From: BobHanson <hansonr@stolaf.edu>
Date: Wed, 3 Jun 2020 20:54:03 +0000 (-0500)
Subject: JAL-3664 support for user.home, user.dir, user
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=f16506aebc33ce6829623aa1d1f60ece3f078347;p=jalview.git

JAL-3664 support for user.home, user.dir, user
---

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index 22c9098..4378457 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -34,6 +34,7 @@ package ext.edu.ucsf.rbvi.strucviz2;
 
 import jalview.bin.Cache;
 import jalview.gui.Preferences;
+import jalview.util.Platform;
 
 import java.io.File;
 import java.io.IOException;
@@ -931,7 +932,7 @@ public class StructureManager
       pathList.add("/usr/local/chimera/bin/chimera");
       pathList.add("/usr/local/bin/chimera");
       pathList.add("/usr/bin/chimera");
-      pathList.add(System.getProperty("user.home") + "/opt/bin/chimera");
+      pathList.add(Platform.getUserPath("opt/bin/chimera"));
     }
     else if (os.startsWith("Windows"))
     {
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index bb26c13..a89714a 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -247,10 +247,8 @@ public class Cache implements ApplicationSingletonI
   /**
    * Sifts settings
    */
-  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
-          .getProperty("user.home") + File.separatorChar
-          + ".sifts_downloads" + File.separatorChar;
-
+  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = Platform.getUserPath(".sifts_downloads/");
+  
   private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
@@ -258,8 +256,7 @@ public class Cache implements ApplicationSingletonI
   /**
    * Identifiers.org download settings
    */
-  private static final String ID_ORG_FILE = System.getProperty("user.home")
-          + File.separatorChar + ".identifiers.org.ids.json";
+  private static final String ID_ORG_FILE = Platform.getUserPath(".identifiers.org.ids.json");
 
   /**
    * Allowed values are PDB or mmCIF
@@ -363,8 +360,7 @@ public class Cache implements ApplicationSingletonI
     propertiesFile = propsFile;
     if (propsFile == null && !propsAreReadOnly)
     {
-      propertiesFile = System.getProperty("user.home") + File.separatorChar
-              + ".jalview_properties";
+      propertiesFile = Platform.getUserPath(".jalview_properties");
     }
     else
     {
diff --git a/src/jalview/datamodel/features/FeatureAttributes.java b/src/jalview/datamodel/features/FeatureAttributes.java
index 1a125c2..655d1eb 100644
--- a/src/jalview/datamodel/features/FeatureAttributes.java
+++ b/src/jalview/datamodel/features/FeatureAttributes.java
@@ -137,7 +137,7 @@ public class FeatureAttributes implements ApplicationSingletonI
          * Parse numeric value unless we have previously
          * seen text data for this attribute type
          */
-        if (type == null || type == Datatype.Number)
+        if (type == null && couldBeNumber(value) || type == Datatype.Number)
         {
           try
           {
@@ -224,6 +224,27 @@ public class FeatureAttributes implements ApplicationSingletonI
   }
 
   /**
+   * This quick check will save significant time avoiding numerous NumberFormatExceptions.
+   * 
+   * @param f
+   * @return
+   */
+  public boolean couldBeNumber(String f)
+  {
+    int len = f.length();
+    if (len == 0)
+      return false;
+    char ch = f.charAt(0);
+    switch (ch) {
+    case '.':
+    case '+':
+    case '-':
+      return len > 1;
+    }
+    return (ch <= '9' &&  ch >= '0');
+  }
+
+  /**
    * Answers true if at least one attribute is known for the given feature type,
    * else false
    * 
diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 9db3df2..5573e0d 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -25,6 +25,7 @@ import jalview.gui.OOMWarning;
 import jalview.json.binding.biojs.BioJSReleasePojo;
 import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
@@ -44,8 +45,7 @@ public class BioJsHTMLOutput extends HTMLOutput
 
   private static TreeMap<String, File> bioJsMSAVersions;
 
