Overhaul of the function discovery and refresh in Appearance

modules/AppearanceAPI/src/main/java/org/gephi/appearance/AttributeFunctionImpl.java

+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.AttributeFunction;
+import org.gephi.appearance.api.Partition;
+import org.gephi.appearance.api.PartitionFunction;
+import org.gephi.appearance.api.Ranking;
+import org.gephi.appearance.api.RankingFunction;
+import org.gephi.appearance.spi.Transformer;
+import org.gephi.appearance.spi.TransformerUI;
+import org.gephi.graph.api.Column;
+import org.gephi.graph.api.Graph;
+
+/**
+ *
+ * @author mbastian
+ */
+public class AttributeFunctionImpl extends FunctionImpl implements RankingFunction, PartitionFunction, AttributeFunction {
+
+    public AttributeFunctionImpl(String id, Graph graph, Column column, Transformer transformer, TransformerUI transformerUI, RankingImpl ranking) {
+        super(id, null, graph, column, transformer, transformerUI, null, ranking);
+    }
+
+    public AttributeFunctionImpl(String id, Graph graph, Column column, Transformer transformer, TransformerUI transformerUI, PartitionImpl partition) {
+        super(id, null, graph, column, transformer, transformerUI, partition, null);
+    }
+
+    @Override
+    public Column getColumn() {
+        return column;
+    }
+
+    @Override
+    public Partition getPartition() {
+        return partition;
+    }
+
+    @Override
+    public Ranking getRanking() {
+        return ranking;
+    }
+
+    @Override
+    public String toString() {
+        return column.getTitle();
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/AttributePartitionImpl.java

+/*
+ Copyright 2008-2013 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2013 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2013 Gephi Consortium.
+ */
+package org.gephi.appearance;
+
+import org.gephi.graph.api.Column;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Index;
+
+/**
+ *
+ * @author mbastian
+ */
+public class AttributePartitionImpl extends PartitionImpl {
+
+    protected final Index index;
+    protected final Column column;
+
+    public AttributePartitionImpl(Column column, Index index) {
+        super();
+        this.column = column;
+        this.index = index;
+    }
+
+    @Override
+    public Object getValue(Element element) {
+        return element.getAttribute(column);
+    }
+
+    @Override
+    public Iterable getValues() {
+        return index.values(column);
+    }
+
+    @Override
+    public int getElementCount() {
+        return index.countElements(column);
+    }
+
+    @Override
+    public int count(Object value) {
+        return index.count(column, value);
+    }
+
+    @Override
+    public float percentage(Object value) {
+        int count = index.count(column, value);
+        return (float) count / index.countElements(column);
+    }
+
+    @Override
+    public int size() {
+        return index.countValues(column);
+    }
+
+    @Override
+    public Column getColumn() {
+        return column;
+    }
+
+    @Override
+    public int hashCode() {
+        int hash = 3;
+        hash = 23 * hash + (this.column != null ? this.column.hashCode() : 0);
+        return hash;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final AttributePartitionImpl other = (AttributePartitionImpl) obj;
+        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
+            return false;
+        }
+        return true;
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/AttributeRankingImpl.java

+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.Interpolator;
+import org.gephi.graph.api.Column;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Index;
+
+/**
+ *
+ * @author mbastian
+ */
+public class AttributeRankingImpl extends RankingImpl {
+
+    protected final Index index;
+    protected final Column column;
+
+    public AttributeRankingImpl(Column column, Index index, Interpolator interpolator) {
+        super(interpolator);
+        this.column = column;
+        this.index = index;
+    }
+
+    @Override
+    protected void refresh() {
+        min = index.getMinValue(column);
+        max = index.getMaxValue(column);
+    }
+
+    @Override
+    public Number getValue(Element element) {
+        return (Number) element.getAttribute(column);
+    }
+
+    @Override
+    public int hashCode() {
+        int hash = 3;
+        hash = 67 * hash + (this.column != null ? this.column.hashCode() : 0);
+        return hash;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final AttributeRankingImpl other = (AttributeRankingImpl) obj;
+        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
+            return false;
+        }
+        return true;
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/DegreeRankingImpl.java

