Package picard.util

Class AbstractInputParser

java.lang.Object
htsjdk.samtools.util.AbstractIterator<String[]>
picard.util.AbstractInputParser
All Implemented Interfaces:
htsjdk.samtools.util.CloseableIterator<String[]>, Closeable, AutoCloseable, Iterable<String[]>, Iterator<String[]>
Direct Known Subclasses:
BasicInputParser
public abstract class AbstractInputParser extends htsjdk.samtools.util.AbstractIterator<String[]> implements Iterable<String[]>, htsjdk.samtools.util.CloseableIterator<String[]>
Class for parsing text files where each line consists of fields separated by whitespace. Code is abstracted into this class so that we can optimize its performance over time. This class assumes that every line will have the same number of whitespace-separated "words" and that lines that start with "#" are comments and should be ignored. Classes that extend this parser can do so simply by implementing their own constructors and the readNextLine(), close(), and getFileName() methods.

  • Constructor Details

    • AbstractInputParser

      public AbstractInputParser()

  • Method Details

    • close

      public abstract void close()
      Closes this stream and releases any system resources associated with it.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface htsjdk.samtools.util.CloseableIterator<String[]>

    • readNextLine

      protected abstract byte[] readNextLine()
      Returns:
      the next line of text from the underlying stream(s) or null if there is no next line

    • getFileName

      public abstract String getFileName()
      Returns:
      the name(s) of the file(s) being parsed, or null if no name is available

    • iterator

      public Iterator<String[]> iterator()
      Specified by:
      iterator in interface Iterable<String[]>
      Returns:
      an iterator over a set of elements of type String[]

    • advance

      protected String[] advance()
      Specified by:
      advance in class htsjdk.samtools.util.AbstractIterator<String[]>

    • calculateWordCount

      protected void calculateWordCount(byte[] line)
      Calculates the number of delimiter-separated "words" in a line and sets the value of wordCount
      Parameters:
      line - representative line from the file

    • isComment

      protected boolean isComment(byte[] line)
      Determines whether a given line is a comment
      Parameters:
      line - the line to evaluate
      Returns:
      true if the line is a comment (and should be ignored) otherwise false

    • isBlank

      protected boolean isBlank(byte[] line)
      Determines whether a given line is a comment
      Parameters:
      line - the line to evaluate
      Returns:
      true if the line is a comment (and should be ignored) otherwise false

    • isDelimiter

      protected boolean isDelimiter(byte b)
      Determines whether a given character is a delimiter
      Parameters:
      b - the character to evaluate
      Returns:
      true if b is a delimiter; otherwise false

    • getWordCount

      protected int getWordCount()

    • setWordCount

      protected void setWordCount(int wordCount)

    • isTreatGroupedDelimitersAsOne

      protected boolean isTreatGroupedDelimitersAsOne()

    • setTreatGroupedDelimitersAsOne

      protected void setTreatGroupedDelimitersAsOne(boolean treatGroupedDelimitersAsOne)

    • isSkipBlankLines

      protected boolean isSkipBlankLines()

    • setSkipBlankLines

      protected void setSkipBlankLines(boolean skipBlankLines)