com.hfg.bio.seq.alignment

Class MSA_Settings

java.lang.Object

com.hfg.bio.seq.alignment.MSA_Settings

All Implemented Interfaces:

Cloneable

public class MSA_Settings
extends Object
implements Cloneable

Container for multiple sequence alignment settings.

Constructor Summary

Constructors

Constructor and Description
MSA_Settings()

Method Summary

Modifier and Type	Method and Description
MSA_Settings	clone()
GapPenalties	getGapPenalties(PairwiseSeqType inPairwiseSeqType)
int	getKMerSize()
Boolean	getPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, PairwiseSeqTerminus inPairwiseSeqTerminus)
boolean	getScoreCaseInsensitive()
SubstitutionMatrix	getSubstitutionMatrix(BioSequenceType inSeqType)
MSA_Settings	setGapPenalties(GapPenalties inValue) Sets the specified gap penalties for both the query and subject.
MSA_Settings	setGapPenalties(PairwiseSeqType inPairwiseSeqType, GapPenalties inValue)
MSA_Settings	setKMerSize(int inValue)
MSA_Settings	setPenalizeTerminalGaps(boolean inValue)
MSA_Settings	setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, boolean inValue)
MSA_Settings	setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, PairwiseSeqTerminus inPairwiseSeqTerminus, boolean inValue)
MSA_Settings	setScoreCaseInsensitive(boolean inValue) If specified as true, the scoring matrix's scoreCaseInsensitive() method is used.
MSA_Settings	setSubstitutionMatrix(SubstitutionMatrix inValue)

Methods inherited from class java.lang.Object

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

Constructor Detail

MSA_Settings

public MSA_Settings()

Method Detail

setKMerSize

public MSA_Settings setKMerSize(int inValue)

getKMerSize

public int getKMerSize()

setSubstitutionMatrix

public MSA_Settings setSubstitutionMatrix(SubstitutionMatrix inValue)

getSubstitutionMatrix

public SubstitutionMatrix getSubstitutionMatrix(BioSequenceType inSeqType)

setScoreCaseInsensitive

public MSA_Settings 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 MSA_Settings 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 MSA_Settings setGapPenalties(PairwiseSeqType inPairwiseSeqType,
                                    GapPenalties inValue)

getGapPenalties

public GapPenalties getGapPenalties(PairwiseSeqType inPairwiseSeqType)

setPenalizeTerminalGaps

public MSA_Settings setPenalizeTerminalGaps(boolean inValue)

setPenalizeTerminalGaps

public MSA_Settings setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType,
                                            boolean inValue)

setPenalizeTerminalGaps

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

getPenalizeTerminalGaps

public Boolean getPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType,
                                       PairwiseSeqTerminus inPairwiseSeqTerminus)

clone

public MSA_Settings clone()

Overrides:

clone in class Object