umcg.genetica.io.text

Class TextFile

java.lang.Object

umcg.genetica.io.text.TextFile

All Implemented Interfaces:

Iterable<String>

Direct Known Subclasses:

PeakFile, QTLTextFile, WigFile

public class TextFile
extends Object
implements Iterable<String>

Author:

harmjan

Field Summary

Fields

Modifier and Type	Field and Description
static Pattern	colon
static Pattern	comma
static int	DEFAULT_BUFFER_SIZE
protected static String	ENCODING
protected File	file
protected BufferedReader	in
protected BufferedWriter	out
static boolean	R
static Pattern	semicolon
static Pattern	space
static Pattern	tab
static boolean	W
protected boolean	writeable

Constructor Summary

Constructors

Constructor and Description
TextFile(File file, boolean mode)
TextFile(File file, boolean mode, int buffersize)
TextFile(String file, boolean mode)
TextFile(String file, boolean mode, int buffersize)

Method Summary

Modifier and Type	Method and Description
void	append(char c)
void	append(CharSequence csq)
void	close()
int	countCols(Pattern p)
int	countLines()
void	flush()
String	getFileName()
Iterator<String>	iterator()
void	open()
String[]	readAsArray()
String[]	readAsArray(int col, Pattern p)
ArrayList<String>	readAsArrayList()
ArrayList<String>	readAsArrayList(int col, Pattern p)
Map<String,String>	readAsHashMap(int col1, int col2)
Map<String,String>	readAsHashMap(int col1, int[] col2, String seperator)
Map<String,String>	readAsHashMap(int col1, int col2, Pattern p)
HashSet<Pair<String,String>>	readAsPairs(int A, int B)
Set<String>	readAsSet(int col, Pattern p)
HashSet<Triple<String,String,String>>	readAsTriple(int A, int B, int C)
String	readLine()
String[]	readLineElems(Pattern p) This method is a wrapper for readLineElemsReturnReference: this method returns default substrings delimited by Pattern p.
Iterable<String[]>	readLineElemsIterable(Pattern p)
String[]	readLineElemsReturnObjects(Pattern p) This method returns a new object for each of the splitted elements, instead of the default action, in which each substring is backed by the original full-length String.
String[]	readLineElemsReturnReference(Pattern p) This method returns default substrings delimited by Pattern p.
void	write(String line)
void	writeList(List l)
void	writeln()
void	writeln(CharSequence csq)
void	writeln(String line)
void	writelnDelimited(Object[] vals, Pattern p)
void	writelnsynced(String str)
void	writelnTabDelimited(Object[] vals)

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

Field Detail

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

See Also:

Constant Field Values

tab

public static final Pattern tab

space

public static final Pattern space

colon

public static final Pattern colon

semicolon

public static final Pattern semicolon

comma

public static final Pattern comma

in

protected BufferedReader in

file

protected File file

W

public static final boolean W

See Also:

Constant Field Values

R

public static final boolean R

See Also:

Constant Field Values

out

protected BufferedWriter out

writeable

protected boolean writeable

ENCODING

protected static final String ENCODING

See Also:

Constant Field Values

Constructor Detail

TextFile

public TextFile(String file,
                boolean mode)
         throws IOException

Throws:

IOException

TextFile

public TextFile(File file,
                boolean mode)
         throws IOException

Throws:

IOException

TextFile

public TextFile(File file,
                boolean mode,
                int buffersize)
         throws IOException

Throws:

IOException

TextFile

public TextFile(String file,
                boolean mode,
                int buffersize)
         throws IOException

Throws:

IOException

Method Detail

open

public final void open()
                throws IOException

Throws:

IOException

readLine

public String readLine()
                throws IOException

Throws:

IOException

write

public void write(String line)
           throws IOException

Throws:

IOException

close

public void close()
           throws IOException

Throws:

IOException

readLineElems

public String[] readLineElems(Pattern p)
                       throws IOException

This method is a wrapper for readLineElemsReturnReference: this method returns default substrings delimited by Pattern p.

Parameters:

p - The Pattern object to split with (e.g. TextFile.tab or Strings.comma)

Returns:

New String objects for each substring delimited by Pattern p

Throws:

IOException

readLineElemsIterable

public Iterable<String[]> readLineElemsIterable(Pattern p)

readLineElemsReturnReference

public String[] readLineElemsReturnReference(Pattern p)
                                      throws IOException

This method returns default substrings delimited by Pattern p. As such, this method may be more memory-efficient in some situations (for example when only a multiple columns should be loaded and stored in memory).

Parameters:

p - The Pattern object to split with (e.g. TextFile.tab or Strings.comma)

Returns:

New String objects for each substring delimited by Pattern p

Throws:

IOException

readLineElemsReturnObjects

public String[] readLineElemsReturnObjects(Pattern p)
                                    throws IOException

This method returns a new object for each of the splitted elements, instead of the default action, in which each substring is backed by the original full-length String. As such, this method may be more memory-efficient in some situations (for example when only a single column should be loaded and stored in memory).

Parameters:

p - The Pattern object to split with (e.g. TextFile.tab or Strings.comma)

Returns:

New String objects for each substring delimited by Pattern p

Throws:

IOException

countLines

public int countLines()
               throws IOException

Throws:

IOException

countCols

public int countCols(Pattern p)
              throws IOException

Throws:

IOException

readAsArray

public String[] readAsArray()
                     throws IOException

Throws:

IOException

readAsArray

public String[] readAsArray(int col,
                            Pattern p)
                     throws IOException

Throws:

IOException

readAsArrayList

public ArrayList<String> readAsArrayList()
                                  throws IOException

Throws:

IOException

readAsArrayList

public ArrayList<String> readAsArrayList(int col,
                                         Pattern p)
                                  throws IOException

Throws:

IOException

writeln

public void writeln(CharSequence csq)
             throws IOException

Throws:

IOException

writeln

public void writeln(String line)
             throws IOException

Throws:

IOException

writeln

public void writeln()
             throws IOException

Throws:

IOException

append

public void append(char c)
            throws IOException

Throws:

IOException

append

public void append(CharSequence csq)
            throws IOException

Throws:

IOException

writelnsynced

public void writelnsynced(String str)
                   throws IOException

Throws:

IOException

writelnTabDelimited

public void writelnTabDelimited(Object[] vals)
                         throws IOException

Throws:

IOException

writelnDelimited

public void writelnDelimited(Object[] vals,
                             Pattern p)
                      throws IOException

Throws:

IOException

readAsHashMap

public Map<String,String> readAsHashMap(int col1,
                                        int col2)
                                 throws IOException

Throws:

IOException

readAsHashMap

public Map<String,String> readAsHashMap(int col1,
                                        int[] col2,
                                        String seperator)
                                 throws IOException

Throws:

IOException

readAsHashMap

public Map<String,String> readAsHashMap(int col1,
                                        int col2,
                                        Pattern p)
                                 throws IOException

Throws:

IOException

readAsSet

public Set<String> readAsSet(int col,
                             Pattern p)
                      throws IOException

Throws:

IOException

writeList

public void writeList(List l)
               throws IOException

Throws:

IOException

getFileName

public String getFileName()

readAsPairs

public HashSet<Pair<String,String>> readAsPairs(int A,
                                                int B)
                                         throws IOException

Throws:

IOException

flush

public void flush()
           throws IOException

Throws:

IOException

readAsTriple

public HashSet<Triple<String,String,String>> readAsTriple(int A,
                                                          int B,
                                                          int C)
                                                   throws IOException

Throws:

IOException

iterator

public Iterator<String> iterator()

Specified by:

iterator in interface Iterable<String>