added missing files for testcases; removed lib directory; using only …

…maven dependencies now
wiwie · Aug 15, 2016 · 79c65d9 · 79c65d9
1 parent 2d5f360
commit 79c65d9
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Showing 25 changed files with 751 additions and 98 deletions.
diff --git a/.classpath b/.classpath
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="test"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+	<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>
diff --git a/.project b/.project
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Wiutils</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+			<triggers>auto,full,incremental,</triggers>
+			<arguments>
+				<dictionary>
+					<key>LaunchConfigHandle</key>
+					<value>&lt;project&gt;/.externalToolBuilders/Makejar.launch</value>
+				</dictionary>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>
diff --git a/lib/junit-addons-1.4.jar b/lib/junit-addons-1.4.jar
diff --git a/lib/logback/slf4j-api-1.6.4-sources.jar b/lib/logback/slf4j-api-1.6.4-sources.jar
diff --git a/lib/logback/slf4j-api-1.6.4.jar b/lib/logback/slf4j-api-1.6.4.jar
diff --git a/lib/pcolt/parallelcolt-0.9.4-doc.zip b/lib/pcolt/parallelcolt-0.9.4-doc.zip
diff --git a/lib/pcolt/parallelcolt-0.9.4-src.zip b/lib/pcolt/parallelcolt-0.9.4-src.zip
diff --git a/lib/pcolt/parallelcolt-0.9.4.jar b/lib/pcolt/parallelcolt-0.9.4.jar
diff --git a/pom.xml b/pom.xml
@@ -0,0 +1,99 @@
+<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>de.wiwie</groupId>
+  <artifactId>Wiutils</artifactId>
+  <version>1.1</version>
+
+  <dependencies>
+  	<dependency>
+    <groupId>junit</groupId>
+    <artifactId>junit</artifactId>
+    <version>4.11</version>
+	<scope>test</scope>
+  </dependency>
+
+                <dependency>
+                        <groupId>junit-addons</groupId>
+                        <artifactId>junit-addons</artifactId>
+                        <version>1.4</version>
+                        <scope>compile</scope>
+                </dependency>
+
+
+                <dependency>
+                        <groupId>ch.qos.logback</groupId>
+                        <artifactId>logback-classic</artifactId>
+                        <version>1.0.9</version>
+                </dependency>
+                <dependency>
+                        <groupId>ch.qos.logback</groupId>
+                        <artifactId>logback-core</artifactId>
+                        <version>1.0.9</version>
+                </dependency>
+                <dependency>
+                        <groupId>ch.qos.logback</groupId>
+                        <artifactId>logback-access</artifactId>
+                        <version>1.0.9</version>
+                </dependency>
+
+                <dependency>
+                        <groupId>net.sourceforge.parallelcolt</groupId>
+                        <artifactId>parallelcolt</artifactId>
+                        <version>0.10.1</version>
+                </dependency>
+
+
+  </dependencies>
+
+  <build>
+    <sourceDirectory>src</sourceDirectory>
+    <testSourceDirectory>test</testSourceDirectory>
+    <plugins>
+      <plugin>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.1</version>
+        <configuration>
+          <source>1.8</source>
+          <target>1.8</target>
+        </configuration>
+      </plugin>
+    </plugins>
+
+  </build>
+        <repositories>
+                <repository>
+                        <id>compbio_maven</id>
+                        <snapshots>
+                                <enabled>true</enabled>
+                        </snapshots>
+                        <releases>
+                        </releases>
+                        <name>CompBio Maven Repository</name>
+                        <url>http://maven.compbio.sdu.dk/repository/snapshots/</url>
+                </repository>
+                <repository>
+                        <id>central_maven</id>
+                        <snapshots>
+                                <enabled>true</enabled>
+                        </snapshots>
+                        <releases>
+                        </releases>
+                        <name>Central Maven</name>
+                        <url>http://central.maven.org/</url>
+                </repository>
+        </repositories>
+
+        <distributionManagement>
+                <repository>
+                  <uniqueVersion>true</uniqueVersion>
+                  <id>archiva.snapshots</id>
+                  <name>Snapshots</name>
+                  <url>http://maven.compbio.sdu.dk/repository/snapshots/</url>
+                  <layout>default</layout>
+                </repository>
+        </distributionManagement>
+
+
+
+
+</project>
diff --git a/src/de/wiwie/wiutils/utils/DoubleArray2D.java b/src/de/wiwie/wiutils/utils/DoubleArray2D.java
@@ -17,8 +17,7 @@ public DoubleArray2D(final int rows, final int columns) {
 		this(rows, columns, false);
 	}
 
-	public DoubleArray2D(final int rows, final int columns,
-			final boolean isSymmetric) {
+	public DoubleArray2D(final int rows, final int columns, final boolean isSymmetric) {
 		super(isSymmetric);
 		if (isSymmetric) {
 			this.array = new double[rows][];
@@ -27,8 +26,26 @@ public DoubleArray2D(final int rows, final int columns,
 			for (int i = 0; i < rows; i++) {
 				this.array[i] = new double[i + 1];
 			}
-		} else
+		} else {
 			this.array = new double[rows][columns];
+		}
+		for (int i = 0; i < this.array.length; i++) {
+			for (int j = 0; j < this.array[i].length; j++) {
+				this.array[i][j] = Double.NaN;
+			}
+		}
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.wiwie.wiutils.utils.NumberArray2D#isSet(int, int)
+	 */
+	@Override
+	public boolean isSet(int x, int y) {
+		if (this.isSymmetric && x < y)
+			return !Double.isNaN(this.array[y][x]);
+		return !Double.isNaN(this.array[x][y]);
 	}
 