-  public static final String DEFAULT_DIR = System.getProperty("user.home")
-          + File.separatorChar + ".biojs_templates" + File.separatorChar;
+  public static final String DEFAULT_DIR = Platform.getUserPath(".biojs_templates/");
 
   public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
           .getDefault("biojs_template_directory", DEFAULT_DIR);
diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index 07eb23e..e898438 100644
--- a/src/jalview/urls/IdentifiersUrlProvider.java
+++ b/src/jalview/urls/IdentifiersUrlProvider.java
@@ -118,11 +118,6 @@ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
       }
     } catch (IOException | ParseException e)
     {
-      // unnecessary e.printStackTrace();
-      // Note how in JavaScript we can grab the first bytes from any file reader. 
-      // Typical report here is "NetworkError" because the file does not exist.
-      // "https://." is coming from System.getProperty("user.home"), but this could
-      // be set by the page developer to anything, of course.
       errorMessage = e.toString();
       idData.clear();
     }
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index d5e28c1..ea5d1e0 100644
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ
diff --git a/swingjs/timestamp b/swingjs/timestamp
index 6c92ed6..ae3f683 100644
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20200601093857 
+20200603155024 
diff --git a/swingjs/ver/3.2.9-j11/SwingJS-site.zip b/swingjs/ver/3.2.9-j11/SwingJS-site.zip
index 5563c76..d5e28c1 100644
Binary files a/swingjs/ver/3.2.9-j11/SwingJS-site.zip and b/swingjs/ver/3.2.9-j11/SwingJS-site.zip differ
diff --git a/swingjs/ver/3.2.9-j11/timestamp b/swingjs/ver/3.2.9-j11/timestamp
index 71722a8..763c0a1 100644
--- a/swingjs/ver/3.2.9-j11/timestamp
+++ b/swingjs/ver/3.2.9-j11/timestamp
@@ -1 +1 @@
-20200528154316 
+20200603075530 
diff --git a/swingjs/ver/3.2.9/SwingJS-site.zip b/swingjs/ver/3.2.9/SwingJS-site.zip
index d5e28c1..ea5d1e0 100644
Binary files a/swingjs/ver/3.2.9/SwingJS-site.zip and b/swingjs/ver/3.2.9/SwingJS-site.zip differ
diff --git a/swingjs/ver/3.2.9/timestamp b/swingjs/ver/3.2.9/timestamp
index 6c92ed6..ae3f683 100644
--- a/swingjs/ver/3.2.9/timestamp
+++ b/swingjs/ver/3.2.9/timestamp
@@ -1 +1 @@
-20200601093857 
+20200603155024 
diff --git a/utils/jalviewjs/_j2sclasslist.txt b/utils/jalviewjs/_j2sclasslist.txt
index e35111e..e60fe60 100644
--- a/utils/jalviewjs/_j2sclasslist.txt
+++ b/utils/jalviewjs/_j2sclasslist.txt
@@ -321,7 +321,7 @@ sun/font/FontDesignMetrics.js
 sun/swing/DefaultLookup.js
 sun/swing/SwingLazyValue.js
 sun/text/resources/FormatData.js
-sun/text/resources/FormatData_en.js
+sun/text/resources/en/FormatData_en.js
 sun/util/resources/LocaleData.js
 swingjs/a2s/A2SContainer.js
 swingjs/a2s/A2SEvent.js
diff --git a/utils/jalviewjs/classlists/_j2sclasslist_jmol.txt b/utils/jalviewjs/classlists/_j2sclasslist_jmol.txt
new file mode 100644
index 0000000..bae181d
--- /dev/null
+++ b/utils/jalviewjs/classlists/_j2sclasslist_jmol.txt
@@ -0,0 +1,232 @@
+jalview/ext/jmol/JalviewJmolBinding.js
+jalview/ext/jmol/JmolCommands.js
+jalview/ext/jmol/JmolParser.js
+jalview/gui/AppJmol.js
+jalview/gui/AppJmolBinding.js
+jalview/gui/StructureViewerBase.js
+jalview/io/StructureFile.js
+jalview/jbgui/GStructureViewer.js
+jalview/renderer/seqfeatures/FeatureColourFinder.js
