Integration of David Corsars Phylip File support
[jalview.git] / nbproject / project.properties
diff --git a/nbproject/project.properties b/nbproject/project.properties
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-###############################################################################
-# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-# Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-# 
-# This file is part of Jalview.
-# 
-# Jalview is free software: you can redistribute it and/or
-# modify it under the terms of the GNU General Public License 
-# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-#  
-# Jalview is distributed in the hope that it will be useful, but 
-# WITHOUT ANY WARRANTY; without even the implied warranty 
-# of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-# PURPOSE.  See the GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
-###############################################################################
-annotation.processing.enabled=true
-annotation.processing.enabled.in.editor=false
-annotation.processing.run.all.processors=true
-annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
-application.title=jalview
-application.vendor=Barton Group
-build.classes.dir=${build.dir}/classes
-build.classes.excludes=**/*.java,**/*.form
-# This directory is removed when the project is cleaned:
-build.dir=build
-build.generated.dir=${build.dir}/generated
-build.generated.sources.dir=${build.dir}/generated-sources
-# Only compile against the classpath explicitly listed here:
-build.sysclasspath=ignore
-build.test.classes.dir=${build.dir}/test/classes
-build.test.results.dir=${build.dir}/test/results
-buildfile=nbbuild.xml
-# Uncomment to specify the preferred debugger connection transport:
-#debug.transport=dt_socket
-debug.classpath=\
-    ${run.classpath}
-debug.test.classpath=\
-    ${run.test.classpath}
-# This directory is removed when the project is cleaned:
-dist.dir=dist
-dist.jar=${dist.dir}/jalview.jar
-dist.javadoc.dir=${dist.dir}/javadoc
-endorsed.classpath=
-excludes=
-file.reference.activation.jar=lib/activation.jar
-file.reference.apache-mime4j-0.6.jar=lib/apache-mime4j-0.6.jar
-file.reference.axis.jar=lib/axis.jar
-file.reference.castor-1.1-cycle-xml.jar=lib/castor-1.1-cycle-xml.jar
-file.reference.commons-codec-1.3.jar=lib/commons-codec-1.3.jar
-file.reference.commons-discovery.jar=lib/commons-discovery.jar
-file.reference.commons-logging-1.1.1.jar=lib/commons-logging-1.1.1.jar
-file.reference.commons-logging.jar=lib/commons-logging.jar
-file.reference.httpclient-4.0.3.jar=lib/httpclient-4.0.3.jar
-file.reference.httpcore-4.0.1.jar=lib/httpcore-4.0.1.jar
-file.reference.httpmime-4.0.3.jar=lib/httpmime-4.0.3.jar
-file.reference.jalview-src=src
-file.reference.jaxrpc.jar=lib/jaxrpc.jar
-file.reference.JGoogleAnalytics_0.3.jar=lib/JGoogleAnalytics_0.3.jar
-file.reference.jhall.jar=lib/jhall.jar
-file.reference.Jmol-12.2.4.jar=lib/Jmol-12.2.4.jar
-file.reference.JmolApplet-12.2.4.jar=appletlib/JmolApplet-12.2.4.jar
-file.reference.log4j-1.2.8.jar=lib/log4j-1.2.8.jar
-file.reference.mail.jar=lib/mail.jar
-file.reference.min-jaba-client.jar=lib/min-jaba-client-2.0.jar
-file.reference.regex.jar=lib/regex.jar
-file.reference.saaj.jar=lib/saaj.jar
-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
-file.reference.varna-3.9-dev.jar=lib/VARNAv3.9.jar
-includes=**
-jar.compress=false
-javac.classpath=\
-    ${libs.plugin.jar.classpath}:\
-    ${file.reference.activation.jar}:\
-    ${file.reference.apache-mime4j-0.6.jar}:\
-    ${file.reference.axis.jar}:\
-    ${file.reference.castor-1.1-cycle-xml.jar}:\
-    ${file.reference.commons-codec-1.3.jar}:\
-    ${file.reference.commons-discovery.jar}:\
-    ${file.reference.commons-logging-1.1.1.jar}:\
-    ${file.reference.commons-logging.jar}:\
-    ${file.reference.regex.jar}:\
-    ${file.reference.saaj.jar}:\
-    ${file.reference.httpclient-4.0.3.jar}:\
-    ${file.reference.httpcore-4.0.1.jar}:\
-    ${file.reference.httpmime-4.0.3.jar}:\
-    ${file.reference.jaxrpc.jar}:\
-    ${file.reference.JGoogleAnalytics_0.3.jar}:\
-    ${file.reference.jhall.jar}:\
-    ${file.reference.Jmol-12.2.4.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}:\
-    ${file.reference.vamsas-client.jar}:\
-    ${file.reference.xml-apis.jar}:\
-    ${file.reference.xercesImpl.jar}:\
-    ${file.reference.wsdl4j.jar}:\
-    ${file.reference.JmolApplet-12.2.4.jar} \
-    ${file.reference.varna-3.9-dev.jar}
-# Space-separated list of extra javac options
-javac.compilerargs=
-javac.deprecation=false
-javac.processorpath=\
-    ${javac.classpath}
-javac.source=1.6
-javac.target=1.6
-javac.test.classpath=\
-    ${javac.classpath}:\
-    ${build.classes.dir}
-javac.test.processorpath=\
-    ${javac.test.classpath}
-javadoc.additionalparam=
-javadoc.author=false
-javadoc.encoding=${source.encoding}
-javadoc.noindex=false
-javadoc.nonavbar=false
-javadoc.notree=false
-javadoc.private=false
-javadoc.splitindex=true
-javadoc.use=true
-javadoc.version=false
-javadoc.windowtitle=
-main.class=jalview.bin.Jalview
-manifest.file=manifest.mf
-meta.inf.dir=${src.dir}/META-INF
-mkdist.disabled=false
-platform.active=default_platform
-run.classpath=\
-    ${javac.classpath}:\
-    ${build.classes.dir}
-# Space-separated list of JVM arguments used when running the project
-# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
-# or test-sys-prop.name=value to set system properties for unit tests):
-run.jvmargs=
-run.test.classpath=\
-    ${javac.test.classpath}:\
-    ${build.test.classes.dir}
-source.encoding=UTF-8
-src.dir=${file.reference.jalview-src}