From: Jim Procter Date: Fri, 1 Oct 2021 09:35:08 +0000 (+0100) Subject: Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons X-Git-Tag: Release_2_11_2_0~30^2^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4a442497ab857be0bf62e080f8461dbdc05fb49b;hp=27dc4596d13971e00f04578d469c5e3eb604757f;p=jalview.git Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons --- diff --git a/j11lib/groovy-all-2.4.12-indy.jar b/j11lib/groovy-all-2.4.21-indy.jar similarity index 58% rename from j11lib/groovy-all-2.4.12-indy.jar rename to j11lib/groovy-all-2.4.21-indy.jar index bb246a3..15ee98d 100644 Binary files a/j11lib/groovy-all-2.4.12-indy.jar and b/j11lib/groovy-all-2.4.21-indy.jar differ diff --git a/j8lib/groovy-all-2.4.12-indy.jar b/j8lib/groovy-all-2.4.21-indy.jar similarity index 58% rename from j8lib/groovy-all-2.4.12-indy.jar rename to j8lib/groovy-all-2.4.21-indy.jar index bb246a3..15ee98d 100644 Binary files a/j8lib/groovy-all-2.4.12-indy.jar and b/j8lib/groovy-all-2.4.21-indy.jar differ diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index fabd577..3b08362 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1105,6 +1105,8 @@ status.collecting_job_results = Collecting job results. status.fetching_db_refs = Fetching db refs status.loading_cached_pdb_entries = Loading Cached PDB Entries status.searching_for_pdb_structures = Searching for PDB Structures +status.searching_3d_beacons = Searching 3D Beacons +status.no_structures_discovered_from_3d_beacons = No models discovered from 3D Beacons status.opening_file_for = opening file for status.colouring_structures = Colouring structures label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java index ba575ae..53b0305 100644 --- a/src/jalview/gui/OptsAndParamsPage.java +++ b/src/jalview/gui/OptsAndParamsPage.java @@ -93,7 +93,7 @@ public class OptsAndParamsPage JLabel optlabel = new JLabel(); - JComboBox val = new JComboBox(); + JComboBox val = new JComboBox<>(); public OptionBox(OptionI opt) { @@ -127,7 +127,7 @@ public class OptsAndParamsPage } } add(enabled, BorderLayout.NORTH); - for (Object str : opt.getPossibleValues()) + for (String str : opt.getPossibleValues()) { val.addItem(str); } @@ -589,7 +589,7 @@ public class OptsAndParamsPage { if (choice) { - choicebox = new JComboBox(); + choicebox = new JComboBox<>(); choicebox.addActionListener(this); controlPanel.add(choicebox, BorderLayout.CENTER); } @@ -632,7 +632,9 @@ public class OptsAndParamsPage }); valueField.setPreferredSize(new Dimension(60, 25)); + valueField.setText(parm.getValue()); slider = makeSlider(parm.getValidValue()); + updateSliderFromValueField(); slider.addChangeListener(this); controlPanel.add(slider, BorderLayout.WEST); diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index caecbba..54aefc4 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -20,22 +20,6 @@ */ package jalview.gui; -import jalview.api.FeatureSettingsModelI; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.SequenceI; -import jalview.fts.core.GFTSPanel; -import jalview.fts.service.pdb.PDBFTSPanel; -import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel; -import jalview.fts.service.uniprot.UniprotFTSPanel; -import jalview.io.FileFormatI; -import jalview.io.gff.SequenceOntologyI; -import jalview.util.DBRefUtils; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.ws.seqfetcher.DbSourceProxy; - import java.awt.BorderLayout; import java.awt.Font; import java.awt.event.ActionEvent; @@ -58,6 +42,22 @@ import javax.swing.JScrollPane; import javax.swing.JTextArea; import javax.swing.SwingConstants; +import jalview.api.FeatureSettingsModelI; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.SequenceI; +import jalview.fts.core.GFTSPanel; +import jalview.fts.service.pdb.PDBFTSPanel; +import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel; +import jalview.fts.service.uniprot.UniprotFTSPanel; +import jalview.io.FileFormatI; +import jalview.io.gff.SequenceOntologyI; +import jalview.util.DBRefUtils; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.seqfetcher.DbSourceProxy; + /** * A panel where the use may choose a database source, and enter one or more * accessions, to retrieve entries from the database. @@ -67,11 +67,50 @@ import javax.swing.SwingConstants; */ public class SequenceFetcher extends JPanel implements Runnable { + private class StringPair + { + private String key; + + private String display; + + public StringPair(String s1, String s2) + { + key = s1; + display = s2; + } + + public StringPair(String s) + { + this(s, s); + } + + public String getKey() + { + return key; + } + + public String getDisplay() + { + return display; + } + + @Override + public String toString() + { + return display; + } + + public boolean equals(StringPair other) + { + return other.key == this.key; + } + } + private static jalview.ws.SequenceFetcher sfetch = null; JLabel exampleAccession; - JComboBox database; + JComboBox database; JCheckBox replacePunctuation; @@ -146,8 +185,8 @@ public class SequenceFetcher extends JPanel implements Runnable frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, - Platform.isAMacAndNotJS() ? 240 : 180); + Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, + Platform.isAMacAndNotJS() ? 