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'STRAP:multiple sequence alignments ' | ||||||||
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public interface SequenceAligner
Classes that provide a calculation of sequence alignments. PACKAGE:charite.christo.interfaces. PACKAGE:charite.christo. With JAVADOC:SequenceAligner#setSequences(String[]) the amino acid sequences of the proteins are set. Alignment starts on invoking JAVADOC:SequenceAligner#compute() STRAP retrieves the result by calling JAVADOC:SequenceAligner#getAlignedSequences(). JAVADOC:SequenceAligner#getMaxNumberOfSequences()may return 2 if the procedure is capable of only pair alignments or the number of allowed proteins. A container of GUI elements for the user is provided on pressing ICON:IC_CONTROLPANEL when the class implements JAVADOC:HasControlPanel. The GUI elements may be used to select gap-panalties or BLOSUM matrices.
Field Summary | |
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static int |
OPTION_USE_SECONDARY_STRUCTURE
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Method Summary | |
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void |
compute()
The time consuming computation. |
byte[][] |
getAlignedSequences()
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int |
getMaxNumberOfSequences()
Multiple aligners are usually not limited in the number of sequences. |
byte[][] |
getSequences()
Return the sequences that have been set with setSequences(String[]) |
boolean |
isLocal()
Local alignment procedures do not align the entire sequences. |
void |
setOptions(long flags)
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void |
setSequences(byte[]... ss)
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Field Detail |
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static final int OPTION_USE_SECONDARY_STRUCTURE
Method Detail |
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void setSequences(byte[]... ss)
byte[][] getSequences()
void compute()
void setOptions(long flags)
byte[][] getAlignedSequences()
int getMaxNumberOfSequences()
boolean isLocal()
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