I have configured a JNLP by altering the following section (codebase is localhost/Jalview/webstart):
<application-desc main-class="jalview.bin.Jalview">
<argument>-props</argument>
<argument>http://localhost/Jalview/webstart/local.properties</argument>
</application-desc>
The properties are not read. Jalview prompts for google tracking and then loads the example file from jalview.org despite the properties indicating not to load an example file and to take it from localhost. Obviously I can't open the Java console until the application has started so can't see what is going on.
Any clues? Are null values allowed in the property fields?
local.properties contains the following (as does my .jalview_properties file)
#---JalviewX Properties File---
#Tue Mar 15 08:03:46 GMT 2011
WRAP_ALIGNMENT=false
AUTO_CALC_CONSENSUS=true
FONT_SIZE=10
SHOW_DBREFS_TOOLTIP=true
PFAM_JVSUFFIX=true
SHOW_CONSENSUS_LOGO=false
PAD_GAPS=false
BUILD_DATE=15 November 2010
FONT_NAME=SansSerif
MSF_JVSUFFIX=true
SHOW_JAVA_CONSOLE=true
SHOW_UNCONSERVED=false
LATEST_VERSION=2.6.1
DEFAULT_COLOUR=None
PILEUP_JVSUFFIX=true
SHOW_GROUP_CONSERVATION=false
ID_ITALICS=true
CLUSTAL_JVSUFFIX=true
ANTI_ALIAS=false
VERSION=2.6.1
RECENT_FILE=
SHOW_JWS1_SERVICES=false
FASTA_JVSUFFIX=true
SHOW_JVSUFFIX=true
SEQUENCE_LINKS=SRS|http\://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all\:$SEQUENCE_ID$]))+-view+SwissEntry
DEFAULT_FILE_FORMAT=Jalview
FONT_STYLE=plain
DAS_LOCAL_SOURCE=
SHOW_CONSENSUS_HISTOGRAM=true
SHOW_GROUP_CONSENSUS=false
VERSION_CHECK=true
SHOW_WSDISCOVERY_ERRORS=true
BLC_JVSUFFIX=true
SHOW_JWS2_SERVICES=true
DAS_REGISTRY_URL=http\://www.dasregistry.org/das1/sources/
SHOW_STARTUP_FILE=false
STARTUP_FILE=http\://localhost/Jalview/examples/exampleFile_2_3.jar
RECENT_URL=http\://localhost/Jalview/examples/exampleFile_2_3.jar
SHOW_FULLSCREEN=false
SHOW_QUALITY=true
SHOW_CONSERVATION=true
WSMENU_BYTYPE=true
GAP_SYMBOL=-
JWS2HOSTURLS=http\://localhost\:8080/jaba
SHOW_ANNOTATIONS=true
USAGESTATS=false
SHOW_IDENTITY=true
SHOW_NPFEATS_TOOLTIP=true
USE_PROXY=false
SORT_ALIGNMENT=No sort
WSMENU_BYHOST=true
DAS_ACTIVE_SOURCE=
PIR_MODELLER=false
LAST_DIRECTORY=
SHOW_ENFIN_SERVICES=true
PIR_JVSUFFIX=true
RIGHT_ALIGN_IDS=false
SHOW_OVERVIEW=false
David Martin PhD
College of Life Sciences
University of Dundee
The University of Dundee is a Scottish Registered Charity, No. SC015096.
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