--- /dev/null
+
+package jalview.bin;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import jalview.gui.Preferences;
+
+/**
+ * Collection of all known applet tags from JalviewLite.
+ * Three cases; can be one or more of these:
+ *
+ * CASE I. args[] name and value for ArgsParser
+ *
+ * CASE II. applet parameter for JalviewJSApp
+ *
+ * CASE III. mapped to a Preference
+ *
+ *
+ * @author hansonr
+ *
+ */
+@SuppressWarnings("serial")
+public class AppletParams extends HashMap<String, Object>
+{
+
+ 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 String getParam(String param, String def)
+ {
+ Object val = get(param);
+ return (val != null ? val.toString() : def);
+ }
+
+ // <applet
+ // code="jalview.bin.JalviewLite" width="140" height="35"
+ // archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+ // <param name="permissions" value="sandbox"/>
+ // <param name="file" value="uniref50.fa"/>
+ // <param name="treeFile" value="ferredoxin.nw"/>
+ // <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555;
+ // D,E=5555FF"/>
+ // <param name="sortByTree" value="True"/>
+ // <param name="showSequenceLogo" value="true"/>
+ // <param name="showGroupConsensus" value="true"/>
+ // <param name="showFullId" value="false"/>
+ // <param name="linkLabel_1" value="Uniprot"/>
+ // <param name="linkUrl_1"
+ // value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+ // <param name="linkLabel_2" value="EMBL-EBI Search"/>
+ // <param name="linkUrl_2"
+ // value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+ // <param name="APPLICATION_URL"
+ // value="http://www.jalview.org/services/launchApp"/>
+ // </applet>
+ //
+ public AppletParams(String outerHTML)
+ {
+ String[] tokens = outerHTML.split("<param");
+ outerHTML = tokens[0];
+ String code = getAttr(outerHTML, "code");
+ if (!code.equals("jalview.bin.JalviewLite"))
+ {
+ return;
+ }
+ for (int i = tokens.length; --i > 0;)
+ {
+ String param = tokens[i];
+ String key = getAttr(param, "name");
+ if (key != null)
+ {
+ String value = getAttr(param, "value");
+ System.out.println("AppletParams " + key + " = \"" + value + "\"");
+ put(key, value);
+ }
+ }
+ put("_width", getAttr(outerHTML, "width"));
+ put("_height", getAttr(outerHTML, "height"));
+ put("_id", getAttr(outerHTML, "id"));
+ put("_name", getAttr(outerHTML, "name"));
+ put("_archive", getAttr(outerHTML, "archive"));
+ put("_code", code);
+ }
+
+ public AppletParams()
+ {
+ }
+
+ public static AppletParams getAppletParams(Map<String, Object> map,
+ List<String> vargs)
+ {
+ AppletParams appletParams = new AppletParams();
+ String resourcePath = getString(map, "resourcePath");
+ if (resourcePath == null)
+ resourcePath = "";
+ if (resourcePath.length() > 0 && !resourcePath.endsWith("/"))
+ {
+ resourcePath += "/";
+ }
+ for (int i = params.length; --i >= 0;)
+ {
+ String prefName = params[i];
+ Object value = map.get(prefName);
+ if (value != null)
+ addParam(vargs, prefName, value, appletParams, resourcePath);
+ }
+ return appletParams;
+ }
+
+ private static String getString(Map<String, Object> map, String key)
+ {
+ Object o = map.get(key);
+ return (o == null ? null : o.toString());
+ }
+
+ public static AppletParams getAppletParams(String[] args,
+ List<String> vargs)
+ {
+ AppletParams appletParams = new AppletParams();
+ String resourcePath = "";
+ for (int i = args.length; --i > 0;) // > 0 is correct, not >=0
+ {
+ if (args[i].startsWith("name=\"Info.resourcePath\""))
+ {
+ resourcePath = getAttr(args[i], "value");
+ if (resourcePath.length() > 0 && !resourcePath.endsWith("/"))
+ {
+ resourcePath += "/";
+ }
+ break;
+ }
+ }
+ for (int i = 1; i < args.length; i++)
+ {
+ String arg = args[i].trim();
+ if (arg.startsWith("name="))
+ {
+ String prefName = getAttr(arg, "name");
+ String value = getAttr(arg, "value");
+ addParam(vargs, prefName, value, appletParams, resourcePath);
+ }
+ }
+ return appletParams;
+ }
+
+ private static void addParam(List<String> vargs, String prefName,
+ Object value, AppletParams appletParams, String resourcePath)
+ {
+
+ // note that Application arguments ARE case-sensitive, but
+ // Applet.getParameter() is not.
