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

All Implemented Interfaces:

Index, MutableIndex

Direct Known Subclasses:

IntervalTreeIndex, LinearIndex
```
public abstract class AbstractIndex
extends Object
implements MutableIndex
```
An abstract implementation of the index class. This class takes care of the basics that are common to all of the current indexing classes; including the version information, common header properties, and reading and writing the header to disk.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

protected static class AbstractIndex.BlockStats

static class AbstractIndex.IndexType

Field Summary

Fields
Modifier and Type	Field	Description
`protected LinkedHashMap<String,ChrIndex>`	`chrIndices`	the map of our chromosome bins
`protected int`	`flags`
`protected String`	`indexedFileMD5`
`protected long`	`indexedFileSize`
`protected long`	`indexedFileTS`
`protected Path`	`indexedPath`
`protected Log`	`logger`
`static int`	`MAGIC_NUMBER`
`protected int`	`version`
`static int`	`VERSION`

Constructor Summary

Constructors
Constructor	Description
`AbstractIndex()`	create an abstract index, with defaults for the version value, and empty properties and chromosome lists
`AbstractIndex(AbstractIndex parent)`
`AbstractIndex(File featureFile)`
`AbstractIndex(String featureFile)`	create an index file from the target feature file
`AbstractIndex(Path featurePath)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`void`	`addProperties(Map<String,String> properties)`
`void`	`addProperty(String key, String value)`
`boolean`	`containsChromosome(String chr)`
`boolean`	`equalsIgnoreProperties(Object obj)`	Returns true if this and obj are 'effectively' equivalent indices.
`void`	`finalizeIndex()`
`List<Block>`	`getBlocks(String chr)`
`List<Block>`	`getBlocks(String chr, int start, int end)`	Query the index.
`protected AbstractIndex.BlockStats`	`getBlockStats(boolean logDetails)`
`abstract Class`	`getChrIndexClass()`	returns the class for the index type
`int`	`getFlags()`
`File`	`getIndexedFile()`	Deprecated. on 03/2017.
`String`	`getIndexedFileMD5()`
`long`	`getIndexedFileSize()`
`long`	`getIndexedFileTS()`
`Path`	`getIndexedPath()`
`Map<String,String>`	`getProperties()`	return a mapping of name to property value
`List<String>`	`getSequenceNames()`
`protected abstract int`	`getType()`	get the index type
`int`	`getVersion()`
`boolean`	`hasFileSize()`
`boolean`	`hasMD5()`
`boolean`	`hasTimestamp()`
`boolean`	`isCurrentVersion()`	check the current version against the version we read in
`protected void`	`printIndexInfo()`
`void`	`read(LittleEndianInputStream dis)`
`void`	`setMD5(String md5)`
`protected String`	`statsSummary()`
`protected void`	`validateIndexHeader(int indexType, LittleEndianInputStream dis)`
`void`	`write(LittleEndianOutputStream stream)`	all indexes are writable to disk
`void`	`write(Path idxPath)`	Writes the index into a path.
`void`	`writeBasedOnFeaturePath(Path featurePath)`	Write an appropriately named and located Index file based on the name and location of the featureFile.

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

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

- Field Detail
  - VERSION
```
public static final int VERSION
```
    See Also:
    
    Constant Field Values
  - MAGIC_NUMBER
```
public static final int MAGIC_NUMBER
```
    See Also:
    
    Constant Field Values
  - version
```
protected int version
```
  - indexedPath
```
protected Path indexedPath
```
  - indexedFileSize
```
protected long indexedFileSize
```
  - indexedFileTS
```
protected long indexedFileTS
```
  - indexedFileMD5
```
protected String indexedFileMD5
```
  - flags
```
protected int flags
```
  - logger
```
protected final Log logger
```
  - chrIndices
```
protected LinkedHashMap<String,ChrIndex> chrIndices
```
    the map of our chromosome bins
- Constructor Detail
  - AbstractIndex
```
public AbstractIndex()
```
    create an abstract index, with defaults for the version value, and empty properties and chromosome lists
  - AbstractIndex
```
public AbstractIndex(String featureFile)
```
    create an index file from the target feature file
    
    Parameters:
    
    featureFile - the feature file to create an index from
  - AbstractIndex
```
public AbstractIndex(File featureFile)
```
  - AbstractIndex
```
public AbstractIndex(Path featurePath)
```
  - AbstractIndex
```
public AbstractIndex(AbstractIndex parent)
```
- Method Detail
  - hasFileSize
```
public boolean hasFileSize()
```
  - hasTimestamp
```
public boolean hasTimestamp()
```
  - hasMD5
```
public boolean hasMD5()
```
  - equalsIgnoreProperties
```
public boolean equalsIgnoreProperties(Object obj)
```
    Description copied from interface: Index
    
    Returns true if this and obj are 'effectively' equivalent indices. Ignores the time stamp on the file, as this may not be the same for even identical indices
    
    Specified by:
    
    equalsIgnoreProperties in interface Index
    
    Parameters:
    
    obj -
    
    Returns:
    
    true if this and obj are 'effectively' equivalent data structures.
  - validateIndexHeader
```
protected void validateIndexHeader(int indexType,
                                   LittleEndianInputStream dis)
                            throws IOException
```
    Throws:
    
    IOException
  - isCurrentVersion
```
public boolean isCurrentVersion()
```
    check the current version against the version we read in
    
    Specified by:
    
    isCurrentVersion in interface Index
    
    Returns:
    
    true if we're up to date, false otherwise
  - getIndexedFile
```
@Deprecated
public File getIndexedFile()
```
    Deprecated.
    on 03/2017. Use getIndexedPath() instead.
    
