Added source-code of EscherConverter.

draeger-lab · Mar 21, 2016 · c3155a4 · c3155a4
1 parent 82f34ac
commit c3155a4
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,4 @@
+/target/
+/.settings/
+/.classpath
+/minimalSysBio.xml
diff --git a/lib/jsbml-2492-incl-libs.jar b/lib/jsbml-2492-incl-libs.jar
diff --git a/lib/org.sbgn-with-dependencies.jar b/lib/org.sbgn-with-dependencies.jar
diff --git a/lib/sysbio.jar b/lib/sysbio.jar
diff --git a/pom.xml b/pom.xml
@@ -0,0 +1,189 @@
+<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>
+  <groupId>edu.ucsd.sbrg</groupId>
+  <artifactId>EscherConverter</artifactId>
+
+  <!-- Output to jar format -->
+  <packaging>jar</packaging>
+
+
+  <!-- =================================================================== -->
+  <!-- General project information                                         -->
+  <!-- =================================================================== -->
+
+  <name>${project.artifactId}</name>
+  <version>0.6</version>
+  <url>https://github.com/SBRG/EscherConverter</url>
+  <inceptionYear>2015</inceptionYear>
+  <description>EscherConverter is a stand-alone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.</description>
+
+  <properties>
+    <jdk.version>1.8</jdk.version>
+    <maven.build.timestamp.format>yyyy</maven.build.timestamp.format>
+    <year>${maven.build.timestamp}</year><!-- This property is used for filtering the variable ${year} in some resource files -->
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <project.license.url>http://www.opensource.org/licenses/mit-license.php</project.license.url>
+    <junit.version>4.11</junit.version>
+  </properties>
+
+  <organization>
+    <name>University of California, San Diego</name>
+    <url>http://sbrg.ucsd.edu</url>
+  </organization>
+
+  <issueManagement>
+    <url>https://github.com/SBRG/EscherConverter/issues</url>
+    <system>GitHub Issues</system>
+  </issueManagement>
+
+  <licenses>
+    <license>
+      <name>MIT License</name>
+      <url>${project.license.url}</url>
+      <distribution>repo</distribution>
+    </license>
+  </licenses>
+
+  <developers>
+    <developer>
+      <email>[email protected]</email>
+      <name>Andreas Dräger</name>
+      <url>https://github.com/draeger/</url>
+      <id>draeger</id>
+    </developer>
+  </developers>
+
+  <!-- =================================================================== -->
+  <!-- Dependencies                                                        -->
+  <!-- =================================================================== -->
+
+  <dependencies>
+
+    <!-- To update or install local non-MAVEN JAR files run the command in the comments -->
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>${junit.version}</version>
+      <scope>test</scope>
+    </dependency>
+
+    <dependency>
+      <!-- mvn install:install-file -Dfile=/path/to/jsbml.jar -DgroupId=org.sbml -DartifactId=JSBML -Dversion=REVISION_NUMBER -Dpackaging=jar -->
+      <groupId>org.sbml</groupId>
+      <artifactId>JSBML</artifactId>
+      <version>2492</version>
+      <scope>compile</scope>
+    </dependency>
+
+    <dependency>
+      <!-- mvn install:install-file -Dfile=/path/to/libSBGN.jar -DgroupId=org -DartifactId=sbgn -Dversion=0.2 -Dpackaging=jar -->
+      <groupId>org</groupId>
+      <artifactId>sbgn</artifactId>
+      <version>0.2</version>
+      <scope>compile</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>com.googlecode.json-simple</groupId>
+      <artifactId>json-simple</artifactId>
+      <version>1.1.1</version>
+    </dependency>
+
+    <dependency>
+      <!-- mvn install:install-file -Dfile=/path/to/sysbio.jar -DgroupId=de.zbit -DartifactId=SysBio -Dversion=REVISION_NUMBER -Dpackaging=jar -->
+      <groupId>de.zbit</groupId>
+      <artifactId>SysBio</artifactId>
+      <version>1390</version> <!-- SVN revision -->
+      <scope>compile</scope>
+    </dependency>
+
+  </dependencies>
+
+
+  <!-- =================================================================== -->
+  <!-- Building                                                            -->
+  <!-- =================================================================== -->
+
+  <!-- To build the project run: -->
+  <!-- mvn clean compile package assembly:single -->
+
+  <build>
+
+    <finalName>${project.artifactId}-${project.version}</finalName>
+
+    <resources>
+      <resource>
+        <directory>src/main/resources</directory>
+        <filtering>true</filtering>
+      </resource>
+    </resources>
+
+    <pluginManagement>
+
+      <plugins>
+
+        <!-- Download source code in Eclipse, best practice [OPTIONAL!] -->
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-eclipse-plugin</artifactId>
+          <version>2.9</version>
+          <configuration>
+            <downloadSources>true</downloadSources>
+            <downloadJavadocs>false</downloadJavadocs>
+          </configuration>
+        </plugin>
+
+        <!-- Set a JDK compiler level -->
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-compiler-plugin</artifactId>
+          <version>3.3</version>
+          <configuration>
+            <source>${jdk.version}</source>
+            <target>${jdk.version}</target>
+          </configuration>
+        </plugin>
+
+        <!-- Assemble executable JAR -->
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-assembly-plugin</artifactId>
+          <version>2.6</version>
+          <configuration>
+            <archive>
+              <manifest>
+                <!--<mainClass>edu.ucsd.sbrg.escher.EscherConverter</mainClass>-->
+                <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+              </manifest>
+            </archive>
+            <descriptorRefs>
+              <descriptorRef>jar-with-dependencies</descriptorRef>
+            </descriptorRefs>
+            <finalName>${project.artifactId}-${project.version}</finalName>
+            <appendAssemblyId>false</appendAssemblyId>
+            <!--<descriptor>assembly.xml</descriptor>--> <!-- Details of the assembly are described in this file -->
+          </configuration>
+          <executions>
+            <execution>
+              <id>make-assembly</id> <!-- this is used for inheritance merges -->
+              <phase>package</phase> <!-- bind to the packaging phase -->
+              <goals>
+                <!-- This will create a JAR with all dependencies -->
+                <!-- mvn clean compile assembly:single -->
+                <goal>single</goal>
+              </goals>
+            </execution>
+          </executions>
+        </plugin>
+
+      </plugins>
+    </pluginManagement>
+
+  </build>
+
+</project>
diff --git a/src/main/java/edu/ucsd/sbrg/escher/AbstractBox.java b/src/main/java/edu/ucsd/sbrg/escher/AbstractBox.java
@@ -0,0 +1,168 @@
+/*
+ * $Id$
+ * $URL$
+ * ---------------------------------------------------------------------
+ * This file is part of the program BioNetView.
+ *
+ * Copyright (C) 2013-2016 by the University of California, San Diego.
+ *
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation. A copy of the license
+ * agreement is provided in the file named "LICENSE.txt" included with
+ * this software distribution and also available online as
+ * <http://www.gnu.org/licenses/lgpl-3.0-standalone.html>.
+ * ---------------------------------------------------------------------
+ */
+package edu.ucsd.sbrg.escher;
+
+/**
+ * 
+ * @author Andreas Dr&auml;ger
+ *
+ */
+public abstract class AbstractBox extends AbstractPosition implements Box {
+
+  /**
+   * 
+   */
+  protected Double height;
+  /**
+   * 
+   */
+  protected Double width;
+
+  /**
+   * 
+   */
+  public AbstractBox() {
+    super();
+    x = y = width = height = null;
+  }
+
+  /**
+   * 
+   * @param box
+   */
+  public AbstractBox(AbstractBox box) {
+    super(box);
+    if (box.isSetHeight()) {
+      setHeight(box.getHeight().doubleValue());
+    }
+    if (box.isSetWidth()) {
+      setWidth(box.getWidth().doubleValue());
+    }
+  }
+
+  /* (non-Javadoc)
+   * @see java.lang.Object#equals(java.lang.Object)
+   */
+  @Override
+  public boolean equals(Object obj) {
+    if (this == obj) {
+      return true;
+    }
+    if (!super.equals(obj)) {
+      return false;
+    }
+    if (getClass() != obj.getClass()) {
+      return false;
+    }
+    AbstractBox other = (AbstractBox) obj;
+    if (height == null) {
+      if (other.height != null) {
+        return false;
+      }
+    } else if (!height.equals(other.height)) {
+      return false;
+    }
+    if (width == null) {
+      if (other.width != null) {
+        return false;
+      }
+    } else if (!width.equals(other.width)) {
+      return false;
+    }
+    return true;
+  }
+
+  /* (non-Javadoc)
+   * @see edu.ucsd.sbrg.escher.Box#getHeight()
+   */
+  @Override
+  public Double getHeight() {
+    return height;
+  }
+
+  /* (non-Javadoc)
+   * @see edu.ucsd.sbrg.escher.Box#getWidth()
+   */
+  @Override
+  public Double getWidth() {
+    return width;
+  }
+
+  /* (non-Javadoc)
+   * @see java.lang.Object#hashCode()
+   */
+  @Override
+  public int hashCode() {
+    final int prime = 31;
+    int result = super.hashCode();
+    result = prime * result + ((height == null) ? 0 : height.hashCode());
+    result = prime * result + ((width == null) ? 0 : width.hashCode());
+    return result;
+  }
+
+  /* (non-Javadoc)
+   * @see edu.ucsd.sbrg.escher.Box#isSetHeight()
+   */
+  @Override
+  public boolean isSetHeight() {
+    return height != null;
+  }
+
+  /* (non-Javadoc)
+   * @see edu.ucsd.sbrg.escher.Box#isSetWidth()
+   */
+  @Override
+  public boolean isSetWidth() {
+    return width != null;
+  }
+
+  /* (non-Javadoc)
+   * @see edu.ucsd.sbrg.escher.Box#setHeight(java.lang.Double)
+   */
+  @Override
+  public void setHeight(Double height) {
+    this.height = height;
+  }
+
+  /* (non-Javadoc)
+   * @see edu.ucsd.sbrg.escher.Box#setWidth(java.lang.Double)
+   */
+  @Override
+  public void setWidth(Double width) {
+    this.width = width;
+  }
+
+  /* (non-Javadoc)
+   * @see java.lang.Object#toString()
+   */
+  @Override
+  public String toString() {
+    StringBuilder builder = new StringBuilder();
+    builder.append(getClass().getSimpleName());
+    builder.append(" [x=");
+    builder.append(x);
+    builder.append(", y=");
+    builder.append(y);
+    builder.append(", width=");
+    builder.append(width);
+    builder.append(", height=");
+    builder.append(height);
+    builder.append("]");
+    return builder.toString();
+  }
+
+}