240 : 180); } private String getFrameTitle() @@ -164,15 +203,25 @@ public class SequenceFetcher extends JPanel implements Runnable database = new JComboBox<>(); database.setFont(JvSwingUtils.getLabelFont()); - database.setPrototypeDisplayValue("ENSEMBLGENOMES "); + StringPair instructionItem = new StringPair( + MessageManager.getString("action.select_ddbb")); + database.setPrototypeDisplayValue(instructionItem); String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb(); Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER); - database.addItem(MessageManager.getString("action.select_ddbb")); + database.addItem(instructionItem); for (String source : sources) { - database.addItem(source); + List slist = sfetch.getSourceProxy(source); + if (slist.size() == 1 && slist.get(0) != null) + { + database.addItem(new StringPair(source, slist.get(0).getDbName())); + } + else + { + database.addItem(new StringPair(source)); + } } - database.setSelectedItem(selectedDb); + setDatabaseSelectedItem(selectedDb); if (database.getSelectedIndex() == -1) { database.setSelectedIndex(0); @@ -183,7 +232,8 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void actionPerformed(ActionEvent e) { - String currentSelection = (String) database.getSelectedItem(); + String currentSelection = ((StringPair) database.getSelectedItem()) + .getKey(); updateExampleQuery(currentSelection); if ("pdb".equalsIgnoreCase(currentSelection)) @@ -310,6 +360,19 @@ public class SequenceFetcher extends JPanel implements Runnable this.add(databasePanel, BorderLayout.NORTH); } + private void setDatabaseSelectedItem(String db) + { + for (int i = 0; i < database.getItemCount(); i++) + { + StringPair sp = database.getItemAt(i); + if (sp != null && db != null && db.equals(sp.getKey())) + { + database.setSelectedIndex(i); + return; + } + } + } + /** * Answers a semi-colon-delimited string with the example query or queries for * the selected database @@ -381,7 +444,8 @@ public class SequenceFetcher extends JPanel implements Runnable */ protected void example_actionPerformed() { - String eq = getExampleQueries((String) database.getSelectedItem()); + String eq = getExampleQueries( + ((StringPair) database.getSelectedItem()).getKey()); textArea.setText(eq); repaint(); } @@ -430,9 +494,9 @@ public class SequenceFetcher extends JPanel implements Runnable text = text.replace(",", ";"); } text = text.replaceAll("(\\s|[; ])+", ";"); - if (!t0.equals(text)) + if (!t0.equals(text)) { - textArea.setText(text); + textArea.setText(text); } if (text.isEmpty()) { @@ -477,8 +541,8 @@ public class SequenceFetcher extends JPanel implements Runnable List presultTitle = new ArrayList<>(); List presult = new ArrayList<>(); List aresult = new ArrayList<>(); - List sources = sfetch - .getSourceProxy((String) database.getSelectedItem()); + List sources = sfetch.getSourceProxy( + ((StringPair) database.getSelectedItem()).getKey()); Iterator proxies = sources.iterator(); String[] qries = textArea.getText().trim().split(";"); List nextFetch = Arrays.asList(qries); @@ -530,23 +594,25 @@ public class SequenceFetcher extends JPanel implements Runnable } catch (Exception e) { showErrorMessage("Error retrieving " + textArea.getText() + " from " - + database.getSelectedItem()); + + ((StringPair) database.getSelectedItem()).getDisplay()); // error // +="Couldn't retrieve sequences from "+database.getSelectedItem(); System.err.println("Retrieval failed for source ='" - + database.getSelectedItem() + "' and query\n'" - + textArea.getText() + "'\n"); + + ((StringPair) database.getSelectedItem()).getDisplay() + + "' and query\n'" + textArea.getText() + "'\n"); e.printStackTrace(); } catch (OutOfMemoryError e) { showErrorMessage("Out of Memory when retrieving " - + textArea.getText() + " from " + database.getSelectedItem() + + textArea.getText() + " from " + + ((StringPair) database.getSelectedItem()).getDisplay() + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n"); e.printStackTrace(); } catch (Error e) { showErrorMessage("Serious Error retrieving " + textArea.getText() - + " from " + database.getSelectedItem()); + + " from " + + ((StringPair) database.getSelectedItem()).getDisplay()); e.printStackTrace(); } @@ -693,7 +759,8 @@ public class SequenceFetcher extends JPanel implements Runnable } catch (OutOfMemoryError oome) { new OOMWarning("fetching " + multiacc + " from " - + database.getSelectedItem(), oome, this); + + ((StringPair) database.getSelectedItem()).getDisplay(), + oome, this); } } @@ -767,12 +834,12 @@ public class SequenceFetcher extends JPanel implements Runnable for (String q : queries) { - // BH 2019.01.25 dbr is never used. -// DBRefEntry dbr = new DBRefEntry(); -// dbr.setSource(proxy.getDbSource()); -// dbr.setVersion(null); + // BH 2019.01.25 dbr is never used. + // DBRefEntry dbr = new DBRefEntry(); + // dbr.setSource(proxy.getDbSource()); + // dbr.setVersion(null); String accId = proxy.getAccessionIdFromQuery(q); -// dbr.setAccessionId(accId); + // dbr.setAccessionId(accId); boolean rfound = false; for (int r = 0, nr = rs.length; r < nr; r++) { @@ -801,15 +868,18 @@ public class SequenceFetcher extends JPanel implements Runnable */ public String getDefaultRetrievalTitle() { - return "Retrieved from " + database.getSelectedItem(); + return "Retrieved from " + + ((StringPair) database.getSelectedItem()).getDisplay(); } + /** * constructs an alignment frame given the data and metadata + * * @param al * @param title * @param currentFileFormat * @param preferredFeatureColours - * @return the alignment + * @return the alignment */ public AlignmentI parseResult(AlignmentI al, String title, FileFormatI currentFileFormat, diff --git a/src/jalview/gui/Slider.java b/src/jalview/gui/Slider.java index 7f18461..714e770 100644 --- a/src/jalview/gui/Slider.java +++ b/src/jalview/gui/Slider.java @@ -16,6 +16,12 @@ import javax.swing.JSlider; public class Slider extends JSlider { /* + * the number of nominal positions the slider represents + * (higher number = more fine-grained positioning) + */ + private static final int SCALE_TICKS = 1000; + + /* * 'true' value corresponding to zero on the slider */ private float trueMin; @@ -57,7 +63,7 @@ public class Slider extends JSlider trueMin = min; trueMax = max; setMinimum(0); - sliderScaleFactor = 100f / (max - min); + sliderScaleFactor = SCALE_TICKS / (max - min); int sliderMax = (int) ((max - min) * sliderScaleFactor); setMaximum(sliderMax); setSliderValue(value); diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 