First commit!

marmof.iml

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="com.carrotsearch:hppc:0.6.1" level="project" />
+    <orderEntry type="library" name="com.google.guava:guava:18.0" level="project" />
+  </component>
+</module>

src/amu/saeed/marmof/BoolArray.java

@@ -0,0 +1,109 @@
+package amu.saeed.marmof;
+
+import java.math.BigInteger;
+import java.util.Arrays;
+
+/**
+ * Created by Saeed on 3/7/14.
+ */
+public class BoolArray implements Comparable<BoolArray> {
+    private boolean[] array;
+
+    public BoolArray(boolean[] array) {
+        this.array = array.clone();
+    }
+
+    private BoolArray() {
+    }
+
+    public static BoolArray buildFrom(boolean[] array) {
+        BoolArray result = new BoolArray();
+        result.array = array;
+        return result;
+    }
+
+    public static boolean[] longToBoolArray(long a, int size) {
+        boolean[] arr = new boolean[size];
+        for (int i = 0; i < size; i++)
+            if ((a & (1L << i)) != 0)
+                arr[i] = true;
+        return arr;
+    }
+
+    public static long boolArrayToLong(boolean[] arr) {
+        if (arr.length > 64)
+            throw new IllegalStateException("Array size is larger than 64: " + arr.length);
+
+        long result = 0;
+        for (int i = 0; i < arr.length; i++)
+            if (arr[i])
+                result |= (1L << i);
+
+        return result;
+    }
+
+    public boolean[] getArray() {
+        return array;
+    }
+
+    public int size() {
+        return getArray().length;
+    }
+
+    public BigInteger getAsBigInt() {
+        BigInteger result = BigInteger.ZERO;
+        for (int i = 0; i < getArray().length; i++)
+            if (getArray()[i])
+                result = result.setBit(i);
+        return result;
+    }
+
+    @Override
+    public String toString() {
+        char[] signature = new char[getArray().length];
+        for (int i = 0; i < getArray().length; i++)
+            if (getArray()[i])
+                signature[i] = '1';
+            else
+                signature[i] = '0';
+        return new String(signature);
+    }
+
+    @Override
+    public boolean equals(Object aThat) {
+        if (this == aThat) return true;
+        if (aThat == null) return false;
+        if (!(aThat instanceof BoolArray)) return false;
+        BoolArray that = (BoolArray) aThat;
+        return Arrays.equals(getArray(), that.getArray());
+    }
+
+    @Override
+    public int hashCode() {
+        if (getArray() == null)
+            return 0;
+        int result = 1;
+        for (int i = 0; i < getArray().length; i++)
+            result = 31 * result + (getArray()[i] ? 1231 : 1237);
+        return result;
+    }
+
+    @Override
+    public int compareTo(BoolArray o) {
+        if (getArray().length < o.getArray().length)
+            return -1;
+        if (getArray().length > o.getArray().length)
+            return 1;
+
+        for (int i = 0; i < getArray().length; i++) {
+            if (getArray()[i] == o.getArray()[i])
+                continue;
+            if (getArray()[i] == true)
+                return 1;
+            else
+                return -1;
+        }
+        return 0;
+    }
+
+}

src/amu/saeed/marmof/FreqMap.java

@@ -0,0 +1,88 @@
+package amu.saeed.marmof;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Created by Saeed on 4/17/14.
+ */
+final public class FreqMap {
+    public HashMap<BoolArray, Count> map = new HashMap<BoolArray, Count>();
+
+    public void add(BoolArray arr, int occurrences) {
+        Count freq = map.get(arr);
+        if (freq == null)
+            map.put(arr, new Count(occurrences));
+        else
+            freq.getAndAdd(occurrences);
+    }
+
+    public void add(BoolArray arr, long occurrences) {
+        Count freq = map.get(arr);
+        if (freq == null)
+            map.put(arr, new Count(occurrences));
+        else
+            freq.getAndAdd(occurrences);
+    }
+
+    public int size() {
+        return map.size();
+    }
+
+    public long totalFreq() {
+        long sum = 0;
+        for (Map.Entry<BoolArray, Count> e : map.entrySet())
+            sum += e.getValue().get();
+        return sum;
+    }
+
+    public void clear() {
+        map.clear();
+    }
+
+    final public class Count {
+        long value;
+
+        Count(int value) {
+            this.value = value;
+        }
+
+        Count(long value) {
+            this.value = value;
+        }
+
+        public long get() {
+            return value;
+        }
+
+        public long getAndAdd(int delta) {
+            long result = value;
+            value = result + delta;
+            return result;
+        }
+
+        public long getAndAdd(long delta) {
+            long result = value;
+            value = result + delta;
+            return result;
+        }
+
+
+        @Override
+        public int hashCode() {
+            return (int) (value ^ (value >>> 32));
+        }
+
+        @Override
+        public boolean equals(Object obj) {
+            return obj instanceof Count && ((Count) obj).value == value;
+        }
+
+        @Override
+        public String toString() {
+            return Long.toString(value);
+        }
+
+    }
+
+}

src/amu/saeed/marmof/Graph.java

@@ -0,0 +1,44 @@
+package amu.saeed.marmof;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * Created by saeed on 5/7/15.
+ */
+public interface Graph {
+    boolean areNeighbor(int v, int w);
+
+    public int[] getNeighbors(int v);
+
+    public void printInfo();
+
+    public int vertexCount();
+
+    public int edgeCount();
+
+    public Set<Integer> getVertices();
+
+    public List<Edge> getEdges();
+
+    public int getDegree(int vertex);
+
+    public SubGraphStructure getSubGraph(int[] vertex_set);
+
+    public long getSubGraphAsLong(int[] vertex_set);
+
+    public boolean hasEdge(int v, int w);
+
+    public void printToFile(String path) throws IOException;
+
+    public final static class Edge {
+        int src;
+        int dest;
+
+        public Edge(int src, int dest) {
+            this.src = src;
+            this.dest = dest;
+        }
+    }
+}