Examples of makeListItem()

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

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    if(smiles != null) ne.addAttribute(new Attribute("SMILES", smiles));
    if(inchi != null) ne.addAttribute(new Attribute("InChI", inchi));
    doc.setTitle(ne);
    Element list = doc.addList();
         
    list.appendChild(doc.makeListItem("Name: " + name));
    list.appendChild(doc.makeListItem("Type: " + type));
    if(smiles != null) list.appendChild(doc.makeListItem("SMILES: " + smiles));
    if(inchi != null) list.appendChild(doc.makeListItem("InChI: " + inchi));
   
    if(inchi != null) {
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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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    if(inchi != null) ne.addAttribute(new Attribute("InChI", inchi));
    doc.setTitle(ne);
    Element list = doc.addList();
         
    list.appendChild(doc.makeListItem("Name: " + name));
    list.appendChild(doc.makeListItem("Type: " + type));
    if(smiles != null) list.appendChild(doc.makeListItem("SMILES: " + smiles));
    if(inchi != null) list.appendChild(doc.makeListItem("InChI: " + inchi));
   
    if(inchi != null) {
      Collection<String> synonyms = ChemNameDictSingleton.getNamesFromInChI(inchi);
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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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    doc.setTitle(ne);
    Element list = doc.addList();
         
    list.appendChild(doc.makeListItem("Name: " + name));
    list.appendChild(doc.makeListItem("Type: " + type));
    if(smiles != null) list.appendChild(doc.makeListItem("SMILES: " + smiles));
    if(inchi != null) list.appendChild(doc.makeListItem("InChI: " + inchi));
   
    if(inchi != null) {
      Collection<String> synonyms = ChemNameDictSingleton.getNamesFromInChI(inchi);
      if(synonyms != null) {
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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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    Element list = doc.addList();
         
    list.appendChild(doc.makeListItem("Name: " + name));
    list.appendChild(doc.makeListItem("Type: " + type));
    if(smiles != null) list.appendChild(doc.makeListItem("SMILES: " + smiles));
    if(inchi != null) list.appendChild(doc.makeListItem("InChI: " + inchi));
   
    if(inchi != null) {
      Collection<String> synonyms = ChemNameDictSingleton.getNamesFromInChI(inchi);
      if(synonyms != null) {
        Element li = doc.makeListItem("Synonyms:");
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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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    if(inchi != null) list.appendChild(doc.makeListItem("InChI: " + inchi));
   
    if(inchi != null) {
      Collection<String> synonyms = ChemNameDictSingleton.getNamesFromInChI(inchi);
      if(synonyms != null) {
        Element li = doc.makeListItem("Synonyms:");
        li.appendChild(doc.makeList(synonyms));
        list.appendChild(li);
      }
    }
   
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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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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&amp;db=pccompound&amp;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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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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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&amp;db=pccompound&amp;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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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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    list.appendChild(doc.makeListItem(doc.makeLink("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&amp;db=pccompound&amp;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&amp;db=pccompound&amp;term=" +
            URLEncoder.encode("\"" + inchi + "\"[InChI]", "UTF-8"), "Search PubChem by InChI")));       
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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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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&amp;db=pccompound&amp;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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Examples of uk.ac.cam.ch.wwmm.ptclib.scixml.SciXMLDocument.makeListItem()

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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&amp;db=pccompound&amp;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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