    Gets the indexed file.
    
    Throws:
    
    UnsupportedOperationException - if the path cannot be represented as a file.
  - getIndexedPath
```
public Path getIndexedPath()
```
  - getIndexedFileSize
```
public long getIndexedFileSize()
```
  - getIndexedFileTS
```
public long getIndexedFileTS()
```
  - getIndexedFileMD5
```
public String getIndexedFileMD5()
```
  - getFlags
```
public int getFlags()
```
  - getVersion
```
public int getVersion()
```
  - setMD5
```
public void setMD5(String md5)
```
  - containsChromosome
```
public boolean containsChromosome(String chr)
```
    Specified by:
    
    containsChromosome in interface Index
    
    Parameters:
    
    chr - the chromosome (or contig) name
    
    Returns:
    
    true if we have an entry; false otherwise
  - finalizeIndex
```
public void finalizeIndex()
```
  - getSequenceNames
```
public List<String> getSequenceNames()
```
    Specified by:
    
    getSequenceNames in interface Index
    
    Returns:
    
    a list of the sequence names we've seen during indexing, in order
  - getBlocks
```
public List<Block> getBlocks(String chr,
                             int start,
                             int end)
```
    Description copied from interface: Index
    
    Query the index.
    
    Specified by:
    
    getBlocks in interface Index
    
    Parameters:
    
    chr - the chromosome
    
    start - the start position
    
    end - the end position
    
    Returns:
    
    a list of blocks that contain the specified interval. Can never return null
  - getBlocks
```
public List<Block> getBlocks(String chr)
```
  - write
```
public void write(LittleEndianOutputStream stream)
           throws IOException
```
    Description copied from interface: Index
    
    all indexes are writable to disk
    
    Specified by:
    
    write in interface Index
    
    Parameters:
    
    stream - the stream to write the index to. Caller must close after invocation.
    
    Throws:
    
    IOException - if the index is unable to write to the specified location
  - write
```
public void write(Path idxPath)
           throws IOException
```
    Description copied from interface: Index
    
    Writes the index into a path.
    
    Specified by:
    
    write in interface Index
    
    Parameters:
    
    idxPath - Where to write the index.
    
    Throws:
    
    IOException - if the index is unable to write to the specified path.
  - writeBasedOnFeaturePath
```
public void writeBasedOnFeaturePath(Path featurePath)
                             throws IOException
```
    Description copied from interface: Index
    
    Write an appropriately named and located Index file based on the name and location of the featureFile. If featureFile is not a normal file, the index will silently not be written.
    
    Specified by:
    
    writeBasedOnFeaturePath in interface Index
    
    Throws:
    
    IOException - if featureFile is not a normal file.
  - read
```
public void read(LittleEndianInputStream dis)
          throws IOException
```
    Throws:
    
    IOException
  - printIndexInfo
```
protected void printIndexInfo()
```
  - getBlockStats
```
protected AbstractIndex.BlockStats getBlockStats(boolean logDetails)
```
  - statsSummary
```
protected String statsSummary()
```
  - addProperty
```
public void addProperty(String key,
                        String value)
```
    Specified by:
    
    addProperty in interface MutableIndex
  - addProperties
```
public void addProperties(Map<String,String> properties)
```
    Specified by:
    
    addProperties in interface MutableIndex
  - getProperties
```
public Map<String,String> getProperties()
```
    return a mapping of name to property value
    
    Specified by:
    
    getProperties in interface Index
    
    Returns:
    
    the mapping of values as an unmodifiable map
  - getType
```
protected abstract int getType()
```
    get the index type
    
    Returns:
    
    The index type
  - getChrIndexClass
```
public abstract Class getChrIndexClass()
```
    returns the class for the index type
    
    Returns:
    
    a Class, from which a new instance can be created

Modifier and Type	Class	Description
`protected static class`	`AbstractIndex.BlockStats`
`static class`	`AbstractIndex.IndexType`

Class AbstractIndex

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.tribble.index.Index

Field Detail

VERSION

MAGIC_NUMBER

version

indexedPath

indexedFileSize

indexedFileTS

indexedFileMD5

flags

logger

chrIndices

Constructor Detail

AbstractIndex

AbstractIndex

AbstractIndex

AbstractIndex

AbstractIndex

Method Detail

hasFileSize

hasTimestamp

hasMD5

equalsIgnoreProperties

validateIndexHeader

isCurrentVersion

getIndexedFile

getIndexedPath

getIndexedFileSize

getIndexedFileTS

getIndexedFileMD5

getFlags

getVersion

setMD5

containsChromosome

finalizeIndex

getSequenceNames

getBlocks

getBlocks

write

write

writeBasedOnFeaturePath

read

printIndexInfo

getBlockStats

statsSummary

addProperty

addProperties

getProperties

getType

getChrIndexClass