4807489..3ecca9b 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -247,13 +247,19 @@ public class StructureChooser extends GStructureChooser @Override public void run() { + progressBar.setProgressBar("status.searching_3d_beacons", progressId); // TODO: warn if no accessions discovered populateSeqsWithoutSourceDBRef(); // redo initial discovery - this time with 3d beacons // Executors. previousWantedFields=null; - initialStructureDiscovery(); + if (!isStructuresDiscovered()) + { + progressBar.setProgressBar("status.no_structures_discovered_from_3d_beacons", progressId); + } else { + progressBar.setProgressBar(null, progressId); + } } }; diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java index 1d240b2..a743694 100644 --- a/src/jalview/io/FileFormat.java +++ b/src/jalview/io/FileFormat.java @@ -244,7 +244,7 @@ public enum FileFormat implements FileFormatI return new PhylipFile(); } }, - GenBank("GenBank Flatfile", "gb", true, false) + GenBank("GenBank Flatfile", "gb, gbk", true, false) { @Override public AlignmentFileReaderI getReader(FileParse source) diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 9420465..67b44d7 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -31,6 +31,8 @@ import java.util.List; import java.util.Map; import java.util.StringTokenizer; import java.util.Vector; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import jalview.analysis.AlignSeq; import jalview.api.FeatureSettingsModelI; @@ -404,12 +406,14 @@ public class DBRefFetcher implements Runnable } else { + Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+"); // generate queries from sequence ID string - StringTokenizer st = new StringTokenizer(sequence.getName(), - "|"); - while (st.hasMoreTokens()) + Matcher tokens = possibleIds.matcher(sequence.getName()); + int p=0; + while (tokens.find(p)) { - String token = st.nextToken(); + String token = tokens.group(); + p = tokens.end(); UPEntry[] presp = null; if (picrClient != null) { diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index a80a530..b9fe52f 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -34,7 +34,6 @@ import jalview.datamodel.SequenceI; import jalview.schemes.ResidueProperties; import jalview.util.StringUtils; import jalview.ws.seqfetcher.DbSourceProxyImpl; -import jalview.xml.binding.embl.ROOT; import jalview.xml.binding.uniprot.DbReferenceType; import jalview.xml.binding.uniprot.Entry; import jalview.xml.binding.uniprot.FeatureType; @@ -43,8 +42,8 @@ import jalview.xml.binding.uniprot.PositionType; import jalview.xml.binding.uniprot.PropertyType; import java.io.InputStream; +import java.net.HttpURLConnection; import java.net.URL; -import java.net.URLConnection; import java.util.ArrayList; import java.util.List; import java.util.Vector; @@ -149,21 +148,27 @@ public class Uniprot extends DbSourceProxyImpl + ".xml"; URL url = new URL(downloadstring); - URLConnection urlconn = url.openConnection(); - InputStream istr = urlconn.getInputStream(); - List entries = getUniprotEntries(istr); - if (entries != null) + HttpURLConnection urlconn = (HttpURLConnection)url.openConnection(); + // anything other than 200 means we don't have data + // TODO: JAL-3882 reuse the EnsemblRestClient's fair + // use/backoff logic to retry when the server tells us to go away + if (urlconn.getResponseCode() == 200) { - List seqs = new ArrayList<>(); - for (Entry entry : entries) + InputStream istr = urlconn.getInputStream(); + List entries = getUniprotEntries(istr); + if (entries != null) { - seqs.add(uniprotEntryToSequence(entry)); + List seqs = new ArrayList<>(); + for (Entry entry : entries) + { + seqs.add(uniprotEntryToSequence(entry)); + } + al = new Alignment(seqs.toArray(new SequenceI[seqs.size()])); } - al = new Alignment(seqs.toArray(new SequenceI[seqs.size()])); } - stopQuery(); return al; + } catch (Exception e) { throw (e); @@ -518,6 +523,11 @@ public class Uniprot extends DbSourceProxyImpl } catch (JAXBException | XMLStreamException | FactoryConfigurationError e) { + if (e instanceof javax.xml.bind.UnmarshalException && e.getCause()!=null && e.getCause() instanceof XMLStreamException && e.getCause().getMessage().contains("[row,col]:[1,1]")) + { + // trying to parse an empty stream + return null; + } e.printStackTrace(); } return entries; diff --git a/utils/install4j/file_associations_auto-Info_plist.xml b/utils/install4j/file_associations_auto-Info_plist.xml index fac86a3..2196a6a 100644 --- a/utils/install4j/file_associations_auto-Info_plist.xml +++ b/utils/install4j/file_associations_auto-Info_plist.xml @@ -197,6 +197,25 @@ CFBundleTypeExtensions +txt + +CFBundleTypeName +ENA Flatfile File +CFBundleTypeIconFile +Jalview-File.icns +CFBundleTypeRole +Editor +CFBundleTypeMIMETypes + +application/x-embl+txt + +LSIsAppleDefaultForType + + + + +CFBundleTypeExtensions + fa fasta @@ -237,6 +256,26 @@ CFBundleTypeExtensions +gb +gbk + +CFBundleTypeName +GenBank Flatfile File +CFBundleTypeIconFile +Jalview-File.icns +CFBundleTypeRole +Editor +CFBundleTypeMIMETypes + +application/x-genbank+txt + +LSIsAppleDefaultForType + + + + +CFBundleTypeExtensions + gff2 CFBundleTypeName diff --git a/utils/install4j/file_associations_auto-install4j8.xml b/utils/install4j/file_associations_auto-install4j8.xml index b14d32a..0d80644 100644 --- a/utils/install4j/file_associations_auto-install4j8.xml +++ b/utils/install4j/file_associations_auto-install4j8.xml @@ -143,9 +143,9 @@ - + - + @@ -188,9 +188,9 @@ - + - + @@ -233,9 +233,9 @@ - + - + @@ -278,9 +278,9 @@ - + - + @@ -323,9 +323,9 @@ - + - + @@ -368,9 +368,9 @@ - + - + @@ -413,9 +413,9 @@ - + - + @@ -448,8 +448,53 @@ + + + + ENA Flatfile (.txt) + Creating file associations... + + + + + + + + + + + + + + ENA Flatfile File + txt + 737 + + + Jalview-File.icns + + + + + + + + + Jalview-File.png + + + application/x-embl+txt + + + Jalview-File.ico + + + + + + - + Fasta (.fa, .fasta) Creating file associations... @@ -458,13 +503,13 @@ - + - + - + Fasta File fa,fasta @@ -494,7 +539,7 @@ - + Jalview Features (.features, .jvfeatures) Creating file associations... @@ -503,13 +548,13 @@ - + - + - + Jalview Features File features,jvfeatures @@ -538,8 +583,53 @@ + + + + GenBank Flatfile (.gb, .gbk) + Creating file associations... + + + + + + + + + + + + + + GenBank Flatfile File + gb,gbk + 737 + + + Jalview-File.icns + + + + + + + + + Jalview-File.png + + + application/x-genbank+txt + + + Jalview-File.ico + + + + + + - + Generic Features Format v2 (.gff2) Creating file associations... @@ -548,13 +638,13 @@ - + - + - + Generic Features Format v2 File gff2 @@ -584,7 +674,7 @@ - + Generic Features Format v3 (.gff3) Creating file associations... @@ -593,13 +683,13 @@ - + - + - + Generic Features Format v3 File gff3 @@ -629,7 +719,7 @@ - + JnetFile (.concise, .jnet) Creating file associations... @@ -638,13 +728,13 @@ - + - + - + JnetFile File concise,jnet @@ -674,7 +764,7 @@ - + MSF (.msf) Creating file associations... @@ -683,13 +773,13 @@ - + - + - + MSF File msf @@ -719,7 +809,7 @@ - + PFAM (.pfam) Creating file associations... @@ -728,13 +818,13 @@ - + - + - + PFAM File pfam @@ -764,7 +854,7 @@ - + PHYLIP (.phy) Creating file associations... @@ -773,13 +863,13 @@ - + - + - + PHYLIP File phy @@ -809,7 +899,7 @@ - + PileUp (.pileup) Creating file associations... @@ -818,13 +908,13 @@ - + - + - + PileUp File pileup @@ -854,7 +944,7 @@ - + PIR (.pir) Creating file associations... @@ -863,13 +953,13 @@ - + - + - + PIR File pir @@ -899,7 +989,7 @@ - + RNAML (.rnaml) Creating file associations... @@ -908,13 +998,13 @@ - + - + - + RNAML File rnaml @@ -944,7 +1034,7 @@ - + Substitution Matrix (.mat) Creating file associations... @@ -953,13 +1043,13 @@ - + - + - + Substitution Matrix File mat @@ -989,7 +1079,7 @@ - + Stockholm (.stk, .sto) Creating file associations... @@ -998,13 +1088,13 @@ - + - + - + Stockholm File stk,sto diff --git a/utils/jalviewjs/classlists/jvexamplefile.txt b/utils/jalviewjs/classlists/jvexamplefile.txt index ae01fe1..fd38213 100644 --- a/utils/jalviewjs/classlists/jvexamplefile.txt +++ b/utils/jalviewjs/classlists/jvexamplefile.txt @@ -1,491 +1,183 @@ - -com/stevesoft/pat/Any.js -com/stevesoft/pat/Bracket.js -com/stevesoft/pat/Branch.js -com/stevesoft/pat/CaseMgr.js -com/stevesoft/pat/DotMulti.js -com/stevesoft/pat/End.js -com/stevesoft/pat/FastBracket.js -com/stevesoft/pat/FastChar.js -com/stevesoft/pat/FastMulti.js -com/stevesoft/pat/NUnicodeAlpha.js -com/stevesoft/pat/NUnicodeCurrency.js -com/stevesoft/pat/NUnicodeDigit.js -com/stevesoft/pat/NUnicodeMath.js -com/stevesoft/pat/NUnicodePunct.js -com/stevesoft/pat/NUnicodeW.js -com/stevesoft/pat/NUnicodeWhite.js -com/stevesoft/pat/NoPattern.js -com/stevesoft/pat/NullPattern.js -com/stevesoft/pat/Or.js -com/stevesoft/pat/OrMark.js -com/stevesoft/pat/Pattern.js -com/stevesoft/pat/PatternSub.js -com/stevesoft/pat/Pthings.js -com/stevesoft/pat/Range.js -com/stevesoft/pat/RegHolder.js -com/stevesoft/pat/RegOpt.js -com/stevesoft/pat/RegRes.js -com/stevesoft/pat/Regex.js -com/stevesoft/pat/ReplaceRule.js -com/stevesoft/pat/Replacer.js -com/stevesoft/pat/Rthings.js -com/stevesoft/pat/Skip.js -com/stevesoft/pat/StrPos.js -com/stevesoft/pat/StringLike.js 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java/awt/event/MouseAdapter.js +java/awt/event/MouseEvent.js +java/awt/event/MouseListener.js java/awt/event/MouseMotionAdapter.js +java/awt/event/MouseMotionListener.js java/awt/event/MouseWheelEvent.js +java/awt/event/MouseWheelListener.js +java/awt/event/TextListener.js +java/awt/event/WindowAdapter.js +java/awt/event/WindowEvent.js +java/awt/event/WindowFocusListener.js +java/awt/event/WindowListener.js +java/awt/event/WindowStateListener.js +java/awt/font/FontRenderContext.js java/awt/font/TextAttribute.js +java/awt/geom/AffineTransform.js +java/awt/geom/Dimension2D.js java/awt/geom/Path2D.js java/awt/geom/PathIterator.js +java/awt/geom/Point2D.js java/awt/geom/RectIterator.js +java/awt/geom/Rectangle2D.js +java/awt/geom/RectangularShape.js java/awt/image/BufferedImage.js java/awt/image/ColorModel.js java/awt/image/DataBuffer.js java/awt/image/DataBufferInt.js java/awt/image/DirectColorModel.js java/awt/image/ImageConsumer.js +java/awt/image/ImageObserver.js java/awt/image/ImageProducer.js java/awt/image/PackedColorModel.js java/awt/image/PixelGrabber.js @@ -494,15 +186,26 @@ java/awt/image/RenderedImage.js java/awt/image/SampleModel.js java/awt/image/SinglePixelPackedSampleModel.js java/awt/image/WritableRaster.js +java/awt/peer/ComponentPeer.js +java/awt/peer/ContainerPeer.js java/awt/peer/DialogPeer.js +java/awt/peer/FramePeer.js java/awt/peer/KeyboardFocusManagerPeer.js +java/awt/peer/LightweightPeer.js +java/awt/peer/WindowPeer.js java/awt/print/Printable.js +java/beans/ChangeListenerMap.js +java/beans/PropertyChangeEvent.js +java/beans/PropertyChangeListener.js +java/beans/PropertyChangeSupport.js java/io/BufferedInputStream.js java/io/BufferedReader.js java/io/BufferedWriter.js java/io/ByteArrayInputStream.js java/io/ByteArrayOutputStream.js java/io/Closeable.js +java/io/DataInput.js +java/io/DataInputStream.js java/io/File.js java/io/FileDescriptor.js java/io/FileInputStream.js @@ -518,41 +221,44 @@ java/io/ObjectStreamField.js java/io/OutputStream.js java/io/OutputStreamWriter.js java/io/PrintStream.js -java/io/PrintWriter.js -java/io/PushbackInputStream.js java/io/Reader.js java/io/StringReader.js java/io/StringWriter.js java/io/Writer.js +java/lang/AbstractStringBuilder.js java/lang/AutoCloseable.js +java/lang/Class.js +java/lang/Enum.js java/lang/Iterable.js java/lang/Readable.js java/lang/Runtime.js +java/lang/StringBuffer.js java/lang/StringBuilder.js +java/lang/Thread.js +java/lang/ThreadGroup.js +java/lang/ThreadLocal.js +java/lang/ref/ReferenceQueue.js +java/lang/reflect/AccessibleObject.js +java/lang/reflect/AnnotatedElement.js java/lang/reflect/Constructor.js java/lang/reflect/Method.js java/math/BigDecimal.js java/math/BigInteger.js java/math/MathContext.js java/math/RoundingMode.js +java/net/ContentHandler.js java/net/HttpURLConnection.js -java/net/HttpsURLConnection.js java/net/URI.js +java/net/URL.js java/net/URLConnection.js -java/net/URLDecoder.js java/net/URLStreamHandler.js -java/nio/Bits.js -java/nio/Buffer.js -java/nio/ByteBuffer.js -java/nio/ByteOrder.js -java/nio/CharBuffer.js -java/nio/HeapByteBuffer.js -java/nio/HeapCharBuffer.js -java/nio/charset/Charset.js -java/nio/charset/CharsetDecoder.js -java/nio/charset/CoderResult.js -java/nio/charset/CodingErrorAction.js -java/security/AccessControlContext.js +java/net/URLStreamHandlerFactory.js +java/net/UnknownHostException.js +java/nio/file/FileSystem.js +java/nio/file/FileSystems.js +java/nio/file/Path.js +java/nio/file/Watchable.js +java/nio/file/spi/FileSystemProvider.js java/security/AccessController.js java/security/PrivilegedAction.js java/security/PrivilegedExceptionAction.js @@ -568,26 +274,46 @@ java/text/Format.js java/text/MessageFormat.js java/text/NumberFormat.js java/text/SimpleDateFormat.js +java/text/spi/BreakIteratorProvider.js +java/text/spi/CollatorProvider.js +java/text/spi/DateFormatProvider.js +java/text/spi/DateFormatSymbolsProvider.js +java/text/spi/DecimalFormatSymbolsProvider.js +java/text/spi/NumberFormatProvider.js +java/util/AbstractCollection.js +java/util/AbstractList.js +java/util/AbstractMap.js java/util/AbstractQueue.js java/util/AbstractSequentialList.js +java/util/AbstractSet.js java/util/ArrayDeque.js +java/util/ArrayList.js +java/util/Arrays.js java/util/BitSet.js java/util/Calendar.js java/util/Collection.js +java/util/Collections.js java/util/ComparableTimSort.js java/util/Comparator.js java/util/Deque.js +java/util/Dictionary.js java/util/DualPivotQuicksort.js java/util/Enumeration.js +java/util/EventListener.js +java/util/EventObject.js java/util/Formatter.js java/util/GregorianCalendar.js +java/util/HashMap.js +java/util/HashSet.js +java/util/Hashtable.js +java/util/IdentityHashMap.js java/util/Iterator.js java/util/LinkedHashMap.js java/util/LinkedHashSet.js java/util/LinkedList.js java/util/List.js java/util/ListIterator.js -java/util/ListResourceBundle.js +java/util/Locale.js java/util/Map.js java/util/NavigableMap.js java/util/NavigableSet.js @@ -595,16 +321,22 @@ java/util/Objects.js java/util/Properties.js java/util/PropertyResourceBundle.js java/util/Queue.js +java/util/Random.js java/util/RandomAccess.js +java/util/RandomAccessSubList.js java/util/ResourceBundle.js +java/util/ServiceLoader.js java/util/Set.js java/util/SortedMap.js java/util/SortedSet.js +java/util/Stack.js java/util/StringTokenizer.js +java/util/SubList.js java/util/TimSort.js java/util/TimeZone.js java/util/TreeMap.js java/util/TreeSet.js +java/util/Vector.js java/util/WeakHashMap.js java/util/concurrent/AbstractExecutorService.js java/util/concurrent/BlockingQueue.js @@ -619,7 +351,6 @@ java/util/concurrent/Semaphore.js java/util/concurrent/ThreadFactory.js java/util/concurrent/ThreadPoolExecutor.js java/util/concurrent/TimeUnit.js -java/util/concurrent/atomic/AtomicBoolean.js java/util/concurrent/atomic/AtomicInteger.js java/util/concurrent/locks/AbstractOwnableSynchronizer.js java/util/concurrent/locks/AbstractQueuedSynchronizer.js @@ -628,14 +359,16 @@ java/util/concurrent/locks/Lock.js java/util/concurrent/locks/ReadWriteLock.js java/util/concurrent/locks/ReentrantLock.js java/util/concurrent/locks/ReentrantReadWriteLock.js -java/util/function/Function.js java/util/jar/JarEntry.js java/util/jar/JarInputStream.js -java/util/logging/Level.js -java/util/logging/Logger.js java/util/regex/MatchResult.js java/util/regex/Matcher.js java/util/regex/Pattern.js +java/util/spi/CalendarDataProvider.js +java/util/spi/CurrencyNameProvider.js +java/util/spi/LocaleNameProvider.js +java/util/spi/LocaleServiceProvider.js +java/util/spi/TimeZoneNameProvider.js java/util/zip/CRC32.js java/util/zip/Inflater.js java/util/zip/InflaterInputStream.js @@ -647,17 +380,20 @@ javajs/api/GenericCifDataParser.js javajs/api/GenericLineReader.js javajs/api/GenericOutputChannel.js javajs/api/JSONEncodable.js -javajs/awt/Font.js -javajs/awt/FontManager.js javajs/util/A4.js +javajs/util/AU.js +javajs/util/AjaxURLConnection.js javajs/util/AjaxURLStreamHandler.js +javajs/util/AjaxURLStreamHandlerFactory.js javajs/util/BS.js javajs/util/Base64.js javajs/util/CU.js javajs/util/CifDataParser.js javajs/util/DF.js javajs/util/Encoding.js +javajs/util/JSThread.js javajs/util/LimitedLineReader.js +javajs/util/Lst.js javajs/util/M3.js javajs/util/M34.js javajs/util/M4.js @@ -665,96 +401,141 @@ javajs/util/OC.js javajs/util/P3.js javajs/util/P3i.js javajs/util/P4.js +javajs/util/PT.js javajs/util/Rdr.js javajs/util/SB.js javajs/util/T3.js javajs/util/T3i.js javajs/util/T4.js javajs/util/V3.js +javax/net/ssl/HttpsURLConnection.js javax/swing/AbstractAction.js -javax/swing/AbstractCellEditor.js -javax/swing/AbstractSpinnerModel.js +javax/swing/AbstractButton.js +javax/swing/AbstractListModel.js javax/swing/Action.js +javax/swing/ActionMap.js +javax/swing/AncestorNotifier.js +javax/swing/ArrayTable.js javax/swing/Autoscroller.js -javax/swing/CellEditor.js +javax/swing/BorderFactory.js +javax/swing/BoundedRangeModel.js +javax/swing/BoxLayout.js +javax/swing/ButtonGroup.js +javax/swing/ButtonModel.js javax/swing/CellRendererPane.js -javax/swing/ColorChooserDialog.js +javax/swing/ClientPropertyKey.js +javax/swing/ComboBoxEditor.js +javax/swing/ComboBoxModel.js javax/swing/ComponentInputMap.js -javax/swing/DefaultCellEditor.js +javax/swing/DefaultBoundedRangeModel.js +javax/swing/DefaultButtonModel.js +javax/swing/DefaultComboBoxModel.js javax/swing/DefaultDesktopManager.js