doc/JalviewJS-startupParams.md

   1 ## JalviewJS startup parameters
   2
   3 TODO -- go through these
   4
   5 # parameters -- from jalview.bin.AppletParams
   6
   7   private final static String[] params = {
   8       "alignpdbfiles",
   9       "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN",
  10       "annotations",
  11       "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
  12       "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
  13       "embedded", "enableSplitFrame", "externalstructureviewer", "features",
  14       "file", "file2", "format", "heightScale", "hidefeaturegroups",
  15       "jalviewhelpurl", "jnetfile", "jpredfile", "label", "linkLabel_",
  16       "linkLabel_1", "linkURL_", "nojmol", "normaliseLogo",
  17       "normaliseSequenceLogo", "oninit", "PDBFILE", "PDBSEQ",
  18       "relaxedidmatch", "resolvetocodebase", "RGB", "scaleProteinAsCdna",
  19       "scoreFile", "separator", "sequence", "showAnnotation", "showbutton",
  20       "showConsensus", "showConsensusHistogram", "showConservation",
  21       "showfeaturegroups", "showFeatureSettings", "showFullId",
  22       "showGroupConsensus", "showGroupConservation", "showOccupancy",
  23       "showQuality", "showSequenceLogo", "showTreeBootstraps",
  24       "showTreeDistances", "showUnconserved", "showUnlinkedTreeNodes",
  25       "sortBy", "sortByTree", "tree", "treeFile", "upperCase",
  26       "userDefinedColour", "widthScale", "windowHeight", "windowWidth",
  27       "wrap", };
  28
  29
  30
  31
  32 # arguments -- from jalview.bin.ArgsParser
  33
  34   public static final String NOCALCULATION = "nocalculation";
  35
  36   public static final String NOMENUBAR = "nomenubar";
  37
  38   public static final String NOSTATUS = "nostatus";
  39
  40   public static final String SHOWOVERVIEW = "showoverview";
  41
  42   //
  43   public static final String ANNOTATIONS = "annotations";
  44
  45   public static final String COLOUR = "colour";
  46
  47   public static final String FEATURES = "features";
  48
  49   public static final String GROOVY = "groovy";
  50
  51   public static final String GROUPS = "groups";
  52
  53   public static final String HEADLESS = "headless";
  54
  55   public static final String JABAWS = "jabaws";
  56
  57   public static final String NOANNOTATION = "no-annotation";
  58
  59   public static final String NOANNOTATION2 = "noannotation"; // BH 2019.05.07
  60
  61   public static final String NODISPLAY = "nodisplay";
  62
  63   public static final String NOGUI = "nogui";
  64
  65   public static final String NONEWS = "nonews";
  66
  67   public static final String NOQUESTIONNAIRE = "noquestionnaire";
  68
  69   public static final String NOSORTBYTREE = "nosortbytree";
  70
  71   public static final String NOUSAGESTATS = "nousagestats";
  72
  73   public static final String OPEN = "open";
  74
  75   public static final String OPEN2 = "open2"; // BH added -- for applet
  76                                               // compatibility; not fully
  77                                               // implemented
  78
  79   public static final String PROPS = "props";
  80
  81   public static final String QUESTIONNAIRE = "questionnaire";
  82
  83   public static final String SETPROP = "setprop";
  84
  85   public static final String SORTBYTREE = "sortbytree";
  86
  87   public static final String TREE = "tree";
  88
  89   public static final String VDOC = "vdoc";
  90
  91   public static final String VSESS = "vsess";
  92