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java.lang.Objectorg.biojava.bio.alignment.SequenceAlignment
public abstract class SequenceAlignment
This Interface provides methods for the alignment of biosequences.
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 String |
formatOutput(String queryName,
String targetName,
String[] align,
String path,
int queryStart,
int queryEnd,
long queryLength,
int targetStart,
int targetEnd,
long targetLength,
double 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(Sequence query,
Sequence 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 double |
pairwiseAlignment(Sequence query,
Sequence 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 double pairwiseAlignment(Sequence query, Sequence subject) throws Exception
query
- subject
-
Exception
public abstract Alignment getAlignment(Sequence query, Sequence subject) throws Exception
query
- subject
-
Exception
public static String formatOutput(String queryName, String targetName, String[] align, String path, int queryStart, int queryEnd, long queryLength, int targetStart, int targetEnd, long targetLength, double 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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