Merge branch 'master' into improve-sync-language-script

CHANGELOG.md

@@ -21,6 +21,9 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 - Move Bibtex and Biblatex mode switcher to File menu
 - Display active edit mode (BibTeX or Biblatex) at window title
 - Implements #444: The search is cleared by either clicking the clear-button or by pressing ESC with having focus in the search field. 
+- Icons are shown as Header for icon columns in the entry table (#315)
+- Tooltips are shown for header columns and contents which are too wide to be displayed in the entry table (#384)
+- Default order in entry table:  # | all file based icons (file, URL/DOI, ...) | all bibtex field based icons (bibtexkey, entrytype, author, title, ...) | all activated special field icons (ranking, quality, ...)
 
 ### Fixed
 - Fixed #434: Revert to old 'JabRef' installation folder name instead of 'jabref'
@@ -32,11 +35,14 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 - Fixes #412: Biblatex preserves capital letters, checking whether letters may be converted to lowercase within the Integrity Check action is obsolete.
 - Fixed #437: The toolbar after the search field is now correctly wrapped when using a small window size for JabRef
 - Fixed #438: Cut, Copy and Paste are now translated correctly in the menu
+- Fixed #443/#445: Fixed sorting and moving special field columns
+- Fixed #498: non-working legacy PDF/PS column removed
 
 ### Removed
 - Removed file history size preference (never available from the UI)
 - Removed jstorImporter because it's hardly ever used, even Jstor.org doesn't support/export said format anymore
-
+- Removed option "Show one letter heading for icon columns" which is obsolete with the fix of #315/384
+- Removed table column "PDF/PS" which refers to legacy fields "ps" resp. "pdf" which are no longer supported (see also fix #498)
 
 
 

src/main/java/net/sf/jabref/JabRef.java

@@ -42,8 +42,8 @@
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.migrations.PreferencesMigrations;
-import net.sf.jabref.model.database.BibtexDatabase;
-import net.sf.jabref.model.entry.BibtexEntry;
+import net.sf.jabref.model.database.BibDatabase;
+import net.sf.jabref.model.entry.BibEntry;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -289,9 +289,9 @@ public Vector<ParserResult> processArguments(String[] args, boolean initialStart
                 String searchTerm = data[0].replace("\\$", " "); //enables blanks within the search term:
                                                                  //? stands for a blank
                 ParserResult pr = loaded.elementAt(loaded.size() - 1);
-                BibtexDatabase dataBase = pr.getDatabase();
+                BibDatabase dataBase = pr.getDatabase();
                 SearchManagerNoGUI smng = new SearchManagerNoGUI(searchTerm, dataBase);
-                BibtexDatabase newBase = smng.getDBfromMatches(); //newBase contains only match entries
+                BibDatabase newBase = smng.getDBfromMatches(); //newBase contains only match entries
 
                 //export database
                 if ((newBase != null) && (newBase.getEntryCount() > 0)) {
@@ -425,7 +425,7 @@ public Vector<ParserResult> processArguments(String[] args, boolean initialStart
                 if (data.length == 2) {
                     ParserResult pr = loaded.firstElement();
                     AuxCommandLine acl = new AuxCommandLine(data[0], pr.getDatabase());
-                    BibtexDatabase newBase = acl.perform();
+                    BibDatabase newBase = acl.perform();
 
                     boolean notSavedMsg = false;
 
@@ -518,7 +518,7 @@ private ParserResult fetch(String fetchCommand) {
 
         System.out.println(Localization.lang("Running Query '%0' with fetcher '%1'.", query, engine) + " "
                 + Localization.lang("Please wait..."));
-        Collection<BibtexEntry> result = new ImportInspectionCommandLine().query(query, fetcher);
+        Collection<BibEntry> result = new ImportInspectionCommandLine().query(query, fetcher);
 
         if ((result == null) || result.isEmpty()) {
             System.out.println(
@@ -849,7 +849,7 @@ private static ParserResult importFile(String argument) {
             if ((data.length > 1) && !"*".equals(data[1])) {
                 System.out.println(Localization.lang("Importing") + ": " + data[0]);
                 try {
-                    List<BibtexEntry> entries;
+                    List<BibEntry> entries;
                     if (OS.WINDOWS) {
                         entries = Globals.importFormatReader.importFromFile(data[1], data[0], JabRef.jrf);
                     } else {

src/main/java/net/sf/jabref/JabRefPreferences.java

@@ -42,6 +42,7 @@
 import net.sf.jabref.gui.entryeditor.EntryEditorTabList;
 import net.sf.jabref.gui.keyboard.KeyBinding;
 import net.sf.jabref.gui.keyboard.KeyBindingRepository;
+import net.sf.jabref.gui.maintable.PersistenceTableColumnListener;
 import net.sf.jabref.gui.preftabs.ImportSettingsTab;
 import net.sf.jabref.importer.fileformat.ImportFormat;
 import net.sf.jabref.logic.autocompleter.AutoCompletePreferences;
@@ -193,7 +194,6 @@ public class JabRefPreferences {
     public static final String FILE_COLUMN = "fileColumn";
     public static final String PREFER_URL_DOI = "preferUrlDoi";
     public static final String URL_COLUMN = "urlColumn";
-    public static final String PDF_COLUMN = "pdfColumn";
     public static final String DISABLE_ON_MULTIPLE_SELECTION = "disableOnMultipleSelection";
     public static final String CTRL_CLICK = "ctrlClick";
     public static final String INCOMPLETE_ENTRY_BACKGROUND = "incompleteEntryBackground";
@@ -232,7 +232,6 @@ public class JabRefPreferences {
     public static final String TOOLBAR_VISIBLE = "toolbarVisible";
     public static final String HIGHLIGHT_GROUPS_MATCHING_ALL = "highlightGroupsMatchingAll";
     public static final String HIGHLIGHT_GROUPS_MATCHING_ANY = "highlightGroupsMatchingAny";
-    public static final String SHOW_ONE_LETTER_HEADING_FOR_ICON_COLUMNS = "showOneLetterHeadingForIconColumns";
     public static final String UPDATE_TIMESTAMP = "updateTimestamp";
     public static final String TIME_STAMP_FIELD = "timeStampField";
     public static final String TIME_STAMP_FORMAT = "timeStampFormat";
@@ -608,7 +607,6 @@ private JabRefPreferences() {
 
         defaults.put(CTRL_CLICK, Boolean.FALSE);
         defaults.put(DISABLE_ON_MULTIPLE_SELECTION, Boolean.FALSE);
-        defaults.put(PDF_COLUMN, Boolean.FALSE);
         defaults.put(URL_COLUMN, Boolean.TRUE);
         defaults.put(PREFER_URL_DOI, Boolean.FALSE);
         defaults.put(FILE_COLUMN, Boolean.TRUE);
@@ -627,8 +625,6 @@ private JabRefPreferences() {
         defaults.put(SpecialFieldsUtils.PREF_AUTOSYNCSPECIALFIELDSTOKEYWORDS, SpecialFieldsUtils.PREF_AUTOSYNCSPECIALFIELDSTOKEYWORDS_DEFAULT);
         defaults.put(SpecialFieldsUtils.PREF_SERIALIZESPECIALFIELDS, SpecialFieldsUtils.PREF_SERIALIZESPECIALFIELDS_DEFAULT);
 
-        defaults.put(SHOW_ONE_LETTER_HEADING_FOR_ICON_COLUMNS, Boolean.FALSE);
-
         defaults.put(USE_OWNER, Boolean.FALSE);
         defaults.put(OVERWRITE_OWNER, Boolean.FALSE);
         defaults.put(ALLOW_TABLE_EDITING, Boolean.FALSE);
@@ -817,6 +813,7 @@ public void setLanguageDependentDefaultValues() {
         defaults.put(CUSTOM_TAB_FIELDS + "_def2", "review");
         defaults.put(CUSTOM_TAB_NAME + "_def2", Localization.lang("Review"));
 
+        defaults.put(EMAIL_SUBJECT, Localization.lang("References"));
     }
 
     public boolean putBracesAroundCapitals(String fieldName) {

src/main/java/net/sf/jabref/MetaData.java

@@ -22,7 +22,7 @@
 import net.sf.jabref.migrations.VersionHandling;
 import net.sf.jabref.logic.labelPattern.AbstractLabelPattern;
 import net.sf.jabref.logic.labelPattern.DatabaseLabelPattern;
-import net.sf.jabref.model.database.BibtexDatabase;
+import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.sql.DBStrings;
 import net.sf.jabref.logic.util.strings.StringUtil;
 
@@ -48,7 +48,7 @@ public class MetaData implements Iterable<String> {
      * must simply make sure the appropriate changes are reflected in the Vector
      * it has been passed.
      */
-    public MetaData(HashMap<String, String> inData, BibtexDatabase db) {
+    public MetaData(HashMap<String, String> inData, BibDatabase db) {
         boolean groupsTreePresent = false;
         Vector<String> flatGroupsData = null;
         Vector<String> treeGroupsData = null;
@@ -221,11 +221,11 @@ public String[] getFileDirectory(String fieldName) {
      * Parse the groups metadata string
      *
      * @param orderedData The vector of metadata strings
-     * @param db          The BibtexDatabase this metadata belongs to
+     * @param db          The BibDatabase this metadata belongs to
      * @param version     The group tree version
      * @return true if parsing was successful, false otherwise
      */
-    private void putGroups(Vector<String> orderedData, BibtexDatabase db, int version) {
+    private void putGroups(Vector<String> orderedData, BibDatabase db, int version) {
         try {
             groupsRoot = VersionHandling.importGroups(orderedData, db,
                     version);

src/main/java/net/sf/jabref/SearchManagerNoGUI.java

@@ -23,26 +23,26 @@
 import org.apache.commons.logging.LogFactory;
 
 import net.sf.jabref.importer.*;
-import net.sf.jabref.model.database.BibtexDatabase;
-import net.sf.jabref.model.entry.BibtexEntry;
+import net.sf.jabref.model.database.BibDatabase;
+import net.sf.jabref.model.entry.BibEntry;
 
 /**
  * @author Silberer, Zirn
  */
 class SearchManagerNoGUI {
 
     private String searchTerm;
-    private final BibtexDatabase database;
-    private BibtexDatabase base;
+    private final BibDatabase database;
+    private BibDatabase base;
 
     private static final Log LOGGER = LogFactory.getLog(SearchManagerNoGUI.class);
 
-    public SearchManagerNoGUI(String term, BibtexDatabase dataBase) {
+    public SearchManagerNoGUI(String term, BibDatabase dataBase) {
         searchTerm = term;
         database = dataBase;
     }
 
-    public BibtexDatabase getDBfromMatches() {
+    public BibDatabase getDBfromMatches() {
         LOGGER.debug("Search term: " + searchTerm);
         if (specifiedYears()) {
             searchTerm = fieldYear();
@@ -56,9 +56,9 @@ public BibtexDatabase getDBfromMatches() {
             return base;
         }
 
-        Collection<BibtexEntry> entries = database.getEntries();
-        Vector<BibtexEntry> matchEntries = new Vector<>();
-        for (BibtexEntry entry : entries) {
+        Collection<BibEntry> entries = database.getEntries();
+        Vector<BibEntry> matchEntries = new Vector<>();
+        for (BibEntry entry : entries) {
             boolean hit = searchQuery.isMatch(entry);
             entry.setSearchHit(hit);
             if (hit) {

src/main/java/net/sf/jabref/bibtex/BibtexEntryWriter.java

@@ -5,7 +5,7 @@
 import net.sf.jabref.JabRefPreferences;
 import net.sf.jabref.exporter.LatexFieldFormatter;
 import net.sf.jabref.logic.util.strings.StringUtil;
-import net.sf.jabref.model.entry.BibtexEntry;
+import net.sf.jabref.model.entry.BibEntry;
 
 import java.io.IOException;
 import java.io.Writer;
@@ -59,7 +59,7 @@ public BibtexEntryWriter(LatexFieldFormatter fieldFormatter, boolean write) {
         this.write = write;
     }
 
-    public void write(BibtexEntry entry, Writer out) throws IOException {
+    public void write(BibEntry entry, Writer out) throws IOException {
         // if the entry has not been modified, write it as it was
         if(!entry.hasChanged()){
             out.write(entry.getParsedSerialization());
@@ -87,14 +87,14 @@ public void write(BibtexEntry entry, Writer out) throws IOException {
      * @param out
      * @throws IOException
      */
-    private void writeRequiredFieldsFirstOptionalFieldsSecondRemainingFieldsThird(BibtexEntry entry, Writer out) throws IOException {
+    private void writeRequiredFieldsFirstOptionalFieldsSecondRemainingFieldsThird(BibEntry entry, Writer out) throws IOException {
         // Write header with type and bibtex-key.
         out.write('@' + entry.getType().getName() + '{');
 
         HashSet<String> writtenFields = new HashSet<>();
 
         writeKeyField(entry, out);
-        writtenFields.add(BibtexEntry.KEY_FIELD);
+        writtenFields.add(BibEntry.KEY_FIELD);
 
         // Write required fields first.
         // Thereby, write the title field first.
@@ -140,7 +140,7 @@ private void writeRequiredFieldsFirstOptionalFieldsSecondRemainingFieldsThird(Bi
         out.write((hasWritten ? Globals.NEWLINE : "") + '}');
     }
 
-    private List<String> getRequiredFieldsSorted(BibtexEntry entry) {
+    private List<String> getRequiredFieldsSorted(BibEntry entry) {
         String entryTypeName = entry.getType().getName();
         List<String> sortedFields = requiredFieldsSorted.get(entryTypeName);
 
@@ -154,7 +154,7 @@ private List<String> getRequiredFieldsSorted(BibtexEntry entry) {
         return sortedFields;
     }
 
-    private List<String> getOptionalFieldsSorted(BibtexEntry entry) {
+    private List<String> getOptionalFieldsSorted(BibEntry entry) {
         String entryTypeName = entry.getType().getName();
         List<String> sortedFields = optionalFieldsSorted.get(entryTypeName);
 
@@ -175,14 +175,14 @@ private List<String> getOptionalFieldsSorted(BibtexEntry entry) {
      * @param out
      * @throws IOException
      */
-    private void writeRequiredFieldsFirstRemainingFieldsSecond(BibtexEntry entry, Writer out) throws IOException {
+    private void writeRequiredFieldsFirstRemainingFieldsSecond(BibEntry entry, Writer out) throws IOException {
         // Write header with type and bibtex-key.
         out.write('@' + entry.getType().getName().toUpperCase(Locale.US) + '{');
 
         writeKeyField(entry, out);
 
         HashSet<String> written = new HashSet<>();
-        written.add(BibtexEntry.KEY_FIELD);
+        written.add(BibEntry.KEY_FIELD);
         boolean hasWritten = false;
         // Write required fields first.
         List<String> fields = entry.getRequiredFieldsFlat();
@@ -219,13 +219,13 @@ private void writeRequiredFieldsFirstRemainingFieldsSecond(BibtexEntry entry, Wr
         out.write((hasWritten ? Globals.NEWLINE : "") + '}');
     }
 
-    private void writeUserDefinedOrder(BibtexEntry entry, Writer out) throws IOException {
+    private void writeUserDefinedOrder(BibEntry entry, Writer out) throws IOException {
         // Write header with type and bibtex-key.
         out.write('@' + entry.getType().getName() + '{');
 
         writeKeyField(entry, out);
         HashMap<String, String> written = new HashMap<>();
-        written.put(BibtexEntry.KEY_FIELD, null);
+        written.put(BibEntry.KEY_FIELD, null);
         boolean hasWritten = false;
 
         // Write user defined fields first.
@@ -265,7 +265,7 @@ private void writeUserDefinedOrder(BibtexEntry entry, Writer out) throws IOExcep
 
