AlignmentScoring (com.hfg API Documentation)

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

All Implemented Interfaces:

Cloneable, Comparable<AlignmentScoring>
```
public class AlignmentScoring
extends Object
implements Cloneable, Comparable<AlignmentScoring>
```
Pairwise sequence alignment scoring data.

Constructor Summary

Constructors
Constructor and Description

AlignmentScoring()

AlignmentScoring(XMLNode inXMLNode)

Constructors
Constructor and Description
`AlignmentScoring()`
`AlignmentScoring(XMLNode inXMLNode)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`calculate(PairwiseSeqAlignment inAlignment)`
`void`	`clear()`
`AlignmentScoring`	`clone()`
`AlignmentScoring`	`combine(AlignmentScoring inValue)`
`int`	`compareTo(AlignmentScoring inObj2)`
`boolean`	`equals(Object inObj2)`
`int`	`getAdjustedComparisonLength()` Doesn't penalize sequence's terminal gaps.
`Float`	`getAdjustedPctIdentity()` Doesn't penalize sequence's terminal gaps.
`int`	`getComparisonLength()`
`Float`	`getEValue()`
`int`	`getNumIdentities()`
`Float`	`getPctIdentity()`
`Float`	`getPValue()`
`Integer`	`getQueryInternalGapLength()` Returns the total number of non-terminal query gap positions where the subject is not a gap.
`Float`	`getScore()`
`List<Range<Integer>>`	`getScoringBoundaries()`
`Float`	`getZScore()`
`int`	`hashCode()`
`AlignmentScoring`	`incrementComparisonLength()`
`AlignmentScoring`	`incrementComparisonLength(int inValue)`
`AlignmentScoring`	`incrementNumIdentities()`
`AlignmentScoring`	`incrementNumIdentities(int inValue)`
`AlignmentScoring`	`setAdjustedPctIdentity(Float inValue)` Sets the percent identity that doesn't penalize sequence's terminal gaps.
`AlignmentScoring`	`setComparisonLength(Integer inValue)`
`AlignmentScoring`	`setEValue(Float inValue)`
`AlignmentScoring`	`setNumIdentities(Integer inValue)`
`AlignmentScoring`	`setPValue(Float inValue)`
`AlignmentScoring`	`setScore(Float inValue)`
`AlignmentScoring`	`setScoringBoundaries(List<Range<Integer>> inValue)` Specifies an optional 1-based list of alignment position ranges which should be considered for scoring.
`AlignmentScoring`	`setZScore(Float inValue)`
`String`	`toString()`
`XMLNode`	`toXMLNode()`

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

Constructor Detail

AlignmentScoring
```
public AlignmentScoring()
```

AlignmentScoring

public AlignmentScoring(XMLNode inXMLNode)

Method Detail

combine

public AlignmentScoring combine(AlignmentScoring inValue)

clone
```
public AlignmentScoring 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(AlignmentScoring inObj2)
```
Specified by:

compareTo in interface Comparable<AlignmentScoring>

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

toString in class Object

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

clear
```
public void clear()
```

setScoringBoundaries
```
public AlignmentScoring setScoringBoundaries(List<Range<Integer>> inValue)
```
Specifies an optional 1-based list of alignment position ranges which should be considered for scoring.

Parameters:

inValue - List of 1-based Ranges to score

Returns:

this AlignmentScoring object to enable method chaining

getScoringBoundaries

public List<Range<Integer>> getScoringBoundaries()

setScore

public AlignmentScoring setScore(Float inValue)

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

setNumIdentities

public AlignmentScoring setNumIdentities(Integer inValue)

incrementNumIdentities

public AlignmentScoring incrementNumIdentities()

incrementNumIdentities

public AlignmentScoring incrementNumIdentities(int inValue)

getNumIdentities
```
public int getNumIdentities()
```

setComparisonLength

public AlignmentScoring setComparisonLength(Integer inValue)

incrementComparisonLength

public AlignmentScoring incrementComparisonLength()

incrementComparisonLength

public AlignmentScoring incrementComparisonLength(int inValue)

getComparisonLength
```
public int getComparisonLength()
```

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

Returns:

the adjusted comparison length

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

setAdjustedPctIdentity
```
public AlignmentScoring setAdjustedPctIdentity(Float inValue)
```
Sets the percent identity that doesn't penalize sequence's terminal gaps.

Returns:

this AlignmentScoring object to enable method chaining

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

Returns:

the adjusted percent identity

setEValue

public AlignmentScoring setEValue(Float inValue)

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

setPValue

public AlignmentScoring setPValue(Float inValue)

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

setZScore

public AlignmentScoring setZScore(Float inValue)

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

getQueryInternalGapLength
```
public Integer getQueryInternalGapLength()
```
Returns the total number of non-terminal query gap positions where the subject is not a gap.

Returns:

the total number of non-terminal query gap positions where the subject is not a gap

calculate

public void calculate(PairwiseSeqAlignment inAlignment)

Class AlignmentScoring

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AlignmentScoring

AlignmentScoring

Method Detail

combine

clone

equals

hashCode

compareTo

toString

toXMLNode

clear

setScoringBoundaries

getScoringBoundaries

setScore

getScore

setNumIdentities

incrementNumIdentities

incrementNumIdentities

getNumIdentities

setComparisonLength

incrementComparisonLength

incrementComparisonLength

getComparisonLength

getAdjustedComparisonLength

getPctIdentity

setAdjustedPctIdentity

getAdjustedPctIdentity

setEValue

getEValue

setPValue

getPValue

setZScore

getZScore

getQueryInternalGapLength

calculate