Class SmithWaterman3DParameters
- java.lang.Object
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- org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters
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- All Implemented Interfaces:
ConfigStrucAligParams
public class SmithWaterman3DParameters extends Object implements ConfigStrucAligParams
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Constructor Summary
Constructors Constructor Description SmithWaterman3DParameters()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Short
getGapExtend()
Short
getGapOpen()
Double
getMaxRmsd()
Integer
getMinLen()
List<String>
getUserConfigHelp()
The help text for each of these parameters.List<String>
getUserConfigParameterNames()
The labels to be displayed to the user for each parameterList<String>
getUserConfigParameters()
get the list of parameters that the user can change through the user interface.List<Class>
getUserConfigTypes()
Get the data types of the parametersvoid
reset()
Set the parameters to the default.void
setGapExtend(Short gapExtend)
void
setGapOpen(Short gapOpen)
void
setMaxRmsd(Double maxRmsd)
void
setMinLen(Integer minLen)
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Constructor Detail
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SmithWaterman3DParameters
public SmithWaterman3DParameters()
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Method Detail
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getUserConfigHelp
public List<String> getUserConfigHelp()
Description copied from interface:ConfigStrucAligParams
The help text for each of these parameters.- Specified by:
getUserConfigHelp
in interfaceConfigStrucAligParams
- Returns:
- help strings
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getUserConfigParameterNames
public List<String> getUserConfigParameterNames()
Description copied from interface:ConfigStrucAligParams
The labels to be displayed to the user for each parameter- Specified by:
getUserConfigParameterNames
in interfaceConfigStrucAligParams
- Returns:
- list of parameter names
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getUserConfigParameters
public List<String> getUserConfigParameters()
Description copied from interface:ConfigStrucAligParams
get the list of parameters that the user can change through the user interface. Parameter names are the same names as the corresponding Get/Set methods.- Specified by:
getUserConfigParameters
in interfaceConfigStrucAligParams
- Returns:
- list of parameters
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getUserConfigTypes
public List<Class> getUserConfigTypes()
Description copied from interface:ConfigStrucAligParams
Get the data types of the parameters- Specified by:
getUserConfigTypes
in interfaceConfigStrucAligParams
- Returns:
- list of parameter classes
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reset
public void reset()
Description copied from interface:ConfigStrucAligParams
Set the parameters to the default.- Specified by:
reset
in interfaceConfigStrucAligParams
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getGapExtend
public Short getGapExtend()
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setGapExtend
public void setGapExtend(Short gapExtend)
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getGapOpen
public Short getGapOpen()
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setGapOpen
public void setGapOpen(Short gapOpen)
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getMaxRmsd
public Double getMaxRmsd()
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setMaxRmsd
public void setMaxRmsd(Double maxRmsd)
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