     }
 
-    private void writeKeyField(BibtexEntry entry, Writer out) throws IOException {
+    private void writeKeyField(BibEntry entry, Writer out) throws IOException {
         String keyField = StringUtil.shaveString(entry.getCiteKey());
         out.write((keyField == null ? "" : keyField) + ',' + Globals.NEWLINE);
     }
@@ -281,7 +281,7 @@ private void writeKeyField(BibtexEntry entry, Writer out) throws IOException {
      *                          it was not set
      * @throws IOException In case of an IO error
      */
-    private boolean writeField(BibtexEntry entry, Writer out, String name, boolean prependWhiteSpace) throws IOException {
+    private boolean writeField(BibEntry entry, Writer out, String name, boolean prependWhiteSpace) throws IOException {
         String field = entry.getField(name);
         // only write field if is is not empty or if empty fields should be included
         // the first condition mirrors mirror behavior of com.jgoodies.common.base.Strings.isNotBlank(str)

src/main/java/net/sf/jabref/bibtex/DuplicateCheck.java

@@ -16,8 +16,8 @@
 package net.sf.jabref.bibtex;
 
 import net.sf.jabref.model.entry.AuthorList;
-import net.sf.jabref.model.database.BibtexDatabase;
-import net.sf.jabref.model.entry.BibtexEntry;
+import net.sf.jabref.model.database.BibDatabase;
+import net.sf.jabref.model.entry.BibEntry;
 
 import java.util.HashMap;
 import java.util.HashSet;
@@ -64,11 +64,11 @@ public class DuplicateCheck {
     /**
      * Checks if the two entries represent the same publication.
      *
-     * @param one BibtexEntry
-     * @param two BibtexEntry
+     * @param one BibEntry
+     * @param two BibEntry
      * @return boolean
      */
-    public static boolean isDuplicate(BibtexEntry one, BibtexEntry two) {
+    public static boolean isDuplicate(BibEntry one, BibEntry two) {
 
         // First check if they are of the same type - a necessary condition:
         if (one.getType() != two.getType()) {
@@ -98,7 +98,7 @@ public static boolean isDuplicate(BibtexEntry one, BibtexEntry two) {
         return req[0] >= DuplicateCheck.duplicateThreshold;
     }
 
-    private static double[] compareFieldSet(String[] fields, BibtexEntry one, BibtexEntry two) {
+    private static double[] compareFieldSet(String[] fields, BibEntry one, BibEntry two) {
         double res = 0;
         double totWeights = 0.;
         for (String field : fields) {
@@ -122,7 +122,7 @@ private static double[] compareFieldSet(String[] fields, BibtexEntry one, Bibtex
         return new double[] {0.5, 0.0};
     }
 
-    private static int compareSingleField(String field, BibtexEntry one, BibtexEntry two) {
+    private static int compareSingleField(String field, BibEntry one, BibEntry two) {
         String s1 = one.getField(field);
         String s2 = two.getField(field);
         if (s1 == null) {
@@ -176,7 +176,7 @@ private static int compareSingleField(String field, BibtexEntry one, BibtexEntry
         }
     }
 
-    public static double compareEntriesStrictly(BibtexEntry one, BibtexEntry two) {
+    public static double compareEntriesStrictly(BibEntry one, BibEntry two) {
         HashSet<String> allFields = new HashSet<>();
         allFields.addAll(one.getFieldNames());
         allFields.addAll(two.getFieldNames());
@@ -200,15 +200,15 @@ public static double compareEntriesStrictly(BibtexEntry one, BibtexEntry two) {
     /**
      * Goes through all entries in the given database, and if at least one of
      * them is a duplicate of the given entry, as per
-     * Util.isDuplicate(BibtexEntry, BibtexEntry), the duplicate is returned.
+     * Util.isDuplicate(BibEntry, BibEntry), the duplicate is returned.
      * The search is terminated when the first duplicate is found.
      *
      * @param database The database to search.
      * @param entry    The entry of which we are looking for duplicates.
      * @return The first duplicate entry found. null if no duplicates are found.
      */
-    public static BibtexEntry containsDuplicate(BibtexDatabase database, BibtexEntry entry) {
-        for (BibtexEntry other : database.getEntries()) {
+    public static BibEntry containsDuplicate(BibDatabase database, BibEntry entry) {
+        for (BibEntry other : database.getEntries()) {
             if (DuplicateCheck.isDuplicate(entry, other)) {
                 return other; // Duplicate found.
             }