moved to maven

Author: tylerperyea

mavenMake.sh

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+mvn install:install-file -Dfile=lib/jchem3.jar -DgroupId=chemaxon -DartifactId=jchem -Dversion=3.0.0 -Dpackaging=jar

pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<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/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>gov.nih.ncats</groupId>
+  <artifactId>lychi</artifactId>
+  <packaging>jar</packaging>
+  <version>0.5.0</version>
+  <name>Lychi</name>
+
+  <repositories>
+    <repository>
+      <id>jboss-repo</id>
+      <url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
+    </repository>
+  </repositories>
+  <properties>
+    <java.version>1.8</java.version>
+    <maven.compiler.plugin.version>2.3.2</maven.compiler.plugin.version>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.target>1.8</maven.compiler.target>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <commonsFileuploadVersion>1.2.1</commonsFileuploadVersion>
+    <commonsIoVersion>2.3</commonsIoVersion>
+    <junitVersion>3.8.2</junitVersion>
+    <log4jVersion>1.2.16</log4jVersion>
+    <commonsLang3Version>3.1</commonsLang3Version>
+    <downloadLabel>Beta</downloadLabel>
+    <gae.version>1.6.5</gae.version>
+    <deploy.dir>binaries</deploy.dir>
+    <sonatypeRepoId>sonatype-nexus-snapshots</sonatypeRepoId>
+    <sonatypeUrl>http://oss.sonatype.org/content/repositories/snapshots</sonatypeUrl>
+    <wikiSvnExec>true</wikiSvnExec>
+  </properties>
+  
+<dependencies>
+    <dependency>
+        <groupId>chemaxon</groupId>
+        <artifactId>jchem</artifactId>
+        <version>3.0.0</version>
+    </dependency>
+    <dependency>
+        <groupId>junit</groupId>
+        <artifactId>junit</artifactId>
+        <version>4.12</version>
+    </dependency>
+</dependencies>
+
+  <build>
+  
+  	<finalName>${project.artifactId}-${project.version}</finalName>
+    <outputDirectory>${deploy.dir}</outputDirectory>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>${maven.compiler.plugin.version}</version>
+        <configuration>
+          <source>${java.version}</source>
+          <target>${java.version}</target>
+          <compilerArgument>-proc:none</compilerArgument>
+        </configuration>
+      </plugin>
+<plugin>
+    <artifactId>maven-assembly-plugin</artifactId>
+    <executions>
+      <execution>
+        <phase>package</phase>
+        <goals>
+          <goal>single</goal>
+        </goals>
+      </execution>
+    </executions>
+
+   <configuration>
+               <archive>
+                  <manifest>
+                     <mainClass>tripod.molvec.ui.Viewer</mainClass>
+                  </manifest>
+               </archive>
+               <descriptorRefs>
+                  <descriptorRef>jar-with-dependencies</descriptorRef>
+               </descriptorRefs>
+            </configuration>
+  </plugin>
+  <!-- 
+  <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>create-distribution</id>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+            <configuration>
+              <finalName>GSRSPull-${project.version}</finalName>
+              <appendAssemblyId>false</appendAssemblyId>
+              <descriptors>
+                <descriptor>assembly/sample.xml</descriptor>
+              </descriptors>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+      -->
+    </plugins>
+    <resources>
+        <resource>
+            <directory>src/main/java</directory>
+            <includes>
+                <include>**/*.html</include>
+				<include>**/*.js</include>
+				<include>**/*.css</include>
+				<include>**/*.png</include>
+            </includes>
+        </resource>
+    </resources>
+  </build>
+</project>

src/lychi/AtomIterator.java src/main/java/lychi/AtomIterator.java

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+package lychi;
+public final class Version {
+   public static final String VERSION = "20170222";    
+   public static final String COMMIT = "fe2ea2a";
+   public static final String USER = "tyler";
+   public static final String TIMESTAMP = "12/14/2018 at 14:53:34 EST";
+   private Version () {}
+   public static void main (String[] argv) {
+      System.out.println("LyChI Version: commit="+COMMIT+" version="+VERSION+" timestamp="+TIMESTAMP+" user="+USER);
+   }
+}