LinearIndex.ChrIndex (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.tribble.index.linear.LinearIndex.ChrIndex

All Implemented Interfaces:

ChrIndex

Enclosing class:

LinearIndex
```
public static class LinearIndex.ChrIndex
extends Object
implements ChrIndex
```
Blocks are organized as a simple flat list:
Block 0 Block 1 Block 2
There's a constant bin width, so that each block corresponds to a specific interval over the genome based on its index, as in:
Block 0: (0 - binWidth] Block 1: (binWidth - 2 * binWidth] Block 2: (2 * binWidth - 3 * binWidth]
Note that covered regions are open on the left ( and closed on the right ].
In general, if block i is the ith block (starting from 0), then block i contains all records that have starting position > (i * binWidth) and <= ((i + 1) * binWidth))

Constructor Summary

Constructors
Constructor and Description

ChrIndex()
Default constructor needed for factory methods -- DO NOT REMOVE

Constructors
Constructor and Description
`ChrIndex()` Default constructor needed for factory methods -- DO NOT REMOVE

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(Object obj)`
`double`	`getAverageFeatureSize()`
`List<Block>`	`getBlocks()`
`List<Block>`	`getBlocks(int start, int end)`
`double`	`getFeaturesPerBlock()`
`String`	`getName()`
`int`	`getNBlocks()`
`int`	`getNFeatures()`
`long`	`getTotalSize()`
`void`	`incrementFeatureCount()`
`LinearIndex.ChrIndex`	`optimize(double threshold)`
`void`	`read(LittleEndianInputStream dis)`
`void`	`updateLongestFeature(int featureLength)`
`void`	`write(LittleEndianOutputStream dos)`

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

- Constructor Detail
  - ChrIndex
```
public ChrIndex()
```
    Default constructor needed for factory methods -- DO NOT REMOVE
- Method Detail
  - getName
```
public String getName()
```
    Specified by:
    
    getName in interface ChrIndex
  - getNBlocks
```
public int getNBlocks()
```
  - getBlocks
```
public List<Block> getBlocks()
```
    Specified by:
    
    getBlocks in interface ChrIndex
    
    Returns:
    
    all blocks in ChrIndex
  - getBlocks
```
public List<Block> getBlocks(int start,
                             int end)
```
    Specified by:
    
    getBlocks in interface ChrIndex
    
    Parameters:
    
    start - the start position, one based
    
    end - the end position, one based
    
    Returns:
    
    a list of blocks that include the region defined from start to stop. Can never return null
  - updateLongestFeature
```
public void updateLongestFeature(int featureLength)
```
  - getNFeatures
```
public int getNFeatures()
```
  - incrementFeatureCount
```
public void incrementFeatureCount()
```
  - write
```
public void write(LittleEndianOutputStream dos)
           throws IOException
```
    Specified by:
    
    write in interface ChrIndex
    
    Throws:
    
    IOException
  - read
```
public void read(LittleEndianInputStream dis)
          throws IOException
```
    Specified by:
    
    read in interface ChrIndex
    
    Throws:
    
    IOException
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - getTotalSize
```
public long getTotalSize()
```
    Returns:
    
    Total size of all blocks
  - getAverageFeatureSize
```
public double getAverageFeatureSize()
```
  - getFeaturesPerBlock
```
public double getFeaturesPerBlock()
```
  - optimize
```
public LinearIndex.ChrIndex optimize(double threshold)
```

Class LinearIndex.ChrIndex

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ChrIndex

Method Detail

getName

getNBlocks

getBlocks

getBlocks

updateLongestFeature

getNFeatures

incrementFeatureCount

write

read

equals

getTotalSize

getAverageFeatureSize

getFeaturesPerBlock

optimize