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<p>......the number of pertussis cases in California was again as high in 2010 as it was in 1947 (Kuehn, <xref ref-type="fig" rid="fim988-bib-0047"/>. Despite a close to 85% worldwide...</p>

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<ref id="fim988-bib-0047"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kuehn</surname><given-names>BM</given-names></name></person-group> (<year>2010</year>) <article-title>Panel backs wider pertussis vaccination to curb outbreaks, prevent deaths</article-title>. <source>JAMA</source> <volume>304</volume>: <fpage>2684</fpage>&#x2013;<lpage>2686</lpage>.</citation></ref>

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Kuehn, <xref ref-type="fig" rid="fim988-bib-0047"/>
<xref ref-type="bibr" rid="fim988-bib-0047">Kuehn, 2010</xref>

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  // Define folder path with the XML files to modify.
   var sFolderXML = "C:\\Temp\\FolderA\\";
   // Define folder path with the XML reference files.
   var sFolderREF = "C:\\Temp\\FolderB\\";

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//== Main ==================================================================

// Verify existence of function GetListOfFiles in this script.
if(typeof(GetListOfFiles) != "function")
{
   UltraEdit.messageBox("Function GetListOfFiles is missing in script.\n\nSee UltraEdit forum topic\n\nhttp://forums.ultraedit.com/viewtopic.php?f=52&t=5442");
}
// Verify existence of function GetFileName in this script.
else if(typeof(GetFileName) != "function")
{
   UltraEdit.messageBox("Function GetFileName is missing in script.\n\nSee UltraEdit forum topic\n\nhttp://forums.ultraedit.com/viewtopic.php?f=52&t=6762");
}
else
{  // The two folder paths below must end with a backslash!

   // Define folder path with the XML files to modify.
   var sFolderXML = "C:\\Temp\\FolderA\\";
   // Define folder path with the XML reference files.
   var sFolderREF = "C:\\Temp\\FolderB\\";

   // Define environment for this script.
   UltraEdit.insertMode();
   UltraEdit.columnModeOff();

   // Define document index numbers for the XML file to modify and
   // the corresponding reference file as they will have later in
   // array of opened documents of UltraEdit/UEStudio.
   var g_nXmlFile = UltraEdit.document.length + 1;
   var g_nRefFile = g_nXmlFile + 1;
   var nListFile  = UltraEdit.document.length;

   // Global counters used for summary information.
   var g_nTotalFound   = 0;
   var g_nTotalUpdated = 0;

   // Enable debug messages for GetListOfFiles and GetFileName.
   var g_nDebugMessage = 2;

   // Get the list of file names of all XML files in specified folder.
   if (GetListOfFiles(0,sFolderXML,"*.xml",false))
   {
      // Creation of list was successful. Select the complete list and
      // load it into an array of strings for opening each file in a loop.
      UltraEdit.activeDocument.selectAll();
      var asFileNames = UltraEdit.activeDocument.selection.split("\r\n");
      if (asFileNames[asFileNames.length-1] == "") asFileNames.pop();
      // Cancel the selection as it looks better on script execution.
      UltraEdit.activeDocument.top();

      // Prepare output window for script process information output.
      UltraEdit.outputWindow.clear();
      if (UltraEdit.outputWindow.visible == false)
      {
         UltraEdit.outputWindow.showWindow(true);
      }

      // Select once Perl regular expression engine.
      UltraEdit.perlReOn();

      // Process now the XML file pairs in a loop.
      for (var nFile = 0; nFile < asFileNames.length; nFile++)
      {
         UltraEdit.open(asFileNames[nFile]);
         UltraEdit.open(sFolderREF+GetFileName(asFileNames[nFile])+"_REF.xml");

         // Always make list file the active file to avoid display updates
         // if the document windows are maximized which reduces total time
         // needed to finish this script.
         UltraEdit.document[nListFile].setActive();

         // Show in output window which file is currently processed.
         UltraEdit.outputWindow.write("Processing file "+asFileNames[nFile]+" ...");

         // Do the actual find and replace in the two XML files.
         FindAndReplace();

         // Close not modified reference file and modified XML file
         // with saving. Attention: The order is important here!
         UltraEdit.closeFile(UltraEdit.document[g_nRefFile].path,2);
         UltraEdit.closeFile(UltraEdit.document[g_nXmlFile].path,1);
      }

      // Close now also the file with the file names without saving.
      UltraEdit.closeFile(UltraEdit.document[nListFile].path,2);

      // Output a short summary information in output window.
      UltraEdit.outputWindow.write("Summary:\n\nTotal number of references found:   "+g_nTotalFound);
      UltraEdit.outputWindow.write("Total number of references updated: "+g_nTotalUpdated);
      UltraEdit.outputWindow.showStatus=false;
   }
}

//== FindAndReplace ========================================================

function FindAndReplace()
{
   var nRefFound = 0;
   var nRefUpdated = 0;
   var bTopPosition = true;
   var bFirstMissing = true;

   // Define once all parameters for the Perl regular expression
   // finds used in both XML files to find the references.
   UltraEdit.document[g_nXmlFile].findReplace.mode=0;
   UltraEdit.document[g_nXmlFile].findReplace.matchCase=true;
   UltraEdit.document[g_nXmlFile].findReplace.matchWord=false;
   UltraEdit.document[g_nXmlFile].findReplace.regExp=true;
   UltraEdit.document[g_nXmlFile].findReplace.searchDown=true;
   if (typeof(UltraEdit.document[g_nXmlFile].findReplace.searchInColumn) == "boolean")
   {
      UltraEdit.document[g_nXmlFile].findReplace.searchInColumn=false;
   }

   UltraEdit.document[g_nRefFile].findReplace.mode=0;
   UltraEdit.document[g_nRefFile].findReplace.matchCase=true;
   UltraEdit.document[g_nRefFile].findReplace.matchWord=false;
   UltraEdit.document[g_nRefFile].findReplace.regExp=true;
   UltraEdit.document[g_nRefFile].findReplace.searchDown=true;
   if (typeof(UltraEdit.document[g_nXmlFile].findReplace.searchInColumn) == "boolean")
   {
      UltraEdit.document[g_nXmlFile].findReplace.searchInColumn=false;
   }

   while(UltraEdit.document[g_nXmlFile].findReplace.find('\\(.*?, *?<xref ref-type="fig" rid="fim[0-9]+-bib-[0-9]+"/>'))
   {
      nRefFound++;
      var sXmlFound = UltraEdit.document[g_nXmlFile].selection;
      var sRID = sXmlFound.replace(/^.*rid="(fim\d+-bib-\d+)"\/>/,"$1");

      var sRefFound = "";
      if(UltraEdit.document[g_nRefFile].findReplace.find('<ref id="'+sRID+'">.*?<year>[0-9]+</year>'))
      {
         sRefFound = UltraEdit.document[g_nRefFile].selection;
      }
      else if(!bTopPosition)
      {  // Identification not found downwards from last found string
         // position. Search in entire file from top to bottom.
         bTopPosition = true;
         UltraEdit.document[g_nRefFile].top();
         if(UltraEdit.document[g_nRefFile].findReplace.find('<ref id="'+sRID+'">.*?<year>[0-9]+</year>'))
         {
            sRefFound = UltraEdit.document[g_nRefFile].selection;
         }
      }
      if(sRefFound.length)
      {
         bTopPosition = false;
         var sYear = sRefFound.replace(/^.*?<year>(\d+)<\/year>/,"$1");
         var sNewRef = sXmlFound.replace(/^\((.*?,) *?<xref ref-type="fig"( rid=".*")\/>/,'(<xref ref-type="bibr"$2>$1 '+sYear+"</xref>");
         UltraEdit.document[g_nXmlFile].write(sNewRef);
         nRefUpdated++;
      }
      else
      {
         if(bFirstMissing)
         {
            bFirstMissing = false;
            UltraEdit.outputWindow.write("");
         }
         UltraEdit.outputWindow.write("Line "+UltraEdit.document[g_nXmlFile].currentLineNum+': "'+sRID+'" not found.');
      }
   }
   g_nTotalFound += nRefFound;
   g_nTotalUpdated += nRefUpdated;
   UltraEdit.outputWindow.write("\nNumber of references found:   "+nRefFound);
   UltraEdit.outputWindow.write("Number of references updated: "+nRefUpdated+"\n");
}