jabaws

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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
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ensure we never check in autogenerated documentation or build artefacts

fix jabaws download link

File puller tester

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

word order

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4814 e3abac25-378b-4346-85de-24260fe3988d

load the driver explicitly

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4813 e3abac25-378b-4346-85de-24260fe3988d

AMI ID update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4809 e3abac25-378b-4346-85de-24260fe3988d

web site minor tweaks

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4808 e3abac25-378b-4346-85de-24260fe3988d

web pages url updates

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4805 e3abac25-378b-4346-85de-24260fe3988d

Bug fix to the stat pages

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4802 e3abac25-378b-4346-85de-24260fe3988d

updated javadoc for the system as well as new redirect address for download app

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4793 e3abac25-378b-4346-85de-24260fe3988d

  1. … 822 more files in changeset.
remove old project javadoc

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4790 e3abac25-378b-4346-85de-24260fe3988d

  1. … 513 more files in changeset.
remove old datamodel javadoc

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4789 e3abac25-378b-4346-85de-24260fe3988d

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    /website/dm_javadoc/allclasses-frame.html
  1. … 224 more files in changeset.