+jalview/structure/StructureListener.js
+jalview/structure/StructureMapping.js
+jalview/structure/StructureMappingcommandSet.js
+jalview/structures/models/AAStructureBindingModel.js
+jalview/structures/models/SequenceStructureBindingModel.js
+jalview/util/CaseInsensitiveString.js
+jalview/util/HttpUtils.js
+jalview/util/MapList.js
+jalview/ws/dbsources/EbiFileRetrievedProxy.js
+jalview/ws/dbsources/Pdb.js
+jalview/ws/seqfetcher/DbSourceProxy.js
+jalview/ws/seqfetcher/DbSourceProxyImpl.js
+java/awt/font/TextAttribute.js
+java/awt/image/ImageProducer.js
+java/awt/image/PixelGrabber.js
+java/io/BufferedWriter.js
+java/io/FilterOutputStream.js
+java/io/OutputStream.js
+java/io/OutputStreamWriter.js
+java/io/PrintStream.js
+java/io/StringWriter.js
+java/io/Writer.js
+javajs/api/BytePoster.js
+javajs/api/GenericOutputChannel.js
+javajs/util/A4.js
+javajs/util/BS.js
+javajs/util/CU.js
+javajs/util/DF.js
+javajs/util/LimitedLineReader.js
+javajs/util/M3.js
+javajs/util/M34.js
+javajs/util/M4.js
+javajs/util/Measure.js
+javajs/util/OC.js
+javajs/util/P3.js
+javajs/util/P3i.js
+javajs/util/P4.js
+javajs/util/T3.js
+javajs/util/T3i.js
+javajs/util/T4.js
+javajs/util/V3.js
+mc_view/Atom.js
+mc_view/Bond.js
+mc_view/PDBChain.js
+mc_view/Residue.js
+org/jmol/adapter/readers/pdb/PdbReader.js
+org/jmol/adapter/smarter/Atom.js
+org/jmol/adapter/smarter/AtomIterator.js
+org/jmol/adapter/smarter/AtomSetCollection.js
+org/jmol/adapter/smarter/AtomSetCollectionReader.js
+org/jmol/adapter/smarter/AtomSetObject.js
+org/jmol/adapter/smarter/Bond.js
+org/jmol/adapter/smarter/BondIterator.js
+org/jmol/adapter/smarter/Resolver.js
+org/jmol/adapter/smarter/SmarterJmolAdapter.js
+org/jmol/adapter/smarter/Structure.js
+org/jmol/api/AtomIndexIterator.js
+org/jmol/api/EventManager.js
+org/jmol/api/GenericFileInterface.js
+org/jmol/api/GenericMouseInterface.js
+org/jmol/api/GenericPlatform.js
+org/jmol/api/Interface.js
+org/jmol/api/JmolAdapter.js
+org/jmol/api/JmolAdapterAtomIterator.js
+org/jmol/api/JmolAdapterBondIterator.js
+org/jmol/api/JmolCallbackListener.js
+org/jmol/api/JmolGraphicsInterface.js
+org/jmol/api/JmolPropertyManager.js
+org/jmol/api/JmolRendererInterface.js
+org/jmol/api/JmolRepaintManager.js
+org/jmol/api/JmolScriptEvaluator.js
+org/jmol/api/JmolScriptFunction.js
+org/jmol/api/JmolScriptManager.js
+org/jmol/api/JmolSelectionListener.js
+org/jmol/api/JmolStatusListener.js
+org/jmol/api/JmolViewer.js
+org/jmol/api/PlatformViewer.js
+org/jmol/api/Translator.js
+org/jmol/atomdata/AtomDataServer.js
+org/jmol/atomdata/RadiusData.js
+org/jmol/awt/AwtFile.js
+org/jmol/awt/AwtFont.js
+org/jmol/awt/Display.js
+org/jmol/awt/Image.js
+org/jmol/awt/Mouse.js
+org/jmol/awt/Platform.js
+org/jmol/bspt/Bspf.js
+org/jmol/bspt/Bspt.js
+org/jmol/bspt/CubeIterator.js
+org/jmol/bspt/Element.js
+org/jmol/bspt/Leaf.js
+org/jmol/bspt/Node.js
+org/jmol/c/CBK.js
+org/jmol/c/FIL.js
+org/jmol/c/PAL.js
+org/jmol/c/STER.js
+org/jmol/c/STR.js
+org/jmol/c/VDW.js
+org/jmol/g3d/CylinderRenderer.js
+org/jmol/g3d/G3DRenderer.js
+org/jmol/g3d/Graphics3D.js
+org/jmol/g3d/HermiteRenderer.js
+org/jmol/g3d/LineRenderer.js
+org/jmol/g3d/Pixelator.js
+org/jmol/g3d/Platform3D.js
+org/jmol/g3d/PrecisionRenderer.js
+org/jmol/g3d/SphereRenderer.js
+org/jmol/g3d/TextRenderer.js
+org/jmol/g3d/TextString.js
+org/jmol/g3d/TriangleRenderer.js
+org/jmol/i18n/GT.js
+org/jmol/i18n/Language.js
