charite.christo.strap.extensions
Class PairAlignerNeoBioPROXY
java.lang.Object
charite.christo.AbstractProxy
charite.christo.strap.AbstractAlignerProxy
charite.christo.strap.extensions.PairAlignerNeoBioPROXY
- All Implemented Interfaces:
- HasPropertyMap, HasScore, SequenceAligner
public class PairAlignerNeoBioPROXY
- extends AbstractAlignerProxy
- implements SequenceAligner, HasScore
HELP
Home: http://neobio.sourceforge.net/
Depending on the settings it produces local or global sequence alignments.
Written in Java
Methods inherited from class charite.christo.AbstractProxy |
dispose, disposeProxy, getControlPanel, getPrgParas, getPropertyMap, getProxy, getScore, getSharedControlPanel, getSharedInstance, interpret, jarFile, jarsContainingNativeLibraries, proxyObject, proxyObjectRun, remoteURLs, setOptions, setSharedInstance, usrShareJava |
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PARA_ALGORITHM
public static final java.lang.String PARA_ALGORITHM
- See Also:
- Constant Field Values
PARA_MATCH
public static final java.lang.String PARA_MATCH
- See Also:
- Constant Field Values
PARA_MISMATCH
public static final java.lang.String PARA_MISMATCH
- See Also:
- Constant Field Values
PARA_GAP
public static final java.lang.String PARA_GAP
- See Also:
- Constant Field Values
GLOBAL_NEEDLEMANWUNSCH
public static final java.lang.String GLOBAL_NEEDLEMANWUNSCH
- See Also:
- Constant Field Values
LOCAL_SMITHWATERMAN
public static final java.lang.String LOCAL_SMITHWATERMAN
- See Also:
- Constant Field Values
GLOBAL_CROCHEMORELANDAUZIVUKELSON
public static final java.lang.String GLOBAL_CROCHEMORELANDAUZIVUKELSON
- See Also:
- Constant Field Values
LOCAL_CROCHEMORELANDAUZIVUKELSON
public static final java.lang.String LOCAL_CROCHEMORELANDAUZIVUKELSON
- See Also:
- Constant Field Values
PairAlignerNeoBioPROXY
public PairAlignerNeoBioPROXY()
getRequiredJars
public java.lang.String getRequiredJars()
- Specified by:
getRequiredJars
in class AbstractProxy
getPropertyFlags
public final long getPropertyFlags()
- Specified by:
getPropertyFlags
in interface SequenceAligner
'The most important classes are StrapAlign, Protein and StrapEvent.'