 	/*
@@ -91,7 +108,6 @@ public boolean equals(Object o) {
 			return false;
 
 		DoubleArray2D other = (DoubleArray2D) o;
-		return this.isSymmetric == other.isSymmetric
-				&& Arrays.deepEquals(this.array, other.array);
+		return this.isSymmetric == other.isSymmetric && Arrays.deepEquals(this.array, other.array);
 	}
 }
diff --git a/src/de/wiwie/wiutils/utils/FloatArray2D.java b/src/de/wiwie/wiutils/utils/FloatArray2D.java
@@ -29,6 +29,21 @@ public FloatArray2D(final int rows, final int columns,
 			}
 		} else
 			this.array = new float[rows][columns];
+		for (int i = 0; i < this.array.length; i++) { 
+			for (int j = 0; j < this.array[i].length; j++) {
+				this.array[i][j] = Float.NaN;
+			}
+		}
+	}
+
+	/* (non-Javadoc)
+	 * @see de.wiwie.wiutils.utils.NumberArray2D#isSet(int, int)
+	 */
+	@Override
+	public boolean isSet(int x, int y) {
+		if (this.isSymmetric && x < y)
+			return !Float.isNaN(this.array[y][x]);
+		return !Float.isNaN(this.array[x][y]);
 	}
 
 	/*

diff --git a/src/de/wiwie/wiutils/utils/NumberArray2D.java b/src/de/wiwie/wiutils/utils/NumberArray2D.java
@@ -23,6 +23,8 @@ public NumberArray2D(final boolean isSymmetric) {
 	public abstract double get(int x, int y);
 
 	public abstract void set(int x, int y, double val);
+
+	public abstract boolean isSet(int x, int y);
 
 	@Override
 	public abstract boolean equals(Object o);

diff --git a/src/de/wiwie/wiutils/utils/Pair.java b/src/de/wiwie/wiutils/utils/Pair.java
@@ -31,7 +31,8 @@ public Pair(final T el1, final U el2) {
 	public boolean equals(final Object p) {
 		if (p instanceof Pair) {
 			final Pair<T, U> other = (Pair<T, U>) p;
-			return other.e1.equals(this.e1) && other.e2.equals(this.e2);
+			return ((this.e1 == null && other.e1 == null) || (other.e1.equals(this.e1)))
+					&& ((this.e2 == null && other.e2 == null) || (other.e2.equals(this.e2)));
 		}
 		return false;
 	}
@@ -54,12 +55,12 @@ public void setSecond(final U newSecond) {
 
 	@Override
 	public int hashCode() {
-		return this.e1.hashCode() + this.e2.hashCode();
+		return (this.e1 != null ? this.e1.hashCode() : 0) + (this.e2 != null ? this.e2.hashCode() : 0);
 	}
 
 	@Override
 	public String toString() {
-		return "(" + this.e1.toString() + "\t" + this.e2.toString() + ")";
+		return "(" + (this.e1 != null ? this.e1.toString() : "null") + "\t" + (this.e2 != null ? this.e2.toString() : "null") + ")";
 	}
 
 	/**

diff --git a/src/de/wiwie/wiutils/utils/ShortArray2D.java b/src/de/wiwie/wiutils/utils/ShortArray2D.java
@@ -17,8 +17,7 @@ public ShortArray2D(final int rows, final int columns) {
 		this(rows, columns, false);
 	}
 
-	public ShortArray2D(final int rows, final int columns,
-			final boolean isSymmetric) {
+	public ShortArray2D(final int rows, final int columns, final boolean isSymmetric) {
 		super(isSymmetric);
 		if (isSymmetric) {
 			this.array = new short[rows][];
@@ -29,6 +28,23 @@ public ShortArray2D(final int rows, final int columns,
 			}
 		} else
 			this.array = new short[rows][columns];
+		for (int i = 0; i < this.array.length; i++) {
+			for (int j = 0; j < this.array[i].length; j++) {
+				this.array[i][j] = Short.MIN_VALUE;
+			}
+		}
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.wiwie.wiutils.utils.NumberArray2D#isSet(int, int)
+	 */
+	@Override
+	public boolean isSet(int x, int y) {
+		if (this.isSymmetric && x < y)
+			return this.array[y][x] != Short.MIN_VALUE;
+		return this.array[x][y] != Short.MIN_VALUE;
 	}
 
 	/*
@@ -91,7 +107,6 @@ public boolean equals(Object o) {
 			return false;
 
 		ShortArray2D other = (ShortArray2D) o;
-		return this.isSymmetric == other.isSymmetric
-				&& Arrays.deepEquals(this.array, other.array);
+		return this.isSymmetric == other.isSymmetric && Arrays.deepEquals(this.array, other.array);
 	}
 }