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- -compbio.data.sequence -
-Class ClustalAlignmentUtil

-
-java.lang.Object
-  extended by compbio.data.sequence.ClustalAlignmentUtil
-
-
-
-
public final class ClustalAlignmentUtil
extends Object
- - -

-Tools to read and write clustal formated files -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
Petr Troshin based on jimp class
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-Field Summary
-static chargapchar - -
-          Dash char to be used as gap char in the alignments
-  - - - - - - - - - - -
-Constructor Summary
ClustalAlignmentUtil() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static booleanisValidClustalFile(InputStream input) - -
-          Please note this method closes the input stream provided as a parameter
-static AlignmentreadClustalFile(File file) - -
-           
-static AlignmentreadClustalFile(InputStream instream) - -
-          Read Clustal formatted alignment.
-static voidwriteClustalAlignment(Writer out, - Alignment alignment) - -
-          Write Clustal formatted alignment Limitations: does not record the - consensus.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Field Detail
- -

-gapchar

-
-public static final char gapchar
-
-
Dash char to be used as gap char in the alignments -

-

-
See Also:
Constant Field Values
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-Constructor Detail
- -

-ClustalAlignmentUtil

-
-public ClustalAlignmentUtil()
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-Method Detail
- -

-readClustalFile

-
-public static Alignment readClustalFile(InputStream instream)
-                                 throws IOException,
-                                        UnknownFileFormatException
-
-
Read Clustal formatted alignment. Limitations: Does not read consensus - - Sequence names as well as the sequences are not guaranteed to be unique! -

-

- -
Throws: -
{@link - IOException} -
{@link - UnknownFileFormatException} -
IOException -
UnknownFileFormatException
-
-
-
- -

-isValidClustalFile

-
-public static boolean isValidClustalFile(InputStream input)
-
-
Please note this method closes the input stream provided as a parameter -

-

-
Parameters:
input - -
Returns:
true if the file is recognised as Clustal formatted alignment, - false otherwise
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-
-
- -

-writeClustalAlignment

-
-public static void writeClustalAlignment(Writer out,
-                                         Alignment alignment)
-                                  throws IOException
-
-
Write Clustal formatted alignment Limitations: does not record the - consensus. Potential bug - records 60 chars length alignment where - Clustal would have recorded 50 chars. -

-

-
Parameters:
out -
alignment - -
Throws: -
IOException
-
-
-
- -

-readClustalFile

-
-public static Alignment readClustalFile(File file)
-                                 throws UnknownFileFormatException,
-                                        IOException
-
-
- -
Throws: -
UnknownFileFormatException -
IOException
-
-
- -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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