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 key = getAttr(arg, "name");
 129         String value = getAttr(arg, "value");
 130         String name = key;
 131         switch (name.toLowerCase())
 132         {
 133         case "alignpdbfiles":
 134           break;
 135         case "annotationcolour_max":
 136           name = "ANNOTATIONCOLOUR_MAX";
 137           break;
 138         case "annotationcolour_min":
 139           name = "ANNOTATIONCOLOUR_MIN";
 140           break;
 141         case "annotations":
 142           value = checkTF(value);
 143           break;
 144         case "application_url":
 145           name = "APPLICATION_URL";
 146           break;
 147         case "automaticscrolling":
 148           name = "automaticScrolling";
 149           break;
 150         case "centrecolumnlabels":
 151           break;
 152         case "defaultcolour":
 153           name = "DEFAULT_COLOUR"; // defaultColour
 154           break;
 155         case "defaultcolournuc":
 156           name = "DEFAULT_COLOUR_NUC";// defaultColourNuc
 157           break;
 158         case "defaultcolourprot":
 159           name = "DEFAULT_COLOUR_PROT";// defaultColourProt";
 160           break;
 161         case "enablesplitframe":
 162           name = "enableSplitFrame";
 163           break;
 164         case "externalstructureviewer":
 165           break;
 166         case "features":
 167           value = resourcePath + value;
 168           break;
 169         case "format":
 170           break;
 171         case "heightscale":
 172           name = "heightScale";
 173           break;
 174         case "hidefeaturegroups":
 175           break;
 176         case "jalviewhelpurl":
 177           break;
 178         case "jnetfile":
 179           value = resourcePath + value;
 180           break;
 181         case "jpredfile":
 182           value = resourcePath + value;
 183           break;
 184         case "label":
 185           break;
 186         case "linklabel_":
 187           name = "linkLabel_";
 188           break;
 189         case "linklabel_1":
 190           name = "linkLabel_1";
 191           break;
 192         case "linkurl_":
 193           name = "linkURL_";
 194           break;
 195         case "nojmol":
 196           break;
 197         case "normaliselogo":
 198           name = "normaliseLogo";
 199           break;
 200         case "normalisesequencelogo":
 201           name = "normaliseSequenceLogo";
 202           break;
 203         case "oninit":
 204           break;
 205         case "pdbfile":
 206           name = "PDBFILE";
 207           break;
 208         case "pdbseq":
 209           name = "PDBSEQ";
 210           break;
 211         case "relaxedidmatch":
 212           break;
 213         case "resolvetocodebase":
 214           break;
 215         case "rgb":
 216           name = "RGB";
 217           break;
 218         case "scaleproteinascdna":
 219           name = "scaleProteinAsCdna";
 220           break;
 221         case "scorefile":
 222           name = "scoreFile";
 223           value = resourcePath + value;
 224           break;
 225         case "separator":
 226           break;
 227         case "sequence":
 228           break;
 229         case "sortby":
 230           name = "sortBy";
 231           break;
 232         case "sortbytree":
 233           value = checkTF(value);
 234           key = null; // taken care of by Jalview
 235           break;
 236         case "tree":
 237         case "treefile":
 238           name = "tree";
 239           value = resourcePath + value;
 240           key = null; // taken care of by Jalview
 241           break;
 242         case "uppercase":
 243           name = "upperCase";
 244           break;
 245         case "userdefinedcolour":
 246           name = "colour";
 247           break;
 248         case "widthscale":
 249           name = "widthScale";
 250           break;
 251         case "windowheight":
 252           name = "windowHeight";
 253           break;
 254         case "windowwidth":
 255           name = "windowWidth";
 256           break;
 257         case "wrap":
 258           break;
 259
 260         // cases not handled in doc/parameters.xlsx
 261         case "debug":
 262           value = checkTF(value);
 263           break;
 264         case "file":
 265           name = "open";
 266           value = resourcePath + value;
 267           break;
 268         case "file2":
 269           value = resourcePath + value;
 270           break;
 271         case "embedded":
 272           value = checkTF(value);
 273           break;
 274         case "showannotation":
 275           name = "SHOW_ANNOTATIONS";
 276           value = checkTF(value);
 277           break;
 278         case "showbutton":
 279           value = checkTF(value);
 280           break;
 281         case "showconsensus":
 282           name = "SHOW_CONSENSUS_LOGO";
 283           value = checkTF(value);
