1 #---JalviewX Properties File---
2 #Fri Apr 25 09:54:25 BST 2014
5 BACKUPFILES_REVERSE_ORDER=false
6 BACKUPFILES_SUFFIX=_BACKUPFILESTESTTMP%n
7 BACKUPFILES_CONFIRM_DELETE_OLD=false
8 BACKUPFILES_NO_MAX=false
9 BACKUPFILES_ENABLED=true
10 BACKUPFILES_SUFFIX_DIGITS=8
13 SHOW_WSDISCOVERY_ERRORS=true
14 LATEST_VERSION=2.8.0b1
15 SHOW_CONSERVATION=true
16 JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
17 JAVA_CONSOLE_SCREEN_WIDTH=450
18 LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
20 SORT_ALIGNMENT=No sort
23 SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
25 RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
30 SHOW_DBREFS_TOOLTIP=true
32 SCREENGEOMETRY_HEIGHT=1600
33 JAVA_CONSOLE_SCREEN_Y=475
34 JAVA_CONSOLE_SCREEN_X=830
37 STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
38 JAVA_CONSOLE_SCREEN_HEIGHT=162
43 SHOW_GROUP_CONSERVATION=false
44 SHOW_JWS2_SERVICES=true
45 SHOW_NPFEATS_TOOLTIP=true
49 RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
50 AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
51 JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
52 SHOW_GROUP_CONSENSUS=false
53 SHOW_CONSENSUS_HISTOGRAM=true
55 AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
56 FIGURE_AUTOIDWIDTH=false
58 ANNOTATIONCOLOUR_MIN=ffc800
59 SHOW_STARTUP_FILE=false
60 RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
61 DEFAULT_FILE_FORMAT=FASTA
62 SHOW_JAVA_CONSOLE=false
68 JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
69 BUILD_DATE=01 November 2013
71 SHOW_CONSENSUS_LOGO=false
72 SCREENGEOMETRY_WIDTH=2560
74 JALVIEW_RSS_WINDOW_SCREEN_Y=0
76 JALVIEW_RSS_WINDOW_SCREEN_X=0
77 SHOW_UNCONSERVED=false
81 ANNOTATIONCOLOUR_MAX=ff0000
82 AUTO_CALC_CONSENSUS=true
84 DAS_ACTIVE_SOURCE=uniprot\t
85 JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
88 SHOW_ENFIN_SERVICES=true
93 #DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
94 DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
95 logs.Jalview.level=DEBUG