+
+ // prefName // CASE III
+
+ String argName = null; // CASE I
+
+ String appletName = prefName.toLowerCase(); // CASE II
+
+ // by nulling one or more of these names, that route will not be used.
+
+ switch (appletName)
+ {
+
+ case "file":
+ argName = "open";
+ prefName = null;
+ value = resourcePath + value;
+ break;
+ case "file2":
+ argName = "open2";
+ prefName = null;
+ value = resourcePath + value;
+ break;
+ case "oninit":
+ case "hidefeaturegroups":
+ // applet parameter only
+ // setting argName to null indicates that we want
+ // JalviewJSApp to take care of this using getParameter or getParameterAsObject
+ prefName = argName = null;
+ break;
+ case "tree":
+ case "treefile":
+ // setting appletName to null indicates that we want
+ // Jalview.doMain to taken care of this as Jalview args
+ argName = "tree";
+ prefName = null;
+ value = resourcePath + value;
+ break;
+
+ case "features":
+ case "jnetfile":
+ case "jpredfile":
+ case "pdbfile":
+ case "scorefile":
+ case "sequence":
+ case "annotations":
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;
+
+ // non-loading preferences
+
+ case "defaultcolour":
+ prefName = Preferences.DEFAULT_COLOUR;
+ break;
+ case "defaultcolournuc":
+ prefName = Preferences.DEFAULT_COLOUR_NUC;
+ break;
+ case "defaultcolourprot":
+ prefName = Preferences.DEFAULT_COLOUR_PROT;
+ break;
+ case "annotationcolour_max":
+ prefName = Preferences.ANNOTATIONCOLOUR_MAX;
+ break;
+ case "annotationcolour_min":
+ prefName = Preferences.ANNOTATIONCOLOUR_MIN;
+ break;
+ case "enablesplitframe":
+ prefName = Preferences.ENABLE_SPLIT_FRAME;
+ break;
+ case "centrecolumnlabels":
+ prefName = Preferences.CENTRE_COLUMN_LABELS;
+ break;
+ case "sortby":
+ prefName = Preferences.SORT_ALIGNMENT; // id, etc.
+ break;
+ case "normalisesequencelogo":
+ prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
+ break;
+ case "relaxedidmatch":
+ prefName = Preferences.RELAXEDSEQIDMATCHING;
+ break;
+ case "scaleproteinascdna":
+ prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
+ break;
+ case "userdefinedcolour":
+ argName = "colour";
+ prefName = Preferences.USER_DEFINED_COLOURS;
+ break;
+ case "wrap":
+ prefName = Preferences.WRAP_ALIGNMENT;
+ break;
+ case "sortbytree":
+ argName = prefName;
+ prefName = Preferences.SORT_BY_TREE;
+ value = checkTF(value);
+ break;
+
+ // implemented; not tested:
+
+ case "pdbseq":
+ case "alignpdbfiles":
+ prefName = null;
+ break;
+ case "format":
+ argName = prefName;
+ break;
+ case "separator":
+ argName = prefName;
+ break;
+
+ // TODO: probably not relevant?
+
+ case "rgb":
+ prefName = null; // TODO no background for application?
