JAL-3033 and more classes for examples core

diff --git a/classlists/jvexamplefile.txt b/classlists/jvexamplefile.txt
index a980e32..ae01fe1 100644 (file)
--- a/classlists/jvexamplefile.txt
+++ b/classlists/jvexamplefile.txt
@@ -1,3 +1,6 @@
+
+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
@@ -20,10 +23,12 @@ 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
@@ -232,10 +237,10 @@ jalview/gui/ViewSelectionMenu.js
 jalview/io/AlignFile.js
 jalview/io/AlignmentFileReaderI.js
 jalview/io/AlignmentFileWriterI.js
+jalview/io/AnnotationFile.js
 jalview/io/AppletFormatAdapter.js
 jalview/io/DataSourceType.js
 jalview/io/FastaFile.js
-com/stevesoft/pat/Bracket.js
 jalview/io/FileFormat.js
 jalview/io/FileFormatI.js
 jalview/io/FileFormats.js
@@ -243,15 +248,18 @@ jalview/io/FileLoader.js
 jalview/io/FileParse.js
 jalview/io/FormatAdapter.js
 jalview/io/IdentifyFile.js
+jalview/io/JPredFile.js
 jalview/io/JalviewFileChooser.js
 jalview/io/JalviewFileFilter.js
 jalview/io/JalviewFileView.js
+jalview/io/JnetAnnotationMaker.js
 jalview/io/NewickFile.js
 jalview/io/PDBFeatureSettings.js
 jalview/io/PIRFile.js
 jalview/io/ScoreMatrixFile.js
 jalview/io/SequenceAnnotationReport.js
 jalview/io/StructureFile.js
+jalview/io/TCoffeeScoreFile.js
 jalview/io/cache/JvCacheableInputBox.js
 jalview/javascript/json/JSON.js
 jalview/javascript/log4j/ConsoleAppender.js
@@ -390,6 +398,7 @@ jalview/xml/binding/jalview/Annotation.js
 jalview/xml/binding/jalview/AnnotationElement.js
 jalview/xml/binding/jalview/Feature.js
 jalview/xml/binding/jalview/JalviewModel.js
+jalview/xml/binding/jalview/ObjectFactory.js
 jalview/xml/binding/jalview/Pdbentry.js
 jalview/xml/binding/jalview/Sequence.js
 jalview/xml/binding/jalview/SequenceSet.js
@@ -822,6 +831,7 @@ 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
@@ -848,6 +858,7 @@ 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
@@ -1161,6 +1172,7 @@ 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