comments and version wget ping timeout fix for when www connection is unavailable due to proxy taking too long to respond
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added SeqSearch service interface. Documented and refactored web service client (tbc - more refactors to come).
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trial fix for parsing NHX style trees to extract the bootstrap values
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potential fix for hang on opening of application window when run in a proxied network environment (splashscreen constructor blocks whilst jalview.jnlp is fetched)
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typo on Jalview help url
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documented and refactored to facilitate headless feature file generation
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added centre column labels menu entry to format menu
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added centre annotation labels menu entry (and commented out SeqSearch web service handler builder code)
130 lines of code changed in:
centrecolumnlabels format menu item and parameter added to applet
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castor debug option cleared
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bugfix for refactoring (webservice windows wouldn't open!!)
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javadoc and refactor of setWebService method to allow headless client operation
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todo for refactoring webservice GUI creation mechanism
4 lines of code changed in:
javadoc for webservice client tutorial
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todos
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javadoc and quiet flag
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fix JPred thread so job aborts if submission fails.
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quick fix for conservation calculation when residue ambiguity codes are used.
130 lines of code changed in:
bug fix for Features/Annotations file parameter parsing in JalviewLite reported and fixed by Daron Standley and Reiko Yamashita. Also enhanced Jmol to allow it to be used to view PDB files retrieved via Classloader in the Applet
106 lines of code changed in: