/** * Implements grammer rule "Authors" * * @param be * @throws IOException */ private void parseAuthors(BibtexEntry be) throws IOException { // read authors and institutions String authors = ""; String institutions = ""; while (this.lastLine != null && !this.lastLine.equals("") && !startsWithKeyword(recognizedFields)) { // read single author String author = null; String institution = null; boolean institutionDone = false; if (this.lastLine.indexOf('(') >= 0) { author = this.lastLine.substring(0, this.lastLine.indexOf('(')).trim(); institutionDone = this.lastLine.indexOf(')') > 0; institution = this.lastLine.substring(this.lastLine.indexOf('(') + 1, institutionDone && this.lastLine.indexOf(')') > this.lastLine.indexOf('(') + 1 ? this.lastLine.indexOf(')') : this.lastLine.length()).trim(); } else { author = this.lastLine.substring(0, this.lastLine.length()).trim(); institutionDone = true; } readLine(); while (!institutionDone && this.lastLine!= null) { institutionDone = this.lastLine.indexOf(')') > 0; institution += this.lastLine.substring(0, institutionDone ? this.lastLine.indexOf(')') : this.lastLine.length()).trim(); readLine(); } if (author != null) { authors += !authors.equals("") ? " and " + author : "" + author; } if (institution != null) { institutions += !institutions.equals("") ? " and " + institution : "" + institution; } } if (!authors.equals("")) { be.setField("author", authors); } if (!institutions.equals("")) { be.setField("institution", institutions); } }
/** * Parse the entries in the source, and return a List of BibtexEntry * objects. */ public List<BibtexEntry> importEntries(InputStream stream, OutputPrinter status) throws IOException { ArrayList<BibtexEntry> bibitems = new ArrayList<BibtexEntry>(); StringBuffer sb = new StringBuffer(); BufferedReader in = new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream)); String str; while ((str = in.readLine()) != null) { if (str.length() < 3) continue; // begining of a new item if (str.substring(0, 6).equals("PMID- ")) sb.append("::").append(str); else { String beg = str.substring(0, 6); if (beg.indexOf(" ") > 0) { sb.append(" ## "); // mark the begining of each field sb.append(str); } else { sb.append("EOLEOL"); // mark the end of each line sb.append(str.trim()); } } } String[] entries = sb.toString().split("::"); // skip the first entry as it is either empty or has document header HashMap<String, String> hm = new HashMap<String, String>(); for (int i = 0; i < entries.length; i++) { String[] fields = entries[i].split(" ## "); if (fields.length == 0) fields = entries[i].split("\n"); String Type = ""; String pages = ""; String shortauthor = ""; String fullauthor = ""; hm.clear(); for (int j = 0; j < fields.length; j++) { System.out.println(">>>"+fields[j]+"<<<"); //empty field don't do anything if (fields[j].length() <= 2) continue; String beg = fields[j].substring(0, 6); String value = fields[j].substring(6); value = value.trim(); if (beg.equals("PT - ")) { // PT = value.replaceAll("JOURNAL ARTICLE", "article").replaceAll("Journal Article", "article"); Type = "article"; //make all of them PT? } else if (beg.equals("TY - ")) { if ("CONF".equals(value)) Type = "inproceedings"; } else if (beg.equals("JO - ")) hm.put("booktitle", value); else if (beg.equals("FAU - ")) { String tmpauthor = value.replaceAll("EOLEOL", " and "); // if there is already someone there then append with "and" if (!"".equals(fullauthor)) fullauthor = fullauthor + " and " + tmpauthor; else fullauthor = tmpauthor; } else if (beg.equals("AU - ")) { String tmpauthor = value.replaceAll("EOLEOL", " and ").replaceAll(" ", ", "); // if there is already someone there then append with "and" if (!"".equals(shortauthor)) shortauthor = shortauthor + " and " + tmpauthor; else shortauthor = tmpauthor; } else if (beg.equals("TI - ")) hm.put("title", value.replaceAll("EOLEOL", " ")); else if (beg.equals("TA - ")) hm.put("journal", value.replaceAll("EOLEOL", " ")); else if (beg.equals("AB - ")) hm.put("abstract", value.replaceAll("EOLEOL", " ")); else if (beg.equals("PG - ")) pages = value.replaceAll("-", "--"); else if (beg.equals("IP - ")) hm.put("number", value); else if (beg.equals("DP - ")) { String[] parts = value.split(" "); // sometimes this is just year, sometimes full date hm.put("year", parts[0]); } else if (beg.equals("VI - ")) hm.put("volume", value); else if (beg.equals("AID - ")) { String[] parts = value.split(" "); if ("[doi]".equals(parts[1])) { hm.put("doi", parts[0]); hm.put("url", "http://dx.doi.org/" + parts[0]); } } } if (!"".equals(pages)) hm.put("pages", pages); if (!"".equals(fullauthor)) hm.put("author", fullauthor); else if (!"".equals(shortauthor)) hm.put("author", shortauthor); BibtexEntry b = new BibtexEntry(BibtexFields.DEFAULT_BIBTEXENTRY_ID, Globals.getEntryType(Type)); // id assumes an existing database so don't // create one here b.setField(hm); // the first bibitem is always empty, presumably as a result of trying // to parse header informaion. So add only if we have at least author or // title fields. if (hm.get("author") != null || hm.get("title") != null) bibitems.add(b); } return bibitems; }
Clone fragments detected by clone detection tool
File path: /jabref-2.10/src/java/net/sf/jabref/imports/RepecNepImporter.java File path: /jabref-2.10/src/java/net/sf/jabref/imports/BiomailImporter.java
Method name: void parseAuthors(BibtexEntry) Method name: List importEntries(InputStream, OutputPrinter)
Number of AST nodes: 1 Number of AST nodes: 3
1
/**
1
/**
2
   * Implements grammer rule "Authors"
2
     * Parse the entries in the source, and return a List of BibtexEntry
3
   *
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     * objects.
4
   * @param be
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     */
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   * @throws IOException
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    public List<BibtexEntry> importEntries(InputStream stream, OutputPrinter status) throws IOException {
6
   */
6
        ArrayList<BibtexEntry> bibitems = new ArrayList<BibtexEntry>();
7
  private void parseAuthors(BibtexEntry be) throws IOException {
7
        StringBuffer sb = new StringBuffer();
8
    // read authors and institutions
8
9
    String authors = "";
9
        BufferedReader in =
10
    String institutions = "";
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                new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream));
11
    while (this.lastLine != null && !this.lastLine.equals("") && !startsWithKeyword(recognizedFields)) {
11
12
      
12
        String str;
13
      // read single author
13
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      String author = null;
14
        while ((str = in.readLine()) != null) {
15
      String institution = null;
15
            if (str.length() < 3)
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      boolean institutionDone = false;
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                continue;
17
      if (this.lastLine.indexOf('(') >= 0) {
17
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        author = this.lastLine.substring(0, this.lastLine.indexOf('(')).trim();
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            // begining of a new item
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        institutionDone = this.lastLine.indexOf(')') > 0;
19
            if (str.substring(0, 6).equals("PMID- "))
20
        institution = this.lastLine.substring(this.lastLine.indexOf('(') + 1, institutionDone && this.lastLine.indexOf(')') > this.lastLine.indexOf('(') + 1 ? this.lastLine.indexOf(')') : this.lastLine.length()).trim();
20
                sb.append("::").append(str);
21
      } else {
21
            else {
22
        author = this.lastLine.substring(0, this.lastLine.length()).trim();
22
                String beg = str.substring(0, 6);
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        institutionDone = true;
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      }
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                if (beg.indexOf(" ") > 0) {
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                    sb.append(" ## "); // mark the begining of each field
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      readLine();
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                    sb.append(str);
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      while (!institutionDone && this.lastLine!= null) {
27
                } else {
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        institutionDone = this.lastLine.indexOf(')') > 0;
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                    sb.append("EOLEOL"); // mark the end of each line
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        institution += this.lastLine.substring(0, institutionDone ? this.lastLine.indexOf(')') : this.lastLine.length()).trim();
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                    sb.append(str.trim());
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        readLine();
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                }
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      }
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            }
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32
        }
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      if (author != null) {
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        authors += !authors.equals("") ? " and " + author : "" + author;
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        String[] entries = sb.toString().split("::");
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      }
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      if (institution != null) {
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        // skip the first entry as it is either empty or has document header
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        institutions += !institutions.equals("") ? " and " + institution : "" + institution;
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        HashMap<String, String> hm = new HashMap<String, String>();
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      }            
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    }
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        for (int i = 0; i < entries.length; i++) {
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            String[] fields = entries[i].split(" ## ");
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    if (!authors.equals("")) {
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      be.setField("author", authors);
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            if (fields.length == 0)
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    }
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                fields = entries[i].split("\n");
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    if (!institutions.equals("")) {
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      be.setField("institution", institutions);
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            String Type = "";
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    }
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            String pages = "";
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  }
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            String shortauthor = "";
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            String fullauthor = "";
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            hm.clear();
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            for (int j = 0; j < fields.length; j++) {
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                System.out.println(">>>"+fields[j]+"<<<");
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                //empty field don't do anything
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                if (fields[j].length() <= 2)
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                    continue;
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                String beg = fields[j].substring(0, 6);
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                String value = fields[j].substring(6);
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                value = value.trim();
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                if (beg.equals("PT  - ")) {
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                    // PT = value.replaceAll("JOURNAL ARTICLE", "article").replaceAll("Journal Article", "article");
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                    Type = "article"; //make all of them PT?
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                } else if (beg.equals("TY  - ")) {
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                    if ("CONF".equals(value))
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                        Type = "inproceedings";
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                } else if (beg.equals("JO  - "))
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                    hm.put("booktitle", value);
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                else if (beg.equals("FAU - ")) {
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                    String tmpauthor = value.replaceAll("EOLEOL", " and ");
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                    // if there is already someone there then append with "and"
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                    if (!"".equals(fullauthor))
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                        fullauthor = fullauthor + " and " + tmpauthor;
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                    else
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                        fullauthor = tmpauthor;
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                } else if (beg.equals("AU  - ")) {
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                    String tmpauthor = value.replaceAll("EOLEOL", " and ").replaceAll(" ", ", ");
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                    // if there is already someone there then append with "and"
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                    if (!"".equals(shortauthor))
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                        shortauthor = shortauthor + " and " + tmpauthor;
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                    else
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                        shortauthor = tmpauthor;
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                } else if (beg.equals("TI  - "))
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                    hm.put("title", value.replaceAll("EOLEOL", " "));
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                else if (beg.equals("TA  - "))
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                    hm.put("journal", value.replaceAll("EOLEOL", " "));
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                else if (beg.equals("AB  - "))
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                    hm.put("abstract", value.replaceAll("EOLEOL", " "));
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                else if (beg.equals("PG  - "))
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                    pages = value.replaceAll("-", "--");
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                else if (beg.equals("IP  - "))
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                    hm.put("number", value);
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                else if (beg.equals("DP  - ")) {
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                    String[] parts = value.split(" "); // sometimes this is just year, sometimes full date
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                    hm.put("year", parts[0]);
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                } else if (beg.equals("VI  - "))
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                    hm.put("volume", value);
101
                else if (beg.equals("AID - ")) {
102
                    String[] parts = value.split(" ");
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                    if ("[doi]".equals(parts[1])) {
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                        hm.put("doi", parts[0]);
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                        hm.put("url", "http://dx.doi.org/" + parts[0]);
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                    }
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                }
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            }
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            if (!"".equals(pages))
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                hm.put("pages", pages);
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            if (!"".equals(fullauthor))
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                hm.put("author", fullauthor);
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            else if (!"".equals(shortauthor))
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                hm.put("author", shortauthor);
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            BibtexEntry b =
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                    new BibtexEntry(BibtexFields.DEFAULT_BIBTEXENTRY_ID, Globals.getEntryType(Type)); // id assumes an existing database so don't
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            // create one here
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            b.setField(hm);
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            // the first bibitem is always empty, presumably as a result of trying
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            // to parse header informaion. So add only if we have at least author or
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            // title fields.
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            if (hm.get("author") != null || hm.get("title") != null)
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                bibitems.add(b);
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        }
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        return bibitems;
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    }

