IMPACT_S

Class FileFormat

java.lang.Object

IMPACT_S.FileFormat

Direct Known Subclasses:

FileFormatConverter, FileFormatReader

public class FileFormat
extends java.lang.Object

Class for storing basic information about Sequence Files.

Author:

Emanuel Maldonado

See Also:

FileFormatReader, FileFormatConverter

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String[]	CFILE_FORMATS Collection of format names, only for ConTest.
static java.lang.String	CLUSTAL_F CLUSTAL format name
static char	CLUSTAL_TYPE CLUSTAL format type
static java.lang.String	DCSE_F DCSE format name (discontinued).
static int	DESTINATION Output files
static java.lang.String	FASTA_F FASTA format name
static char	FASTA_TYPE FASTA format type
static java.lang.String[]	FILEFORMATS Collection of format names.
static java.lang.String	MASE_F MASE format name
static char	MASE_TYPE MASE format type
protected java.io.File	msafileIn
protected java.io.File	msafileOut
protected static java.lang.String	PCLASSIC_F Phylip Classic format
protected static java.lang.String	PEXTENDED_F Phylip Extended format
static java.lang.String[]	PHYLIP_FTYPES PHYLIP Format types for either Interleaved or Sequential: Classic/Extended
static char	PHYLIP_TYPE PHYLIP format type
static java.lang.String	PHYLIPG_F PHYLIP GENERIC format name
static java.lang.String	PHYLIPI_F PHYLIP INTERLEAVED format name
static java.lang.String	PHYLIPS_F PHYLIP SEQUENTIAL format name
static int	SOURCE Input files

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	FileFormat() FileFormat empty constructor.
protected	FileFormat(java.lang.String filepath, int srcdest) Initialize FileFormat.

Method Summary

Modifier and Type	Method and Description
protected java.io.BufferedReader	getBR() Get file reader.
protected java.io.Writer	getBW() Get file writer.
protected boolean	isWhite(java.lang.String line) Determine if a given line is consists of only white space (space or tab).
protected void	setInputFile(java.lang.String infile) Set input file for reading data.
protected void	setOutputFile(java.lang.String outfile) Set output file for saving data.

Methods inherited from class java.lang.Object

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

Field Detail

SOURCE

public static final int SOURCE

Input files

See Also:

Constant Field Values

DESTINATION

public static final int DESTINATION

Output files

See Also:

Constant Field Values

FASTA_TYPE

public static final char FASTA_TYPE

FASTA format type

See Also:

Constant Field Values

MASE_TYPE

public static final char MASE_TYPE

MASE format type

See Also:

Constant Field Values

PHYLIP_TYPE

public static final char PHYLIP_TYPE

PHYLIP format type

See Also:

Constant Field Values

CLUSTAL_TYPE

public static final char CLUSTAL_TYPE

CLUSTAL format type

See Also:

Constant Field Values

FASTA_F

public static final java.lang.String FASTA_F

FASTA format name

See Also:

Constant Field Values

MASE_F

public static final java.lang.String MASE_F

MASE format name

See Also:

Constant Field Values

PHYLIPG_F

public static final java.lang.String PHYLIPG_F

PHYLIP GENERIC format name

See Also:

Constant Field Values

PHYLIPI_F

public static final java.lang.String PHYLIPI_F

PHYLIP INTERLEAVED format name

See Also:

Constant Field Values

PHYLIPS_F

public static final java.lang.String PHYLIPS_F

PHYLIP SEQUENTIAL format name

See Also:

Constant Field Values

CLUSTAL_F

public static final java.lang.String CLUSTAL_F

CLUSTAL format name

See Also:

Constant Field Values

DCSE_F

public static final java.lang.String DCSE_F

DCSE format name (discontinued). Only for ConTest.

See Also:

Constant Field Values

FILEFORMATS

public static final java.lang.String[] FILEFORMATS

Collection of format names. Expanded version.

CFILE_FORMATS

public static final java.lang.String[] CFILE_FORMATS

Collection of format names, only for ConTest. Shorter version.

PCLASSIC_F

protected static final java.lang.String PCLASSIC_F

Phylip Classic format

See Also:

Constant Field Values

PEXTENDED_F

protected static final java.lang.String PEXTENDED_F

Phylip Extended format

See Also:

Constant Field Values

PHYLIP_FTYPES

public static final java.lang.String[] PHYLIP_FTYPES

PHYLIP Format types for either Interleaved or Sequential: Classic/Extended

msafileIn

protected java.io.File msafileIn

msafileOut

protected java.io.File msafileOut

Constructor Detail

FileFormat

protected FileFormat()

FileFormat empty constructor.

FileFormat

protected FileFormat(java.lang.String filepath,
                     int srcdest)

Initialize FileFormat.

Parameters:

filepath - file absolute path.

srcdest - decide if for input (SOURCE) or output (DESTINATION).

Method Detail

setOutputFile

protected void setOutputFile(java.lang.String outfile)

Set output file for saving data.

Parameters:

outfile - file absolute path.

setInputFile

protected void setInputFile(java.lang.String infile)

Set input file for reading data.

Parameters:

infile - file absolute path.

getBW

protected java.io.Writer getBW()

Get file writer.

Returns:

writer.

getBR

protected java.io.BufferedReader getBR()

Get file reader.

Returns:

buffered reader.

isWhite

protected boolean isWhite(java.lang.String line)

Determine if a given line is consists of only white space (space or tab). If line is empty, returns true;

Parameters:

line - to test (not null).

Returns:

true if all is space; false otherwise.