+/*
+ Copyright 2008-2013 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2013 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2013 Gephi Consortium.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.Interpolator;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.Node;
+
+/**
+ *
+ * @author mbastian
+ */
+public class DegreeRankingImpl extends RankingImpl {
+
+    private final Graph graph;
+
+    public DegreeRankingImpl(Graph graph, Interpolator interpolator) {
+        super(interpolator);
+        this.graph = graph;
+    }
+
+    @Override
+    public Number getValue(Element element) {
+        return graph.getDegree((Node) element);
+    }
+
+    @Override
+    protected void refresh() {
+        if (graph.getNodeCount() > 0) {
+            int minV = Integer.MAX_VALUE;
+            int maxV = Integer.MIN_VALUE;
+            for (Node n : graph.getNodes()) {
+                int degree = graph.getDegree(n);
+                minV = Math.min(degree, minV);
+                maxV = Math.max(degree, maxV);
+            }
+            min = minV;
+            max = maxV;
+        }
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/EdgeTypePartitionImpl.java

+/*
+ Copyright 2008-2013 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2013 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2013 Gephi Consortium.
+ */
+package org.gephi.appearance;
+
+import java.util.Arrays;
+import org.gephi.graph.api.Column;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphModel;
+
+/**
+ *
+ * @author mbastian
+ */
+public class EdgeTypePartitionImpl extends PartitionImpl {
+
+    protected final Graph graph;
+    protected final GraphModel model;
+
+    public EdgeTypePartitionImpl(Graph graph) {
+        super();
+        this.graph = graph;
+        this.model = graph.getModel();
+    }
+
+    @Override
+    public Iterable getValues() {
+        return Arrays.asList(model.getEdgeTypeLabels());
+    }
+
+    @Override
+    public Object getValue(Element element) {
+        return ((Edge) element).getTypeLabel();
+    }
+
+    @Override
+    public int getElementCount() {
+        return graph.getEdgeCount();
+    }
+
+    @Override
+    public int count(Object value) {
+        return graph.getEdgeCount(model.getEdgeType(value));
+    }
+
+    @Override
+    public float percentage(Object value) {
+        int count = count(value);
+        return (float) count / graph.getEdgeCount();
+    }
+
+    @Override
+    public int size() {
+        return model.getEdgeTypeCount();
+    }
+
+    @Override
+    public Column getColumn() {
+        return null;
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/EdgeWeightRankingImpl.java

+/*
+ Copyright 2008-2013 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2013 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2013 Gephi Consortium.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.Interpolator;
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Graph;
+
+/**
+ *
+ * @author mbastian
+ */
+public class EdgeWeightRankingImpl extends RankingImpl {
+
+    private final Graph graph;
+
+    public EdgeWeightRankingImpl(Graph graph, Interpolator interpolator) {
+        super(interpolator);
+        this.graph = graph;
+    }
+
+    @Override
+    public Number getValue(Element element) {
+        return ((Edge) element).getWeight();
+    }
+
+    @Override
+    protected void refresh() {
+        if (graph.getEdgeCount() > 0) {
+            double minV = Double.MAX_VALUE;
+            double maxV = Double.MIN_VALUE;
+            for (Edge e : graph.getEdges()) {
+                double weight = e.getWeight();
+                minV = Math.min(weight, minV);
+                maxV = Math.max(weight, maxV);
+            }
+            min = minV;
+            max = maxV;
+        }
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/FunctionImpl.java

@@ -41,11 +41,7 @@
  */
 package org.gephi.appearance;
 
-import org.gephi.appearance.api.Partition;
-import org.gephi.appearance.api.PartitionFunction;
-import org.gephi.appearance.api.Ranking;
-import org.gephi.appearance.api.RankingFunction;
-import org.gephi.appearance.api.SimpleFunction;
+import org.gephi.appearance.api.Function;
 import org.gephi.appearance.spi.PartitionTransformer;
 import org.gephi.appearance.spi.RankingTransformer;
 import org.gephi.appearance.spi.SimpleTransformer;
@@ -53,35 +49,31 @@ import org.gephi.appearance.spi.Transformer;
 import org.gephi.appearance.spi.TransformerUI;
 import org.gephi.graph.api.Column;
 import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Graph;
 
 /**
  *
  * @author mbastian
  */
-public class FunctionImpl implements RankingFunction, PartitionFunction, SimpleFunction {
+public abstract class FunctionImpl implements Function {
 
-    protected final AppearanceModelImpl model;
+    protected final String id;
+    protected final String name;
+    protected final Graph graph;
     protected final Column column;
     protected final Transformer transformer;
     protected final TransformerUI transformerUI;
     protected final PartitionImpl partition;
     protected final RankingImpl ranking;
 
-    public FunctionImpl(AppearanceModelImpl model, Column column, Transformer transformer, TransformerUI transformerUI) {
-        this(model, column, transformer, transformerUI, null, null);
-    }
-
-    public FunctionImpl(AppearanceModelImpl model, Column column, Transformer transformer, TransformerUI transformerUI, RankingImpl ranking) {
-        this(model, column, transformer, transformerUI, null, ranking);
-    }
-
-    public FunctionImpl(AppearanceModelImpl model, Column column, Transformer transformer, TransformerUI transformerUI, PartitionImpl partition) {
-        this(model, column, transformer, transformerUI, partition, null);
-    }
-
-    public FunctionImpl(AppearanceModelImpl model, Column column, Transformer transformer, TransformerUI transformerUI, PartitionImpl partition, RankingImpl ranking) {
-        this.model = model;
+    protected FunctionImpl(String id, String name, Graph graph, Column column, Transformer transformer, TransformerUI transformerUI, PartitionImpl partition, RankingImpl ranking) {
+        if (id == null) {
+            throw new NullPointerException("The id can't be null");
+        }
+        this.id = id;
+        this.name = name;
         this.column = column;
+        this.graph = graph;
         try {
             this.transformer = transformer.getClass().newInstance();
         } catch (Exception ex) {
@@ -97,23 +89,14 @@ public class FunctionImpl implements RankingFunction, PartitionFunction, SimpleF
         if (isSimple()) {
             ((SimpleTransformer) transformer).transform(element);
         } else if (isRanking()) {
-            Number val = (Number) element.getAttribute(column);
+            Number val = ranking.getValue(element);
             ((RankingTransformer) transformer).transform(element, ranking, val);
         } else if (isPartition()) {
-            Object val = element.getAttribute(column);
+            Object val = partition.getValue(element);
             ((PartitionTransformer) transformer).transform(element, partition, val);
         }
     }
 
-    @Override
-    public Column getColumn() {
-        return column;
-    }
-
-    public AppearanceModelImpl getModel() {
-        return model;
-    }
-
     @Override
     public Transformer getTransformer() {
         return transformer;
@@ -126,7 +109,7 @@ public class FunctionImpl implements RankingFunction, PartitionFunction, SimpleF
 
     @Override
     public boolean isSimple() {
-        return column == null;
+        return ranking == null && partition == null;
     }
 
     @Override
@@ -145,39 +128,30 @@ public class FunctionImpl implements RankingFunction, PartitionFunction, SimpleF
     }
 
     @Override
-    public Partition getPartition() {
-        return partition;
-    }
-
-    @Override
-    public Ranking getRanking() {
-        return ranking;
+    public Graph getGraph() {
+        return graph;
     }
 
     @Override
     public String toString() {
-        if (column != null) {
-            if (column.getTitle() != null) {
-                return column.getTitle();
-            } else {
-                return column.getId();
-            }
+        if (name != null) {
+            return name;
         }
-        return super.toString();
+        return id;
     }
 
