jabaws

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this looks like the same pattern of scheduler settings as in ServiceStatus - if you wanted to be more Java-ish, you'd have a generic ScheduledEventAttribute class that manipulated a given servlet c...

this looks like the same pattern of scheduler settings as in ServiceStatus - if you wanted to be more Java-ish, you'd have a generic ScheduledEventAttribute class that manipulated a given servlet context's attributes to create/update these stats

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JWS-121: Service status and usage statistics show cached results for faster loads
JWS-121: Service status and usage statistics show cached results for faster loads
I guess Geoff only wants updated looks here, so I guess this could be an improvement as well.

I guess Geoff only wants updated looks here, so I guess this could be an improvement as well.

So Geoff does not want JPred to included in the next release. My understanding is that if Jabaws 2.1 includes a previous version of Jpred, it should be removed...

So Geoff does not want JPred to included in the next release. My understanding is that if Jabaws 2.1 includes a previous version of Jpred, it should be removed...

Thanks Jim Procter! Gonna read it and get my way around. Also, I am going to remove the file, was more to see whether the pushing was working...

Thanks Jim Procter! Gonna read it and get my way around. Also, I am going to remove the file, was more to see whether the pushing was working...

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Rather than create cryptic .txt files in the jabaws source repository (where they will stay forever), I suggest you instead use the JWS Jira project. We have some (now slightly out of date) notes ...

Rather than create cryptic .txt files in the jabaws source repository (where they will stay forever), I suggest you instead use the JWS Jira project.

We have some (now slightly out of date) notes on how the jalview team does this on the wiki. The take home message, however, is that before you start coding, or whatever, use the issue tracker to decide what to code/write/fix, and log your progress. You may even discover issues that you wanted to fix that have already been lodged by someone else !

Remember: If it doesn't happen on the bug tracker, then it hasn't happened yet

No, really.

For more info see: https://wiki.jalview.org/index.php/Development#Pick_something_to_work_on_from_issues.jalview.org

I suspect an epic is called for here, since there will be a number of issues for each tool

I suspect an epic is called for here, since there will be a number of issues for each tool

Again, this should be a new, separate issue.

Again, this should be a new, separate issue.

Suggest you create an epic to collect issues for improving the stats page (or create a component and a series of issues tagged to it)

Suggest you create an epic to collect issues for improving the stats page (or create a component and a series of issues tagged to it)

Is this for downloading JABAWS ? Again, you should create an 'Improvement' on the JWS project to tag this - since it goes into the release notes for the updated version

Is this for downloading JABAWS ?

Again, you should create an 'Improvement' on the JWS project to tag this - since it goes into the release notes for the updated version

Suggest you create a task for this

Suggest you create a task for this

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Added a new document for logging the goals and todos (work in progress)
Added a new document for logging the goals and todos (work in progress)
Fix problem with test data for RNAalifold

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    /webservices/compbio/ws/client/WSTester.java
Replace logo files

Change version: 2.0.1 -> 2.5

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Fix logging problem

Add missing binaty and statis library

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Add missing doc files

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    /binaries/src/ViennaRNA/doc/latex/1_88_84__epars_8h.tex
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    /binaries/src/ViennaRNA/doc/latex/1_88_84__intloops_8h_source.tex
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Replace Progs/RNAalifold with x64 binary and add all other programs

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    /binaries/src/ViennaRNA/Progs/RNA2Dfold
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    /binaries/src/ViennaRNA/Progs/RNALalifold
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    /binaries/src/ViennaRNA/Progs/RNALfold
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    /binaries/src/ViennaRNA/Progs/RNAPKplex
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    /binaries/src/ViennaRNA/Progs/RNAaliduplex
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    /binaries/src/ViennaRNA/Progs/RNAalifold
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    /binaries/src/ViennaRNA/Progs/RNAcofold
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    /binaries/src/ViennaRNA/Progs/RNAdistance
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    /binaries/src/ViennaRNA/Progs/RNAduplex
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    /binaries/src/ViennaRNA/Progs/RNAeval
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    /binaries/src/ViennaRNA/Progs/RNAfold
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    /binaries/src/ViennaRNA/Progs/RNAheat
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    /binaries/src/ViennaRNA/Progs/RNAinverse
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    /binaries/src/ViennaRNA/Progs/RNApaln
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    /binaries/src/ViennaRNA/Progs/RNAparconv
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merged conf/Executable.properties

Parameter bug fixed, Jalview will now run some parameters

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    /conf/settings/RNAalifoldOptionsOnly.xml
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    /conf/settings/RNAalifoldParameters.xml
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    /webservices/compbio/ws/server/WSUtil.java
A secondary parameters file with some Jalview friendly parameters

JWS-71 - nominal Limits for RNAFold service - necessary so 'drmaa library not found' exception isn't raised when submitting to cluster

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

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    /conf/settings/RNAalifoldOptionsOnly.xml
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    /conf/settings/RNAalifoldParameters.xml
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    /datamodel/compbio/data/sequence/Range.java
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    /datamodel/compbio/data/sequence/Score.java
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    /runner/compbio/runner/structure/RNAalifold.java
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    /webservices/compbio/data/msa/FoldWS.java
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    /webservices/compbio/ws/client/Services.java
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    /webservices/compbio/ws/server/WSUtil.java
JWS-69 RNAalifold Linux Binary

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    /binaries/src/ViennaRNA/Progs/RNAalifold
Merge branch 'RNAalifold' of https://source.jalview.org/git/jabaws into RNAalifold

conf/Executable.properties and compilebin.sh updated for linux.

Category.java updated to include new category for RNA folding. RNAalifoldParameters.xml cut down to a number of parameters which I think are needed and which work easily with Jalview

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    /conf/settings/RNAalifoldParameters.xml
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    /datamodel/compbio/data/sequence/Score.java
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    /webservices/compbio/data/msa/Category.java