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jprocter <jprocter@compbio.dundee.ac.uk> in jabaws

Merge branch 'JABAWS_Release_2_0' of https://source.jalview.org/git/jabaws into develop

JWS-48 patch to ensure JAX-WS 2.1 client code source generation with JAX-WS 2.2 libraries

JWS-43 development deployment context changed to "jabaws" so TestNG web service client tests can run against the development server

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    /.settings/org.eclipse.wst.common.component
JWS-47 patch test to default local JABAWS server and source tidy

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    /testsrc/compbio/ws/client/TestIUPredWS.java
JWS-47 override custom/preset analize methods so the input can be validated appropriately for AACons

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    /webservices/compbio/ws/server/AAConWS.java
JWS-47 AACons validation shouldn't be done for generic analysis services

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

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    /testsrc/compbio/ws/client/TestIUPredWS.java
JWS-44 - attempt to make a file executable if it is supposed to be executable according to jabaws configuration.

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    /engine/compbio/engine/client/PathValidator.java
JWS-43 eclipse project metadata for dynamic web project directly deployable on development server

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    /.settings/org.eclipse.wst.common.component
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    /.settings/org.eclipse.wst.common.project.facet.core.xml
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    /.settings/org.eclipse.wst.jsdt.ui.superType.container
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    /.settings/org.eclipse.wst.jsdt.ui.superType.name
Merge branch 'JWS-27-jronn' into develop

Merge branch 'JWS-27-jronn' into JABAWS_Release_2_0

JWS-27 replaced JRonn with patched biojava 3.0.4 version which runs correctly for large sets of sequences in multithreaded mode

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    /binaries/windows/bj3.0.4p-jronn.jar
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    /binaries/windows/bj3.0.4p-jronn.jar.readme
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    /binaries/windows/bj3.0.4p-jronn.patch
Merge branch 'JWS-29' into develop

Merge branch 'JWS-29' into JABAWS_Release_2_0

JWS-29 patch fixes bug - wierd workaround since "^\\s*>" caused scanner to advance to end of file rather than start of next FASTA header

test demonstrating JWS-29 assertion failure

Merge branch 'JWS-36' into JABAWS_Release_2_0

Merge branch 'JWS-36' into develop

JWS-36 patched Scores writer to put spaces between ranges and space separated scores

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    /datamodel/compbio/data/sequence/Score.java
Merge branch 'JWS-35' into JABAWS_Release_2_0

patch fixes JWS-35

patch fixes JWS-35

test for JWS-35 - check that range and first value of prediction for each method matches expected values

test for JWS-35 - check that range and first value of prediction for each method matches expected values

remove jabaws 3 development code

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    /engine/compbio/engine/cluster/dundee/_Queue.java
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    /engine/compbio/engine/conf/_Key.java
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    /runner/compbio/pipeline/_jpred/BlastParser.java
  1. … 30 more files in changeset.
ensure we never check in autogenerated documentation or build artefacts

fix jabaws download link