test/jalview/hmmer/testProps.jvprops

   1 #---JalviewX Properties File---
   2 #Fri Apr 25 09:54:25 BST 2014
   3 SCREEN_Y=768
   4 SCREEN_X=936
   5 SHOW_WSDISCOVERY_ERRORS=true
   6 LATEST_VERSION=2.8.0b1
   7 SHOW_CONSERVATION=true
   8 JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
   9 JAVA_CONSOLE_SCREEN_WIDTH=450
  10 LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
  11 ID_ITALICS=true
  12 SORT_ALIGNMENT=No sort
  13 SHOW_IDENTITY=true
  14 WSMENU_BYHOST=false
  15 SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
  16 SHOW_FULLSCREEN=false
  17 RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
  18 FONT_NAME=SansSerif
  19 BLC_JVSUFFIX=true
  20 VERSION_CHECK=false
  21 YEAR=2011
  22 SHOW_DBREFS_TOOLTIP=true
  23 MSF_JVSUFFIX=true
  24 SCREENGEOMETRY_HEIGHT=1600
  25 JAVA_CONSOLE_SCREEN_Y=475
  26 JAVA_CONSOLE_SCREEN_X=830
  27 PFAM_JVSUFFIX=true
  28 PIR_JVSUFFIX=true
  29 STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
  30 JAVA_CONSOLE_SCREEN_HEIGHT=162
  31 PIR_MODELLER=false
  32 GAP_SYMBOL=-
  33 SHOW_QUALITY=true
  34 SHOW_OCCUPANCY=true
  35 SHOW_GROUP_CONSERVATION=false
  36 SHOW_JWS2_SERVICES=true
  37 SHOW_NPFEATS_TOOLTIP=true
  38 FONT_STYLE=plain
  39 ANTI_ALIAS=false
  40 SORT_BY_TREE=false
  41 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\=$ALIGNMENT\:format\='FASTA',writeasfile$
  42 AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
  43 JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
  44 SHOW_GROUP_CONSENSUS=false
  45 SHOW_CONSENSUS_HISTOGRAM=true
  46 SHOW_OVERVIEW=false
  47 AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  48 FIGURE_AUTOIDWIDTH=false
  49 SCREEN_WIDTH=900
  50 ANNOTATIONCOLOUR_MIN=ffc800
  51 SHOW_STARTUP_FILE=false
  52 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
  53 DEFAULT_FILE_FORMAT=FASTA
  54 SHOW_JAVA_CONSOLE=false
  55 VERSION=2.8b1
  56 FIGURE_USERIDWIDTH=
  57 WSMENU_BYTYPE=false
  58 DEFAULT_COLOUR=None
  59 NOQUESTIONNAIRES=true
  60 JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
  61 BUILD_DATE=01 November 2013
  62 PILEUP_JVSUFFIX=true
  63 SHOW_CONSENSUS_LOGO=false
  64 SCREENGEOMETRY_WIDTH=2560
  65 SHOW_ANNOTATIONS=true
  66 JALVIEW_RSS_WINDOW_SCREEN_Y=0
  67 USAGESTATS=false
  68 JALVIEW_RSS_WINDOW_SCREEN_X=0
  69 SHOW_UNCONSERVED=false
  70 SHOW_JVSUFFIX=true
  71 DAS_LOCAL_SOURCE=
  72 SCREEN_HEIGHT=650
  73 ANNOTATIONCOLOUR_MAX=ff0000
  74 AUTO_CALC_CONSENSUS=true
  75 FASTA_JVSUFFIX=true
  76 DAS_ACTIVE_SOURCE=uniprot\t
  77 JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
  78 PAD_GAPS=false
  79 CLUSTAL_JVSUFFIX=true
  80 SHOW_ENFIN_SERVICES=true
  81 FONT_SIZE=10
  82 RIGHT_ALIGN_IDS=false
  83 USE_PROXY=false
  84 WRAP_ALIGNMENT=false
  85 #DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
  86 DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
  87 logs.Jalview.level=DEBUG
  88 HMMER_PATH=/Users/gmcarstairs/software/hmmer-3.1b2-macosx-intel/binaries