src/jalview/bin/AppletParams.java

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