From: BobHanson <hansonr@stolaf.edu>
Date: Thu, 19 Mar 2020 13:15:46 +0000 (-0500)
Subject: SwingJS runtime update 3.2.9-v1b
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=d7e1a6002a8d491a14592a763828b4f8af7d720d

SwingJS runtime update 3.2.9-v1b

- mostly fixes from recent SwingJS work involving
 -- expanded FileSystem and temp file management
 -- super-fast HashMap (faster than Java!), HashTable,
    StringBuilder, StringBuffer, NumberFormat, DecimalFormat
 -- improved ResourceBundle
 -- full Locale information
 -- additional BufferedImage/ColorModel/Raster support
- fixes temp files not cached (JSTempFile, for Jmol)
- fixes AbstractStringBuilder.replace() typo
- reverts recent HashSet acceleration due to Jalview
  using String.hashCode() for display order of features
---

diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt
index 425e51f..0f9253e 100644
--- a/_j2sclasslist.txt
+++ b/_j2sclasslist.txt
@@ -90,8 +90,6 @@ jalview/datamodel/features/FeatureMatcherI.js
 jalview/datamodel/features/FeatureMatcherSet.js
 jalview/datamodel/features/FeatureMatcherSetI.js
 jalview/datamodel/features/FeatureStore.js
-jalview/datamodel/features/FeatureStoreI.js
-jalview/datamodel/features/FeatureStoreJS.js
 
 jalview/datamodel/features/SequenceFeatures.js
 jalview/datamodel/features/SequenceFeaturesI.js
diff --git a/build-libjs.xml b/build-libjs.xml
index 3fb3cd3..c632310 100644
--- a/build-libjs.xml
+++ b/build-libjs.xml
@@ -1,9 +1,28 @@
 <?xml version="1.0"?>
 <!--
- * just a crude zip up of non-Jalview classes for development purposes -BH 2018
- *
- * external JAR class treatment for JavaScript: see src2/README_SWINGJS.txt
- * 
+
+This ANT task creates the follwing .zip files in the libjs directory:
+
+intervalstore-site.zip
+MiGLayout-site.zip
+VARNA-site.zip
+ 
+Some source files from other projects need to be transpiled, but they do not need to be part of the 
+Java compilation. In fact, some of them (MiGLayout) should NOT be part of the Java compilation, because
+the implementation is not complete. 
+
+The solution was to store these files "off-classpath" in srcjar/ and just transfer them temporarily 
+to the classpath (in src2/), compile, and delete the temporary java files. 
+
+The sequence is:
+
+1) copy files from srcjar/ to src2/
+2) let the transpiler do its job on them (automatically, if Project...Build Automatically is checked)
+3) run this ANT task
+4) delete the *.java files in src2/
+
+
+  
  -->
 
 <project name="jalviewX" default="zipall" basedir="."
diff --git a/libjs/MiGLayout-site.zip b/libjs/MiGLayout-site.zip
index 10d6927..24c2511 100644
Binary files a/libjs/MiGLayout-site.zip and b/libjs/MiGLayout-site.zip differ
diff --git a/libjs/VARNA-site.zip b/libjs/VARNA-site.zip
index 36610bd..152c5c2 100644
Binary files a/libjs/VARNA-site.zip and b/libjs/VARNA-site.zip differ
diff --git a/libjs/intervalstore-site.zip b/libjs/intervalstore-site.zip
index 60a44d3..a3c42b9 100644
Binary files a/libjs/intervalstore-site.zip and b/libjs/intervalstore-site.zip differ
diff --git a/swingjs/DEV_NOTES.txt b/swingjs/DEV_NOTES.txt
index 169c29b..751d81c 100644
--- a/swingjs/DEV_NOTES.txt
+++ b/swingjs/DEV_NOTES.txt
@@ -1,17 +1,10 @@
-This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt  
+This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
 
-_j2sclasslist.txt		the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
+_j2sclasslist.txt 
 
-net.sj.j2s.core.jar		Java8 transpiler (place in eclipse/dropins)
+the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
 
-net.sj.j2s.core-j11.jar	Java 11 transpiler (place in eclipse/dropins)
 
-SwingJS-site.zip		the full site directory for SwingJS including all files not in the test/ directory.
-
-timestamp				the date this directory was last modified  yyyymmddhhmmss
-
-
-Note: 
-
-If the name of the jar file in eclipse/dropins changes, be sure to restart Eclipse with the -clean option.
+SwingJS-site.zip
 
+the full site directory for SwingJS including all files not in the test/ directory.
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index f644a9f..fea1f31 100644
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ
diff --git a/swingjs/timestamp b/swingjs/timestamp
index 2d2725a..4a9ea38 100644
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20200318200931 
+20200319075611 
diff --git a/swingjs/ver/3.2.9/SwingJS-site.zip b/swingjs/ver/3.2.9/SwingJS-site.zip
index f644a9f..fea1f31 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 2d2725a..4a9ea38 100644
--- a/swingjs/ver/3.2.9/timestamp
+++ b/swingjs/ver/3.2.9/timestamp
@@ -1 +1 @@
-20200318200931 
+20200319075611