IMPACT_S

Class FileFormatReader

java.lang.Object

IMPACT_S.FileFormat

IMPACT_S.FileFormatReader

public class FileFormatReader
extends FileFormat

Class to handle the reading/writing of non-aligned sequences files.

Author:

Emanuel Maldonado

See Also:

FileFormat, FileFormatConverter

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
FileFormatReader(java.lang.String filepath, java.lang.String format, int io) FileFormatReader constructor method.

Method Summary

Modifier and Type	Method and Description
java.lang.String	getSequence(int index) Get specific sequence by given index.
java.lang.String	getSequenceTitle(int index) Get specific sequence title, given index location.
java.lang.String[]	getTaxaNames() Get all sequences titles or names.
boolean	readSeqsFormatFile() Read MSA file for instantiated source file and format.
void	setEnableOutput(java.lang.String outfile, java.lang.String outformat) Enable saving sequences to file. This is useful when data read previously from file should not be lost and thus still used for saving.
void	setSequence(java.lang.String sequence, java.lang.String seqname) Set a single sequence with its name.
boolean	setSequences(java.lang.String[][] sequences, java.lang.String[] seqnames) Set a set of sequences with their names in matching order.
boolean	setSequences(java.lang.String[] sequences, java.lang.String[] seqnames) Set a set of sequences with their names in matching order.
void	writeSeqsToFile() Write all sequences to file using chosen format.
void	writeSeqToFile(int index) Write specific sequence to file using chosen 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

FileFormatReader

public FileFormatReader(java.lang.String filepath,
                        java.lang.String format,
                        int io)

FileFormatReader constructor method. Initialize with given input or output file path and corresponding format.

Parameters:

filepath - input/output file path.

format - corresponding format.

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

Method Detail

getSequence

public java.lang.String getSequence(int index)

Get specific sequence by given index.

Parameters:

index - of specific sequence.

Returns:

sequence selected by given index.

getSequenceTitle

public java.lang.String getSequenceTitle(int index)

Get specific sequence title, given index location.

Parameters:

index - location of sequence title.

Returns:

name for given index.

getTaxaNames

public java.lang.String[] getTaxaNames()

Get all sequences titles or names.

Returns:

names.

setSequence

public void setSequence(java.lang.String sequence,
                        java.lang.String seqname)

Set a single sequence with its name. This is always placed as index 0, so values will be overwritten if called again.

Parameters:

sequence - any sequence regardless of its format.

seqname - sequence corresponding title.

See Also:

setSequences(java.lang.String[], java.lang.String[]), setSequences(java.lang.String[][], java.lang.String[])

setSequences

public boolean setSequences(java.lang.String[][] sequences,
                            java.lang.String[] seqnames)

Set a set of sequences with their names in matching order. Both arguments must have the same number of elements: number of sequences must be same as the number of names.

Parameters:

sequences - any set of sequences regardless of its type.

seqnames - sequences corresponding titles.

Returns:

false if number of elements differs (in which case nothing is done); true, otherwise.

See Also:

setSequences(java.lang.String[], java.lang.String[]), setSequence(java.lang.String, java.lang.String)

setSequences

public boolean setSequences(java.lang.String[] sequences,
                            java.lang.String[] seqnames)

Set a set of sequences with their names in matching order. Both arguments must have the same number of elements: number of sequences must be same as the number of names.

Parameters:

sequences - any set of sequences regardless of its type.

seqnames - sequences corresponding titles.

Returns:

false if number of elements differs (in which case nothing is done); true, otherwise.

See Also:

setSequences(java.lang.String[][], java.lang.String[]), setSequence(java.lang.String, java.lang.String)

setEnableOutput

public void setEnableOutput(java.lang.String outfile,
                            java.lang.String outformat)

Enable saving sequences to file.
This is useful when data read previously from file should not be lost and thus still used for saving.

Parameters:

outfile - output file absolute path.

outformat - output file format.

readSeqsFormatFile

public boolean readSeqsFormatFile()

Read MSA file for instantiated source file and format.

Returns:

true when success; false, otherwise.

writeSeqsToFile

public void writeSeqsToFile()

Write all sequences to file using chosen format.

writeSeqToFile

public void writeSeqToFile(int index)

Write specific sequence to file using chosen format.

Parameters:

index - index of selected sequence.