IMPACT_S

Class FileFormatConverter

java.lang.Object

IMPACT_S.FileFormat

IMPACT_S.FileFormatConverter

public class FileFormatConverter
extends FileFormat

Implementation of functions to read/write several formats of MSA files. Accepts at most 2500 taxa, and 10000 sites (sequence size).

Author:

Emanuel Maldonado

See Also:

GUIFileFormatConverter, AlignmentEditor, FileFormat, FileFormatReader

Field Summary

Fields inherited from class IMPACT_S.FileFormat

CFILE_FORMATS, CLUSTAL_F, CLUSTAL_TYPE, DCSE_F, DESTINATION, FASTA_F, FASTA_TYPE, FILEFORMATS, MASE_F, MASE_TYPE, msafileIn, msafileOut, PCLASSIC_F, PEXTENDED_F, PHYLIP_FTYPES, PHYLIP_TYPE, PHYLIPG_F, PHYLIPI_F, PHYLIPS_F, SOURCE

Constructor Summary

Constructors

Constructor and Description
FileFormatConverter() Initialize File Converter.
FileFormatConverter(java.io.File fromfl, java.lang.String fromfmt, java.io.File tofl, java.lang.String tofmt) Build file converter with source and destination files.
FileFormatConverter(java.io.File file, java.lang.String format, int io) Build file converter with file and format.

Method Summary

Modifier and Type	Method and Description
boolean	convert_totmp(java.lang.String[] phy_options) Creation of a temporary file, for phyml submission. Temporary file must be of format Phylip (Interleaved or Sequential). If source file, is of any other format convert to either Interleaved or Sequential according to user choice in phyml options.
boolean	convert(java.io.File fromfl, java.lang.String fromfmt, java.io.File tofl, java.lang.String tofmt) Convert from file with format, to file with format.
int	getMaxTaxaNameSize(java.lang.String[] taxa) Get maximum size for given taxa names.
int	getSequenceCount() Get number of sequences, possibly if file loaded.
java.lang.String[][]	getSequences() Get sequences.
int	getSiteCount() Get number of sites, possibly if file loaded.
java.lang.String[]	getTaxaNames() Get taxa names.
boolean	readMSAfile() Read MSA file for instantiated source file and format.
void	setPhylipFormatType(java.lang.String type) Use phylip format type in read/write phylip files.
void	setSequenceCount(int count) Set number of sequences to value of count.
void	setSequences(java.lang.String[][] msa) Set sequences to msa value.
void	setSiteCount(int count) Set number of sites to value of count.
void	setTaxaNames(java.lang.String[] names) Set taxa names to names value.
void	writeMSAFile() Write to instantiated destination MSA file and format.

Methods inherited from class IMPACT_S.FileFormat

getBR, getBW, isWhite, setInputFile, setOutputFile

Methods inherited from class java.lang.Object

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

Constructor Detail

FileFormatConverter

public FileFormatConverter()

Initialize File Converter. No instantiation is performed.

FileFormatConverter

public FileFormatConverter(java.io.File file,
                           java.lang.String format,
                           int io)

Build file converter with file and format.

Parameters:

file - to read or write

format - file format

io - decide if these arguments are for read (input) or write (output) file. Values: SOURCE , DESTINATION.

FileFormatConverter

public FileFormatConverter(java.io.File fromfl,
                           java.lang.String fromfmt,
                           java.io.File tofl,
                           java.lang.String tofmt)

Build file converter with source and destination files.

Parameters:

fromfl - source file.

fromfmt - source file format.

tofl - destination file.

tofmt - destination file format.

Method Detail

convert

public boolean convert(java.io.File fromfl,
                       java.lang.String fromfmt,
                       java.io.File tofl,
                       java.lang.String tofmt)

Convert from file with format, to file with format.

Parameters:

fromfl - source file.

fromfmt - source file format.

tofl - destination file.

tofmt - destination file format.

Returns:

success when value is true; no success otherwise false

convert_totmp

public boolean convert_totmp(java.lang.String[] phy_options)

Creation of a temporary file, for phyml submission.

Temporary file must be of format Phylip (Interleaved or Sequential).

If source file, is of any other format convert to either Interleaved or Sequential according to user choice in phyml options. Else use same format.

Parameters:

phy_options - phyml options, choices made by the user. Used to know phylip type when input format is not phylip.

Returns:

success when value is true; no success otherwise false

getSequenceCount

public int getSequenceCount()

Get number of sequences, possibly if file loaded.

Returns:

number of sequences.

getSiteCount

public int getSiteCount()

Get number of sites, possibly if file loaded.

Returns:

number of sites.

setSiteCount

public void setSiteCount(int count)

Set number of sites to value of count.

Parameters:

count - the number of sites.

setSequenceCount

public void setSequenceCount(int count)

Set number of sequences to value of count.

Parameters:

count - the number of sequences.

getSequences

public java.lang.String[][] getSequences()

Get sequences.

Returns:

sequences.

getTaxaNames

public java.lang.String[] getTaxaNames()

Get taxa names.

Returns:

taxaNames.

setSequences

public void setSequences(java.lang.String[][] msa)

Set sequences to msa value.

Parameters:

msa - sequences pass to file converter.

setTaxaNames

public void setTaxaNames(java.lang.String[] names)

Set taxa names to names value.

Parameters:

names - of taxa to pass to file converter.

setPhylipFormatType

public void setPhylipFormatType(java.lang.String type)

Use phylip format type in read/write phylip files.

1. Classic - Taxa names limited to 10 characters maximum size.
2. Extended - Taxa names have variable size.

Parameters:

type - values are Classic / Extended.

See Also:

FileFormat.PCLASSIC_F, FileFormat.PEXTENDED_F

readMSAfile

public boolean readMSAfile()

Read MSA file for instantiated source file and format.

Returns:

true when success; false, otherwise.

writeMSAFile

public void writeMSAFile()

Write to instantiated destination MSA file and format.

getMaxTaxaNameSize

public int getMaxTaxaNameSize(java.lang.String[] taxa)

Get maximum size for given taxa names.

Parameters:

taxa - array of taxa names.

Returns:

maximum size among given taxa names.