+ break;
+ case "externalstructureviewer":
+ break;
+ case "application_url":
+ break;
+ case "automaticscrolling":
+ break;
+ case "heightscale":
+ break;
+ case "jalviewhelpurl":
+ break;
+ case "label":
+ break;
+ case "linklabel_":
+ prefName = "linkLabel_";
+ break;
+ case "linklabel_1":
+ prefName = "linkLabel_1";
+ break;
+ case "linkurl_":
+ prefName = "linkURL_";
+ break;
+
+ // unknown:
+
+ case "nojmol":
+ case "normaliselogo":
+ case "resolvetocodebase":
+ case "uppercase":
+ case "widthscale":
+ case "windowheight":
+ case "windowwidth":
+ prefName = null;
+ break;
+
+ // TRUE/FALSE
+
+ case "debug":
+ case "embedded":
+ case "showbutton":
+ value = checkTF(value);
+ break;
+ case "showannotation":
+ prefName = Preferences.SHOW_ANNOTATIONS;
+ value = checkTF(value);
+ break;
+ case "showconsensus":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showconsensushistogram":
+ prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
+ value = checkTF(value);
+ break;
+ case "showconservation":
+ prefName = Preferences.SHOW_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showgroupconsensus":
+ prefName = Preferences.SHOW_GROUP_CONSENSUS;
+ value = checkTF(value);
+ break;
+ case "showgroupconservation":
+ prefName = Preferences.SHOW_GROUP_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showoccupancy":
+ prefName = Preferences.SHOW_OCCUPANCY;
+ value = checkTF(value);
+ break;
+ case "showquality":
+ prefName = Preferences.SHOW_QUALITY;
+ value = checkTF(value);
+ break;
+ case "showsequencelogo":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showunconserved":
+ prefName = Preferences.SHOW_UNCONSERVED;
+ value = checkTF(value);
+ break;
+ case "showfeaturegroups":
+ case "showfeaturesettings":
+ case "showfullid":
+ case "showtreebootstraps":
+ case "showtreedistances":
+ case "showunlinkedtreenodes":
+ value = checkTF(value);
+ break;
+ default:
+ if (appletName.startsWith("pdbfile")
+ || appletName.startsWith("sequence") && Character
+ .isDigit(appletName.charAt(appletName.length() - 1)))
+ {
+ // could be pdbFile2, for example
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;
+ }
+ // or one of the app preference names
+ break;
+ }
+
+ // CASE I. args[] name and value for ArgsParser
+ //
+ // If given an argument name,
+ // put name and value into application args
+ if (value != null && argName != null)
+ {
+ vargs.add(argName);
+ if (value != "true")
+ {
+ vargs.add(value.toString());
+ }
+ }
+
+ // CASE II. applet parameter for JalviewJSApp
+
+ if (value == null)
+ {
+ value = "false";
+ }
+ System.out.println("AppletParams propName=" + prefName + " argName="
+ + argName + " appletName=" + appletName + " value=" + value);
+ if (appletName != null)
+ {
+ appletParams.put(appletName, value);
+ }
+
+ // CASE III. mapped to a Preference
+
+ if (prefName != null)
+ {
+ Cache.setPropertyNoSave(prefName, value.toString());
+ }
+ }
+
+ /**
+ * Check for a single-argument option.
+ *
+ * @param value
+ * @return "true" or null
+ */
+ private static String checkTF(Object value)
+ {
+ return (("" + value).toLowerCase() == "true" ? "true" : null);
+ }
+
+ /**
+ * Crude applet innerHTML parser
+ *
+ * @param tag
+ * @param attr
+ * @return
+ */
+ private static String getAttr(String tag, String attr)
+ {
+ int pt = tag.indexOf(attr + "=\"");
+ if (pt < 0)
+ {
+ System.out
+ .println("AppletParams did not read " + attr + " in " + tag);
+ return null;
+ }
+ // <param name="sortByTree" value="True"/>
+ int pt1 = pt + attr.length() + 2;
+ int pt2 = tag.indexOf("\"", pt1);
+ return (pt < 0 ? null : tag.substring(pt1, pt2));
+ }
+
+ public static void main(String[] args)
+ {
+ new AppletParams("<applet\r\n"
+ + " code=\"jalview.bin.JalviewLite\" width=\"140\" height=\"35\"\r\n"
+ + " archive=\"jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar\"> \r\n"
+ + " <param name=\"permissions\" value=\"sandbox\"/>\r\n"
+ + " <param name=\"file\" value=\"uniref50.fa\"/>\r\n"
+ + " <param name=\"treeFile\" value=\"ferredoxin.nw\"/>\r\n"
+ + " <param name=\"userDefinedColour\" value=\"C=yellow; R,K,H=FF5555; D,E=5555FF\"/>\r\n"
+ + " <param name=\"sortByTree\" value=\"True\"/>\r\n"
+ + " <param name=\"showSequenceLogo\" value=\"true\"/>\r\n"
+ + " <param name=\"showGroupConsensus\" value=\"true\"/>\r\n"
+ + " <param name=\"showFullId\" value=\"false\"/>\r\n"
+ + " <param name=\"linkLabel_1\" value=\"Uniprot\"/>\r\n"
+ + " <param name=\"linkUrl_1\" value=\"http://www.uniprot.org/uniprot/$SEQUENCE_ID$\"/>\r\n"
+ + " <param name=\"linkLabel_2\" value=\"EMBL-EBI Search\"/>\r\n"
+ + " <param name=\"linkUrl_2\" value=\"http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$\"/>\r\n"
+ + " <param name=\"APPLICATION_URL\" value=\"http://www.jalview.org/services/launchApp\"/>\r\n"
+ + " </applet>");
+ }
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff