test/jalview/bin/commandsTest3.jvprops

   1 #---JalviewX Properties File---
   2 #Tue May 28 14:24:20 BST 2024
   3 SHOW_CONSERVATION=true
   4 USE_PROXY=false
   5 SHOW_OCCUPANCY=false
   6 SHOW_UNCONSERVED=false
   7 MEMORY_CUSTOMISED_SETTINGS=false
   8 EPS_RENDERING=Prompt each time
   9 MAP_WITH_SIFTS=false
  10 SHOW_ENFIN_SERVICES=true
  11 JAVA_CONSOLE_SCREEN_WIDTH=900
  12 HIDDEN_COLOUR=2c2c2c
  13 YEAR=2018
  14 SORT_ANNOTATIONS=NONE
  15 SCREEN_HEIGHT=1930
  16 SHOW_STARTUP_FILE=true
  17 SCREENGEOMETRY_HEIGHT=2160
  18 JALVIEW_NEWS_RSS_LASTMODIFIED=22 May 2024, 16\:43\:10
  19 STRUCT_FROM_PDB=true
  20 RIGHT_ALIGN_IDS=false
  21 SHOW_ANNOTATIONS=true
  22 PIR_JVSUFFIX=true
  23 ADD_TEMPFACT_ANN=true
  24 GAP_COLOUR=c0c0c0
  25 SHOW_IDENTITY=true
  26 PIR_MODELLER=false
  27 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\=$ALIGNMENT\:format\='Fasta',writeasfile$
  28 FASTA_JVSUFFIX=true
  29 PROXY_AUTH=false
  30 FIGURE_FIXEDIDWIDTH=
  31 SHOW_JAVA_CONSOLE=false
  32 SCALE_PROTEIN_TO_CDNA=false
  33 BACKUPFILES_SAVED=.bak%n\t3\tfalse\tfalse\t3\tfalse
  34 AUTO_CALC_CONSENSUS=true
  35 SCREEN_WIDTH=1900
  36 SCREEN_X=22
  37 SHOW_GROUP_CONSENSUS=false
  38 SCREEN_Y=0
  39 LAST_DIRECTORY=/home/bsoares/Work/git/develop/jalview/examples
  40 JAVA_CONSOLE_SCREEN_Y=368
  41 JAVA_CONSOLE_SCREEN_X=1010
  42 DEFAULT_COLOUR_PROT=None
  43 SORT_ALIGNMENT=No sort
  44 MEMORY_JVMMEMPC=90
  45 SHOW_AUTOCALC_ABOVE=true
  46 PFAM_JVSUFFIX=true
  47 WSMENU_BYHOST=false
  48 DEFAULT_URL=EMBL-EBI Search
  49 HTML_RENDERING=Prompt each time
  50 AUTHORS=J Procter, M Carstairs, B Soares, K Mourao, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
  51 SHOW_OV_HIDDEN_AT_START=false
  52 MSF_JVSUFFIX=true
  53 SHOW_DBREFS_TOOLTIP=true
  54 FONT_NAME=SansSerif
  55 STARTUP_FILE=/home/bsoares/Work/git/develop/jalview/examples/uniref50.fa
  56 USE_LEGACY_GAP=false
  57 DEFAULT_FILE_FORMAT=Fasta
  58 VERSION=Test
  59 CLUSTAL_JVSUFFIX=true
  60 GAP_SYMBOL=-
  61 JAVA_CONSOLE_SCREEN_HEIGHT=1328
  62 DEFAULT_COLOUR_NUC=None
  63 FONT_STYLE=plain
  64 USAGESTATS=true
  65 JAVA_COMPILE_VERSION=8
  66 PAD_GAPS=false
  67 ADD_SS_ANN=true
  68 AUTHORFNAMES=Jim Procter, Mungo Carstairs, Ben Soares, Kira Mourao, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
  69 SHOW_FULLSCREEN=false
  70 ID_ITALICS=true
  71 SHOW_CONSENSUS_LOGO=false
  72 RECENT_FILE=examples/uniref50.fa\t/home/bsoares/Work/git/develop/jalview/examples/uniref50.fa\t/home/bsoares/Downloads/mview-I20240419-154802-0673-19607440-p1m-aln-html.txt\t/home/bsoares/Work/Journal_Club/2024-04-24/examples/jalview_biojs_msaviewer.html\t/home/bsoares/Work/Journal_Club/2024-04-24/examples/jalview_embedded_svg.html\t./estrogenReceptorCdna.fa\t/home/bsoares/Work/git/develop/jalview/examples/exampleFile_2_7.jar\t/home/bsoares/Work/git/develop/jalview/test.jvp\t/home/bsoares/Work/git/develop/jalview/test.fa\t./test/files/annotation_label_width/sample.a2m\t/home/bsoares/Work/git/develop/jalview/test/files/annotation_label_width/sample.a2m
  73 SHOW_QUALITY=true
  74 SHOW_WSDISCOVERY_ERRORS=true
  75 LATEST_VERSION=2.11.3.3
  76 ANNOTATIONCOLOUR_MIN=ffc800
  77 SHOW_JVSUFFIX=true
  78 SCREENGEOMETRY_WIDTH=3840
  79 SHOW_NPFEATS_TOOLTIP=true
  80 MEMORY_JVMMEMMAX=32g
  81 SVG_RENDERING=Prompt each time
  82 VERSION_CHECK=true
  83 WRAP_ALIGNMENT=false
  84 BACKUPFILES_ENABLED=true
  85 RECENT_URL=http\://jalview.org/examples/uniref50.fa\thttps\://jalview.org/examples/plantfdx.fa\thttps\://www.jalview.org/tutorial/schools/Spike-7BNM-Jmol.jvp\thttp\://www.jalview.org/tutorial/schools/Spike-7BNM-Jmol.jvp\thttps\://jalview.org/examples/uniref50.fa\thttps\://www.jalview.org/examples/exampleFile_2_7.jvp
  86 EXPORT_EMBBED_BIOJSON=true
  87 SORT_BY_TREE=false
  88 AUTOSUPERIMPOSE=true
  89 JALVIEW_RSS_WINDOW_SCREEN_X=0
  90 JALVIEW_RSS_WINDOW_SCREEN_Y=0
  91 BLC_JVSUFFIX=true
  92 ANNOTATIONCOLOUR_MAX=ff0000
  93 ANTI_ALIAS=true
  94 JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=577
  95 JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
  96 SHOW_JWS2_SERVICES=true
  97 FONT_SIZE=10
  98 BACKUPFILES_FC_INCLUDE=false
  99 BACKUPFILES_PRESET=1
 100 SHOW_OVERVIEW=false
 101 WSMENU_BYTYPE=false
 102 SHOW_GROUP_CONSERVATION=false
 103 FIGURE_AUTOIDWIDTH=false
 104 STRUCTURE_DISPLAY=JMOL
 105 PILEUP_JVSUFFIX=true
 106 SEQUENCE_LINKS=EMBL-EBI Search|https\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
 107 JALVIEW_RSS_WINDOW_SCREEN_WIDTH=534
 108 SHOW_CONSENSUS_HISTOGRAM=true