gracefully cope with non-standard nucleotide or amino acid symbols in pairwise alignment.

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index a982580..2425b74 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -42,6 +42,7 @@
                <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
                <echo message="See docs/building.html and the comments in build file for other targets."/>
            <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
+           <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
        </target>
 
 
@@ -264,6 +265,7 @@
                                </fileset>
                                <fileset dir="${packageDir}">
                                        <include name="*.jar"/>
+                                       <include name="*_*.jar"/>
                                        <exclude name="jalview.jar"/>
                                </fileset>
                                <property name="jalview.version" value="${JALVIEW_VERSION}"/>