public BibtexEntry makeBibtexEntry() {
BibtexEntry e = new BibtexEntry(IdGenerator.next(), BibtexEntryTypes.INCOLLECTION);
e.setField("title", "Marine finfish larviculture in Europe");
e.setField("bibtexkey", "shields01");
e.setField("year", "2001");
e.setField("author", "Kevin Shields");
return e;
}
private static BibtexEntry getTestEntry() {
if (PreviewPrefsTab.entry != null) {
return PreviewPrefsTab.entry;
}
PreviewPrefsTab.entry = new BibtexEntry(IdGenerator.next(), BibtexEntryType.getType("article"));
PreviewPrefsTab.entry.setField(BibtexFields.KEY_FIELD, "conceicao1997");
PreviewPrefsTab.entry.setField(
"author",
"Luis E. C. Conceic{\\~a}o and Terje van der Meeren and Johan A. J. Verreth and M S. Evjen and D. F. Houlihan and H. J. Fyhn");
PreviewPrefsTab.entry.setField(
"title",
"Amino acid metabolism and protein turnover in larval turbot (Scophthalmus maximus) fed natural zooplankton or Artemia");
PreviewPrefsTab.entry.setField("year", "1997");
PreviewPrefsTab.entry.setField("journal", "Marine Biology");
PreviewPrefsTab.entry.setField("month", "January");
PreviewPrefsTab.entry.setField("number", "2");
PreviewPrefsTab.entry.setField("volume", "123");
PreviewPrefsTab.entry.setField("pdf", "conceicao1997.pdf");
PreviewPrefsTab.entry.setField("pages", "255--265");
PreviewPrefsTab.entry.setField(
"keywords", "energetics, artemia, metabolism, amino acid, turbot");
PreviewPrefsTab.entry.setField(
"url", "http://ejournals.ebsco.com/direct.asp?ArticleID=TYY4NT82XA9H7R8PFPPV");
PreviewPrefsTab.entry.setField(
"abstract",
"Abstract The present paper studied the influence of different food regimes "
+ "on the free amino acid (FAA) pool, the rate of protein turnover, the flux of amino acids, and "
+ "their relation to growth of larval turbot (Scophthalmus maximus L.) from first feeding until "
+ "metamorphosis. The amino acid profile of protein was stable during the larval period although "
+ "some small, but significant, differences were found. Turbot larvae had proteins which were rich "
+ "in leucine and aspartate, and poor in glutamate, suggesting a high leucine requirement. The "
+ "profile of the FAA pool was highly variable and quite different from the amino acid profile in "
+ "protein. The proportion of essential FAA decreased with development. High contents of free tyrosine "
+ "and phenylalanine were found on Day 3, while free taurine was present at high levels throughout "
+ "the experimental period. Larval growth rates were positively correlated with taurine levels, "
+ "suggesting a dietary dependency for taurine and/or sulphur amino acids.\n\nReduced growth rates in "
+ "Artemia-fed larvae were associated with lower levels of free methionine, indicating that this diet "
+ "is deficient in methionine for turbot larvae. Leucine might also be limiting turbot growth as the "
+ "different diet organisms had lower levels of this amino acid in the free pool than was found in the "
+ "larval protein. A previously presented model was used to describe the flux of amino acids in growing "
+ "turbot larvae. The FAA pool was found to be small and variable. It was estimated that the daily dietary "
+ "amino acid intake might be up to ten times the larval FAA pool. In addition, protein synthesis and "
+ "protein degradation might daily remove and return, respectively, the equivalent of up to 20 and 10 "
+ "times the size of the FAA pool. In an early phase (Day 11) high growth rates were associated with a "
+ "relatively low protein turnover, while at a later stage (Day 17), a much higher turnover was observed.");
return PreviewPrefsTab.entry;
}
private BibtexEntry parseNextEntry(String allText, int startIndex) {
BibtexEntry entry = null;
int index = allText.indexOf("<div class=\"detail", piv);
int endIndex = allText.indexOf("</div>", index);
if (index >= 0 && endIndex > 0) {
endIndex += 6;
piv = endIndex;
String text = allText.substring(index, endIndex);
BibtexEntryType type = null;
String sourceField = null;
String typeName = "";
Matcher typeMatcher = typePattern.matcher(text);
if (typeMatcher.find()) {
typeName = typeMatcher.group(1);
if (typeName.equalsIgnoreCase("IEEE Journals & Magazines")
