src/jalview/bin/AppletParams.java

   1 package jalview.bin;
   2
   3 import jalview.gui.Preferences;
   4
   5 import java.util.HashMap;
   6 import java.util.Map;
   7 import java.util.Vector;
   8
   9 /**
  10  * Collection of all known applet tags from JalviewLite
  11  *
  12  * @author hansonr
  13  *
  14  */
  15 @SuppressWarnings("serial")
  16 public class AppletParams extends HashMap<String, String>
  17 {
  18
  19   private final static String[] params = { "alignpdbfiles",
  20       Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN,
  21       "annotations",
  22       "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
  23       "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
  24       "embedded", "enableSplitFrame", "externalstructureviewer", "features",
  25       "file", "file2", "format", "heightScale", "hidefeaturegroups",
  26       "jalviewhelpurl", "jnetfile", "jpredfile", "label", "linkLabel_",
  27       "linkLabel_1", "linkURL_", "nojmol", "normaliseLogo",
  28       "normaliseSequenceLogo", "oninit", "PDBFILE", "PDBSEQ",
  29       "relaxedidmatch", "resolvetocodebase", "RGB", "scaleProteinAsCdna",
  30       "scoreFile", "separator", "sequence", "showAnnotation", "showbutton",
  31       "showConsensus", "showConsensusHistogram", "showConservation",
  32       "showfeaturegroups", "showFeatureSettings", "showFullId",
  33       "showGroupConsensus", "showGroupConservation", "showOccupancy",
  34       "showQuality", "showSequenceLogo", "showTreeBootstraps",
  35       "showTreeDistances", "showUnconserved", "showUnlinkedTreeNodes",
  36       "sortBy", "sortByTree", "tree", "treeFile", "upperCase",
  37       "userDefinedColour", "widthScale", "windowHeight", "windowWidth",
  38       "wrap", };
  39
  40   public AppletParams(Map<String, String> info)
  41   {
  42     for (int i = params.length; --i >= 0;)
  43     {
  44       put(params[i], info.get(params[i]));
  45     }
  46   }
  47
  48   public String getParam(String param, String def)
  49   {
  50     String val = get(param);
  51     return (val != null ? val : def);
  52   }
  53
  54   // <applet
  55   // code="jalview.bin.JalviewLite" width="140" height="35"
  56   // archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  57   // <param name="permissions" value="sandbox"/>
  58   // <param name="file" value="uniref50.fa"/>
  59   // <param name="treeFile" value="ferredoxin.nw"/>
  60   // <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555;
  61   // D,E=5555FF"/>
  62   // <param name="sortByTree" value="True"/>
  63   // <param name="showSequenceLogo" value="true"/>
  64   // <param name="showGroupConsensus" value="true"/>
  65   // <param name="showFullId" value="false"/>
  66   // <param name="linkLabel_1" value="Uniprot"/>
  67   // <param name="linkUrl_1"
  68   // value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  69   // <param name="linkLabel_2" value="EMBL-EBI Search"/>
  70   // <param name="linkUrl_2"
  71   // value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  72   // <param name="APPLICATION_URL"
  73   // value="http://www.jalview.org/services/launchApp"/>
  74   // </applet>
  75   //
  76   public AppletParams(String outerHTML)
  77   {
  78     String[] tokens = outerHTML.split("<param");
  79     outerHTML = tokens[0];
  80     String code = getAttr(outerHTML, "code");
  81     if (!code.equals("jalview.bin.JalviewLite"))
  82     {
  83       return;
  84     }
  85     for (int i = tokens.length; --i > 0;)
  86     {
  87       String param = tokens[i];
  88       String key = getAttr(param, "name");
  89       if (key != null)
  90       {
  91         String value = getAttr(param, "value");
  92         System.out.println("AppletParams " + key + " = \"" + value + "\"");
  93         put(key, value);
  94       }
  95     }
