1 ## JalviewJS startup parameters
3 TODO -- go through these
5 # parameters -- from jalview.bin.AppletParams
7 private final static String[] params = {
9 "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN",
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",
32 # arguments -- from jalview.bin.ArgsParser
34 public static final String NOCALCULATION = "nocalculation";
36 public static final String NOMENUBAR = "nomenubar";
38 public static final String NOSTATUS = "nostatus";
40 public static final String SHOWOVERVIEW = "showoverview";
43 public static final String ANNOTATIONS = "annotations";
45 public static final String COLOUR = "colour";
47 public static final String FEATURES = "features";
49 public static final String GROOVY = "groovy";
51 public static final String GROUPS = "groups";
53 public static final String HEADLESS = "headless";
55 public static final String JABAWS = "jabaws";
57 public static final String NOANNOTATION = "no-annotation";
59 public static final String NOANNOTATION2 = "noannotation"; // BH 2019.05.07
61 public static final String NODISPLAY = "nodisplay";
63 public static final String NOGUI = "nogui";
65 public static final String NONEWS = "nonews";
67 public static final String NOQUESTIONNAIRE = "noquestionnaire";
69 public static final String NOSORTBYTREE = "nosortbytree";
71 public static final String NOUSAGESTATS = "nousagestats";
73 public static final String OPEN = "open";
75 public static final String OPEN2 = "open2"; // BH added -- for applet
76 // compatibility; not fully
79 public static final String PROPS = "props";
81 public static final String QUESTIONNAIRE = "questionnaire";
83 public static final String SETPROP = "setprop";
85 public static final String SORTBYTREE = "sortbytree";
87 public static final String TREE = "tree";
89 public static final String VDOC = "vdoc";
91 public static final String VSESS = "vsess";