From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 7 Sep 2018 13:51:13 +0000 (+0100)
Subject: JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch... 
X-Git-Tag: Release_2_10_5~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=446084b4f697fedea2053fc6486265b35906c7fe;p=jalview.git

JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch along with instructions for rebuilding the jar
---

diff --git a/.classpath b/.classpath
index 549b185..b19436c 100644
--- a/.classpath
+++ b/.classpath
@@ -49,7 +49,7 @@
 	<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
 	<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
 	<classpathentry kind="lib" path="lib/htsjdk-1.133.jar"/>
-	<classpathentry kind="lib" path="lib/VAqua5.jar"/>
+	<classpathentry kind="lib" path="lib/VAqua5-patch.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
 	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 7779627..7d4ffc7 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -50,7 +50,7 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 
-vaqua: v5 (latest stable) by Alan Snyder et al. GPLv2 with Classpath exception, also includes contributions from Quaqua: downloaded from http://violetlib.org/vaqua/overview.html
+vaqua5-patch: This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
 
 lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
 
diff --git a/doc/patching-vaqua.txt b/doc/patching-vaqua.txt
new file mode 100644
index 0000000..65c9974
--- /dev/null
+++ b/doc/patching-vaqua.txt
@@ -0,0 +1,27 @@
+VAqua5-patched.jar - how the patch was created
+
+1. Download VAqua5 source from https://violetlib.org/release/vaqua/5/VAqua5Source.zip
+2. Unzip to a directory and apply this patch
+
+diff --git a/src/org/violetlib/aqua/fc/AquaFileChooserUI.java b/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
+index 833366d..61f66e5 100644
+--- a/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
++++ b/src/org/violetlib/aqua/fc/AquaFileChooserUI.java
+@@ -1171,7 +1171,8 @@ public class AquaFileChooserUI extends BasicFileChooserUI {
+         goToFolderCancelButtonText = getString("FileChooser.goToFolderCancelButtonText", l, "Cancel");
+         goToFolderAcceptButtonText = getString("FileChooser.goToFolderAcceptButtonText", l, "Accept");
+         goToFolderErrorText = getString("FileChooser.goToFolderErrorText", l, "The folder can\u2019t be found.");
+-        defaultInitialSaveFileName = getString("FileChooser.defaultSaveFileName", l, "Untitled");
++        // Don't set an initial filename for saving (or loading) !  
++       // defaultInitialSaveFileName = getString("FileChooser.defaultSaveFileName", l, "Untitled");
+     }
+ 
+     /**
+
+3. Ensure XCode is installed, along with command line tools and the OSX developer packs
+ - you should have /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
+
+4. Download the VAqua rendering library from violetlib.org and save to the VAqua source's lib folder as lib/VAquaRendering.jar
+
+5. change to the release directory and execute 'ant' - a few warnings are generated but providing a final jar is created, all is good!
+
diff --git a/lib/VAqua5.jar b/lib/VAqua5-patch.jar
similarity index 100%
rename from lib/VAqua5.jar
rename to lib/VAqua5-patch.jar
diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index a3be720..c69d554 100755
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -2337,7 +2337,7 @@ and any path to a file to save to the file]]></string>
                 <string><![CDATA[664]]></string>
               </property>
               <property name="sourceName">
-                <string><![CDATA[VAqua5.jar]]></string>
+                <string><![CDATA[VAqua5-patch.jar]]></string>
               </property>
               <property name="overrideUnixPermissions">
                 <boolean>false</boolean>
@@ -2355,7 +2355,7 @@ and any path to a file to save to the file]]></string>
                 <boolean>true</boolean>
               </property>
               <property name="destinationName">
-                <string><![CDATA[VAqua5.jar]]></string>
+                <string><![CDATA[VAqua5-patch.jar]]></string>
               </property>
               <property name="fileSize">
                 <long>1370564</long>