Merge branch 'bug/JAL-1643_File-chooser-improvement' into develop

Conflicts:
	.classpath

diff --git a/.classpath b/.classpath
index a1fb44d..c110217 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -49,13 +49,12 @@
        <classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
        <classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
        <classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
+       <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
+       <classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
+       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
        <classpathentry kind="lib" path="lib/xml-apis.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
-       <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
-       <classpathentry kind="lib" path="lib/quaqua-filechooser-only.jar"/>
-       
-       
+       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
        <classpathentry kind="output" path="classes"/>
 </classpath>

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index ea44193..824a604 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -42,6 +42,8 @@ xml-apis.jar
 json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
 jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/
 
+quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
+
 Additional dependencies
 
 examples/javascript/deployJava.js : http://java.com/js/deployJava.js

diff --git a/build.xml b/build.xml
index d8ebe1e..478e936 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -349,9 +349,14 @@
             <include name="*.jar" />
             <include name="*_*.jar" />
             <exclude name="jalview.jar" />
+               <exclude name="*jnilib.jar"/>
           </fileset>
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
+               <fileset dir="${packageDir}" os="Mac OS X">
+                       <include name="*quaqua*.jnilib.jar"/>
+               </fileset>
         </resources>
+       
         <application_desc main_class="jalview.bin.Jalview">
         </application_desc>
         <security>

diff --git a/lib/libquaqua-8.0.jnilib.jar b/lib/libquaqua-8.0.jnilib.jar
new file mode 100644 (file)
index 0000000..79383b0
Binary files /dev/null and b/lib/libquaqua-8.0.jnilib.jar differ

diff --git a/lib/libquaqua.jnilib b/lib/libquaqua.jnilib
deleted file mode 100644 (file)
index a3c9e8a..0000000
Binary files a/lib/libquaqua.jnilib and /dev/null differ

diff --git a/lib/libquaqua64-8.0.jnilib.jar b/lib/libquaqua64-8.0.jnilib.jar
new file mode 100644 (file)
index 0000000..efb46a4
Binary files /dev/null and b/lib/libquaqua64-8.0.jnilib.jar differ

diff --git a/lib/libquaqua64.jnilib b/lib/libquaqua64.jnilib
deleted file mode 100644 (file)
index 5378540..0000000
Binary files a/lib/libquaqua64.jnilib and /dev/null differ

diff --git a/lib/quaqua-filechooser-only.jar b/lib/quaqua-filechooser-only-8.0.jar
similarity index 100%
rename from lib/quaqua-filechooser-only.jar
rename to lib/quaqua-filechooser-only-8.0.jar

diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index d77a93b..64f42cd 100755 (executable)
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -2186,6 +2186,162 @@ and any path to a file to save to the file]]></string>
                                                        </property>
                                                </object>
                                        </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="841f46efeefab93">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[libqaqua64.jnilib]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[libqaqua64.jnilib]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>16046</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeefab93">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[libquaqua.jnilib]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[libquaqua.jnilib]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>16046</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
+                                       <method name="addElement">
+                                               <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1936efeefab93">
+                                                       <property name="belongsToUninstallPhase">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                                       <property name="unixPermissions">
+                                                               <string><![CDATA[664]]></string>
+                                                       </property>
+                                                       <property name="sourceName">
+                                                               <string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
+                                                       </property>
+                                                       <property name="overrideUnixPermissions">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="sourcePath">
+                                                               <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+                                                       </property>
+                                                       <property name="shouldUninstall">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledCancel">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="rollbackEnabledError">
+                                                               <boolean>true</boolean>
+                                                       </property>
+                                                       <property name="destinationName">
+                                                               <string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
+                                                       </property>
+                                                       <property name="fileSize">
+                                                               <long>16046</long>
+                                                       </property>
+                                                       <property name="macBinary">
+                                                               <boolean>false</boolean>
+                                                       </property>
+                                                       <property name="targetCheckKind">
+                                                               <int>0</int>
+                                                       </property>
+                                                       <property name="ruleExpression">
+                                                               <string><![CDATA[]]></string>
+                                                       </property>
+                                               </object>
+                                       </method>
                                </object>
                        </property>
                        <property name="rulesFailedMessage">
@@ -6567,6 +6723,10 @@ and any path to a file to read from that file]]></string>
                                                                                <object refID="f46c2f42ab93"/>
                                                                                <object refID="1f46cffffab93"/>
                                                                                <object refID="1f46efeefab93"/>
+                                                                               <object refID="841f46efeefab93"/>
+                                                                               <object refID="9a1f46efeefab93"/>
+                                                                               <object refID="1936efeefab93"/>
+                                                                               
                                                                                <object class="com.zerog.ia.installer.actions.InstallFile" objectID="f44fc5b2aba1">
                                                                                        <property name="belongsToUninstallPhase">
                                                                                                <boolean>false</boolean>
@@ -7144,6 +7304,7 @@ and any path to a file to read from that file]]></string>
                                                                                                <object refID="f46c2f42ab93"/>
                                                                                                <object refID="1f46cffffab93"/>
                                                                                                <object refID="1f46efeefab93"/>
+                                                                                               <object refID="1936efeefab93"/>
                                                                                        </visualChildren>
                                                                                </object>
                                                                                <object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="f44fc5d5aba1">