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Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

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Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added to ScoreManager.

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Reverted some testing changes in TestRNAalifoldWS so that it will run successfully.

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    ./client/TestRNAalifoldWS.java
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RNAStruct replaced by RNAStructScoreManager. Why does webservice getAnnotation method still return a ScoreManager Not an RNAStructScoreManager?!?

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    ./client/TestRNAalifoldWS.java
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Webservice working with ScoreManager

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Alifold results are now parsed and stored in a ScoreManager object

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Webservice which implements FoldWS and returns String. Parameters.xml file updated in line with the RunnerConfig schema.

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Webservice works! but only supports some parameters. Replacing RNAstuct with String.

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    ./client/TestRNAalifoldWS.java
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change code style

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JWS-50 patch AAConWS test for refactoring of calculation parameters to a series of options

JWS-61 test demonstrating compound option value problem with JABAWS client

JWS-47 patch test to default local JABAWS server and source tidy

JWS-47 new customAnalize test for IUPredWS - with several unaligned sequences of different lengths.

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    ./client/TestIUPredWS.java
File puller tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4832 e3abac25-378b-4346-85de-24260fe3988d

adding one more window web service into the test case

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4524 e3abac25-378b-4346-85de-24260fe3988d

Fixes to testcase, take into account the new WS

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4487 e3abac25-378b-4346-85de-24260fe3988d

Expose a few methods of Client and WSTester as API for Jim, new distributables.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4343 e3abac25-378b-4346-85de-24260fe3988d

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Slight refactoring

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4342 e3abac25-378b-4346-85de-24260fe3988d

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Fixes for failed test cases (most was due to the data being used or problems with test cases themselves)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4303 e3abac25-378b-4346-85de-24260fe3988d

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Refactoring of all SequenceAnnotation web services New version of Metro Definition for IUPred exec Stubs regenerated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4280 e3abac25-378b-4346-85de-24260fe3988d

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More work to disorder prediction client & services.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4236 e3abac25-378b-4346-85de-24260fe3988d

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further work on registry & WSTester nearly there

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4229 e3abac25-378b-4346-85de-24260fe3988d

  1. … 4 more files in changeset.
Adding registry web service and changes to WStester and JWS2Client code. Bugs in input/ouput setup for a few web services fixed

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4223 e3abac25-378b-4346-85de-24260fe3988d

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    ./client/WSTesterTester.java
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    ./server/RegistryWSTester.java
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Replace Map<String, HashSet<Score>> with ScoreManager and ScoreHolder classes to compensate for JAXB inability to serialize Maps. Propagate the changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3733 e3abac25-378b-4346-85de-24260fe3988d

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Replace Map<String, HashSet<Score>> with ScoreManager and ScoreHolder classes to compensate for JAXB inability to serialize Maps. Propagate the changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3731 e3abac25-378b-4346-85de-24260fe3988d

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Disembl and Jronn web services work. Modified to produce raw scores Globplot script is added into binaries. Annotation IF renamed to SequenceAnnotation and getAnnotation() method returns Map<String, Set<Score>> result instead of Set<Score> to unify. Changes cause by this is propagated.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3704 e3abac25-378b-4346-85de-24260fe3988d

  1. … 17 more files in changeset.
AAConWS further work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3550 e3abac25-378b-4346-85de-24260fe3988d

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    ./client/AAConWSClientExample.java
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Further work on AAConWS

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3534 e3abac25-378b-4346-85de-24260fe3988d

  1. … 9 more files in changeset.
More javadocs

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3458 e3abac25-378b-4346-85de-24260fe3988d

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AAConWS further work and test cases

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3424 e3abac25-378b-4346-85de-24260fe3988d

  1. … 24 more files in changeset.