BasicInputParser (picard 2.18.2 API)

java.lang.Object
- htsjdk.samtools.util.AbstractIterator<String[]>
- - picard.util.AbstractInputParser
  - - picard.util.BasicInputParser

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<String[]>, Closeable, AutoCloseable, Iterable<String[]>, Iterator<String[]>

Direct Known Subclasses:

CsvInputParser, TabbedInputParser
```
public class BasicInputParser
extends AbstractInputParser
```
TextFileParser which reads a single text file.

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

Constructor Summary

Constructors
Constructor	Description
`BasicInputParser(boolean treatGroupedDelimitersAsOne, int wordCount, File... files)`	Constructor.
`BasicInputParser(boolean treatGroupedDelimitersAsOne, int wordCount, InputStream... inputStreams)`
`BasicInputParser(boolean treatGroupedDelimitersAsOne, File... files)`	Constructor.
`BasicInputParser(boolean treatGroupedDelimitersAsOne, InputStream... inputStreams)`	Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`advanceFile()`
`void`	`close()`	Closes the underlying stream
`String`	`getCurrentLine()`	Provides access to the current (just parsed) line in pre-parsed format.
`int`	`getCurrentLineNumber()`	NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
`String`	`getFileName()`	Gets the name of the file being parsed
`protected byte[]`	`readNextLine()`	Workhorse method that reads the next line from the underlying reader

Methods inherited from class picard.util.AbstractInputParser
advance, calculateWordCount, getWordCount, isBlank, isComment, isDelimiter, isSkipBlankLines, isTreatGroupedDelimitersAsOne, iterator, setSkipBlankLines, setTreatGroupedDelimitersAsOne, setWordCount

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
  - BasicInputParser
```
public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        InputStream... inputStreams)
```
    Constructor. Opens up a buffered reader and reads the first line.
    
    Parameters:
    
    inputStreams - the file(s) to parse, in order
  - BasicInputParser
```
public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        int wordCount,
                        InputStream... inputStreams)
```
  - BasicInputParser
```
public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        File... files)
```
    Constructor. Opens up a buffered reader and reads the first line.
    
    Parameters:
    
    files - the file(s) to parse, in order
  - BasicInputParser
```
public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        int wordCount,
                        File... files)
```
    Constructor. In addition to opening and priming the files, it sets the number of whitespace-separated "words" per line.
    
    Parameters:
    
    files - the file(s) to parse
    
    wordCount - number of whitespace-separated "words" per line
- Method Detail
  - readNextLine
```
protected byte[] readNextLine()
```
    Workhorse method that reads the next line from the underlying reader
    
    Specified by:
    
    readNextLine in class AbstractInputParser
    
    Returns:
    
    String or null if there is no next line
  - advanceFile
```
protected void advanceFile()
```
  - close
```
public void close()
```
    Closes the underlying stream
    
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface htsjdk.samtools.util.CloseableIterator<String[]>
    
    Specified by:
    
    close in class AbstractInputParser
  - getFileName
```
public String getFileName()
```
    Gets the name of the file being parsed
    
    Specified by:
    
    getFileName in class AbstractInputParser
    
    Returns:
    
    the name of the file being parsed
  - getCurrentLine
```
public String getCurrentLine()
```
    Provides access to the current (just parsed) line in pre-parsed format. NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
  - getCurrentLineNumber
```
public int getCurrentLineNumber()
```
    NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().

Class BasicInputParser

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractIterator

Constructor Summary

Method Summary

Methods inherited from class picard.util.AbstractInputParser

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

BasicInputParser

BasicInputParser

BasicInputParser

BasicInputParser

Method Detail

readNextLine

advanceFile

close

getFileName

getCurrentLine

getCurrentLineNumber