javax/swing/DefaultListCellRenderer.js javax/swing/DefaultListSelectionModel.js javax/swing/DefaultRowSorter.js +javax/swing/DefaultSingleSelectionModel.js javax/swing/DesktopManager.js javax/swing/DropMode.js +javax/swing/FocusManager.js javax/swing/Icon.js javax/swing/ImageIcon.js javax/swing/InputMap.js -javax/swing/JColorChooser.js +javax/swing/InternalFrameFocusTraversalPolicy.js +javax/swing/JApplet.js +javax/swing/JButton.js +javax/swing/JCheckBox.js +javax/swing/JCheckBoxMenuItem.js +javax/swing/JComboBox.js +javax/swing/JComponent.js javax/swing/JDesktopPane.js javax/swing/JDialog.js -javax/swing/JFileChooser.js -javax/swing/JFormattedTextField.js +javax/swing/JFrame.js javax/swing/JInternalFrame.js +javax/swing/JLabel.js +javax/swing/JLayeredPane.js javax/swing/JList.js +javax/swing/JMenu.js +javax/swing/JMenuBar.js +javax/swing/JMenuItem.js javax/swing/JOptionPane.js +javax/swing/JPanel.js +javax/swing/JPopupMenu.js javax/swing/JProgressBar.js -javax/swing/JRadioButton.js +javax/swing/JRadioButtonMenuItem.js +javax/swing/JRootPane.js +javax/swing/JScrollBar.js javax/swing/JScrollPane.js -javax/swing/JSlider.js -javax/swing/JSpinner.js +javax/swing/JSeparator.js javax/swing/JTabbedPane.js javax/swing/JTable.js javax/swing/JTextArea.js javax/swing/JTextField.js +javax/swing/JToggleButton.js javax/swing/JToolTip.js javax/swing/JViewport.js javax/swing/JWindow.js javax/swing/KeyStroke.js +javax/swing/KeyboardManager.js +javax/swing/LayoutComparator.js +javax/swing/LayoutFocusTraversalPolicy.js javax/swing/ListCellRenderer.js +javax/swing/ListModel.js javax/swing/ListSelectionModel.js +javax/swing/LookAndFeel.js +javax/swing/MenuElement.js javax/swing/MenuSelectionManager.js +javax/swing/MutableComboBoxModel.js javax/swing/Popup.js javax/swing/PopupFactory.js -javax/swing/RowFilter.js +javax/swing/RepaintManager.js +javax/swing/RootPaneContainer.js javax/swing/RowSorter.js javax/swing/ScrollPaneConstants.js javax/swing/ScrollPaneLayout.js javax/swing/Scrollable.js +javax/swing/SingleSelectionModel.js +javax/swing/SizeRequirements.js javax/swing/SortOrder.js -javax/swing/SpinnerModel.js -javax/swing/SpinnerNumberModel.js -javax/swing/Spring.js -javax/swing/SpringLayout.js +javax/swing/SortingFocusTraversalPolicy.js +javax/swing/SwingConstants.js +javax/swing/SwingContainerOrderFocusTraversalPolicy.js +javax/swing/SwingDefaultFocusTraversalPolicy.js +javax/swing/SwingPaintEventDispatcher.js +javax/swing/SwingUtilities.js javax/swing/Timer.js javax/swing/ToolTipManager.js +javax/swing/TransferHandler.js +javax/swing/UIDefaults.js +javax/swing/UIManager.js javax/swing/ViewportLayout.js +javax/swing/WindowConstants.js +javax/swing/border/AbstractBorder.js +javax/swing/border/BevelBorder.js +javax/swing/border/Border.js javax/swing/border/CompoundBorder.js +javax/swing/border/EmptyBorder.js +javax/swing/border/EtchedBorder.js javax/swing/border/LineBorder.js -javax/swing/border/MatteBorder.js -javax/swing/border/TitledBorder.js -javax/swing/colorchooser/AbstractColorChooserPanel.js -javax/swing/colorchooser/CenterLayout.js -javax/swing/colorchooser/ColorChooserComponentFactory.js -javax/swing/colorchooser/ColorSelectionModel.js -javax/swing/colorchooser/DefaultColorSelectionModel.js -javax/swing/colorchooser/DefaultPreviewPanel.js -javax/swing/colorchooser/DefaultRGBChooserPanel.js -javax/swing/colorchooser/DefaultSwatchChooserPanel.js -javax/swing/colorchooser/MainSwatchPanel.js -javax/swing/colorchooser/RecentSwatchPanel.js -javax/swing/colorchooser/SmartGridLayout.js -javax/swing/colorchooser/SwatchPanel.js +javax/swing/event/AncestorEvent.js +javax/swing/event/AncestorListener.js javax/swing/event/CaretEvent.js javax/swing/event/CaretListener.js javax/swing/event/CellEditorListener.js +javax/swing/event/ChangeEvent.js +javax/swing/event/ChangeListener.js javax/swing/event/DocumentEvent.js javax/swing/event/DocumentListener.js +javax/swing/event/EventListenerList.js +javax/swing/event/HyperlinkListener.js javax/swing/event/InternalFrameAdapter.js javax/swing/event/InternalFrameEvent.js javax/swing/event/InternalFrameListener.js +javax/swing/event/ListDataEvent.js +javax/swing/event/ListDataListener.js javax/swing/event/ListSelectionEvent.js javax/swing/event/ListSelectionListener.js +javax/swing/event/MenuEvent.js javax/swing/event/MenuKeyListener.js javax/swing/event/MenuListener.js javax/swing/event/MouseInputListener.js @@ -767,17 +548,23 @@ javax/swing/event/TableModelEvent.js javax/swing/event/TableModelListener.js javax/swing/event/UndoableEditEvent.js javax/swing/event/UndoableEditListener.js -javax/swing/filechooser/FileFilter.js -javax/swing/filechooser/FileView.js +javax/swing/plaf/ActionMapUIResource.js +javax/swing/plaf/BorderUIResource.js +javax/swing/plaf/ColorUIResource.js javax/swing/plaf/ComponentInputMapUIResource.js +javax/swing/plaf/ComponentUI.js +javax/swing/plaf/DimensionUIResource.js +javax/swing/plaf/FontUIResource.js javax/swing/plaf/InputMapUIResource.js +javax/swing/plaf/InsetsUIResource.js +javax/swing/plaf/UIResource.js javax/swing/plaf/basic/BasicBorders.js +javax/swing/plaf/basic/BasicGraphicsUtils.js javax/swing/table/AbstractTableModel.js javax/swing/table/DefaultTableCellRenderer.js javax/swing/table/DefaultTableColumnModel.js javax/swing/table/DefaultTableModel.js javax/swing/table/JTableHeader.js -javax/swing/table/TableCellEditor.js javax/swing/table/TableCellRenderer.js javax/swing/table/TableColumn.js javax/swing/table/TableColumnModel.js @@ -785,21 +572,18 @@ javax/swing/table/TableModel.js javax/swing/table/TableRowSorter.js javax/swing/text/AbstractDocument.js javax/swing/text/AttributeSet.js +javax/swing/text/BoxView.js javax/swing/text/Caret.js +javax/swing/text/CompositeView.js javax/swing/text/DefaultCaret.js javax/swing/text/DefaultEditorKit.js -javax/swing/text/DefaultFormatter.js -javax/swing/text/DefaultFormatterFactory.js