-->
<project name="jalviewX" default="usage" basedir=".">
<target name="help" depends="usage" />
- <target name="usage">
+ <target name="usage" depends="init">
<echo message="~~~Jalview Ant build.xml Usage~~~~" />
<echo message="Targets include:" />
<echo message="usage - default target, displays this message" />
<echo message=" this needs a keystore and key. See docs/building.html for more information." />
<echo message="compileApplet - compiles all necessary files for Applet" />
<echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
+ <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
+ <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
<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" />
<include name="*.jar"/>
</fileset> -->
</path>
-
+
<!-- Jalview Version String displayed by application on startup and used to check for updates -->
<property name="JALVIEW_VERSION" value="DEVELOPMENT" />
-
+
<property name="INSTALLATION" value="Source" />
-
+
<!-- 2.4 (VAMSAS)" -->
<!-- Include debugging information in javac true or false -->
<property name="javac.debug" value="true" />
<!-- Key Password -->
<property name="jalview.key.pass" value="alignmentisfun" />
+ <property name="testng-groups" value="Functional" />
+
<!-- Don't change anything below here unless you know what you are doing! -->
<!-- Url path for WebStart in JNLP file -->
<property name="WebStartLocation" value="http://www.jalview.org/webstart" />
<!-- Webstart Image - looked for in resources/images -->
- <property name="WebStartImage" value="JalviewLogo_big.png"/>
+ <property name="WebStartImage" value="JalviewLogo_big.png" />
<!-- J2SE version needed for webstart launch -->
<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
- <property name="j2sev" value="1.7+"/>
- <!-- Java Compilation settings - source and target javac version -->
- <property name="javac.source" value="1.7"/>
- <property name="javac.target" value="1.7"/>
-
+ <property name="j2sev" value="1.7+" />
+ <!-- Java Compilation settings - source and target javac version -->
+ <property name="javac.source" value="1.7" />
+ <property name="javac.target" value="1.7" />
+
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<property name="application.codebase" value="*.jalview.org" />
<property name="jsonSimple" value="json_simple-1.1.jar" />
<property name="javaJson" value="java-json.jar" />
<property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <property name="reportDir" value="test-reports" />
- <property name="testDir" value="test" />
- <property name="testOutputDir" value="tests" />
+ <property name="reportDir" value="test-reports" />
+ <property name="testDir" value="test" />
+ <property name="testOutputDir" value="tests" />
<!-- switch to indicate if we should obfuscate jalviewLite -->
<!-- <property name="donotobfuscate" value="true"/> -->
<!-- switch to exclude associations from generated jnlp files -->
<include name="**/*.jar" />
</fileset>
<fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
+ <include name="plugin.jar" />
</fileset>
<fileset dir="appletlib">
<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
<include name="${jmolJar}" />
<include name="${varnaJar}" />
</fileset>
-
+ </path>
+ <path id="test.classpath">
+ <pathelement path="${outputDir}" />
+ <path refid="build.classpath" />
</path>
<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
<!-- The Location of the java 1.1.8 jdk -->
<!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-->
<!-- jre for 1.4 version -->
- <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+ <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
<!-- the classpath for building the 1.1 applet -->
<path id="jalviewlite.deps">
<include name="lib/classes.zip" />
</fileset>
<fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
+ <include name="plugin.jar" />
</fileset>
<pathelement location="appletlib/${jmolJar}" />
<pathelement location="lib/${varnaJar}" />
<pathelement location="lib/${jsoup}" />
<pathelement location="lib/${jsonSimple}" />
<pathelement location="lib/${javaJson}" />
-
+
</path>
<!-- default location for outputting javadoc -->
- <property name="javadocDir" value="${packageDir}/javadoc"/>
+ <property name="javadocDir" value="${packageDir}/javadoc" />
</target>
<tstamp prefix="build">
<format property="date" pattern="dd MMMM yyyy" />
</tstamp>
- <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
- <arg value="rev-parse"/>
- <arg value="--short"/>
- <arg value="HEAD"/>
+ <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
+ <arg value="rev-parse" />
+ <arg value="--short" />
+ <arg value="HEAD" />
</exec>
<exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
- <arg value="rev-parse"/>
- <arg value="--abbrev-ref"/>
- <arg value="HEAD"/>
+ <arg value="rev-parse" />
+ <arg value="--abbrev-ref" />
+ <arg value="HEAD" />
</exec>
<properties file="${outputDir}/.build_properties">
<header>
---Jalview Build Details---
- </header>
+ </header>
<property name="VERSION" value="${JALVIEW_VERSION}" />
<property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
<property name="BUILD_DATE" value="${build.date}" />
<target name="clean" depends="init">
<!-- not efficient yet. -->
- <delete dir="${outputDir}" includes="*,**/*"/>
+ <delete dir="${outputDir}" includes="*,**/*" />
</target>
<target name="distclean" depends="init, clean">
<exclude name="com/stevesoft/**" />
</javac>
</target>
-
-
+
+
<target name="testclean" depends="init">
- <delete dir="${testOutputDir}" includes="*,**/*"/>
+ <delete dir="${testOutputDir}" includes="*,**/*" />
</target>
-
- <target name="prepareTests" depends="init">
- <mkdir dir="${testOutputDir}" />
- <copy todir="${testOutputDir}">
- <fileset dir=".">
- <include name="${docDir}/**/*.*" />
- <include name="${helpDir}/**/*.*" />
- <include name="${libDir}/*.jar" />
- </fileset>
- <fileset dir="${resourceDir}">
- <include name="**/*.*" />
- </fileset>
- </copy>
- </target>
-
- <target name="buildTests" depends="prepareTests">
- <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
- debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
- </javac>
- <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
- debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
- </javac>
+
+ <target name="prepareTests" depends="init,testclean">
+ <mkdir dir="${testOutputDir}" />
</target>
-
- <taskdef name="testng" classname="org.testng.TestNGAntTask" >
- <classpath location="utils/testnglibs/testng.jar" />
- </taskdef>
-
+
+ <target name="buildTests" depends="build,buildindices,prepareTests">
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
+ </javac>
+ </target>
+
+ <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
+
<target name="testng" depends="buildTests">
- <testng classpathref="build.classpath" outputDir="${reportDir}"
- haltOnFailure="false">
- <classpath location="${testOutputDir}" />
- <xmlfileset dir="utils" includes="jalview_testng.xml" />
- </testng>
+ <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
+ verbose="2">
+ <classpath>
+ <pathelement location="${testOutputDir}" />
+ <path refid="test.classpath" />
+ </classpath>
+ <classfileset dir="${testOutputDir}" includes="**/*.class" />
+ </testng>
</target>
-
+
<target name="buildindices" depends="init, prepare" unless="help.uptodate">
<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
<arg line="html" />
<target name="makefulldist" depends="makedist">
<copy todir="${packageDir}">
<fileset dir="${resourceDir}/images">
- <include name="${WebStartImage}"/>
+ <include name="${WebStartImage}" />
</fileset>
</copy>
</fileset>
</jar>
- <mkdir dir="${packageDir}/JNLP-INF"/>
+ <mkdir dir="${packageDir}/JNLP-INF" />
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
<param name="inih" value="*" />
- <param name="maxh" value="*"/>
+ <param name="maxh" value="*" />
</antcall>
<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
</jar>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
<param name="inih" value="10M" />
- <param name="maxh" value="256M"/>
+ <param name="maxh" value="256M" />
</antcall>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+ <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
<param name="inih" value="128M" />
- <param name="maxh" value="512M"/>
+ <param name="maxh" value="512M" />
</antcall>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+ <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
<param name="inih" value="256M" />
- <param name="maxh" value="1024M"/>
+ <param name="maxh" value="1024M" />
</antcall>
<!-- finally, need to postprocess to add in associations at end of 'information' element
<include name="*.jar" />
<include name="*_*.jar" />
<exclude name="jalview.jar" />
- <exclude name="*jnilib.jar"/>
+ <exclude name="*jnilib.jar" />
</fileset>
- </resources>
+ </resources>
<resources os="Mac OS X">
<property name="jalview.version" value="${JALVIEW_VERSION}" />
- <fileset dir="${packageDir}">
- <include name="*quaqua*.jnilib.jar"/>
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*quaqua*.jnilib.jar" />
+ </fileset>
</resources>
-
+
<application_desc main_class="jalview.bin.Jalview">
</application_desc>
<security>
</jnlp>
</presetdef>
- <jnlpf toFile="${jnlpFile}"/>
+ <jnlpf toFile="${jnlpFile}" />
</target>
<target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
- <echo message="Not adding JNLP File Associations"/>
+ <echo message="Not adding JNLP File Associations" />
</target>
<target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
<association mime-type="application-x/ext-file" extensions="jvp"/>
</information>]]></replacevalue>
</replace>
- <echo message="Added file associations to JNLP file"/>
+ <echo message="Added file associations to JNLP file" />
</target>
<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
</target>
<!-- clean dir if it already existed -->
<delete>
<fileset dir="${packageDir}">
- <include name="*.jar"/>
+ <include name="*.jar" />
</fileset>
</delete>
<jar destfile="${packageDir}/${outputJar}" index="true">
<!-- Compile, package and obfuscate Jalview Applet -->
-<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
<target name="compileApplet" depends="init,clean">
<mkdir dir="${outputDir}" />
- <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
- classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
- excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
</target>
<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
<copy todir="${outputDir}/lang">
<fileset dir="${resourceDir}/lang">
- <include name="**.*"/>
+ <include name="**.*" />
</fileset>
</copy>
<jar destfile="in.jar" index="true">
<injar file="in.jar" />
<outjar file="${jalviewLiteJar}" />
<libraryjar refid="obfuscateDeps.path" />
- <dontwarn/>
+ <dontwarn />
<keep access="public" type="class" name="jalview.bin.JalviewLite">
<field access="public" />
<method access="public" />
<include name="jalview-jalopy.xml" />
<include name="JalviewApplet.jpx" />
<include name="JalviewX.jpx" />
- <include name="nbbuild.xml"/>
- <include name="nbproject/genfiles.properties"/>
- <include name="nbproject/project.properties"/>
- <include name="nbproject/project.xml"/>
+ <include name="nbbuild.xml" />
+ <include name="nbproject/genfiles.properties" />
+ <include name="nbproject/project.properties" />
+ <include name="nbproject/project.xml" />
<include name="${sourceDir}/*.java" />
<include name="${sourceDir}/**/*.java" />
<include name="${sourceDir}/**/*.cdr" />
<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
<copy todir="${packageDir}/examples">
<fileset dir="examples">
- <include name="**/*"/>
- <include name="javascript/*"/>
- <include name="jmol/*"/>
+ <include name="**/*" />
+ <include name="javascript/*" />
+ <include name="jmol/*" />
</fileset>
<fileset dir=".">
<include name="${jalviewLiteJar}" />
</fileset>
<fileset dir="appletlib">
- <include name="**/*"/>
+ <include name="**/*" />
</fileset>
</copy>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
<jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
<manifest>
- <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+ <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
<!-- <attribute name="Permissions" value="sandbox" /> -->
<!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Codebase" value="${applet.codebase}"/>
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
</manifest>
</jar>
<signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
</presetdef>
<!-- create differently privileged artefacts -->
<copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
<copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
<ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
<ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
<ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
<fileset dir="${packageDir}/examples">
- <exclude name="u_*.jar"/>
+ <exclude name="u_*.jar" />
<include name="${jalviewLiteJar}" />
<include name="${jmolJar}" />
<include name="${javaJson}" />
</signjar>
<!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
<copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- <!-- finally, replace any launchApp servlet tags with a version specification -->
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
- <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html"/>
- </fileset>
- </replace>
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
- <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html"/>
- </fileset>
- </replace>
+ <!-- finally, replace any launchApp servlet tags with a version specification -->
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp"]]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp']]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
</target>
<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package com.stevesoft.pat;
-
-import static org.testng.AssertJUnit.assertEquals;
-
-import java.io.IOException;
-import java.io.StringWriter;
-
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-/**
- * Test class refactored from RegexWriter main method
- */
-public class RegexWriterTest
-{
-
- /**
- * Asserts that the result of performing 'replaceAll' on the input using the
- * regular expression is the same as the output of a RegexWriter, constructed
- * from the regular expression, writing out each character of the input
- * string.
- *
- * @param re
- * a regular expression
- * @param inp
- * an input string
- * @throws Exception
- */
-
- @Test(groups = { "Functional" }, dataProvider = "testWriteParam")
- void test(String re, String inp) throws IOException
- {
- StringWriter sw = new StringWriter();
- Regex rex = Regex.perlCode(re);
- String res1 = rex.replaceAll(inp);
- RegexWriter rw = new RegexWriter(rex, sw);
- for (int i = 0; i < inp.length(); i++)
- {
- rw.write(inp.charAt(i));
- }
- rw.close();
- String res2 = sw.toString();
- if (!res1.equals(res2))
- {
- System.out.println("re=" + re);
- System.out.println("inp=" + inp);
- System.out.println("res1=" + res1);
- System.out.println("res2=" + res2);
- assertEquals(res1, res2);
- }
- }
-
- // @Test(groups ={ "Functional" })
- // public void testWrite() throws IOException
- // {
- // for (int n = 1; n <= 1; n++)
- // {
- // test("s/x/y/", "-----x123456789");
- // test("s/x/y/", "x123456789");
- // test("s/x/y/", "-----x");
- // test("s/x.*?x/y/", ".xx..x..x...x...x....x....x");
- // test("s/x.*x/[$&]/", "--x........x--xx");
- // test("s/x.*x/[$&]/", "--x........x------");
- // test("s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb");
- // test("s/.$/a/", "123");
- // test("s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb");
- // test("s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb");
- // test("s/$/a/", "bbb");
- // test("s/^/a/", "bbb");
- // test("s/^/a/", "");
- // test("s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx");
- // test("s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
- // test("s/x/$&/", "xxx");
- // }
- // }
-
- @DataProvider(name = "testWriteParam")
- public Object[][] regexTestParams()
- {
- return new Object[][] { { "s/x/y/", "-----x123456789" },
- { "s/x/y/", "x123456789" }, { "s/x/y/", "-----x" },
- { "s/x.*?x/y/", ".xx..x..x...x...x....x....x" },
- { "s/x.*x/[$&]/", "--x........x--xx" },
- { "s/x.*x/[$&]/", "--x........x------" },
- { "s/.$/a/m", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb" },
- { "s/.$/a/", "123" },
- { "s/.$/a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb" },
- { "s/^./a/", "bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb" },
- { "s/$/a/", "bbb" }, { "s/^/a/", "bbb" }, { "s/^/a/", "" },
- { "s{.*}{N}", "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx" },
- { "s/.{0,7}/y/", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" },
- { "s/x/$&/", "xxx" } };
- }
-}
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
-<suite name="Suite" parallel="none">
- <test verbose="2" name="Test">
- <classes>
- <class name="jalview.gui.AlignViewportTest"/>
- <class name="jalview.util.ShiftListTest"/>
- <class name="jalview.util.ColorUtilsTest"/>
- <class name="jalview.gui.PDBSearchPanelTest"/>
- <class name="MCview.PDBfileTest"/>
- <class name="jalview.io.BioJsHTMLOutputTest"/>
- <class name="jalview.io.JSONFileTest"/>
- <class name="jalview.ext.jmol.PDBFileWithJmolTest"/>
- <class name="jalview.ws.jabaws.RNAStructExportImport"/>
- <class name="jalview.ext.paradise.TestAnnotate3D"/>
- <class name="MCview.PDBChainTest"/>
- <class name="jalview.io.StockholmFileTest"/>
- <class name="jalview.schemes.ScoreMatrixPrinter"/>
- <class name="jalview.datamodel.SearchResultsTest"/>
- <class name="jalview.ws.seqfetcher.DasSequenceFetcher"/>
- <class name="jalview.util.DBRefUtilsTest"/>
- <class name="jalview.analysis.CrossRefTest"/>
- <class name="jalview.ws.jabaws.MinJabawsClientTests"/>
- <class name="jalview.datamodel.AlignedCodonTest"/>
- <class name="MCview.AtomTest"/>
- <class name="jalview.gui.PopupMenuTest"/>
- <class name="jalview.viewmodel.styles.ViewStyleTest"/>
- <class name="jalview.io.AnnotationFileIOTest"/>
- <class name="jalview.ws.jws2.ParameterUtilsTest"/>
- <class name="jalview.io.RNAMLfileTest"/>
- <class name="jalview.analysis.AlignmentUtilsTests"/>
- <class name="jalview.gui.SequenceRendererTest"/>
- <class name="jalview.bin.CommandLineOperations"/>
- <class name="jalview.gui.PaintRefresherTest"/>
- <class name="jalview.ws.seqfetcher.DbRefFetcherTest"/>
- <class name="jalview.datamodel.AlignmentAnnotationTests"/>
- <class name="jalview.schemes.ResiduePropertiesTest"/>
- <class name="jalview.ext.rbvi.chimera.ChimeraCommandsTest"/>
- <class name="MCview.ResidueTest"/>
- <class name="jalview.io.PhylipFileTests"/>
- <class name="jalview.util.MappingUtilsTest"/>
- <class name="jalview.ws.jabaws.DisorderAnnotExportImport"/>
- <class name="jalview.analysis.GroupingTest"/>
- <class name="jalview.analysis.AnnotationSorterTest"/>
- <class name="jalview.io.FileIOTester"/>
- <class name="jalview.util.MapListTest"/>
- <class name="jalview.datamodel.ColumnSelectionTest"/>
- <class name="jalview.ext.rbvi.chimera.ChimeraConnect"/>
- <class name="jalview.gui.ProgressBarTest"/>
- <class name="jalview.analysis.AlignmentAnnotationUtilsTest"/>
- <class name="jalview.structure.StructureSelectionManagerTest"/>
- <class name="jalview.io.TCoffeeScoreFileTest"/>
- <class name="jalview.analysis.AAFrequencyTest"/>
- <class name="jalview.ws.dbsources.PDBRestClientTest"/>
- <class name="jalview.analysis.DnaTest"/>
- <class name="jalview.util.StringUtilsTest"/>
- <class name="jalview.structures.models.AAStructureBindingModelTest"/>
- <class name="jalview.gui.JvSwingUtilsTest"/>
- <class name="jalview.analysis.CodingUtilsTest"/>
- <class name="jalview.io.AnnotatedPDBFileInputTest"/>
- <class name="jalview.ws.rest.ShmmrRSBSService"/>
- <class name="jalview.io.NewickFileTests"/>
- <class name="jalview.analysis.ParsePropertiesTest"/>
- <class name="MCview.BondTest"/>
- <class name="jalview.commands.EditCommandTest"/>
- <class name="jalview.ext.rbvi.chimera.JalviewChimeraView"/>
- <class name="jalview.ws.jabaws.JpredJabaStructExportImport"/>
- <class name="jalview.gui.HelpTest"/>
- <class name="jalview.datamodel.AlignedCodonIteratorTest"/>
- <class name="jalview.datamodel.xdb.embl.EmblFileTest"/>
- <class name="jalview.util.ComparisonTest"/>
- <class name="jalview.util.QuickSortTest"/>
- <class name="jalview.ws.PDBSequenceFetcherTest"/>
- <class name="jalview.analysis.scoremodels.FeatureScoreModelTest"/>
- <class name="jalview.io.Jalview2xmlTests"/>
- <class name="jalview.ws.rest.RestClientTest"/>
- <class name="jalview.datamodel.AlignedCodonFrameTest"/>
- <class name="jalview.datamodel.MappingTest"/>
- <class name="jalview.datamodel.AlignmentTest"/>
- <class name="jalview.ws.dbsources.UniprotTest"/>
- <class name="jalview.gui.AnnotationChooserTest"/>
- <class name="jalview.structure.Mapping"/>
- <class name="jalview.datamodel.SequenceTest"/>
- <class name="jalview.datamodel.PDBEntryTest"/>
- <class name="jalview.gui.StructureChooserTest"/>
- <class name="jalview.schemes.DnaCodonTests"/>
- <class name="com.stevesoft.pat.RegexWriterTest"/>
- <class name="jalview.datamodel.DBRefEntryTest"/>
- <class name="jalview.gui.FontChooserTest"/>
- <class name="jalview.analysis.TestAlignSeq"/>
- <class name="jalview.datamodel.SeqCigarTest"/>
- <class name="jalview.gui.JAL1353bugdemo"/>
- <class name="jalview.datamodel.AlignmentViewTest"/>
- </classes>
- </test> <!-- Test -->
-</suite> <!-- Suite -->
git://source.jalview.org / jalview.git / commitdiff