From: Jim Procter Date: Mon, 6 Oct 2014 16:26:54 +0000 (+0100) Subject: JAL-848 reinstate netbeans files from Phylip patch branch X-Git-Tag: Release_2_8_2b1^2~46^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7fe71b0a74e5a5938688048232297cf1e7813d1b;p=jalview.git JAL-848 reinstate netbeans files from Phylip patch branch --- diff --git a/nbbuild.xml b/nbbuild.xml new file mode 100644 index 0000000..1fbf3c9 --- /dev/null +++ b/nbbuild.xml @@ -0,0 +1,100 @@ + + + + + + + + + + + + Builds, tests, and runs the project jalview. + + + + + + + + + + diff --git a/nbproject/genfiles.properties b/nbproject/genfiles.properties new file mode 100644 index 0000000..158e222 --- /dev/null +++ b/nbproject/genfiles.properties @@ -0,0 +1,25 @@ +############################################################################### +# 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 . +############################################################################### +nbbuild.xml.data.CRC32=f5d3c6c2 +nbbuild.xml.script.CRC32=307ee084 +nbbuild.xml.stylesheet.CRC32=28e38971@1.43.1.45 +# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml. +# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you. +nbproject/build-impl.xml.data.CRC32=f5d3c6c2 +nbproject/build-impl.xml.script.CRC32=7a2a3bf9 +nbproject/build-impl.xml.stylesheet.CRC32=0c01fd8e@1.43.1.45 diff --git a/nbproject/project.properties b/nbproject/project.properties new file mode 100644 index 0000000..b505d62 --- /dev/null +++ b/nbproject/project.properties @@ -0,0 +1,145 @@ +############################################################################### +# 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 . +############################################################################### +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} diff --git a/nbproject/project.xml b/nbproject/project.xml new file mode 100644 index 0000000..6c49988 --- /dev/null +++ b/nbproject/project.xml @@ -0,0 +1,31 @@ + + + + org.netbeans.modules.java.j2seproject + + + jalview + + + + + + +