					
					
						

							See real code fragment
							
							See real code fragment
						
					
					
				

			

			

			
    
			
			
  1. 
				
    
					{Refactorable}
				
    
				
    
					
    
						
    
							Mapping Summary
							
								
    
									Number of mapped statements3
								
    
								
    
									Number of unmapped statements in the first code fragment0
								
    
								
    
									Number of unmapped statements in the second code fragment0
								
    
								
    
									Time elapsed for statement mapping (ms)0.0
								
    
								
    
									Similarity Score1.000
								
    
							
    
								Clone typeType 2
							
    
						    			
						
    
					
				
    
			
    
			
    
				Mapped Statements
				
					
    
						ID
						Statement
						
						ID
						Statement
					
    
					
    21
    institutions += !institutions.equals("") ? " and " + institution : "" + institution;
    21
    institutions += !institutions.equals("") ? " and " + institution : "" + institution;
    43
    if (!"".equals(fullauthor))
    Differences
    Expression1Expression2Difference
    ""fullauthorTYPE_COMPATIBLE_REPLACEMENT
    institutions""TYPE_COMPATIBLE_REPLACEMENT
    institutionsfullauthorVARIABLE_NAME_MISMATCH
    institutionsfullauthorVARIABLE_NAME_MISMATCH
    " and "fullauthorTYPE_COMPATIBLE_REPLACEMENT
    institution" and "TYPE_COMPATIBLE_REPLACEMENT
    " and " + institutionfullauthor + " and " + tmpauthorINFIX_EXTENDED_OPERAND_NUMBER_MISMATCH
    "" + institutiontmpauthorTYPE_COMPATIBLE_REPLACEMENT
    		43
    if (!"".equals(fullauthor))
                                                                                                    
    44
    fullauthor = fullauthor + " and " + tmpauthor;
    Differences
    Expression1Expression2Difference
    institutionsfullauthorVARIABLE_NAME_MISMATCH
    " and "fullauthorTYPE_COMPATIBLE_REPLACEMENT
    institution" and "TYPE_COMPATIBLE_REPLACEMENT
    " and " + institutionfullauthor + " and " + tmpauthorINFIX_EXTENDED_OPERAND_NUMBER_MISMATCH
    		44
    fullauthor = fullauthor + " and " + tmpauthor;
            
    else
                                                      
    45
    fullauthor = tmpauthor;
    Differences
    Expression1Expression2Difference
    institutionsfullauthorVARIABLE_NAME_MISMATCH
    "" + institutiontmpauthorTYPE_COMPATIBLE_REPLACEMENT
    		45
    fullauthor = tmpauthor;
    
				    
			
    
			
    
				Precondition Violations (0)
				
					
    
						Row
						Violation
					
    
					
				    
			
    
			
    2.