PairwiseSeqAlignment (com.hfg API Documentation)

java.lang.Object
- com.hfg.bio.seq.alignment.PairwiseSeqAlignment

All Implemented Interfaces:: Cloneable, Comparable<PairwiseSeqAlignment>

public class PairwiseSeqAlignment
extends Object
implements Cloneable, Comparable<PairwiseSeqAlignment>

Pairwise sequence alignment container.

Constructor Summary

Constructors
Constructor and Description

PairwiseSeqAlignment(AlignedQuery inAlignedQuery, AlignedSubject inAlignedSubject)

PairwiseSeqAlignment(XMLNode inXMLNode)

Constructors
Constructor and Description
`PairwiseSeqAlignment(AlignedQuery inAlignedQuery, AlignedSubject inAlignedSubject)`
`PairwiseSeqAlignment(XMLNode inXMLNode)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clearCachedValues()`
`PairwiseSeqAlignment`	`clone()`
`int`	`compareTo(PairwiseSeqAlignment inObj2)`
`boolean`	`equals(Object inObj2)`
`void`	`extendAlignedQuery()` In the case of a local query vs.
`Integer`	`getAdjustedComparisonLength()` Doesn't penalize sequence's terminal gaps.
`Float`	`getAdjustedPctIdentity()` Doesn't penalize sequence's terminal gaps.
`AlignedQuery`	`getAlignedQuery()`
`AlignedSubject`	`getAlignedSubject()`
`Integer`	`getComparisonLength()`
`Float`	`getEValue()`
`Integer`	`getNumIdentities()`
`Float`	`getPctIdentity()`
`Float`	`getPValue()`
`Float`	`getScore()`
`AlignmentScoring`	`getScoring()` Returns the alignment scoring object.
`PairwiseSettings`	`getSettings()`
`PairwiseSeqAlignment`	`getSubalignment(int inZeroIndexedStart)`
`PairwiseSeqAlignment`	`getSubalignment(int inZeroIndexedStart, int inLimit)`
`Float`	`getZScore()`
`int`	`hashCode()`
`void`	`invert()` Swaps the query and the subject.
`Integer`	`length()`
`PairwiseSeqAlignment`	`setAlignedQuery(AlignedQuery inValue)`
`PairwiseSeqAlignment`	`setAlignedSubject(AlignedSubject inValue)`
`PairwiseSeqAlignment`	`setEValue(Float inValue)`
`PairwiseSeqAlignment`	`setPValue(Float inValue)`
`PairwiseSeqAlignment`	`setScore(Float inValue)`
`PairwiseSeqAlignment`	`setSettings(PairwiseSettings inValue)`
`PairwiseSeqAlignment`	`setZScore(Float inValue)`
`String`	`showScoring()` Method helpful for understanding the per-residue scoring breakdown.
`String`	`toString()`
`XMLNode`	`toXMLNode()`

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

PairwiseSeqAlignment

public PairwiseSeqAlignment(AlignedQuery inAlignedQuery,
                            AlignedSubject inAlignedSubject)

PairwiseSeqAlignment

public PairwiseSeqAlignment(XMLNode inXMLNode)

Method Detail

clone
```
public PairwiseSeqAlignment clone()
```
Overrides:

clone in class Object

equals
```
public boolean equals(Object inObj2)
```
Overrides:

equals in class Object

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class Object

compareTo
```
public int compareTo(PairwiseSeqAlignment inObj2)
```
Specified by:

compareTo in interface Comparable<PairwiseSeqAlignment>

setSettings

public PairwiseSeqAlignment setSettings(PairwiseSettings inValue)

getSettings
```
public PairwiseSettings getSettings()
```

clearCachedValues
```
public void clearCachedValues()
```

setAlignedQuery

public PairwiseSeqAlignment setAlignedQuery(AlignedQuery inValue)

getAlignedQuery
```
public AlignedQuery getAlignedQuery()
```

setAlignedSubject

public PairwiseSeqAlignment setAlignedSubject(AlignedSubject inValue)

getAlignedSubject

public AlignedSubject getAlignedSubject()

length
```
public Integer length()
```

getScoring
```
public AlignmentScoring getScoring()
```
Returns the alignment scoring object.

Returns:

the alignment scoring object

setScore

public PairwiseSeqAlignment setScore(Float inValue)

getScore
```
public Float getScore()
```

getNumIdentities
```
public Integer getNumIdentities()
```

getComparisonLength
```
public Integer getComparisonLength()
```

getAdjustedComparisonLength
```
public Integer getAdjustedComparisonLength()
```
Doesn't penalize sequence's terminal gaps.

Returns:

the adjusted comparison length

getPctIdentity
```
public Float getPctIdentity()
```

getAdjustedPctIdentity
```
public Float getAdjustedPctIdentity()
```
Doesn't penalize sequence's terminal gaps.

Returns:

the adjusted percent identity

setEValue

public PairwiseSeqAlignment setEValue(Float inValue)

getEValue
```
public Float getEValue()
```

setPValue

public PairwiseSeqAlignment setPValue(Float inValue)

getPValue
```
public Float getPValue()
```

setZScore

public PairwiseSeqAlignment setZScore(Float inValue)

getZScore
```
public Float getZScore()
```

showScoring
```
public String showScoring()
```
Method helpful for understanding the per-residue scoring breakdown.

Returns:

ASCII display of the per-residue scoring

toString
```
public String toString()
```
Overrides:

toString in class Object

toXMLNode
```
public XMLNode toXMLNode()
```

getSubalignment

public PairwiseSeqAlignment getSubalignment(int inZeroIndexedStart)

getSubalignment

public PairwiseSeqAlignment getSubalignment(int inZeroIndexedStart,
                                            int inLimit)

extendAlignedQuery
```
public void extendAlignedQuery()
```
In the case of a local query vs. a global subject, this method can be used to extend the local query in both directions to match where subject residues are present.

invert
```
public void invert()
```
Swaps the query and the subject.

Class PairwiseSeqAlignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PairwiseSeqAlignment

PairwiseSeqAlignment

Method Detail

clone

equals

hashCode

compareTo

setSettings

getSettings

clearCachedValues

setAlignedQuery

getAlignedQuery

setAlignedSubject

getAlignedSubject

length

getScoring

setScore

getScore

getNumIdentities

getComparisonLength

getAdjustedComparisonLength

getPctIdentity

getAdjustedPctIdentity

setEValue

getEValue

setPValue

getPValue

setZScore

getZScore

showScoring

toString

toXMLNode

getSubalignment

getSubalignment

extendAlignedQuery

invert