Package htsjdk.tribble.index

Class AbstractIndex

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.

  • Field Details

    • VERSION

      public static final int VERSION
      See Also:

    • MAGIC_NUMBER

      public static final int MAGIC_NUMBER
      See Also:

    • 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 Details

    • 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 Details

    • 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