit it.
public java.lang.String seqString()
It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.
public java.lang.String subStr(int start, int end) throws java.lang.IndexOutOfBoundsException
This should use the same rules as seqString.
start
- the first symbol to includeend
- the last symbol to include
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