picard.util

Class DelimitedTextFileWithHeaderIterator

java.lang.Object

picard.util.DelimitedTextFileWithHeaderIterator

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<DelimitedTextFileWithHeaderIterator.Row>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<DelimitedTextFileWithHeaderIterator.Row>

public class DelimitedTextFileWithHeaderIterator
extends java.lang.Object
implements htsjdk.samtools.util.CloseableIterator<DelimitedTextFileWithHeaderIterator.Row>

Iterate through a delimited text file in which columns are found by looking at a header line rather than by position. TODO: This effectively replaces TabbedTextFileWithHeaderParser although the latter hasn't been modified to use this code instead.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	DelimitedTextFileWithHeaderIterator.Row

Constructor Summary

Constructors

Constructor and Description
DelimitedTextFileWithHeaderIterator(BasicInputParser parser)

Method Summary

Modifier and Type	Method and Description
void	close()
java.util.Set<java.lang.String>	columnLabels()
java.util.Set<java.lang.String>	getColumnNames()
int	getCurrentLineNumber()
boolean	hasColumn(java.lang.String columnLabel)
boolean	hasNext()
DelimitedTextFileWithHeaderIterator.Row	next()
void	remove()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

DelimitedTextFileWithHeaderIterator

public DelimitedTextFileWithHeaderIterator(BasicInputParser parser)

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.

getCurrentLineNumber

public int getCurrentLineNumber()

getColumnNames

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

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<DelimitedTextFileWithHeaderIterator.Row>

next

public DelimitedTextFileWithHeaderIterator.Row next()

Specified by:

next in interface java.util.Iterator<DelimitedTextFileWithHeaderIterator.Row>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<DelimitedTextFileWithHeaderIterator.Row>

close

public void close()

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<DelimitedTextFileWithHeaderIterator.Row>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable