public final class ClustalAlignmentUtil
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static char |
gapchar
Dash char to be used as gap char in the alignments
|
private static java.util.logging.Logger |
log |
private static int |
maxNameLength |
private static int |
minNameHolderLength |
private static int |
oneLineAlignmentLength |
private static java.lang.String |
spacer |
Constructor and Description |
---|
ClustalAlignmentUtil() |
Modifier and Type | Method and Description |
---|---|
static boolean |
isValidClustalFile(java.io.InputStream input)
Please note this method closes the input stream provided as a parameter
|
static Alignment |
readClustalFile(java.io.File file) |
static Alignment |
readClustalFile(java.io.InputStream instream)
Read Clustal formatted alignment.
|
static void |
writeClustalAlignment(java.io.Writer out,
Alignment alignment)
Write Clustal formatted alignment Limitations: does not record the
consensus.
|
private static final java.util.logging.Logger log
public static final char gapchar
private static final java.lang.String spacer
private static final int maxNameLength
private static final int minNameHolderLength
private static final int oneLineAlignmentLength
public static Alignment readClustalFile(java.io.InputStream instream) throws java.io.IOException, UnknownFileFormatException
{@link
- IOException}{@link
- UnknownFileFormatException}java.io.IOException
UnknownFileFormatException
public static boolean isValidClustalFile(java.io.InputStream input)
input
- public static void writeClustalAlignment(java.io.Writer out, Alignment alignment) throws java.io.IOException
out
- alignment
- java.io.IOException
public static Alignment readClustalFile(java.io.File file) throws UnknownFileFormatException, java.io.IOException
UnknownFileFormatException
java.io.IOException