X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FUnknownFileFormatException.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FUnknownFileFormatException.html;h=cd3ae7ba6378e2f74f3b9d1b2692777caca1d0aa;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html new file mode 100644 index 0000000..cd3ae7b --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html @@ -0,0 +1,305 @@ + + + + + + +Uses of Class compbio.data.sequence.UnknownFileFormatException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.UnknownFileFormatException

+
+ + + + + + + + + + + + + +
+Packages that use UnknownFileFormatException
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
compbio.runnerUtilities commonly used by all runners. 
+  +

+ + + + + +
+Uses of UnknownFileFormatException in compbio.data.sequence
+  +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Methods in compbio.data.sequence that throw UnknownFileFormatException
+static List<FastaSequence>SequenceUtil.openInputStream(String inFilePath) + +
+          Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
+static AlignmentClustalAlignmentUtil.readClustalFile(File file) + +
+           
+static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) + +
+          Read Clustal formatted alignment.
+static HashMap<String,Set<Score>>SequenceUtil.readDisembl(InputStream input) + +
+          > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
+static HashMap<String,Set<Score>>SequenceUtil.readGlobPlot(InputStream input) + +
+          > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
+static Map<String,Score>SequenceUtil.readIUPred(File result) + +
+          Read IUPred output
+static Map<String,Score>SequenceUtil.readJRonn(File result) + +
+           
+static Map<String,Score>SequenceUtil.readJRonn(InputStream inStream) + +
+          Reader for JRonn horizontal file format
+  +

+ + + + + +
+Uses of UnknownFileFormatException in compbio.runner
+  +

+ + + + + + + + + + + + + +
Methods in compbio.runner that throw UnknownFileFormatException
+static AlignmentUtil.readClustalFile(String workDirectory, + String clustFile) + +
+           
+static Map<String,Score>Util.readJronnFile(String workDirectory, + String clustFile) + +
+           
+  +

+

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