htsjdk.tribble.index

Class DynamicIndexCreator

java.lang.Object

htsjdk.tribble.index.TribbleIndexCreator

htsjdk.tribble.index.DynamicIndexCreator

All Implemented Interfaces:

IndexCreator

public class DynamicIndexCreator
extends TribbleIndexCreator

A DynamicIndexCreator creates the proper index based on an IndexFactory.IndexBalanceApproach and the characteristics of the file. Ultimately this is either a LinearIndex or an IntervalTreeIndex, with index parameters based on whether seek time or file size is to be minimized.

Field Summary

Fields inherited from class htsjdk.tribble.index.TribbleIndexCreator

properties

Constructor Summary

Constructors

Constructor and Description
DynamicIndexCreator(java.io.File inputFile, IndexFactory.IndexBalanceApproach iba)

Method Summary

Modifier and Type	Method and Description
void	addFeature(Feature f, long filePosition) Add a feature to the index
void	addProperty(java.lang.String key, java.lang.String value)
Index	finalizeIndex(long finalFilePosition) Create the index, given the stream of features passed in to this point
protected static java.util.LinkedHashMap<java.lang.Double,TribbleIndexCreator>	scoreIndexes(double densityOfFeatures, java.util.Map<IndexFactory.IndexType,TribbleIndexCreator> indexes, int longestFeature, IndexFactory.IndexBalanceApproach iba) score the available indexes for the specified density and feature lengths The scoring method is trying to determine how many features would be returned for a sample one base query; or: (features/seek).

Methods inherited from class htsjdk.tribble.index.TribbleIndexCreator

setIndexSequenceDictionary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DynamicIndexCreator

public DynamicIndexCreator(java.io.File inputFile,
                           IndexFactory.IndexBalanceApproach iba)

Method Detail

finalizeIndex

public Index finalizeIndex(long finalFilePosition)

Description copied from interface: IndexCreator

Create the index, given the stream of features passed in to this point

Parameters:

finalFilePosition - the final file position, for indexes that have to close out with the final position

Returns:

an index object

addFeature

public void addFeature(Feature f,
                       long filePosition)

Description copied from interface: IndexCreator

Add a feature to the index

Parameters:

f - the feature, of which start, end, and contig must be filled in

filePosition - the current file position, at the beginning of the specified feature

scoreIndexes

protected static java.util.LinkedHashMap<java.lang.Double,TribbleIndexCreator> scoreIndexes(double densityOfFeatures,
                                                                                            java.util.Map<IndexFactory.IndexType,TribbleIndexCreator> indexes,
                                                                                            int longestFeature,
                                                                                            IndexFactory.IndexBalanceApproach iba)

score the available indexes for the specified density and feature lengths The scoring method is trying to determine how many features would be returned for a sample one base query; or: (features/seek). For the interval index this is clear: it's the bin size (interval is binned by feature count). for Linear indexes it's the density of features X the number of bins we need to retrieve (which is determined by the bin size X the longest feature).

Parameters:

densityOfFeatures - the density of features (features/base)

indexes - Map from IndexType -> IndexCreator

longestFeature - the longest feature we've found

iba - the index balancing approach

Returns:

the best index available for the target indexes

addProperty

public void addProperty(java.lang.String key,
                        java.lang.String value)

Overrides:

addProperty in class TribbleIndexCreator