picard.util

Class TabbedTextFileWithHeaderParser

java.lang.Object

picard.util.TabbedTextFileWithHeaderParser

All Implemented Interfaces:

java.lang.Iterable<TabbedTextFileWithHeaderParser.Row>

public class TabbedTextFileWithHeaderParser
extends java.lang.Object
implements java.lang.Iterable<TabbedTextFileWithHeaderParser.Row>

Parse a tabbed text file in which columns are found by looking at a header line rather than by position.

Author:

alecw@broadinstitute.org

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	TabbedTextFileWithHeaderParser.Row

Constructor Summary

Constructors

Constructor and Description
TabbedTextFileWithHeaderParser(java.io.File file)
TabbedTextFileWithHeaderParser(java.io.File file, java.lang.String[] columnHeaders)
TabbedTextFileWithHeaderParser(TabbedInputParser parser)

Method Summary

Modifier and Type	Method and Description
void	close() Release all resources associated with the parser.
java.util.Set<java.lang.String>	columnLabels()
java.util.List<java.lang.String>	columnLabelsList()
java.util.Set<java.lang.String>	getColumnNames()
int	getCurrentLineNumber()
boolean	hasColumn(java.lang.String columnLabel)
htsjdk.samtools.util.CloseableIterator<TabbedTextFileWithHeaderParser.Row>	iterator() Creates the iterator object.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

TabbedTextFileWithHeaderParser

public TabbedTextFileWithHeaderParser(TabbedInputParser parser)

TabbedTextFileWithHeaderParser

public TabbedTextFileWithHeaderParser(java.io.File file)

TabbedTextFileWithHeaderParser

public TabbedTextFileWithHeaderParser(java.io.File file,
                                      java.lang.String[] columnHeaders)

Method Detail

hasColumn

public boolean hasColumn(java.lang.String columnLabel)

Parameters:

columnLabel -

Returns:

True if the given column label appears in the header.

columnLabels

public java.util.Set<java.lang.String> columnLabels()

Returns:

The set of column labels for this file in no particular order.

columnLabelsList

public java.util.List<java.lang.String> columnLabelsList()

Returns:

The column labels for this file as a List, in no particular order.

iterator

public htsjdk.samtools.util.CloseableIterator<TabbedTextFileWithHeaderParser.Row> iterator()

Creates the iterator object. It is illegal to have more than one iterator extant on the same parser object.

Specified by:

iterator in interface java.lang.Iterable<TabbedTextFileWithHeaderParser.Row>

close

public void close()

Release all resources associated with the parser. Iteration will not work after this has been called.

getCurrentLineNumber

public int getCurrentLineNumber()

getColumnNames

public java.util.Set<java.lang.String> getColumnNames()