javax/swing/text/Document.js -javax/swing/text/DocumentFilter.js javax/swing/text/EditorKit.js javax/swing/text/Element.js javax/swing/text/GapContent.js javax/swing/text/GapVector.js -javax/swing/text/InternationalFormatter.js javax/swing/text/JTextComponent.js javax/swing/text/MutableAttributeSet.js -javax/swing/text/NumberFormatter.js javax/swing/text/PlainDocument.js javax/swing/text/PlainView.js javax/swing/text/Position.js @@ -813,7 +597,7 @@ javax/swing/text/TabExpander.js javax/swing/text/TextAction.js javax/swing/text/Utilities.js javax/swing/text/View.js -javax/swing/tree/TreeCellEditor.js +javax/swing/text/WrappedPlainView.js javax/swing/tree/TreeNode.js javax/swing/undo/AbstractUndoableEdit.js javax/swing/undo/CompoundEdit.js @@ -831,15 +615,11 @@ javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js javax/xml/bind/annotation/adapters/XmlAdapter.js javax/xml/bind/helpers/AbstractUnmarshallerImpl.js javax/xml/bind/helpers/DefaultValidationEventHandler.js -javax/xml/datatype/DatatypeFactory.js javax/xml/datatype/XMLGregorianCalendar.js javax/xml/namespace/QName.js javax/xml/stream/XMLInputFactory.js +javax/xml/stream/XMLStreamConstants.js javax/xml/stream/XMLStreamReader.js -mc_view/Atom.js -mc_view/Bond.js -mc_view/PDBChain.js -mc_view/Residue.js net/miginfocom/layout/AC.js net/miginfocom/layout/AnimSpec.js net/miginfocom/layout/BoundSize.js @@ -858,7 +638,6 @@ net/miginfocom/layout/UnitValue.js net/miginfocom/swing/MigLayout.js net/miginfocom/swing/SwingComponentWrapper.js net/miginfocom/swing/SwingContainerWrapper.js -org/apache/xerces/jaxp/datatype/DatatypeFactoryImpl.js org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js org/jmol/adapter/readers/cif/CifReader.js org/jmol/adapter/readers/cif/MMCifReader.js @@ -874,9 +653,9 @@ org/jmol/adapter/smarter/Resolver.js org/jmol/adapter/smarter/SmarterJmolAdapter.js org/jmol/adapter/smarter/Structure.js org/jmol/adapter/smarter/StructureIterator.js -org/jmol/adapter/smarter/XtalSymmetry.js org/jmol/api/AtomIndexIterator.js org/jmol/api/EventManager.js +org/jmol/api/FontManager.js org/jmol/api/GenericFileInterface.js org/jmol/api/GenericMouseInterface.js org/jmol/api/GenericPlatform.js @@ -886,9 +665,9 @@ org/jmol/api/JmolAdapterAtomIterator.js org/jmol/api/JmolAdapterBondIterator.js org/jmol/api/JmolAdapterStructureIterator.js org/jmol/api/JmolCallbackListener.js +org/jmol/api/JmolFilesReaderInterface.js org/jmol/api/JmolGraphicsInterface.js org/jmol/api/JmolMeasurementClient.js -org/jmol/api/JmolPropertyManager.js org/jmol/api/JmolRendererInterface.js org/jmol/api/JmolRepaintManager.js org/jmol/api/JmolScriptEvaluator.js @@ -920,6 +699,8 @@ org/jmol/c/PAL.js org/jmol/c/STER.js org/jmol/c/STR.js org/jmol/c/VDW.js +org/jmol/dssx/Bridge.js +org/jmol/dssx/DSSP.js org/jmol/g3d/CylinderRenderer.js org/jmol/g3d/G3DRenderer.js org/jmol/g3d/Graphics3D.js @@ -936,6 +717,7 @@ org/jmol/i18n/GT.js org/jmol/i18n/Language.js org/jmol/i18n/Resource.js org/jmol/io/FileReader.js +org/jmol/io/FilesReader.js org/jmol/modelset/Atom.js org/jmol/modelset/AtomCollection.js org/jmol/modelset/AtomIteratorWithinModel.js @@ -945,9 +727,11 @@ org/jmol/modelset/BondIterator.js org/jmol/modelset/BondIteratorSelected.js org/jmol/modelset/Chain.js org/jmol/modelset/Group.js +org/jmol/modelset/HBond.js org/jmol/modelset/LabelToken.js org/jmol/modelset/Measurement.js org/jmol/modelset/MeasurementData.js +org/jmol/modelset/MeasurementPending.js org/jmol/modelset/Model.js org/jmol/modelset/ModelLoader.js org/jmol/modelset/ModelSet.js @@ -965,12 +749,9 @@ org/jmol/modelsetbio/BioPolymer.js org/jmol/modelsetbio/BioResolver.js org/jmol/modelsetbio/Helix.js org/jmol/modelsetbio/Monomer.js -org/jmol/modelsetbio/NucleicMonomer.js -org/jmol/modelsetbio/NucleicPolymer.js -org/jmol/modelsetbio/PhosphorusMonomer.js -org/jmol/modelsetbio/PhosphorusPolymer.js org/jmol/modelsetbio/ProteinStructure.js org/jmol/modelsetbio/Sheet.js +org/jmol/modelsetbio/Turn.js org/jmol/render/BallsRenderer.js org/jmol/render/BbcageRenderer.js org/jmol/render/CageRenderer.js @@ -1000,6 +781,7 @@ org/jmol/script/ScriptFunction.js org/jmol/script/ScriptManager.js org/jmol/script/ScriptMathProcessor.js org/jmol/script/ScriptParam.js +org/jmol/script/ScriptQueueThread.js org/jmol/script/ScriptTokenParser.js org/jmol/script/T.js org/jmol/scriptext/CmdExt.js @@ -1008,6 +790,7 @@ org/jmol/scriptext/ScriptExt.js org/jmol/shape/AtomShape.js org/jmol/shape/Balls.js org/jmol/shape/Bbcage.js +org/jmol/shape/Echo.js org/jmol/shape/FontLineShape.js org/jmol/shape/Frank.js org/jmol/shape/Hover.js @@ -1027,6 +810,7 @@ org/jmol/symmetry/SymmetryInfo.js org/jmol/symmetry/UnitCell.js org/jmol/thread/HoverWatcherThread.js org/jmol/thread/JmolThread.js +org/jmol/thread/TimeoutThread.js org/jmol/util/BSUtil.js org/jmol/util/BoxInfo.js org/jmol/util/C.js @@ -1036,6 +820,7 @@ org/jmol/util/DefaultLogger.js org/jmol/util/Edge.js org/jmol/util/Elements.js org/jmol/util/Escape.js +org/jmol/util/Font.js org/jmol/util/GData.js org/jmol/util/Geodesic.js org/jmol/util/Int2IntHash.js @@ -1063,7 +848,6 @@ org/jmol/viewer/JC.js org/jmol/viewer/ModelManager.js org/jmol/viewer/MotionPoint.js org/jmol/viewer/MouseState.js -org/jmol/viewer/PropertyManager.js org/jmol/viewer/SelectionManager.js org/jmol/viewer/ShapeManager.js org/jmol/viewer/StateManager.js @@ -1072,6 +856,7 @@ org/jmol/viewer/TransformManager.js org/jmol/viewer/Viewer.js org/jmol/viewer/binding/Binding.js org/jmol/viewer/binding/JmolBinding.js +org/json/simple/parser/ParseException.js org/xml/sax/AttributeList.js org/xml/sax/Attributes.js org/xml/sax/ContentHandler.js @@ -1079,11 +864,18 @@ org/xml/sax/InputSource.js org/xml/sax/Parser.js org/xml/sax/XMLReader.js org/xml/sax/ext/Attributes2.js -sun/awt/AWTAccessor.js +sun/awt/AWTAutoShutdown.js +sun/awt/AppContext.js sun/awt/CausedFocusEvent.js +sun/awt/ComponentFactory.js