migration from svn

.checkstyle

+<?xml version="1.0" encoding="UTF-8"?>
+
+<fileset-config file-format-version="1.2.0" simple-config="false" sync-formatter="false"/>

.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="src/main/resources"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.gitignore

+target/
+map_images/
+CellDesigner-plugin/target/
+annotation/target/
+annotation/minerva-big/
+commons/target/
+comparison/target/
+console/target/
+converter/target/
+converter-CellDesigner/target/
+converter-SBGNML/target/
+*.png
+target/
+debian/minerva*
+debian/src/*.sql
+*.war
+editor/target/
+model/target/
+model-command/target/
+pathvisio/target/
+persist/target/
+quadTrees/target/
+reactome/target/
+rest-api/target/
+web/target/
+web/src/main/webapp/svnversion.txt

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>MapViewer-parent</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+		<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.core.resources.prefs

+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/test/java=UTF-8
+encoding/<project>=UTF-8

.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning

.settings/org.eclipse.m2e.core.prefs

+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

.settings/org.eclipse.wst.validation.prefs

+DELEGATES_PREFERENCE=delegateValidatorList
+USER_BUILD_PREFERENCE=enabledBuildValidatorListorg.eclipse.wst.wsi.ui.internal.WSIMessageValidator;
+USER_MANUAL_PREFERENCE=enabledManualValidatorListorg.eclipse.wst.wsi.ui.internal.WSIMessageValidator;
+USER_PREFERENCE=overrideGlobalPreferencesfalse
+eclipse.preferences.version=1
+override=false
+suspend=false
+vals/org.eclipse.jst.jsf.facelet.ui.FaceletHTMLValidator/global=FF01
+vals/org.eclipse.jst.jsp.core.JSPBatchValidator/global=FF01
+vals/org.eclipse.jst.jsp.core.JSPContentValidator/global=FF01
+vals/org.eclipse.jst.jsp.core.TLDValidator/global=FF01
+vals/org.eclipse.wst.dtd.core.dtdDTDValidator/global=FF01
+vals/org.eclipse.wst.html.core.HTMLValidator/global=FF01
+vals/org.eclipse.wst.wsdl.validation.wsdl/global=FF02158org.eclipse.wst.wsdl.validation.internal.eclipse.Validator
+vals/org.eclipse.wst.xml.core.xml/global=FF03
+vals/org.eclipse.wst.xsd.core.xsd/global=FF02162org.eclipse.wst.xsd.core.internal.validation.eclipse.Validator
+vals/org.eclipse.wst.xsl.core.xsl/global=FF02
+vf.version=3

CellDesigner-plugin/.checkstyle

+<?xml version="1.0" encoding="UTF-8"?>
+
+<fileset-config file-format-version="1.2.0" simple-config="false" sync-formatter="false">
+  <fileset name="src" enabled="true" check-config-name="MapViewer checkstyle" local="false">
+    <file-match-pattern match-pattern="src/main/." include-pattern="true"/>
+  </fileset>
+</fileset-config>

CellDesigner-plugin/.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

CellDesigner-plugin/.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>MapViewer-CellDesigner-plugin</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
+	</natures>
+</projectDescription>

CellDesigner-plugin/.settings/org.eclipse.core.resources.prefs

+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
+encoding/<project>=UTF-8

CellDesigner-plugin/.settings/org.eclipse.jdt.core.prefs

+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.8

CellDesigner-plugin/.settings/org.eclipse.m2e.core.prefs

+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

CellDesigner-plugin/build.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project name="CellDesigner plugin" default="main" basedir=".">
+	<property environment="env"/>
+	<property name="build.dir" value="target" />
+	<property name="mvn.home" value="${env.M2_HOME}" />
+	<property name="celldesigner.home" value="C:/Program Files (x86)/CellDesigner4.4/" />
+	<property name="celldesigner.deploy.dir" value="${celldesigner.home}/plugin/" />
+	<property name="plugin.name" value="mv_plugin" />
+	<property name="jar.file" value="CellDesigner-plugin-1.0-jar-with-dependencies.jar" />
+
+	<target name="maven-build">
+		<exec executable="${mvn.home}/bin/mvn.bat" >
+			 <arg line="clean" />
+		</exec>
+		<exec executable="${mvn.home}/bin/mvn.bat" >
+			 <arg line="-Dmaven.test.skip=true install" />
+		</exec>
+	</target>
+
+	<target name="jar-exists">
+    <available file="${celldesigner.home}/plugin/${plugin.name}.jar" property="jar.exists"/>
+	</target>
+	
+	<target name="remove-jar" depends="jar-exists" if="jar.exists">
+		<delete file="${celldesigner.home}/plugin/${plugin.name}.jar" />
+	</target>
+
+	<target name="deploy" depends="remove-jar">
+		<copy file="${build.dir}/${jar.file}" todir="${celldesigner.deploy.dir}" />
+		<move file="${celldesigner.deploy.dir}/${jar.file}" tofile="${celldesigner.deploy.dir}/${plugin.name}.jar"/>
+	</target>
+
+	<target name="main" depends="maven-build, deploy"/>
+
+</project>
\ No newline at end of file

CellDesigner-plugin/install.xml

+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" 
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+  <id>jar-with-dependencies</id>
+  <formats>
+    <format>jar</format>
+  </formats>
+  <includeBaseDirectory>false</includeBaseDirectory>
+  <dependencySets>
+    <dependencySet>
+      <outputDirectory>/</outputDirectory>
+      <useProjectArtifact>true</useProjectArtifact>
+      <unpack>true</unpack>
+      <scope>runtime</scope>
+      <excludes>
+      	<exclude>jp.sbi:celldesigner</exclude>
+      	<exclude>org.sbml:libsbml</exclude>
+      	
+      </excludes>
+    </dependencySet>
+  </dependencySets>
+</assembly>
\ No newline at end of file

CellDesigner-plugin/pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>lcsb.mapviewer</groupId>
+    <artifactId>parent</artifactId>
+    <version>1.0</version>
+  </parent>
+  <artifactId>CellDesigner-plugin</artifactId>
+  	<!-- dependency from the MapViewer model -->
+
+  <repositories>
+		<repository>
+	    <id>central</id>
+    	<url>http://repo.maven.apache.org/maven2/</url>
+		</repository>
+
+		<repository>
+   		<id>repo</id>
+    	<releases>
+       	<enabled>true</enabled>
+       	<checksumPolicy>ignore</checksumPolicy>
+    	</releases>
+    	<snapshots>
+        <enabled>false</enabled>
+    	</snapshots>
+    	<url>file://${project.basedir}/repo</url>
+		</repository>
+
+	</repositories>
+
+<build>
+  <plugins>
+    <plugin>
+      <artifactId>maven-assembly-plugin</artifactId>
+      <executions>
+    		<execution>
+      		<id>make-assembly</id> <!-- this is used for inheritance merges -->
+      		<phase>package</phase> <!-- bind to the packaging phase -->
+      		<goals>
+        		<goal>single</goal>
+      		</goals>
+      		<configuration>
+        		<descriptor>install.xml</descriptor>
+      		</configuration>
+    		</execution>
+  		</executions>
+    </plugin>
+  </plugins>
+</build>
+	
+	
+	<dependencies>
+		<dependency>
+            <groupId>lcsb.mapviewer</groupId>
+            <artifactId>model</artifactId>
+            <version>1.0</version>
+		</dependency>
+
+		<dependency>
+            <groupId>lcsb.mapviewer</groupId>
+            <artifactId>commons</artifactId>
+            <version>1.0</version>
+    </dependency>
+
+		<dependency>
+            <groupId>lcsb.mapviewer</groupId>
+            <artifactId>converter-CellDesigner</artifactId>
+            <version>1.0</version>
+		</dependency>
+
+		<dependency>
+			<groupId>jp.sbi</groupId>
+			<artifactId>celldesigner</artifactId>
+			<version>${celldesigner.version}</version>
+		</dependency>
+    
+		<dependency>
+			<groupId>org.sbml</groupId>
+			<artifactId>libsbml</artifactId>
+			<version>${libsbml.version}</version>
+		</dependency>
+    
+  </dependencies>
+  
+</project>
\ No newline at end of file

CellDesigner-plugin/repo/jp/sbi/celldesigner/4.4/celldesigner-4.4.pom

+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>jp.sbi</groupId>
+  <artifactId>celldesigner</artifactId>
+  <version>4.4</version>
+  <description>POM was created from install:install-file</description>
+</project>

CellDesigner-plugin/repo/jp/sbi/celldesigner/maven-metadata-local.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<metadata>
+  <groupId>jp.sbi</groupId>
+  <artifactId>celldesigner</artifactId>
+  <versioning>
+    <release>4.4</release>
+    <versions>
+      <version>4.4</version>
+    </versions>
+    <lastUpdated>20150326110056</lastUpdated>
+  </versioning>
+</metadata>