All Implemented Interfaces:

java.lang.Comparable
```
public class AnchorDataPHG
 implements Comparable<T>
                    
```
THis class differs from AnchorData in WGS_whatever as it includes more fields to match what is stored in PHGSchema's anchor_haplotypes. Specifically it includes ave_allele_depth and additional_data May 26, 2017: Class updated to include gene_start and gene_end These values needed when trimming anchors. The stored anchors have sequence of merged genes whose GFF start/end positions overlapped with 1000bp flanking on each end. THis 1000bp may be less is the distance between 2 genes is less than 2000bps.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description

Constructor Summary

Constructors
Constructor	Description
`AnchorDataPHG(Range<Position> interval, String asmContig, int asmStart, int asmEnd, String asmStrand, String gvcf, String sequence, int asmFileId, int gvcfFileId)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`static String`	`getChecksumForString(String seq, String protocol)`
`Range<Position>`	`intervalCoordinates()`
`String`	`asmContig()`
`int`	`asmStart()`
`int`	`asmEnd()`
`String`	`asmStrand()`
`String`	`gvcf()`
`String`	`sequence()`
`int`	`seqLen()`
`String`	`seqHash()`
`int`	`asmFileId()`
`int`	`gvcfFileId()`
`boolean`	`equals(Object obj)`
`int`	`hashCode()`
`int`	`compareTo(AnchorDataPHG other)`

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

Constructor Detail

AnchorDataPHG

AnchorDataPHG(Range<Position> interval, String asmContig, int asmStart, int asmEnd, String asmStrand, String gvcf, String sequence, int asmFileId, int gvcfFileId)

Method Detail

getChecksumForString

 static String getChecksumForString(String seq, String protocol)

intervalCoordinates
```
 Range<Position> intervalCoordinates()
```

asmContig
```
 String asmContig()
```

asmStart
```
 int asmStart()
```

asmEnd
```
 int asmEnd()
```

asmStrand
```
 String asmStrand()
```

gvcf
```
 String gvcf()
```

sequence
```
 String sequence()
```

seqLen
```
 int seqLen()
```

seqHash
```
 String seqHash()
```

asmFileId
```
 int asmFileId()
```

gvcfFileId
```
 int gvcfFileId()
```

equals
```
 boolean equals(Object obj)
```

hashCode
```
 int hashCode()
```

compareTo
```
 int compareTo(AnchorDataPHG other)
```

Class AnchorDataPHG

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AnchorDataPHG

Method Detail

getChecksumForString

intervalCoordinates

asmContig

asmStart

asmEnd

asmStrand

gvcf

sequence

seqLen

seqHash

asmFileId

gvcfFileId

equals

hashCode

compareTo