sun/awt/EventQueueItem.js -sun/awt/KeyboardFocusManagerPeerProvider.js +sun/awt/MostRecentKeyValue.js +sun/awt/MostRecentThreadAppContext.js +sun/awt/PaintEventDispatcher.js +sun/awt/PostEventQueue.js +sun/awt/RequestFocusController.js sun/awt/SunGraphicsCallback.js +sun/awt/SunToolkit.js sun/awt/image/DataStealer.js sun/awt/image/IntegerComponentRaster.js sun/awt/image/IntegerInterleavedRaster.js @@ -1094,20 +886,18 @@ sun/font/EAttribute.js sun/font/FontDesignMetrics.js sun/java2d/StateTrackable.js sun/java2d/StateTrackableDelegate.js -sun/nio/cs/ArrayDecoder.js -sun/nio/cs/HistoricallyNamedCharset.js -sun/nio/cs/StandardCharsets.js -sun/nio/cs/ThreadLocalCoders.js -sun/nio/cs/UTF_8.js -sun/nio/cs/Unicode.js +sun/net/www/MessageHeader.js sun/swing/DefaultLookup.js sun/swing/StringUIClientPropertyKey.js +sun/swing/SwingLazyValue.js sun/swing/SwingUtilities2.js sun/swing/UIAction.js sun/swing/UIClientPropertyKey.js sun/swing/table/DefaultTableCellHeaderRenderer.js sun/text/resources/FormatData.js -sun/text/resources/FormatData_en.js +sun/text/resources/en/FormatData_en.js +sun/text/resources/en/FormatData_en_GB.js +sun/text/resources/en/FormatData_en_US.js sun/util/calendar/AbstractCalendar.js sun/util/calendar/BaseCalendar.js sun/util/calendar/CalendarDate.js @@ -1115,22 +905,56 @@ sun/util/calendar/CalendarSystem.js sun/util/calendar/CalendarUtils.js sun/util/calendar/Gregorian.js sun/util/calendar/ZoneInfo.js +sun/util/calendar/ZoneInfoFile.js +sun/util/locale/BaseLocale.js +sun/util/locale/LanguageTag.js +sun/util/locale/LocaleUtils.js +sun/util/locale/provider/AuxLocaleProviderAdapter.js +sun/util/locale/provider/AvailableLanguageTags.js +sun/util/locale/provider/CalendarDataProviderImpl.js +sun/util/locale/provider/CalendarDataUtility.js +sun/util/locale/provider/CalendarProviderImpl.js +sun/util/locale/provider/DateFormatProviderImpl.js +sun/util/locale/provider/JRELocaleProviderAdapter.js +sun/util/locale/provider/LocaleDataMetaInfo.js +sun/util/locale/provider/LocaleProviderAdapter.js +sun/util/locale/provider/LocaleResources.js +sun/util/locale/provider/LocaleServiceProviderPool.js +sun/util/locale/provider/ResourceBundleBasedAdapter.js +sun/util/locale/provider/SPILocaleProviderAdapter.js sun/util/resources/LocaleData.js -swingjs/JSAbstractDocument.js -swingjs/JSCharSet.js -swingjs/JSDnD.js -swingjs/JSDocumentEvent.js +sun/util/resources/ParallelListResourceBundle.js +sun/util/spi/CalendarProvider.js +swingjs/JSApp.js +swingjs/JSAppletThread.js +swingjs/JSAppletViewer.js +swingjs/JSDummyApplet.js +swingjs/JSFileSystem.js swingjs/JSFocusPeer.js -swingjs/JSGraphicsCompositor.js +swingjs/JSFontMetrics.js +swingjs/JSFrameViewer.js +swingjs/JSGraphics2D.js +swingjs/JSGraphicsConfiguration.js +swingjs/JSGraphicsEnvironment.js swingjs/JSImage.js swingjs/JSImagekit.js swingjs/JSKeyEvent.js swingjs/JSMenuManager.js -swingjs/JSPlainDocument.js -swingjs/JSTempFile.js +swingjs/JSMouse.js +swingjs/JSScreenDevice.js +swingjs/JSThreadGroup.js +swingjs/JSToolkit.js +swingjs/JSUtil.js swingjs/a2s/A2SContainer.js swingjs/a2s/Dialog.js -swingjs/api/JSMinimalAbstractDocument.js +swingjs/api/Interface.js +swingjs/api/JSUtilI.js +swingjs/api/js/DOMNode.js +swingjs/api/js/HTML5Canvas.js +swingjs/api/js/HTML5CanvasContext2D.js +swingjs/api/js/JSFunction.js +swingjs/api/js/JSInterface.js +swingjs/jquery/JQueryUI.js swingjs/json/JSON.js swingjs/jzlib/Adler32.js swingjs/jzlib/CRC32.js @@ -1142,42 +966,66 @@ swingjs/jzlib/Inflate.js swingjs/jzlib/Inflater.js swingjs/jzlib/InflaterInputStream.js swingjs/jzlib/ZStream.js -swingjs/plaf/BasicArrowButton.js +swingjs/plaf/BasicComboBoxEditor.js +swingjs/plaf/BasicComboBoxRenderer.js swingjs/plaf/BasicHTML.js +swingjs/plaf/ButtonListener.js swingjs/plaf/CellHolder.js -swingjs/plaf/CenterLayout.js +swingjs/plaf/DefaultMenuLayout.js +swingjs/plaf/HTML5LookAndFeel.js swingjs/plaf/JSAppletUI.js -swingjs/plaf/JSColorChooserUI.js +swingjs/plaf/JSButtonUI.js +swingjs/plaf/JSCheckBoxMenuItemUI.js +swingjs/plaf/JSCheckBoxUI.js +swingjs/plaf/JSComboBoxUI.js +swingjs/plaf/JSComboPopupList.js +swingjs/plaf/JSComponentUI.js swingjs/plaf/JSDesktopIconUI.js swingjs/plaf/JSDesktopPaneUI.js swingjs/plaf/JSDialogUI.js -swingjs/plaf/JSFormattedTextFieldUI.js +swingjs/plaf/JSEventHandler.js +swingjs/plaf/JSFrameUI.js swingjs/plaf/JSGraphicsUtils.js swingjs/plaf/JSInternalFrameUI.js +swingjs/plaf/JSLabelUI.js +swingjs/plaf/JSLayeredPaneUI.js +swingjs/plaf/JSLightweightUI.js swingjs/plaf/JSListUI.js +swingjs/plaf/JSMenuBarUI.js +swingjs/plaf/JSMenuItemUI.js +swingjs/plaf/JSMenuUI.js +swingjs/plaf/JSOptionPaneUI.js +swingjs/plaf/JSPanelUI.js +swingjs/plaf/JSPopupMenuSeparatorUI.js +swingjs/plaf/JSPopupMenuUI.js swingjs/plaf/JSPopupUI.js swingjs/plaf/JSProgressBarUI.js +swingjs/plaf/JSRadioButtonMenuItemUI.js +swingjs/plaf/JSRadioButtonUI.js +swingjs/plaf/JSRootPaneUI.js +swingjs/plaf/JSScrollBarUI.js swingjs/plaf/JSScrollPaneUI.js -swingjs/plaf/JSSpinnerUI.js +swingjs/plaf/JSSeparatorUI.js +swingjs/plaf/JSSliderUI.js swingjs/plaf/JSTabbedPaneUI.js swingjs/plaf/JSTableHeaderUI.js swingjs/plaf/JSTableUI.js swingjs/plaf/JSTextAreaUI.js swingjs/plaf/JSTextFieldUI.js swingjs/plaf/JSTextUI.js -swingjs/plaf/JSTextViewUI.js swingjs/plaf/JSToolTipUI.js swingjs/plaf/JSViewportUI.js +swingjs/plaf/JSWindowUI.js +swingjs/plaf/LazyActionMap.js +swingjs/plaf/Resizer.js swingjs/plaf/TextListener.js swingjs/xml/JSJAXBClass.js swingjs/xml/JSJAXBContext.js swingjs/xml/JSJAXBContextFactory.js -swingjs/xml/JSJAXBDatatypeFactory.js swingjs/xml/JSJAXBField.js swingjs/xml/JSJAXBUnmarshaller.js swingjs/xml/JSSAXAttributes.js swingjs/xml/JSSAXParser.js swingjs/xml/JSXMLGregorianCalendarImpl.js swingjs/xml/JSXMLInputFactory.js -swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Any.js -swingjs/xml/JSXMLStreamReader.jscom/stevesoft/pat/Boundary.js +swingjs/xml/JSXMLStreamReader.js