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java.lang.Objectorg.biojava.bio.alignment.SequenceAlignment
public abstract class SequenceAlignment
This Interface provides methods for the alignment of bio-sequences.
Constructor Summary | |
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SequenceAlignment()
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Method Summary | |
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abstract List |
alignAll(SequenceIterator source,
SequenceDB subjectDB)
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static StringBuffer |
formatOutput(String queryName,
String targetName,
String[] align,
String path,
int queryStart,
int queryEnd,
long queryLength,
int targetStart,
int targetEnd,
long targetLength,
int editdistance,
long time)
This method provides a BLAST-like formated alignment from the given String s, in which the sequence coordinates and the
information "Query" or "Target", respectively is added to each line. |
abstract Alignment |
getAlignment(SymbolList query,
SymbolList subject)
This method also performs a sequence alignment of the two given sequences but it returns an Alignment object instead of the score. |
abstract String |
getAlignmentString()
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abstract int |
pairwiseAlignment(SymbolList query,
SymbolList subject)
Performs a pairwise sequence alignment of the two given sequences. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SequenceAlignment()
Method Detail |
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public abstract String getAlignmentString() throws Exception
BioException
Exception
public abstract List alignAll(SequenceIterator source, SequenceDB subjectDB) throws Exception
source
- a SequenceIterator containing a set of sequences to be aligned
withsubjectDB
- the SequenceDB containing another set of sequences.
NoSuchElementException
Exception
public abstract int pairwiseAlignment(SymbolList query, SymbolList subject) throws Exception
query
- subject
-
Exception
public abstract Alignment getAlignment(SymbolList query, SymbolList subject) throws Exception
query
- subject
-
Exception
public static StringBuffer formatOutput(String queryName, String targetName, String[] align, String path, int queryStart, int queryEnd, long queryLength, int targetStart, int targetEnd, long targetLength, int editdistance, long time)
String
s, in which the sequence coordinates and the
information "Query" or "Target", respectively is added to each line. Each
line contains 60 sequence characters including the gap symbols plus the
meta information. There is one white line between two pairs of sequences.
queryName
- name of the query sequencetargetName
- name of the target sequencealign
- a String
-array, where the index 0 is the query
sequence and index 1 the target sequence (for instance
new String[] {myQuerySequence.seqString(), myTargetSequence.seqString()}
)path
- the "path", that means a String containing white spaces and pipe
("|") symbols, which makes matches visible. The two strings in
align
have to have the same length and also the
same length than this path
.queryStart
- the start position in the query, where the alignment starts. For
example zero for normal Needleman-Wunsch-Alignments.queryEnd
- the end position, that means the sequence coordinate, which is the
last symbol of the query sequence. Counting starts at zero!queryLength
- The length of the query sequence without gaps.targetStart
- These are all the same for the target. Have a look at these above.targetEnd
- targetLength
- editdistance
- time
- The time in milliseconds, which was needed to generate the
alignment.
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