+org/jmol/i18n/Resource.js
+org/jmol/io/FileReader.js
+org/jmol/modelset/Atom.js
+org/jmol/modelset/AtomCollection.js
+org/jmol/modelset/AtomIteratorWithinModel.js
+org/jmol/modelset/Bond.js
+org/jmol/modelset/BondCollection.js
+org/jmol/modelset/BondIterator.js
+org/jmol/modelset/BondIteratorSelected.js
+org/jmol/modelset/Chain.js
+org/jmol/modelset/Group.js
+org/jmol/modelset/Model.js
+org/jmol/modelset/ModelLoader.js
+org/jmol/modelset/ModelSet.js
+org/jmol/modelset/Orientation.js
+org/jmol/modelset/Structure.js
+org/jmol/modelsetbio/AlphaMonomer.js
+org/jmol/modelsetbio/AlphaPolymer.js
+org/jmol/modelsetbio/BioModel.js
+org/jmol/modelsetbio/BioModelSet.js
+org/jmol/modelsetbio/BioPolymer.js
+org/jmol/modelsetbio/BioResolver.js
+org/jmol/modelsetbio/Helix.js
+org/jmol/modelsetbio/Monomer.js
+org/jmol/modelsetbio/ProteinStructure.js
+org/jmol/render/BallsRenderer.js
+org/jmol/render/FontLineShapeRenderer.js
+org/jmol/render/FrankRenderer.js
+org/jmol/render/RepaintManager.js
+org/jmol/render/ShapeRenderer.js
+org/jmol/render/SticksRenderer.js
+org/jmol/renderbio/BackboneRenderer.js
+org/jmol/renderbio/BioShapeRenderer.js
+org/jmol/renderbio/CartoonRenderer.js
+org/jmol/renderbio/RocketsRenderer.js
+org/jmol/renderbio/StrandsRenderer.js
+org/jmol/script/ContextToken.js
+org/jmol/script/SV.js
+org/jmol/script/ScriptCompiler.js
+org/jmol/script/ScriptContext.js
+org/jmol/script/ScriptError.js
+org/jmol/script/ScriptEval.js
+org/jmol/script/ScriptExpr.js
+org/jmol/script/ScriptFlowContext.js
+org/jmol/script/ScriptFunction.js
+org/jmol/script/ScriptManager.js
+org/jmol/script/ScriptMathProcessor.js
+org/jmol/script/ScriptParam.js
+org/jmol/script/ScriptTokenParser.js
+org/jmol/script/T.js
+org/jmol/scriptext/MathExt.js
+org/jmol/shape/AtomShape.js
+org/jmol/shape/Balls.js
+org/jmol/shape/Frank.js
+org/jmol/shape/Mesh.js
+org/jmol/shape/Shape.js
+org/jmol/shape/Sticks.js
+org/jmol/shapebio/Backbone.js
+org/jmol/shapebio/BioShape.js
+org/jmol/shapebio/BioShapeCollection.js
+org/jmol/shapebio/Cartoon.js
+org/jmol/shapebio/Rockets.js
+org/jmol/thread/HoverWatcherThread.js
+org/jmol/thread/JmolThread.js
+org/jmol/util/BSUtil.js
+org/jmol/util/BoxInfo.js
+org/jmol/util/C.js
+org/jmol/util/ColorEncoder.js
+org/jmol/util/CommandHistory.js
+org/jmol/util/DefaultLogger.js
+org/jmol/util/Edge.js
+org/jmol/util/Elements.js
+org/jmol/util/Escape.js
+org/jmol/util/GData.js
+org/jmol/util/Geodesic.js
+org/jmol/util/Int2IntHash.js
+org/jmol/util/Int2IntHashEntry.js
+org/jmol/util/Logger.js
+org/jmol/util/LoggerInterface.js
+org/jmol/util/MeshSurface.js
+org/jmol/util/Node.js
+org/jmol/util/Normix.js
+org/jmol/util/Point3fi.js
+org/jmol/util/Rectangle.js
+org/jmol/util/Rgb16.js
+org/jmol/util/Shader.js
+org/jmol/util/SimpleEdge.js
+org/jmol/util/SimpleNode.js
+org/jmol/util/TempArray.js
+org/jmol/viewer/ActionManager.js
+org/jmol/viewer/AnimationManager.js
+org/jmol/viewer/ColorManager.js
+org/jmol/viewer/FileManager.js
+org/jmol/viewer/Gesture.js
+org/jmol/viewer/GlobalSettings.js
+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
+org/jmol/viewer/StatusManager.js
+org/jmol/viewer/TransformManager.js
+org/jmol/viewer/Viewer.js
+org/jmol/viewer/binding/Binding.js
+org/jmol/viewer/binding/JmolBinding.js
+sun/awt/image/OffScreenImageSource.js
+sun/font/AttributeValues.js
+sun/font/EAttribute.js
\ No newline at end of file