  96     put("_width", getAttr(outerHTML, "width"));
  97     put("_height", getAttr(outerHTML, "height"));
  98     put("_id", getAttr(outerHTML, "id"));
  99     put("_name", getAttr(outerHTML, "name"));
 100     put("_archive", getAttr(outerHTML, "archive"));
 101     put("_code", code);
 102   }
 103
 104   public AppletParams()
 105   {
 106     // TODO Auto-generated constructor stub
 107   }
 108
 109   public static AppletParams getAppletParams(String[] args,
 110           Vector<String> vargs)
 111   {
 112     AppletParams appletParams = new AppletParams();
 113     String resourcePath = null;
 114     for (int i = args.length; --i > 0;) // > 0 is correct, not >=0
 115     {
 116       if (args[i].startsWith("name=\"Info.resourcePath\""))
 117       {
 118         resourcePath = getAttr(args[i], "value");
 119         if (resourcePath.length() > 0 && !resourcePath.endsWith("/"))
 120         {
 121           resourcePath += "/";
 122         }
 123         break;
 124       }
 125     }
 126     for (int i = 1; i < args.length; i++)
 127     {
 128       String arg = args[i].trim();
 129       if (arg.startsWith("name="))
 130       {
 131         String appName = getAttr(arg, "name");
 132         String value = getAttr(arg, "value");
 133         String appletName = appName.toLowerCase();
 134
 135         // note that Application arguments ARE case-sensitive, but
 136         // Applet.getParameter() is not.
 137
 138         switch (appletName)
 139         {
 140
 141         // tested, working:
 142
 143         case "file":
 144           appName = "open";
 145           value = resourcePath + value;
 146           appletName = null;
 147           break;
 148         case "file2":
 149           value = resourcePath + value;
 150           appName = null;
 151           break;
 152         case "jnetfile":
 153           value = resourcePath + value;
 154           appName = null;
 155           break;
 156         case "jpredfile":
 157           value = resourcePath + value;
 158           appName = null;
 159           break;
 160         case "features":
 161           value = resourcePath + value;
 162           appName = null;
 163           break;
 164         case "pdbfile":
 165           value = resourcePath + value;
 166           appName = null;
 167           break;
 168         case "tree":
 169         case "treefile":
 170           appName = "tree";
 171           value = resourcePath + value;
 172           appletName = null; // taken care of by Jalview
 173           break;
 174         case "defaultcolour":
 175           appName = Preferences.DEFAULT_COLOUR;
 176           break;
 177         case "defaultcolournuc":
 178           appName = Preferences.DEFAULT_COLOUR_NUC;
 179           break;
 180         case "defaultcolourprot":
 181           appName = Preferences.DEFAULT_COLOUR_PROT;
 182           break;
 183
 184         // implemented; not tested:
 185
 186         case "oninit":
 187           appName = null;
 188           break;
 189         case "annotations":
 190           value = resourcePath + value;
 191           appName = null;
 192           break;
 193         case "annotationcolour_max":
 194           appName = Preferences.ANNOTATIONCOLOUR_MAX;
 195           break;
 196         case "annotationcolour_min":
 197           appName = Preferences.ANNOTATIONCOLOUR_MIN;
 198           break;
 199         case "enablesplitframe":
 200           appName = Preferences.ENABLE_SPLIT_FRAME;
 201           break;
 202         case "hidefeaturegroups":
 203           break;
 204         case "centrecolumnlabels":
 205           appName = null;
 206           break;
 207         case "pdbseq":
 208           appName = null;
 209           break;
 210         case "sortby":
 211           appName = Preferences.SORT_ALIGNMENT; // id, etc.
