src/jalview/bin/AppletParams.java

   1 package jalview.bin;
   2
   3 import java.util.HashMap;
   4 import java.util.Map;
   5
   6 /**
   7  * Collection of all known applet tags from JalviewLite
   8  *
   9  * @author hansonr
  10  *
  11  */
  12 @SuppressWarnings("serial")
  13 public class AppletParams extends HashMap<String, String>
  14 {
  15
  16   private final static String[] params = { "alignpdbfiles",
  17       "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN", "annotations",
  18       "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
  19       "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
  20       "embedded", "enableSplitFrame", "externalstructureviewer", "features",
  21       "file", "file2", "format", "heightScale", "hidefeaturegroups",
  22       "jalviewhelpurl", "jnetfile", "jpredfile", "label", "linkLabel_",
  23       "linkLabel_1", "linkURL_", "nojmol", "normaliseLogo",
  24       "normaliseSequenceLogo", "oninit", "PDBFILE", "PDBSEQ",
  25       "relaxedidmatch", "resolvetocodebase", "RGB", "scaleProteinAsCdna",
  26       "scoreFile", "separator", "sequence", "showAnnotation", "showbutton",
  27       "showConsensus", "showConsensusHistogram", "showConservation",
  28       "showfeaturegroups", "showFeatureSettings", "showFullId",
  29       "showGroupConsensus", "showGroupConservation", "showOccupancy",
  30       "showQuality", "showSequenceLogo", "showTreeBootstraps",
  31       "showTreeDistances", "showUnconserved", "showUnlinkedTreeNodes",
  32       "sortBy", "sortByTree", "tree", "treeFile", "upperCase",
  33       "userDefinedColour", "widthScale", "windowHeight", "windowWidth",
  34       "wrap", };
  35
  36   public AppletParams(Map<String, String> info)
  37   {
  38     for (int i = params.length; --i >= 0;)
  39     {
  40       put(params[i], info.get(params[i]));
  41     }
  42   }
  43
  44   public String getParam(String param, String def)
  45   {
  46     String val = get(param);
  47     return (val != null ? val : def);
  48   }
  49
  50   // <applet
  51   // code="jalview.bin.JalviewLite" width="140" height="35"
  52   // archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  53   // <param name="permissions" value="sandbox"/>
  54   // <param name="file" value="uniref50.fa"/>
  55   // <param name="treeFile" value="ferredoxin.nw"/>
  56   // <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555;
  57   // D,E=5555FF"/>
  58   // <param name="sortByTree" value="True"/>
  59   // <param name="showSequenceLogo" value="true"/>
  60   // <param name="showGroupConsensus" value="true"/>
  61   // <param name="showFullId" value="false"/>
  62   // <param name="linkLabel_1" value="Uniprot"/>
  63   // <param name="linkUrl_1"
  64   // value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  65   // <param name="linkLabel_2" value="EMBL-EBI Search"/>
  66   // <param name="linkUrl_2"
  67   // value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  68   // <param name="APPLICATION_URL"
  69   // value="http://www.jalview.org/services/launchApp"/>
  70   // </applet>
  71   //
  72   public AppletParams(String outerHTML)
  73   {
  74     String[] tokens = outerHTML.split("<param");
  75     outerHTML = tokens[0];
  76     String code = getAttr(outerHTML, "code");
  77     if (!code.equals("jalview.bin.JalviewLite"))
  78     {
  79       return;
  80     }
  81     for (int i = tokens.length; --i > 0;)
  82     {
  83       String param = tokens[i];
  84       String key = getAttr(param, "name");
  85       if (key != null)
  86       {
  87         String value = getAttr(param, "value");
  88         System.out.println("AppletParams " + key + " = \"" + value + "\"");
  89         put(key, value);
  90       }
  91     }
  92     put("_width", getAttr(outerHTML, "width"));
  93     put("_height", getAttr(outerHTML, "height"));
  94     put("_id", getAttr(outerHTML, "id"));
  95     put("_name", getAttr(outerHTML, "name"));
  96     put("_archive", getAttr(outerHTML, "archive"));
  97     put("_code", code);
  98   }
  99
 100   /**
 101    * Crude applet innerHTML parser
 102    *
 103    * @param tag
 104    * @param attr
 105    * @return
 106    */
 107   private String getAttr(String tag, String attr)
 108   {
 109     int pt = tag.indexOf(attr + "=\"");
 110     if (pt < 0)
 111     {
 112       System.out
 113               .println("AppletParams did not read " + attr + " in " + tag);
 114       return null;
 115     }
 116     // <param name="sortByTree" value="True"/>
 117     int pt1 = pt + attr.length() + 2;
 118     int pt2 = tag.indexOf("\"", pt1);
 119     return (pt < 0 ? null : tag.substring(pt1, pt2));
 120   }
 121
 122   public static void main(String[] args)
 123   {
 124     new AppletParams("<applet\r\n"
 125             + "    code=\"jalview.bin.JalviewLite\" width=\"140\" height=\"35\"\r\n"
 126             + "    archive=\"jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar\">  \r\n"
 127             + "  <param name=\"permissions\" value=\"sandbox\"/>\r\n"
 128             + "  <param name=\"file\" value=\"uniref50.fa\"/>\r\n"
 129             + "  <param name=\"treeFile\" value=\"ferredoxin.nw\"/>\r\n"
 130             + "  <param name=\"userDefinedColour\" value=\"C=yellow; R,K,H=FF5555; D,E=5555FF\"/>\r\n"
 131             + "  <param name=\"sortByTree\" value=\"True\"/>\r\n"
 132             + "  <param name=\"showSequenceLogo\" value=\"true\"/>\r\n"
 133             + "  <param name=\"showGroupConsensus\" value=\"true\"/>\r\n"
 134             + "  <param name=\"showFullId\" value=\"false\"/>\r\n"
 135             + "    <param name=\"linkLabel_1\" value=\"Uniprot\"/>\r\n"
 136             + "    <param name=\"linkUrl_1\" value=\"http://www.uniprot.org/uniprot/$SEQUENCE_ID$\"/>\r\n"
 137             + "    <param name=\"linkLabel_2\" value=\"EMBL-EBI Search\"/>\r\n"
 138             + "    <param name=\"linkUrl_2\" value=\"http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$\"/>\r\n"
 139             + "    <param name=\"APPLICATION_URL\" value=\"http://www.jalview.org/services/launchApp\"/>\r\n"
 140             + "     </applet>");
 141   }
 142
 143 }