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 java.lang.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 java.lang.Short
getGapExtend()
java.lang.Short
getGapOpen()
java.util.List<java.lang.String>
getUserConfigHelp()
The help text for each of these parameters.java.util.List<java.lang.String>
getUserConfigParameterNames()
The labels to be displayed to the user for each parameterjava.util.List<java.lang.String>
getUserConfigParameters()
get the list of parameters that the user can change through the user interface.java.util.List<java.lang.Class>
getUserConfigTypes()
Get the data types of the parametersvoid
reset()
Set the parameters to the default.void
setGapExtend(java.lang.Short gapExtend)
void
setGapOpen(java.lang.Short gapOpen)
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Method Detail
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getUserConfigHelp
public java.util.List<java.lang.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 java.util.List<java.lang.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 java.util.List<java.lang.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 java.util.List<java.lang.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 java.lang.Short getGapExtend()
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setGapExtend
public void setGapExtend(java.lang.Short gapExtend)
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getGapOpen
public java.lang.Short getGapOpen()
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setGapOpen
public void setGapOpen(java.lang.Short gapOpen)
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