public class FileFormat
extends java.lang.Object
FileFormatReader,
FileFormatConverter| 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
|
| Modifier | Constructor and Description |
|---|---|
protected |
FileFormat()
FileFormat empty constructor.
|
protected |
FileFormat(java.lang.String filepath,
int srcdest)
Initialize FileFormat.
|
| 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.
|
public static final int SOURCE
public static final int DESTINATION
public static final char FASTA_TYPE
public static final char MASE_TYPE
public static final char PHYLIP_TYPE
public static final char CLUSTAL_TYPE
public static final java.lang.String FASTA_F
public static final java.lang.String MASE_F
public static final java.lang.String PHYLIPG_F
public static final java.lang.String PHYLIPI_F
public static final java.lang.String PHYLIPS_F
public static final java.lang.String CLUSTAL_F
public static final java.lang.String DCSE_F
public static final java.lang.String[] FILEFORMATS
public static final java.lang.String[] CFILE_FORMATS
protected static final java.lang.String PCLASSIC_F
protected static final java.lang.String PEXTENDED_F
public static final java.lang.String[] PHYLIP_FTYPES
protected java.io.File msafileIn
protected java.io.File msafileOut
protected FileFormat()
protected FileFormat(java.lang.String filepath,
int srcdest)
filepath - file absolute path.srcdest - decide if for input (SOURCE) or output (DESTINATION).protected void setOutputFile(java.lang.String outfile)
outfile - file absolute path.protected void setInputFile(java.lang.String infile)
infile - file absolute path.protected java.io.Writer getBW()
protected java.io.BufferedReader getBR()
protected boolean isWhite(java.lang.String line)
line - to test (not null).