 212           break;
 213         case "sortbytree":
 214           appName = Preferences.SORT_BY_TREE;
 215           value = checkTF(value);
 216           appletName = null; // taken care of by Jalview
 217           break;
 218         case "format":
 219           break;
 220
 221         // probably not relevant:
 222
 223         case "externalstructureviewer":
 224           break;
 225         case "alignpdbfiles":
 226           break;
 227         case "application_url":
 228           appName = "APPLICATION_URL";
 229           break;
 230         case "automaticscrolling":
 231           appName = "automaticScrolling";
 232           break;
 233         case "heightscale":
 234           appName = "heightScale";
 235           break;
 236         case "jalviewhelpurl":
 237           break;
 238         case "label":
 239           break;
 240         case "linklabel_":
 241           appName = "linkLabel_";
 242           break;
 243         case "linklabel_1":
 244           appName = "linkLabel_1";
 245           break;
 246         case "linkurl_":
 247           appName = "linkURL_";
 248           break;
 249         case "rgb":
 250           appName = null; // no background for application
 251           break;
 252
 253         // unknown:
 254
 255         case "nojmol":
 256           break;
 257         case "normaliselogo":
 258           appName = Preferences.NORMALISE_LOGO;
 259           break;
 260         case "normalisesequencelogo":
 261           appName = Preferences.NORMALISE_CONSENSUS_LOGO;
 262           break;
 263         case "relaxedidmatch":
 264           break;
 265         case "resolvetocodebase":
 266           break;
 267         case "scaleproteinascdna":
 268           appName = "scaleProteinAsCdna";
 269           break;
 270         case "separator":
 271           break;
 272         case "sequence":
 273           break;
 274         case "uppercase":
 275           appName = "upperCase";
 276           break;
 277         case "userdefinedcolour":
 278           appName = "colour";
 279           break;
 280         case "widthscale":
 281           appName = "widthScale";
 282           break;
 283         case "windowheight":
 284           appName = "windowHeight";
 285           break;
 286         case "windowwidth":
 287           appName = "windowWidth";
 288           break;
 289         case "wrap":
 290           appName = Preferences.WRAP_ALIGNMENT;
 291           break;
 292         case "scorefile":
 293           appName = "scoreFile";
 294           value = resourcePath + value;
 295           break;
 296
 297         // TRUE/FALSE
 298
 299         case "debug":
 300           value = checkTF(value);
 301           break;
 302         case "embedded":
 303           value = checkTF(value);
 304           break;
 305         case "showbutton":
 306           value = checkTF(value);
 307           break;
 308         case "showannotation":
 309           appName = Preferences.SHOW_ANNOTATIONS;
 310           value = checkTF(value);
 311           break;
 312         case "showconsensus":
 313           appName = Preferences.SHOW_CONSENSUS_LOGO;
 314           value = checkTF(value);
 315           break;
 316         case "showconsensushistogram":
 317           appName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
 318           value = checkTF(value);
 319           break;
 320         case "showconservation":
 321           appName = Preferences.SHOW_CONSERVATION;
 322           value = checkTF(value);
 323           break;
 324         case "showgroupconsensus":
 325           appName = Preferences.SHOW_GROUP_CONSENSUS;
 326           value = checkTF(value);
 327           break;
 328         case "showgroupconservation":
 329           appName = Preferences.SHOW_GROUP_CONSERVATION;
 330           value = checkTF(value);
 331           break;
 332         case "showoccupancy":
 333           appName = Preferences.SHOW_OCCUPANCY;
 334           value = checkTF(value);
 335           break;
 336         case "showquality":
 337           appName = Preferences.SHOW_QUALITY;
 338           value = checkTF(value);
 339           break;
 340         case "showsequencelogo":
 341           appName = Preferences.SHOW_CONSENSUS_LOGO;
