LinearIndex (htsjdk 2.14.3 API)

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

All Implemented Interfaces:

Index, MutableIndex
```
public class LinearIndex
extends AbstractIndex
```
Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in genomic coordinates). Features are allocated to bins by start position. The longest feature in each recorded and used to adjust the start position of a query to include all bins that might have a feature that overlaps the query interval. This works well for feature sets of approximately homogeneous length, or whose longest feature is on the order of the bin width or less.
magicNumber integer type integer version integer filename null terminated character array filesize long lastModified long md5 String flags integer
------ LINEAR INDEX nChromosomes integer

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class LinearIndex.ChrIndex
Blocks are organized as a simple flat list:
- Nested classes/interfaces inherited from class htsjdk.tribble.index.AbstractIndex
  AbstractIndex.BlockStats, AbstractIndex.IndexType

Nested Classes
Modifier and Type	Class	Description
`static class`	`LinearIndex.ChrIndex`	Blocks are organized as a simple flat list:

Field Summary

Fields
Modifier and Type Field Description

static boolean enableAdaptiveIndexing

static int INDEX_TYPE

static double MAX_FEATURES_PER_BIN
- Fields inherited from class htsjdk.tribble.index.AbstractIndex
  chrIndices, flags, indexedFileMD5, indexedFileSize, indexedFileTS, indexedPath, logger, MAGIC_NUMBER, version, VERSION

Fields
Modifier and Type	Field	Description
`static boolean`	`enableAdaptiveIndexing`
`static int`	`INDEX_TYPE`
`static double`	`MAX_FEATURES_PER_BIN`

Constructor Summary

Constructors
Constructor	Description
`LinearIndex(InputStream inputStream)`	Load from file.
`LinearIndex(String featureFile)`	Initialize with default parameters
`LinearIndex(Path featurePath)`	Initialize with default parameters
`LinearIndex(List<LinearIndex.ChrIndex> indices, File featureFile)`	Initialize using the specified `indices`
`LinearIndex(List<LinearIndex.ChrIndex> indices, Path featureFile)`	Initialize using the specified `indices`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Class`	`getChrIndexClass()`	returns the class for the index type
`List<String>`	`getSequenceNames()`
`protected int`	`getType()`	get the index type
`boolean`	`isCurrentVersion()`	check the current version against the version we read in
`Index`	`optimize()`
`Index`	`optimize(double threshold)`	Adapative optimization of the linear index
`protected void`	`setTS(long ts)`
`void`	`writeTable(PrintStream out)`	Code to convert linear index to a text table for analysis

Methods inherited from class htsjdk.tribble.index.AbstractIndex
addProperties, addProperty, containsChromosome, equalsIgnoreProperties, finalizeIndex, getBlocks, getBlocks, getBlockStats, getFlags, getIndexedFile, getIndexedFileMD5, getIndexedFileSize, getIndexedFileTS, getIndexedPath, getProperties, getVersion, hasFileSize, hasMD5, hasTimestamp, printIndexInfo, read, setMD5, statsSummary, validateIndexHeader, write, write, writeBasedOnFeaturePath

Methods inherited from interface htsjdk.tribble.index.Index
write, writeBasedOnFeatureFile

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

- Field Detail
  - MAX_FEATURES_PER_BIN
```
public static final double MAX_FEATURES_PER_BIN
```
  - INDEX_TYPE
```
public static final int INDEX_TYPE
```
  - enableAdaptiveIndexing
```
public static boolean enableAdaptiveIndexing
```
- Constructor Detail
  - LinearIndex
```
public LinearIndex(List<LinearIndex.ChrIndex> indices,
                   Path featureFile)
```
    Initialize using the specified indices
    
    Parameters:
    
    indices -
    
    featureFile -
  - LinearIndex
```
public LinearIndex(List<LinearIndex.ChrIndex> indices,
                   File featureFile)
```
    Initialize using the specified indices
    
    Parameters:
    
    indices -
    
    featureFile -
  - LinearIndex
```
public LinearIndex(String featureFile)
```
    Initialize with default parameters
    
    Parameters:
    
    featureFile - File for which this is an index
  - LinearIndex
```
public LinearIndex(Path featurePath)
```
    Initialize with default parameters
    
    Parameters:
    
    featurePath - Path for which this is an index
  - LinearIndex
```
public LinearIndex(InputStream inputStream)
            throws IOException
```
    Load from file.
    
    Parameters:
    
    inputStream - This method assumes that the input stream is already buffered as appropriate.
    
    Throws:
    
    IOException
- Method Detail
  - isCurrentVersion
```
public boolean isCurrentVersion()
```
    Description copied from class: AbstractIndex
    
    check the current version against the version we read in
    
    Specified by:
    
    isCurrentVersion in interface Index
    
    Overrides:
    
    isCurrentVersion in class AbstractIndex
    
    Returns:
    
    true if we're up to date, false otherwise
  - getType
```
protected int getType()
```
    Description copied from class: AbstractIndex
    
    get the index type
    
    Specified by:
    
    getType in class AbstractIndex
    
    Returns:
    
    The index type
  - getSequenceNames
```
public List<String> getSequenceNames()
```
    Specified by:
    
    getSequenceNames in interface Index
    
    Overrides:
    
    getSequenceNames in class AbstractIndex
    
    Returns:
    
    a list of the sequence names we've seen during indexing, in order
  - getChrIndexClass
```
public Class getChrIndexClass()
```
    Description copied from class: AbstractIndex
    
    returns the class for the index type
    
    Specified by:
    
    getChrIndexClass in class AbstractIndex
    
    Returns:
    
    a Class, from which a new instance can be created
  - optimize
```
public Index optimize(double threshold)
```
    Adapative optimization of the linear index
    
    Parameters:
    
    threshold - threshold to use for optimizing each constituent chrIndex
    
    Returns:
    
    The new optimized index
  - optimize
```
public Index optimize()
```
  - writeTable
```
public void writeTable(PrintStream out)
```
    Code to convert linear index to a text table for analysis
    
    Parameters:
    
    out - Stream to which to write out table to
  - setTS
```
protected final void setTS(long ts)
```

Class LinearIndex

Nested Class Summary

Nested classes/interfaces inherited from class htsjdk.tribble.index.AbstractIndex

Field Summary

Fields inherited from class htsjdk.tribble.index.AbstractIndex

Constructor Summary

Method Summary

Methods inherited from class htsjdk.tribble.index.AbstractIndex

Methods inherited from interface htsjdk.tribble.index.Index

Methods inherited from class java.lang.Object

Field Detail

MAX_FEATURES_PER_BIN

INDEX_TYPE

enableAdaptiveIndexing

Constructor Detail

LinearIndex

LinearIndex

LinearIndex

LinearIndex

LinearIndex

Method Detail

isCurrentVersion

getType

getSequenceNames

getChrIndexClass

optimize

optimize

writeTable

setTS