|| typeName.equalsIgnoreCase("IEEE Early Access Articles")
|| typeName.equalsIgnoreCase("IET Journals & Magazines")
|| typeName.equalsIgnoreCase("AIP Journals & Magazines")
|| typeName.equalsIgnoreCase("AVS Journals & Magazines")
|| typeName.equalsIgnoreCase("IBM Journals & Magazines")
|| typeName.equalsIgnoreCase("TUP Journals & Magazines")
|| typeName.equalsIgnoreCase("BIAI Journals & Magazines")) {
type = BibtexEntryType.getType("article");
sourceField = "journal";
} else if (typeName.equalsIgnoreCase("IEEE Conference Publications")
|| typeName.equalsIgnoreCase("IET Conference Publications")
|| typeName.equalsIgnoreCase("VDE Conference Publications")) {
type = BibtexEntryType.getType("inproceedings");
sourceField = "booktitle";
} else if (typeName.equalsIgnoreCase("IEEE Standards")
|| typeName.equalsIgnoreCase("Standards")) {
type = BibtexEntryType.getType("standard");
sourceField = "number";
} else if (typeName.equalsIgnoreCase("IEEE eLearning Library Courses")) {
type = BibtexEntryType.getType("Electronic");
sourceField = "note";
} else if (typeName.equalsIgnoreCase("Wiley-IEEE Press eBook Chapters")
|| typeName.equalsIgnoreCase("MIT Press eBook Chapters")
|| typeName.equalsIgnoreCase("IEEE USA Books & eBooks")) {
type = BibtexEntryType.getType("inCollection");
sourceField = "booktitle";
}
}
if (type == null) {
type = BibtexEntryType.getType("misc");
sourceField = "note";
System.err.println("Type detection failed. Use MISC instead.");
unparseable++;
System.err.println(text);
}
entry = new BibtexEntry(IdGenerator.next(), type);
if (typeName.equalsIgnoreCase("IEEE Standards")) {
entry.setField("organization", "IEEE");
}
if (typeName.equalsIgnoreCase("Wiley-IEEE Press eBook Chapters")) {
entry.setField("publisher", "Wiley-IEEE Press");
} else if (typeName.equalsIgnoreCase("MIT Press eBook Chapters")) {
entry.setField("publisher", "MIT Press");
} else if (typeName.equalsIgnoreCase("IEEE USA Books & eBooks")) {
entry.setField("publisher", "IEEE USA");
}
if (typeName.equalsIgnoreCase("IEEE Early Access Articles")) {
entry.setField("note", "Early Access");
}
Set<String> fields = fieldPatterns.keySet();
for (String field : fields) {
Matcher fieldMatcher = Pattern.compile(fieldPatterns.get(field)).matcher(text);
if (fieldMatcher.find()) {
entry.setField(field, htmlConverter.format(fieldMatcher.group(1)));
if (field.equals("title") && fieldMatcher.find()) {
String sec_title = htmlConverter.format(fieldMatcher.group(1));
if (entry.getType() == BibtexEntryType.getStandardType("standard")) {
sec_title = sec_title.replaceAll("IEEE Std ", "");
}
entry.setField(sourceField, sec_title);
}
if (field.equals("pages") && fieldMatcher.groupCount() == 2) {
entry.setField(field, fieldMatcher.group(1) + "-" + fieldMatcher.group(2));
}
}
}
Matcher authorMatcher = authorPattern.matcher(text);
// System.out.println(text);
StringBuilder authorNames = new StringBuilder("");
int authorCount = 0;
while (authorMatcher.find()) {
if (authorCount >= 1) {
authorNames.append(" and ");
}
authorNames.append(htmlConverter.format(authorMatcher.group(1)));
// System.out.println(authorCount + ": " + authorMatcher.group(1));
authorCount++;
}
entry.setField("author", authorNames.toString());
if (entry.getField("author") == null
|| entry.getField("author").startsWith("a href")
|| entry
.getField("author")
.startsWith("Topic(s)")) { // Fix for some documents without authors
entry.setField("author", "");
}
if (entry.getType() == BibtexEntryType.getStandardType("inproceedings")
&& entry.getField("author").equals("")) {
entry.setType(BibtexEntryType.getStandardType("proceedings"));
}
if (includeAbstract) {
index = text.indexOf("id=\"abstract");
if (index >= 0) {
endIndex = text.indexOf("</div>", index) + 6;
text = text.substring(index, endIndex);
Matcher absMatcher = absPattern.matcher(text);
if (absMatcher.find()) {
// Clean-up abstract
String abstr = absMatcher.group(1);
abstr = abstr.replaceAll("<span class='snippet'>([\\w]+)</span>", "$1");
entry.setField("abstract", htmlConverter.format(abstr));
}
}
}
}
if (entry == null) {
return null;
} else {
return cleanup(entry);
}
}