 284           break;
 285         case "showconsensushistogram":
 286           name = "SHOW_CONSENSUS_HISTOGRAM";
 287           value = checkTF(value);
 288           break;
 289         case "showconservation":
 290           name = "SHOW_CONSERVATION";
 291           value = checkTF(value);
 292           break;
 293         case "showfeaturegroups":
 294           value = checkTF(value);
 295           break;
 296         case "showfeaturesettings":
 297           name = "showFeatureSettings";
 298           value = checkTF(value);
 299           break;
 300         case "showfullid":
 301           name = "showFullId";
 302           value = checkTF(value);
 303           break;
 304         case "showgroupconsensus":
 305           name = "SHOW_GROUP_CONSENSUS";
 306           value = checkTF(value);
 307           break;
 308         case "showgroupconservation":
 309           name = "SHOW_GROUP_CONSERVATION";
 310           value = checkTF(value);
 311           break;
 312         case "showoccupancy":
 313           name = "SHOW_OCCUPANCY";
 314           value = checkTF(value);
 315           break;
 316         case "showquality":
 317           name = "SHOW_QUALITY";
 318           value = checkTF(value);
 319           break;
 320         case "showsequencelogo":
 321           name = "showSequenceLogo";
 322           value = checkTF(value);
 323           break;
 324         case "showtreebootstraps":
 325           name = "showTreeBootstraps";
 326           value = checkTF(value);
 327           break;
 328         case "showtreedistances":
 329           name = "showTreeDistances";
 330           value = checkTF(value);
 331           break;
 332         case "showunconserved":
 333           name = "showUnconserved";
 334           value = checkTF(value);
 335           break;
 336         case "showunlinkedtreenodes":
 337           name = "showUnlinkedTreeNodes";
 338           value = checkTF(value);
 339           break;
 340         default:
 341           break;
 342         }
 343         if (value != null)
 344         {
 345           vargs.add(name);
 346           if (value != "true")
 347           {
 348             vargs.add(value);
 349           }
 350         }
 351         if (value == null)
 352         {
 353           value = "false";
 354         }
 355         System.out.println("AppletParams name=" + name + " value=" + value);
 356         Cache.setPropertyNoSave(name, value);
 357         if (key != null)
 358         {
 359           appletParams.put(key, value);
 360         }
 361       }
 362     }
 363     return appletParams;
 364   }
 365
 366   /**
 367    * Check for a single-argument option.
 368    *
 369    * @param value
 370    * @return "true" or null
 371    */
 372   private static String checkTF(String value)
 373   {
 374     return (value.toLowerCase() == "true" ? "true" : null);
 375   }
 376
 377   /**
 378    * Crude applet innerHTML parser
 379    *
 380    * @param tag
 381    * @param attr
 382    * @return
 383    */
 384   private static String getAttr(String tag, String attr)
 385   {
 386     int pt = tag.indexOf(attr + "=\"");
 387     if (pt < 0)
 388     {
 389       System.out
 390               .println("AppletParams did not read " + attr + " in " + tag);
 391       return null;
 392     }
 393     // <param name="sortByTree" value="True"/>
 394     int pt1 = pt + attr.length() + 2;
 395     int pt2 = tag.indexOf("\"", pt1);
 396     return (pt < 0 ? null : tag.substring(pt1, pt2));
 397   }
 398
 399   public static void main(String[] args)
 400   {
 401     new AppletParams("<applet\r\n"
 402             + "    code=\"jalview.bin.JalviewLite\" width=\"140\" height=\"35\"\r\n"
 403             + "    archive=\"jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar\">  \r\n"
 404             + "  <param name=\"permissions\" value=\"sandbox\"/>\r\n"
 405             + "  <param name=\"file\" value=\"uniref50.fa\"/>\r\n"
 406             + "  <param name=\"treeFile\" value=\"ferredoxin.nw\"/>\r\n"
 407             + "  <param name=\"userDefinedColour\" value=\"C=yellow; R,K,H=FF5555; D,E=5555FF\"/>\r\n"
 408             + "  <param name=\"sortByTree\" value=\"True\"/>\r\n"
 409             + "  <param name=\"showSequenceLogo\" value=\"true\"/>\r\n"
 410             + "  <param name=\"showGroupConsensus\" value=\"true\"/>\r\n"
 411             + "  <param name=\"showFullId\" value=\"false\"/>\r\n"
 412             + "    <param name=\"linkLabel_1\" value=\"Uniprot\"/>\r\n"
 413             + "    <param name=\"linkUrl_1\" value=\"http://www.uniprot.org/uniprot/$SEQUENCE_ID$\"/>\r\n"
 414             + "    <param name=\"linkLabel_2\" value=\"EMBL-EBI Search\"/>\r\n"
 415             + "    <param name=\"linkUrl_2\" value=\"http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$\"/>\r\n"
 416             + "    <param name=\"APPLICATION_URL\" value=\"http://www.jalview.org/services/launchApp\"/>\r\n"
 417             + "     </applet>");
 418   }
 419
 420 }