ConfigStrucAligParams
public class CECPParameters extends CeParameters
CeCPMain
Modifier and Type | Class | Description |
---|---|---|
static class |
CECPParameters.DuplicationHint |
CeParameters.ScoringStrategy
Modifier and Type | Field | Description |
---|---|---|
static int |
DEFAULT_MIN_CP_LENGTH |
|
protected CECPParameters.DuplicationHint |
duplicationHint |
|
protected java.lang.Integer |
minCPLength |
DEFAULT_GAP_EXTENSION, DEFAULT_GAP_OPEN, DEFAULT_oRmsdThr, DEFAULT_SUBSTITUTION_MATRIX, DISTANCE_INCREMENT, distanceIncrement, gapExtension, gapOpen, maxGapSize, maxNrIterationsForOptimization, maxOptRMSD, oRmsdThr, rmsdThr, rmsdThrJoin, scoringStrategy, seqWeight, showAFPRanges, sideChainScoringType, substitutionMatrix, winSize
Constructor | Description |
---|---|
CECPParameters() |
Modifier and Type | Method | Description |
---|---|---|
CECPParameters.DuplicationHint |
getDuplicationHint() |
|
java.lang.Integer |
getMinCPLength() |
|
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 parameter
|
java.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 parameters
|
void |
reset() |
Set the parameters to the default.
|
void |
setDuplicationHint(CECPParameters.DuplicationHint duplicationHint) |
|
void |
setMinCPLength(java.lang.Integer minCPLength) |
|
java.lang.String |
toString() |
getDistanceIncrement, getGapExtension, getGapOpen, getMaxGapSize, getMaxNrIterationsForOptimization, getMaxOptRMSD, getORmsdThr, getRmsdThr, getRmsdThrJoin, getScoringStrategy, getSeqWeight, getSubstitutionMatrix, getWinSize, isShowAFPRanges, setDistanceIncrement, setGapExtension, setGapOpen, setMaxGapSize, setMaxNrIterationsForOptimization, setMaxOptRMSD, setORmsdThr, setRmsdThr, setRmsdThrJoin, setScoringStrategy, setSeqWeight, setShowAFPRanges, setSubstitutionMatrix, setWinSize
public static final int DEFAULT_MIN_CP_LENGTH
protected CECPParameters.DuplicationHint duplicationHint
protected java.lang.Integer minCPLength
public java.lang.String toString()
toString
in class CeParameters
public void reset()
ConfigStrucAligParams
reset
in interface ConfigStrucAligParams
reset
in class CeParameters
public java.util.List<java.lang.String> getUserConfigHelp()
ConfigStrucAligParams
getUserConfigHelp
in interface ConfigStrucAligParams
getUserConfigHelp
in class CeParameters
public java.util.List<java.lang.String> getUserConfigParameters()
ConfigStrucAligParams
getUserConfigParameters
in interface ConfigStrucAligParams
getUserConfigParameters
in class CeParameters
public java.util.List<java.lang.String> getUserConfigParameterNames()
ConfigStrucAligParams
getUserConfigParameterNames
in interface ConfigStrucAligParams
getUserConfigParameterNames
in class CeParameters
public java.util.List<java.lang.Class> getUserConfigTypes()
ConfigStrucAligParams
getUserConfigTypes
in interface ConfigStrucAligParams
getUserConfigTypes
in class CeParameters
public CECPParameters.DuplicationHint getDuplicationHint()
public void setDuplicationHint(CECPParameters.DuplicationHint duplicationHint)
public java.lang.Integer getMinCPLength()
public void setMinCPLength(java.lang.Integer minCPLength)