All Implemented Interfaces:

java.lang.Comparable
```
public class PairedSimilarFragment
 implements Comparable<T>
                    
```
Class that holds reference and assembly alignment data to be sorted and filtered in a longest path algorithm.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`public int`	`refStartPos`
`public int`	`refEndPos`
`public int`	`asmStartPos`
`public int`	`asmEndPos`
`public double`	`score`
`public int`	`strand`

Constructor Summary

Constructors
Constructor	Description
`PairedSimilarFragment(int refStartPos, int refEndPos, int asmStartPos, int asmEndPos, double score, int strand)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`int`	`getRefStartPos()`
`void`	`setRefStartPos(int position)`
`int`	`getRefEndPos()`
`void`	`setRefEndPos(int position)`
`int`	`getAsmStartPos()`
`void`	`setAsmStartPos(int position)`
`int`	`getAsmEndPos()`
`void`	`setAsmEndPos(int position)`
`double`	`getScore()`
`void`	`setScore(double score)`
`int`	`getStrand()`
`void`	`setStrand(int strand)`
`int`	`compareTo(PairedSimilarFragment compareFruit)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PairedSimilarFragment

PairedSimilarFragment(int refStartPos, int refEndPos, int asmStartPos, int asmEndPos, double score, int strand)

Method Detail

getRefStartPos
```
 int getRefStartPos()
```

setRefStartPos
```
 void setRefStartPos(int position)
```

getRefEndPos
```
 int getRefEndPos()
```

setRefEndPos
```
 void setRefEndPos(int position)
```

getAsmStartPos
```
 int getAsmStartPos()
```

setAsmStartPos
```
 void setAsmStartPos(int position)
```

getAsmEndPos
```
 int getAsmEndPos()
```

setAsmEndPos
```
 void setAsmEndPos(int position)
```

getScore
```
 double getScore()
```

setScore
```
 void setScore(double score)
```

getStrand
```
 int getStrand()
```

setStrand
```
 void setStrand(int strand)
```

compareTo

 int compareTo(PairedSimilarFragment compareFruit)

Class PairedSimilarFragment

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PairedSimilarFragment

Method Detail

getRefStartPos

setRefStartPos

getRefEndPos

setRefEndPos

getAsmStartPos

setAsmStartPos

getAsmEndPos

setAsmEndPos

getScore

setScore

getStrand

setStrand

compareTo