AbstractInputParser (picard 2.18.2 API)

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.

Field Summary
- Fields inherited from class htsjdk.samtools.util.AbstractIterator
  next

Constructor Summary

Constructors
Constructor Description

AbstractInputParser()

Constructors
Constructor	Description
`AbstractInputParser()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected String[]`	`advance()`
`protected void`	`calculateWordCount(byte[] line)`	Calculates the number of delimiter-separated "words" in a line and sets the value of `wordCount`
`abstract void`	`close()`	Closes this stream and releases any system resources associated with it.
`abstract String`	`getFileName()`
`protected int`	`getWordCount()`
`protected boolean`	`isBlank(byte[] line)`	Determines whether a given line is a comment
`protected boolean`	`isComment(byte[] line)`	Determines whether a given line is a comment
`protected boolean`	`isDelimiter(byte b)`	Determines whether a given character is a delimiter
`protected boolean`	`isSkipBlankLines()`
`protected boolean`	`isTreatGroupedDelimitersAsOne()`
`Iterator<String[]>`	`iterator()`
`protected abstract byte[]`	`readNextLine()`
`protected void`	`setSkipBlankLines(boolean skipBlankLines)`
`protected void`	`setTreatGroupedDelimitersAsOne(boolean treatGroupedDelimitersAsOne)`
`protected void`	`setWordCount(int wordCount)`

Methods inherited from class htsjdk.samtools.util.AbstractIterator
hasNext, isIterating, next, peek, remove

Methods inherited from interface htsjdk.samtools.util.CloseableIterator
stream, toList

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface java.util.Iterator
forEachRemaining, hasNext, next, remove

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

- Constructor Detail
  - AbstractInputParser
```
public AbstractInputParser()
```
- Method Detail
  - 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)
```

Class AbstractInputParser

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractIterator

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.util.AbstractIterator

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.lang.Iterable

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Constructor Detail

AbstractInputParser

Method Detail

close

readNextLine

getFileName

iterator

advance

calculateWordCount

isComment

isBlank

isDelimiter

getWordCount

setWordCount

isTreatGroupedDelimitersAsOne

setTreatGroupedDelimitersAsOne

isSkipBlankLines

setSkipBlankLines