X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2FClustalAlignmentUtil.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2FClustalAlignmentUtil.html;h=879d7672e7a0df041fdb39e404ad4682ecb3a080;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..879d767 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,387 @@ + + + + + + +ClustalAlignmentUtil + + + + + + + + + + + + +
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+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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
+
+
+ +

+ + + + + + + + + + + +
+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
+  +

+ + + + + + + + +
+Field Detail
+ +

+gapchar

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

+

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

+ClustalAlignmentUtil

+
+public ClustalAlignmentUtil()
+
+
+ + + + + + + + +
+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
+
+
+
+ +

+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
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
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+ + + +
+ + +