added notes on third party library licencing and updated netbeans builder library...

diff --git a/.classpath b/.classpath
index bb761d8..fe89cba 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -14,10 +14,11 @@
        <classpathentry kind="lib" path="lib/wsdl4j.jar"/>
        <classpathentry kind="lib" path="lib/xercesImpl.jar"/>
        <classpathentry kind="lib" path="lib/xml-apis.jar"/>
+
        <classpathentry kind="lib" path="lib/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
        <classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
        <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
-       <classpathentry kind="lib" path="lib/min-jaba-client.jar" sourcepath="/clustengine"/>
+       <classpathentry kind="lib" path="lib/min-jaba-client.jar" sourcepath="/clustengine/datamodel"/>
        <classpathentry kind="lib" path="lib/Jmol-12.1.13.jar" sourcepath="/Jmol"/>
        <classpathentry kind="lib" path="appletlib/JmolApplet-12.1.13.jar"/>
        <classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
@@ -38,6 +39,8 @@
                        <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
                </attributes>
        </classpathentry>
+       <classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
+       <classpathentry exported="true" kind="var" path="GROOVY_ECLIPSE_HOME/groovy-all-1.0.jar"/>
        <classpathentry kind="output" path="classes"/>
 </classpath>

diff --git a/.project b/.project
index a4ddc99..8794563 100644 (file)
--- a/.project
+++ b/.project
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-       <name>Jalview Release</name>
+       <name>Jalview Release 2.7</name>
        <comment></comment>
        <projects>
        </projects>
@@ -25,6 +25,21 @@
                                </dictionary>
                        </arguments>
                </buildCommand>
+               <buildCommand>
+                       <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+                       <triggers>full,incremental,</triggers>
+                       <arguments>
+                               <dictionary>
+                                       <key>LaunchConfigHandle</key>
+                                       <value>&lt;project&gt;/.externalToolBuilders/buildapplet [Builder].launch</value>
+                               </dictionary>
+                       </arguments>
+               </buildCommand>
+               <buildCommand>
+                       <name>org.codehaus.groovy.eclipse.groovyBuilder</name>
+                       <arguments>
+                       </arguments>
+               </buildCommand>
        </buildSpec>
        <natures>
                <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
@@ -32,5 +47,6 @@
                <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
                <nature>de.tud.st.ispace.builder.ISpaceNature</nature>
                <nature>org.eclipse.jem.beaninfo.BeanInfoNature</nature>
+               <nature>org.codehaus.groovy.eclipse.groovyNature</nature>
        </natures>
 </projectDescription>

diff --git a/README b/README
index bfc65f5..10f032b 100755 (executable)
--- a/README
+++ b/README
@@ -4,11 +4,13 @@ Jalview Readme
 
 The source is available as a tar file and comes complete with the GNU General Public License. 
 
-To build the application you will need a J2SDK 1.5+. 
+To build the application you will need a J2SDK 1.6+. 
 
 An Ant build file (build.xml) is provided, you will need to install Apache Ant first. 
 Run ant to view usage which will display a list of useful build targets.
 
+Jalview is primarily developed with eclipse, and a .project file is provided to simplify importing the source into your own eclipse workspace. A NetBeans nbbuild.xml file is also provided for developing Jalview with NetBeans - but this is not officially supported.
+
 You may also be able to use Borland JBuilder to build Jalview. A JBuilder project file 
 (JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided, 
 but the library dependencies are almost certainly out of date. See the build.xml 

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
new file mode 100644 (file)
index 0000000..2671d8c
--- /dev/null
+++ b/THIRDPARTYLIBS
@@ -0,0 +1,32 @@
+The Jalview Desktop relies on a number of third-party libraries.
+These can be found in the lib directory, with additional compile
+time dependencies in the utils directory.
+
+Licencing information for each library is given below:
+
+JGoogleAnalytics_0.3.jar       APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
+Jmol-12.1.13.jar       GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+activation.jar 
+apache-mime4j-0.6.jar
+axis.jar
+castor-1.1-cycle-xml.jar
+commons-codec-1.3.jar
+commons-discovery.jar
+commons-logging-1.1.1.jar
+commons-logging.jar
+httpclient-4.0.3.jar
+httpcore-4.0.1.jar
+httpmime-4.0.3.jar
+jaxrpc.jar
+jhall.jar
+log4j-1.2.8.jar
+mail.jar
+miglayout-4.0-swing.jar        BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt
+min-jaba-client.jar
+regex.jar
+saaj.jar
+vamsas-client.jar
+wsdl4j.jar
+xercesImpl.jar
+xml-apis.jar
+

diff --git a/nbproject/project.properties b/nbproject/project.properties
index 99c33eb..87df84d 100644 (file)
--- a/nbproject/project.properties
+++ b/nbproject/project.properties
@@ -53,6 +53,7 @@ file.reference.vamsas-client.jar=lib/vamsas-client.jar
 file.reference.wsdl4j.jar=lib/wsdl4j.jar
 file.reference.xercesImpl.jar=lib/xercesImpl.jar
 file.reference.xml-apis.jar=lib/xml-apis.jar
+file.reference.miglayout-4.0-swing.jar=lib/miglayout-4.0-swing.jar
 includes=**
 jar.compress=false
 javac.classpath=\
@@ -74,6 +75,7 @@ javac.classpath=\
     ${file.reference.JGoogleAnalytics_0.3.jar}:\
     ${file.reference.jhall.jar}:\
     ${file.reference.Jmol-12.1.13.jar}:\
+    ${file.reference.miglayout-4.0-swing.jar}:\
     ${file.reference.log4j-1.2.8.jar}:\
     ${file.reference.mail.jar}:\
     ${file.reference.min-jaba-client.jar}:\