X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Findex-files%2Findex-2.html;h=e4c2e1d898bd63636e0a2757374c0cefc2ca7f05;hb=ab3a154bf48a5a143b05eab120f53396fc53bda3;hp=a9214d257629722116a1d9a1baf83b0b2df133ad;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git
diff --git a/website/dm_javadoc/index-files/index-2.html b/website/dm_javadoc/index-files/index-2.html
index a9214d2..e4c2e1d 100644
--- a/website/dm_javadoc/index-files/index-2.html
+++ b/website/dm_javadoc/index-files/index-2.html
@@ -2,12 +2,12 @@
-
+
C-Index
-
+
@@ -82,25 +82,94 @@ function windowTitle()
C
-- ChunkHolder - Class in compbio.metadata
- Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.
- ChunkHolder(String, long) -
+
- CancelJob - Class in compbio.data.msa.jaxws
-
- CancelJob() -
+Constructor for class compbio.data.msa.jaxws.CancelJob
+
-
+
- cancelJob(String) -
+Method in interface compbio.data.msa.JManagement
+
- Stop running the job
jobId
but leave its output untouched
+ - CancelJobResponse - Class in compbio.data.msa.jaxws
-
- CancelJobResponse() -
+Constructor for class compbio.data.msa.jaxws.CancelJobResponse
+
-
+
- Category - Class in compbio.data.msa
- Class that splits
Services
to categories. - CATEGORY_ALIGNMENT -
+Static variable in class compbio.data.msa.Category
+
- All of the Category names
+
- CATEGORY_CONSERVATION -
+Static variable in class compbio.data.msa.Category
+
-
+
- CATEGORY_DISORDER -
+Static variable in class compbio.data.msa.Category
+
-
+
- checkService(Services) -
+Method in class compbio.ws.client.WSTester
+
- Test JABA web service
+
- ChunkHolder - Class in compbio.metadata
- Represents a chunk of a string data together with the position in a file for
+ the next read operation.
- ChunkHolder(String, long) -
Constructor for class compbio.metadata.ChunkHolder
-
+
- cleanProteinSequence(String) -
+Static method in class compbio.data.sequence.SequenceUtil
+
- Remove all non AA chars from the sequence
- cleanSequence(String) -
Static method in class compbio.data.sequence.SequenceUtil
- Removes all whitespace chars in the sequence string
+
- close() -
+Method in class compbio.data.sequence.FastaReader
+
- Call this method to close the connection to the input file if you want to
+ free up the resources.
+
- closeSilently(Logger, Closeable) -
+Static method in class compbio.data.sequence.SequenceUtil
+
- Closes the Closable and logs the exception if any
+
- CLUSTAL_INFO -
+Static variable in enum compbio.ws.client.Services
+
-
+
- CLUSTAL_OMEGA_INFO -
+Static variable in enum compbio.ws.client.Services
+
-
- ClustalAlignmentUtil - Class in compbio.data.sequence
- Tools to read and write clustal formated files
- ClustalAlignmentUtil() -
Constructor for class compbio.data.sequence.ClustalAlignmentUtil
-
-
- compbio.ws.client - package compbio.ws.client
-
- connect(String, Jws2Client.Services) -
+
- compareTo(Range) -
+Method in class compbio.data.sequence.Range
+
-
+
- compareTo(Score) -
+Method in class compbio.data.sequence.Score
+
-
+
- compbio.data.msa.jaxws - package compbio.data.msa.jaxws
-
- connect() -
+Static method in class compbio.ws.client.AAConClient
+
- Connects to a AACon web service by the host and the service name
+
- connect(String, Services) -
Static method in class compbio.ws.client.Jws2Client
-
- Connects to a web service by the host and the service name
-
- copyAndValidateRConfig(RunnerConfig<?>) -
+
- Connects to a web service by the host and the service name web service
+ type
+
- connectToRegistry(String) -
+Static method in class compbio.ws.client.Jws2Client
+
- Get a connection of JABAWS registry
+
- ConservationMethod - Enum in compbio.data.sequence
- Enumeration listing of all the supported methods.
- copyAndValidateRConfig(RunnerConfig<?>) -
Method in class compbio.metadata.RunnerConfig
-
- countMatchesInSequence(String, String) -
Static method in class compbio.data.sequence.FastaSequence
-
+
- CustomAlign - Class in compbio.data.msa.jaxws
-
- CustomAlign() -
+Constructor for class compbio.data.msa.jaxws.CustomAlign
+
-
+
- customAlign(List<FastaSequence>, List<Option<T>>) -
+Method in interface compbio.data.msa.MsaWS
+
- Align a list of sequences with options.
+
- CustomAlignResponse - Class in compbio.data.msa.jaxws
-
- CustomAlignResponse() -
+Constructor for class compbio.data.msa.jaxws.CustomAlignResponse
+
-
+
- CustomAnalize - Class in compbio.data.msa.jaxws
-
- CustomAnalize() -
+Constructor for class compbio.data.msa.jaxws.CustomAnalize
+
-
+
- customAnalize(List<FastaSequence>, List<Option<T>>) -
+Method in interface compbio.data.msa.SequenceAnnotation
+
- Analyse the sequences according to custom settings defined in options
+ list.
+
- CustomAnalizeResponse - Class in compbio.data.msa.jaxws
-
- CustomAnalizeResponse() -
+Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse
+
-