Local gradle pulbish and project refactoring into packages

.gitignore

@@ -11,6 +11,13 @@
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
 
+# Java Files #
+*.jar
+
+# Intellij Idea
+.idea
+
 # Gradle stuff
 build/
 .gradle/
+gradle

README.md

@@ -96,10 +96,28 @@ You can clone the code, compile, and build the JAR file the regular command-line
 way.
 
 We use [Gradle](https://gradle.org/) for connvenience.
-- [install Gradle](https://gradle.org/install)
+- **(on Linux or Mac)** run `chmod +x gradlew`
 - run `gradle test` for unit tests (currently correctness tests)
 - run `gradle build` to find the `apted.jar` file in `build/libs/`
 
+## Deploying to local maven repository
+
+You can publish the project into your local maven repository to import into other projects.
+
+- run `gradle publishToMavenLocal` 
+
+To use APTED in another project:
+
+```
+repositories {
+  mavenLocal()
+}
+
+dependencies {
+  compile 'at.unisalzburg:apted:1.0'
+}
+  ```
+
 ## Javadoc documentation
 
 Run `gradle javadoc` to generate documentation. Then, open in your browser

build.gradle

@@ -1,4 +1,8 @@
+group 'at.unisalzburg'
+version '1.0'
+
 apply plugin: 'java'
+apply plugin: "maven-publish"
 
 // Dependency repository.
 repositories {
@@ -11,13 +15,6 @@ dependencies {
                 'com.google.code.gson:gson:2.8.0'
 }
 
-// Specify main class for the JAR file.
-jar {
-    manifest {
-        attributes 'Main-Class': 'util.CommandLine'
-    }
-}
-
 // Include test classes and private members into javadoc.
 javadoc {
   classpath += sourceSets.test.compileClasspath
@@ -29,3 +26,27 @@ javadoc {
 test {
   testLogging.showStandardStreams = true
 }
+
+// For publishing in MavenLocal
+task sourcesJar(type: Jar, dependsOn: "classes") {
+  classifier = 'sources'
+
+  from sourceSets.main.allSource
+  from sourceSets.test.allSource
+}
+
+publishing {
+    publications {
+        mavenJava(MavenPublication) {
+            groupId 'at.unisalzburg'
+            artifactId 'apted'
+            version '1.0'
+
+            from components.java
+
+            artifact sourcesJar {
+                classifier "sources"
+            }
+        }
+    }
+}

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,6 @@
+#Thu May 18 15:43:57 CEST 2017
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-all.zip

gradlew

@@ -0,0 +1,172 @@
+#!/usr/bin/env sh
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Escape application args
+save ( ) {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
+
+exec "$JAVACMD" "$@"

src/main/java/costmodel/CostModel.java → src/main/java/at/unisalzburg/apted/costmodel/CostModel.java

@@ -21,9 +21,9 @@
  * SOFTWARE.
  */
 
-package costmodel;
+package at.unisalzburg.apted.costmodel;
 
-import node.Node;
+import at.unisalzburg.apted.node.Node;
 
 /**
  * This interface specifies the methods to implement for a custom cost model.

src/main/java/costmodel/PerEditOperationStringNodeDataCostModel.java → src/main/java/at/unisalzburg/apted/costmodel/PerEditOperationStringNodeDataCostModel.java

@@ -21,14 +21,13 @@
  * SOFTWARE.
  */
 
-package costmodel;
+package at.unisalzburg.apted.costmodel;
 
-import costmodel.CostModel;
-import node.Node;
-import node.StringNodeData;
+import at.unisalzburg.apted.node.Node;
+import at.unisalzburg.apted.node.StringNodeData;
 
 /**
- * This is a cost model defined on {@link node.StringNodeData} with a fixed cost
+ * This is a cost model defined on {@link at.unisalzburg.apted.node.StringNodeData} with a fixed cost
  * per edit operation.
  */
 public class PerEditOperationStringNodeDataCostModel implements CostModel<StringNodeData> {

src/main/java/costmodel/StringUnitCostModel.java → src/main/java/at/unisalzburg/apted/costmodel/StringUnitCostModel.java

@@ -21,11 +21,10 @@
  * SOFTWARE.
  */
 
-package costmodel;
+package at.unisalzburg.apted.costmodel;
 
-import costmodel.CostModel;
-import node.Node;
-import node.StringNodeData;
+import at.unisalzburg.apted.node.Node;
+import at.unisalzburg.apted.node.StringNodeData;
 
 /**
  * This is a unit-nost model defined on string labels.

src/main/java/distance/APTED.java → src/main/java/at/unisalzburg/apted/distance/APTED.java

@@ -21,14 +21,14 @@
  * SOFTWARE.
  */
 
-package distance;
+package at.unisalzburg.apted.distance;
 
 import java.util.Arrays;
 import java.util.LinkedList;
 import java.util.Stack;
-import node.Node;
-import node.NodeIndexer;
-import costmodel.CostModel;
+import at.unisalzburg.apted.node.Node;
+import at.unisalzburg.apted.node.NodeIndexer;
+import at.unisalzburg.apted.costmodel.CostModel;
 
 /**
  * Implements APTED algorithm [1,2].
@@ -76,14 +76,14 @@ public class APTED<C extends CostModel, D> {
   /**
    * Indexer of the source tree.
    *
-   * @see node.NodeIndexer
+   * @see at.unisalzburg.apted.node.NodeIndexer
    */
   private NodeIndexer it1;
 
   /**
    * Indexer of the destination tree.
    *
-   * @see node.NodeIndexer
+   * @see at.unisalzburg.apted.node.NodeIndexer
    */
   private NodeIndexer it2;
 

src/main/java/distance/AllPossibleMappingsTED.java → src/main/java/at/unisalzburg/apted/distance/AllPossibleMappingsTED.java

@@ -21,14 +21,14 @@
  * SOFTWARE.
  */
 
-package distance;
+package at.unisalzburg.apted.distance;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
-import node.Node;
-import node.NodeIndexer;
-import costmodel.CostModel;
+import at.unisalzburg.apted.node.Node;
+import at.unisalzburg.apted.node.NodeIndexer;
+import at.unisalzburg.apted.costmodel.CostModel;
 
 /**
  * Implements an exponential algorithm for the tree edit distance. It computes
@@ -43,14 +43,14 @@ public class AllPossibleMappingsTED<C extends CostModel, D> {
   /**
    * Indexer of the source tree.
    *
-   * @see node.NodeIndexer
+   * @see at.unisalzburg.apted.node.NodeIndexer
    */
   private NodeIndexer it1;
 
   /**
    * Indexer of the destination tree.
    *
-   * @see node.NodeIndexer
+   * @see at.unisalzburg.apted.node.NodeIndexer
    */
   private NodeIndexer it2;