Merge branch 'Jalview-JS/develop' into merge_js_develop

[jalview.git] / doc / JalviewJS-startupParams.md

diff --git a/doc/JalviewJS-startupParams.md b/doc/JalviewJS-startupParams.md
new file mode 100644 (file)
index 0000000..9ff3352
--- /dev/null
+++ b/doc/JalviewJS-startupParams.md
@@ -0,0 +1,92 @@
+## 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";
+