TODO -- go through these
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", };
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";