## JalviewJS startup parameters

TODO -- go through these

# parameters -- from jalview.bin.AppletParams

  private final static String[] params = { 
      "alignpdbfiles",
      "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN",
      "annotations",
      "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
      "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
      "embedded", "enableSplitFrame", "externalstructureviewer", "features",
      "file", "file2", "format", "heightScale", "hidefeaturegroups",
      "jalviewhelpurl", "jnetfile", "jpredfile", "label", "linkLabel_",
      "linkLabel_1", "linkURL_", "nojmol", "normaliseLogo",
      "normaliseSequenceLogo", "oninit", "PDBFILE", "PDBSEQ",
      "relaxedidmatch", "resolvetocodebase", "RGB", "scaleProteinAsCdna",
      "scoreFile", "separator", "sequence", "showAnnotation", "showbutton",
      "showConsensus", "showConsensusHistogram", "showConservation",
      "showfeaturegroups", "showFeatureSettings", "showFullId",
      "showGroupConsensus", "showGroupConservation", "showOccupancy",
      "showQuality", "showSequenceLogo", "showTreeBootstraps",
      "showTreeDistances", "showUnconserved", "showUnlinkedTreeNodes",
      "sortBy", "sortByTree", "tree", "treeFile", "upperCase",
      "userDefinedColour", "widthScale", "windowHeight", "windowWidth",
      "wrap", };




# arguments -- from jalview.bin.ArgsParser

  public static final String NOCALCULATION = "nocalculation";

  public static final String NOMENUBAR = "nomenubar";

  public static final String NOSTATUS = "nostatus";

  public static final String SHOWOVERVIEW = "showoverview";

  //
  public static final String ANNOTATIONS = "annotations";

  public static final String COLOUR = "colour";

  public static final String FEATURES = "features";

  public static final String GROOVY = "groovy";

  public static final String GROUPS = "groups";

  public static final String HEADLESS = "headless";

  public static final String JABAWS = "jabaws";

  public static final String NOANNOTATION = "no-annotation";

  public static final String NOANNOTATION2 = "noannotation"; // BH 2019.05.07

  public static final String NODISPLAY = "nodisplay";

  public static final String NOGUI = "nogui";

  public static final String NONEWS = "nonews";

  public static final String NOQUESTIONNAIRE = "noquestionnaire";

  public static final String NOSORTBYTREE = "nosortbytree";

  public static final String NOUSAGESTATS = "nousagestats";

  public static final String OPEN = "open";

  public static final String OPEN2 = "open2"; // BH added -- for applet
                                              // compatibility; not fully
                                              // implemented

  public static final String PROPS = "props";

  public static final String QUESTIONNAIRE = "questionnaire";

  public static final String SETPROP = "setprop";

  public static final String SORTBYTREE = "sortbytree";

  public static final String TREE = "tree";

  public static final String VDOC = "vdoc";

  public static final String VSESS = "vsess";