private void typeDeletion(String name) {
BibtexEntryType type = BibtexEntryType.getType(name);
if (type instanceof CustomEntryType) {
if (BibtexEntryType.getStandardType(name) == null) {
int reply =
JOptionPane.showConfirmDialog(
frame,
Globals.lang(
"All entries of this " + "type will be declared " + "typeless. Continue?"),
Globals.lang("Delete custom format") + " '" + StringUtil.nCase(name) + '\'',
JOptionPane.YES_NO_OPTION,
JOptionPane.WARNING_MESSAGE);
if (reply != JOptionPane.YES_OPTION) {
return;
}
}
BibtexEntryType.removeType(name);
updateTypesForEntries(StringUtil.nCase(name));
changed.remove(name);
reqLists.remove(name);
optLists.remove(name);
if (biblatexMode) {
opt2Lists.remove(name);
}
}
// messageLabel.setText("'"+type.getName()+"' "+
// Globals.lang("is a standard type."));
}
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);
}
}
private void applyChanges() {
valueChanged(new ListSelectionEvent(new JList(), 0, 0, false));
// Iterate over our map of required fields, and list those types if necessary:
List<String> types = typeComp.getFields();
for (Map.Entry<String, List<String>> stringListEntry : reqLists.entrySet()) {
if (!types.contains(stringListEntry.getKey())) {
continue;
}
List<String> reqFields = stringListEntry.getValue();
List<String> optFields = optLists.get(stringListEntry.getKey());
List<String> opt2Fields = opt2Lists.get(stringListEntry.getKey());
String[] reqStr = new String[reqFields.size()];
reqStr = reqFields.toArray(reqStr);
String[] optStr = new String[optFields.size()];
optStr = optFields.toArray(optStr);
String[] opt2Str;
if (opt2Fields != null) {
opt2Str = opt2Fields.toArray(new String[opt2Fields.size()]);
} else {
opt2Str = new String[0];
}
// If this type is already existing, check if any changes have
// been made
boolean changesMade = true;
if (defaulted.contains(stringListEntry.getKey())) {
// This type should be reverted to its default setup.
// System.out.println("Defaulting: "+typeName);
String nm = StringUtil.nCase(stringListEntry.getKey());
BibtexEntryType.removeType(nm);
updateTypesForEntries(nm);
continue;
}
BibtexEntryType oldType = BibtexEntryType.getType(stringListEntry.getKey());
if (oldType != null) {
String[] oldReq = oldType.getRequiredFields(), oldOpt = oldType.getOptionalFields();
if (biblatexMode) {
String[] priOpt = oldType.getPrimaryOptionalFields();
String[] secOpt = Util.getRemainder(oldOpt, priOpt);
if (equalArrays(oldReq, reqStr)
&& equalArrays(oldOpt, optStr)
&& equalArrays(secOpt, opt2Str)) {
changesMade = false;
}
} else if (equalArrays(oldReq, reqStr) && equalArrays(oldOpt, optStr)) {
changesMade = false;
}
}
if (changesMade) {
// System.out.println("Updating: "+typeName);
CustomEntryType typ =
biblatexMode
? new CustomEntryType(
StringUtil.nCase(stringListEntry.getKey()), reqStr, optStr, opt2Str)
: new CustomEntryType(StringUtil.nCase(stringListEntry.getKey()), reqStr, optStr);
BibtexEntryType.ALL_TYPES.put(stringListEntry.getKey().toLowerCase(), typ);
updateTypesForEntries(typ.getName());
}
}
Set<Object> toRemove = new HashSet<Object>();
for (String o : BibtexEntryType.ALL_TYPES.keySet()) {
if (!types.contains(o)) {
toRemove.add(o);
}
}
// Remove those that should be removed:
if (!toRemove.isEmpty()) {
for (Object aToRemove : toRemove) {
typeDeletion((String) aToRemove);
}
}
updateTables();
}
@Override
public void valueChanged(ListSelectionEvent e) {
if (e.getValueIsAdjusting()) {
return;
}
if (lastSelected != null) {
// The entry type lastSelected is now unselected, so we store the current settings
// for that type in our two maps.
reqLists.put(lastSelected, reqComp.getFields());
optLists.put(lastSelected, optComp.getFields());
if (biblatexMode) {
opt2Lists.put(lastSelected, optComp2.getFields());
}
}
String s = typeComp.getFirstSelected();
if (s == null) {
return;
}
List<String> rl = reqLists.get(s);
if (rl == null) {
BibtexEntryType type = BibtexEntryType.getType(s);
if (type != null) {
String[] rf = type.getRequiredFieldsForCustomization(), of = type.getOptionalFields();
List<String> req, opt;
if (rf != null) {
req = java.util.Arrays.asList(rf);
} else {
req = new ArrayList<String>();
}
if (!biblatexMode) {
if (of != null) {
opt = java.util.Arrays.asList(of);
} else {
opt = new ArrayList<String>();
}
} else {
String[] priOf = type.getPrimaryOptionalFields();
if (priOf != null) {
opt = java.util.Arrays.asList(priOf);
} else {
opt = new ArrayList<String>();
}
List<String> opt2 = new ArrayList<String>();
if (of != null) {
for (String anOf : of) {
if (!opt.contains(anOf)) {
opt2.add(anOf);
}
}
}
optComp2.setFields(opt2);
optComp2.setEnabled(true);
}
reqComp.setFields(req);
reqComp.setEnabled(true);
optComp.setFields(opt);
optComp.setEnabled(true);
} else {
// New entry, veintle
reqComp.setFields(new ArrayList<String>());
reqComp.setEnabled(true);
optComp.setFields(new ArrayList<String>());
optComp.setEnabled(true);
if (biblatexMode) {
optComp2.setFields(new ArrayList<String>());
optComp2.setEnabled(true);
}
new FocusRequester(reqComp);
}
} else {
reqComp.setFields(rl);
optComp.setFields(optLists.get(s));
if (biblatexMode) {
optComp2.setFields(opt2Lists.get(s));
}
}
lastSelected = s;
typeComp.enable(s, changed.contains(lastSelected) && !defaulted.contains(lastSelected));
}
/** Remove all types from the menu. Then cycle through all available types, and add them. */
private void populateTypeMenu() {
typeMenu.removeAll();
for (String key : BibtexEntryType.getAllTypes()) {
typeMenu.add(new ChangeTypeAction(BibtexEntryType.getType(key), panel));
}
}