com.hfg.bio.seq.alignment

Class PairwiseSettings

java.lang.Object

com.hfg.bio.seq.alignment.PairwiseSettings

All Implemented Interfaces:

Cloneable

public class PairwiseSettings
extends Object
implements Cloneable

Container for pairwise sequence alignment settings.

Constructor Summary

Constructors

Constructor and Description
PairwiseSettings()

Method Summary

Modifier and Type	Method and Description
PairwiseSettings	clone()
boolean	getCalculateStatisticalScores()
boolean	getDumpMatrices()
GapPenalties	getGapPenalties(PairwiseSeqType inPairwiseSeqType)
Integer	getMaxLocalAlignmentResults()
Integer	getMinLocalAlignmentLength()
int	getMinNumOfBackgroundCycles()
Integer	getMinQueryMatchLength()
Integer	getMinRawScore()
Boolean	getPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, PairwiseSeqTerminus inPairwiseSeqTerminus)
PairwiseAlignmentType	getQueryAlignmentType()
boolean	getScoreCaseInsensitive()
PairwiseAlignmentType	getSubjectAlignmentType()
boolean	getSubjectTemplateMode()
SubstitutionMatrix	getSubstitutionMatrix(BioSequenceType inSeqType)
PairwiseSettings	setAlignmentType(PairwiseAlignmentType inValue)
PairwiseSettings	setCalculateStatisticalScores(boolean inValue) Specifies whether or not to calculate an E-value, P-value, and Z score by generating background alignments.
PairwiseSettings	setDumpMatrices(boolean inValue)
PairwiseSettings	setGapPenalties(GapPenalties inValue) Sets the specified gap penalties for both the query and subject.
PairwiseSettings	setGapPenalties(PairwiseSeqType inPairwiseSeqType, GapPenalties inValue)
PairwiseSettings	setMaxLocalAlignmentResults(Integer inValue)
PairwiseSettings	setMinLocalAlignmentLength(Integer inValue)
PairwiseSettings	setMinNumOfBackgroundCycles(int inValue)
PairwiseSettings	setMinQueryMatchLength(Integer inValue) Specifies the minimum number of non-gap characters for the query in the alignment.
PairwiseSettings	setMinRawScore(Integer inValue)
PairwiseSettings	setPenalizeTerminalGaps(boolean inValue)
PairwiseSettings	setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, boolean inValue)
PairwiseSettings	setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, PairwiseSeqTerminus inPairwiseSeqTerminus, boolean inValue)
PairwiseSettings	setQueryAlignmentType(PairwiseAlignmentType inValue)
PairwiseSettings	setScoreCaseInsensitive(boolean inValue) If specified as true, the scoring matrix's scoreCaseInsensitive() method is used.
PairwiseSettings	setSubjectAlignmentType(PairwiseAlignmentType inValue)
PairwiseSettings	setSubjectTemplateMode(boolean inValue) If specified as true, query gaps are not penalized if they exist in the subject.
PairwiseSettings	setSubstitutionMatrix(SubstitutionMatrix inValue)

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PairwiseSettings

public PairwiseSettings()

Method Detail

setSubstitutionMatrix

public PairwiseSettings setSubstitutionMatrix(SubstitutionMatrix inValue)

getSubstitutionMatrix

public SubstitutionMatrix getSubstitutionMatrix(BioSequenceType inSeqType)

setMaxLocalAlignmentResults

public PairwiseSettings setMaxLocalAlignmentResults(Integer inValue)

getMaxLocalAlignmentResults

public Integer getMaxLocalAlignmentResults()

setMinLocalAlignmentLength

public PairwiseSettings setMinLocalAlignmentLength(Integer inValue)

getMinLocalAlignmentLength

public Integer getMinLocalAlignmentLength()

setMinQueryMatchLength

public PairwiseSettings setMinQueryMatchLength(Integer inValue)

Specifies the minimum number of non-gap characters for the query in the alignment.

Parameters:

inValue - the minimum number of non-gap characters for the query in the alignment

Returns:

this settings object to facilitate method chaining

getMinQueryMatchLength

public Integer getMinQueryMatchLength()

setMinRawScore

public PairwiseSettings setMinRawScore(Integer inValue)

getMinRawScore

public Integer getMinRawScore()

setSubjectTemplateMode

public PairwiseSettings setSubjectTemplateMode(boolean inValue)

If specified as true, query gaps are not penalized if they exist in the subject.

Parameters:

inValue - whether or not to apply subject template mode scoring

Returns:

this settings object (for possible method chaining)

getSubjectTemplateMode

public boolean getSubjectTemplateMode()

setScoreCaseInsensitive

public PairwiseSettings setScoreCaseInsensitive(boolean inValue)

If specified as true, the scoring matrix's scoreCaseInsensitive() method is used.

Parameters:

inValue - whether or not scoring is case insensitive

Returns:

this settings object (for possible method chaining)

getScoreCaseInsensitive

public boolean getScoreCaseInsensitive()

setGapPenalties

public PairwiseSettings setGapPenalties(GapPenalties inValue)

Sets the specified gap penalties for both the query and subject.

Parameters:

inValue - GapPenalties to apply

Returns:

this settings object (for possible method chaining)

setGapPenalties

public PairwiseSettings setGapPenalties(PairwiseSeqType inPairwiseSeqType,
                                        GapPenalties inValue)

getGapPenalties

public GapPenalties getGapPenalties(PairwiseSeqType inPairwiseSeqType)

setPenalizeTerminalGaps

public PairwiseSettings setPenalizeTerminalGaps(boolean inValue)

setPenalizeTerminalGaps

public PairwiseSettings setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType,
                                                boolean inValue)

setPenalizeTerminalGaps

public PairwiseSettings setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType,
                                                PairwiseSeqTerminus inPairwiseSeqTerminus,
                                                boolean inValue)

getPenalizeTerminalGaps

public Boolean getPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType,
                                       PairwiseSeqTerminus inPairwiseSeqTerminus)

setAlignmentType

public PairwiseSettings setAlignmentType(PairwiseAlignmentType inValue)

setQueryAlignmentType

public PairwiseSettings setQueryAlignmentType(PairwiseAlignmentType inValue)

getQueryAlignmentType

public PairwiseAlignmentType getQueryAlignmentType()

setSubjectAlignmentType

public PairwiseSettings setSubjectAlignmentType(PairwiseAlignmentType inValue)

getSubjectAlignmentType

public PairwiseAlignmentType getSubjectAlignmentType()

setMinNumOfBackgroundCycles

public PairwiseSettings setMinNumOfBackgroundCycles(int inValue)

getMinNumOfBackgroundCycles

public int getMinNumOfBackgroundCycles()

setCalculateStatisticalScores

public PairwiseSettings setCalculateStatisticalScores(boolean inValue)

Specifies whether or not to calculate an E-value, P-value, and Z score by generating background alignments.

Parameters:

inValue - whether or not to calculate statistical measures for the alignment

Returns:

this settings object (for possible method chaining)

getCalculateStatisticalScores

public boolean getCalculateStatisticalScores()

setDumpMatrices

public PairwiseSettings setDumpMatrices(boolean inValue)

getDumpMatrices

public boolean getDumpMatrices()

clone

public PairwiseSettings clone()

Overrides:

clone in class Object