Package uk.ac.cam.ch.wwmm.ptclib.scixml

Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeLink()

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    String scrubbedName = name;
    if(scrubbedName.endsWith("s")) scrubbedName = scrubbedName.substring(0, scrubbedName.length()-1);
    scrubbedName = scrubbedName.replaceAll("\u00ad", "");
    String urlName = URLEncoder.encode(scrubbedName, "UTF-8");
   
    list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=pccompound&term=" +
        URLEncoder.encode("\"" + scrubbedName + "\"[CSYN]", "UTF-8"), "Search PubChem for " + scrubbedName)));
    //list.appendChild(doc.makeListItem(doc.makeLink("PubChem?name=" + urlName, "Fetch structures for " + scrubbedName + " from PubChem")));
    if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlName +
        "&type=word&resultsType=snippets", "Search local by name")));
    if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("/ChemNameDict?action=stop&word=" + urlName, "Add " + scrubbedName + " as stopword")));
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    String urlName = URLEncoder.encode(scrubbedName, "UTF-8");
   
    list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=pccompound&term=" +
        URLEncoder.encode("\"" + scrubbedName + "\"[CSYN]", "UTF-8"), "Search PubChem for " + scrubbedName)));
    //list.appendChild(doc.makeListItem(doc.makeLink("PubChem?name=" + urlName, "Fetch structures for " + scrubbedName + " from PubChem")));
    if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlName +
        "&type=word&resultsType=snippets", "Search local by name")));
    if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("/ChemNameDict?action=stop&word=" + urlName, "Add " + scrubbedName + " as stopword")));

    if(inchi != null) {
      String urlInchi = URLEncoder.encode(inchi, "UTF-8");
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    list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=pccompound&term=" +
        URLEncoder.encode("\"" + scrubbedName + "\"[CSYN]", "UTF-8"), "Search PubChem for " + scrubbedName)));
    //list.appendChild(doc.makeListItem(doc.makeLink("PubChem?name=" + urlName, "Fetch structures for " + scrubbedName + " from PubChem")));
    if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlName +
        "&type=word&resultsType=snippets", "Search local by name")));
    if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("/ChemNameDict?action=stop&word=" + urlName, "Add " + scrubbedName + " as stopword")));

    if(inchi != null) {
      String urlInchi = URLEncoder.encode(inchi, "UTF-8");
      list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=pccompound&term=" +
            URLEncoder.encode("\"" + inchi + "\"[InChI]", "UTF-8"), "Search PubChem by InChI")));       
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        "&type=word&resultsType=snippets", "Search local by name")));
    if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("/ChemNameDict?action=stop&word=" + urlName, "Add " + scrubbedName + " as stopword")));

    if(inchi != null) {
      String urlInchi = URLEncoder.encode(inchi, "UTF-8");
      list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=pccompound&term=" +
            URLEncoder.encode("\"" + inchi + "\"[InChI]", "UTF-8"), "Search PubChem by InChI")));       
      if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlInchi +
          "&type=inchi&resultsType=snippets", "Search local by InChI")));
      if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlInchi +
          "&type=inchi&resultsType=compoundsList", "Search local for co-occuring compounds")));
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    if(inchi != null) {
      String urlInchi = URLEncoder.encode(inchi, "UTF-8");
      list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=pccompound&term=" +
            URLEncoder.encode("\"" + inchi + "\"[InChI]", "UTF-8"), "Search PubChem by InChI")));       
      if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlInchi +
          "&type=inchi&resultsType=snippets", "Search local by InChI")));
      if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlInchi +
          "&type=inchi&resultsType=compoundsList", "Search local for co-occuring compounds")));
    }
   
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      String urlInchi = URLEncoder.encode(inchi, "UTF-8");
      list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=pccompound&term=" +
            URLEncoder.encode("\"" + inchi + "\"[InChI]", "UTF-8"), "Search PubChem by InChI")));       
      if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlInchi +
          "&type=inchi&resultsType=snippets", "Search local by InChI")));
      if(!cutDown) list.appendChild(doc.makeListItem(doc.makeLink("Search?query=" + urlInchi +
          "&type=inchi&resultsType=compoundsList", "Search local for co-occuring compounds")));
    }
   
    if(ontIDs != null) {
      String [] oo = ontIDs.split("\\s+");
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          String pid = ontID.substring(4, ontID.length());
          String lastDigit = pid.substring(pid.length()-1, pid.length());
          String penultimateDigit = pid.substring(pid.length()-2, pid.length()-1);
         
          list.appendChild(doc.makeListItem(doc.makeLink("http://wwmm.ch.cam.ac.uk/polymers/polyinfo/" +
              penultimateDigit + "/" + lastDigit + "/" + pid + "/" + pid + ".html", "Get polymer data for " + ontID)));
         
        }
       
       
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        }
       
       
        else {

          list.appendChild(doc.makeListItem(doc.makeLink("http://www.ebi.ac.uk/ontology-lookup/browse.do?termId=" +
            urlOntID, "Look up " + ontID + " using EBI Ontology Lookup Service")));
        }
      }
    }
   
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      Element list = doc.addList();
      File [] dirs = new File(Oscar3Props.getInstance().workspace, "corpora").listFiles();
      for(int i=0;i<dirs.length;i++) {
        String name = dirs[i].getName();
        if(dirs[i].isDirectory() && !name.startsWith("."))  {
          Element a = doc.makeLink("Search?setcorpus=" + URLEncoder.encode(name, "UTF-8"), name);
          list.appendChild(doc.makeListItem(a));
        }
      }

      Element a = doc.makeLink("Search?settoscrap", "ScrapBook");
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          Element a = doc.makeLink("Search?setcorpus=" + URLEncoder.encode(name, "UTF-8"), name);
          list.appendChild(doc.makeListItem(a));
        }
      }

      Element a = doc.makeLink("Search?settoscrap", "ScrapBook");
      list.appendChild(doc.makeListItem(a));

      a = doc.makeLink("Search?indexall", "Index entire workspace");
      list.appendChild(doc.makeListItem(a));
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