 342           value = checkTF(value);
 343           break;
 344         case "showfeaturegroups":
 345           value = checkTF(value);
 346           break;
 347         case "showfeaturesettings":
 348           appName = "showFeatureSettings";
 349           value = checkTF(value);
 350           break;
 351         case "showfullid":
 352           appName = "showFullId";
 353           value = checkTF(value);
 354           break;
 355         case "showtreebootstraps":
 356           appName = "showTreeBootstraps";
 357           value = checkTF(value);
 358           break;
 359         case "showtreedistances":
 360           appName = "showTreeDistances";
 361           value = checkTF(value);
 362           break;
 363         case "showunconserved":
 364           appName = Preferences.SHOW_UNCONSERVED;
 365           value = checkTF(value);
 366           break;
 367         case "showunlinkedtreenodes":
 368           appName = "showUnlinkedTreeNodes";
 369           value = checkTF(value);
 370           break;
 371         default:
 372           // could be pdbFile2, for example
 373           // or one of the app preference names
 374           break;
 375         }
 376         if (value != null)
 377         {
 378           vargs.add(appName);
 379           if (value != "true")
 380           {
 381             vargs.add(value);
 382           }
 383         }
 384         if (value == null)
 385         {
 386           value = "false";
 387         }
 388         System.out.println("AppletParams appName=" + appName + "appletName="
 389                 + appletName + " value=" + value);
 390         Cache.setPropertyNoSave(appName, value);
 391         if (appletName != null)
 392         {
 393           appletParams.put(appletName, value);
 394         }
 395       }
 396     }
 397     return appletParams;
 398   }
 399
 400   /**
 401    * Check for a single-argument option.
 402    *
 403    * @param value
 404    * @return "true" or null
 405    */
 406   private static String checkTF(String value)
 407   {
 408     return (value.toLowerCase() == "true" ? "true" : null);
 409   }
 410
 411   /**
 412    * Crude applet innerHTML parser
 413    *
 414    * @param tag
 415    * @param attr
 416    * @return
 417    */
 418   private static String getAttr(String tag, String attr)
 419   {
 420     int pt = tag.indexOf(attr + "=\"");
 421     if (pt < 0)
 422     {
 423       System.out
 424               .println("AppletParams did not read " + attr + " in " + tag);
 425       return null;
 426     }
 427     // <param name="sortByTree" value="True"/>
 428     int pt1 = pt + attr.length() + 2;
 429     int pt2 = tag.indexOf("\"", pt1);
 430     return (pt < 0 ? null : tag.substring(pt1, pt2));
 431   }
 432
 433   public static void main(String[] args)
 434   {
 435     new AppletParams("<applet\r\n"
 436             + "    code=\"jalview.bin.JalviewLite\" width=\"140\" height=\"35\"\r\n"
 437             + "    archive=\"jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar\">  \r\n"
 438             + "  <param name=\"permissions\" value=\"sandbox\"/>\r\n"
 439             + "  <param name=\"file\" value=\"uniref50.fa\"/>\r\n"
 440             + "  <param name=\"treeFile\" value=\"ferredoxin.nw\"/>\r\n"
 441             + "  <param name=\"userDefinedColour\" value=\"C=yellow; R,K,H=FF5555; D,E=5555FF\"/>\r\n"
 442             + "  <param name=\"sortByTree\" value=\"True\"/>\r\n"
 443             + "  <param name=\"showSequenceLogo\" value=\"true\"/>\r\n"
 444             + "  <param name=\"showGroupConsensus\" value=\"true\"/>\r\n"
 445             + "  <param name=\"showFullId\" value=\"false\"/>\r\n"
 446             + "    <param name=\"linkLabel_1\" value=\"Uniprot\"/>\r\n"
 447             + "    <param name=\"linkUrl_1\" value=\"http://www.uniprot.org/uniprot/$SEQUENCE_ID$\"/>\r\n"
 448             + "    <param name=\"linkLabel_2\" value=\"EMBL-EBI Search\"/>\r\n"
 449             + "    <param name=\"linkUrl_2\" value=\"http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$\"/>\r\n"
 450             + "    <param name=\"APPLICATION_URL\" value=\"http://www.jalview.org/services/launchApp\"/>\r\n"
 451             + "     </applet>");
 452   }
 453
 454 }