     @Override
     public int hashCode() {
         int hash = 5;
-        hash = 47 * hash + (this.column != null ? this.column.hashCode() : 0);
-        hash = 47 * hash + (this.transformer != null ? this.transformer.hashCode() : 0);
-        hash = 47 * hash + (this.partition != null ? this.partition.hashCode() : 0);
-        hash = 47 * hash + (this.ranking != null ? this.ranking.hashCode() : 0);
+        hash = 97 * hash + (this.id != null ? this.id.hashCode() : 0);
         return hash;
     }
 
     @Override
     public boolean equals(Object obj) {
+        if (this == obj) {
+            return true;
+        }
         if (obj == null) {
             return false;
         }
@@ -185,16 +159,7 @@ public class FunctionImpl implements RankingFunction, PartitionFunction, SimpleF
             return false;
         }
         final FunctionImpl other = (FunctionImpl) obj;
-        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
-            return false;
-        }
-        if (this.transformer != other.transformer && (this.transformer == null || !this.transformer.equals(other.transformer))) {
-            return false;
-        }
-        if (this.partition != other.partition && (this.partition == null || !this.partition.equals(other.partition))) {
-            return false;
-        }
-        if (this.ranking != other.ranking && (this.ranking == null || !this.ranking.equals(other.ranking))) {
+        if ((this.id == null) ? (other.id != null) : !this.id.equals(other.id)) {
             return false;
         }
         return true;

modules/AppearanceAPI/src/main/java/org/gephi/appearance/GraphFunctionImpl.java

+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.GraphFunction;
+import org.gephi.appearance.api.Partition;
+import org.gephi.appearance.api.PartitionFunction;
+import org.gephi.appearance.api.Ranking;
+import org.gephi.appearance.api.RankingFunction;
+import org.gephi.appearance.spi.Transformer;
+import org.gephi.appearance.spi.TransformerUI;
+import org.gephi.graph.api.Graph;
+
+/**
+ *
+ * @author mbastian
+ */
+public class GraphFunctionImpl extends FunctionImpl implements GraphFunction, RankingFunction, PartitionFunction {
+
+    public GraphFunctionImpl(String id, String name, Graph graph, Transformer transformer, TransformerUI transformerUI, RankingImpl ranking) {
+        super(id, name, graph, null, transformer, transformerUI, null, ranking);
+    }
+
+    public GraphFunctionImpl(String id, String name, Graph graph, Transformer transformer, TransformerUI transformerUI, PartitionImpl partition) {
+        super(id, name, graph, null, transformer, transformerUI, partition, null);
+    }
+
+    @Override
+    public PartitionImpl getPartition() {
+        return partition;
+    }
+
+    @Override
+    public RankingImpl getRanking() {
+        return ranking;
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/InDegreeRankingImpl.java

+/*
+ Copyright 2008-2013 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2013 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2013 Gephi Consortium.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.Interpolator;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Node;
+
+/**
+ *
+ * @author mbastian
+ */
+public class InDegreeRankingImpl extends RankingImpl {
+
+    private final DirectedGraph graph;
+
+    public InDegreeRankingImpl(DirectedGraph graph, Interpolator interpolator) {
+        super(interpolator);
+        this.graph = graph;
+    }
+
+    @Override
+    public Number getValue(Element element) {
+        return graph.getInDegree((Node) element);
+    }
+
+    @Override
+    protected void refresh() {
+        if (graph.getNodeCount() > 0) {
+            int minV = Integer.MAX_VALUE;
+            int maxV = Integer.MIN_VALUE;
+            for (Node n : graph.getNodes()) {
+                int degree = graph.getInDegree(n);
+                minV = Math.min(degree, minV);
+                maxV = Math.max(degree, maxV);
+            }
+            min = minV;
+            max = maxV;
+        }
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/OutDegreeRankingImpl.java

+/*
+ Copyright 2008-2013 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2013 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2013 Gephi Consortium.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.Interpolator;
+import org.gephi.graph.api.DirectedGraph;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Node;
+
+/**
+ *
+ * @author mbastian
+ */
+public class OutDegreeRankingImpl extends RankingImpl {
+
+    private final DirectedGraph graph;
+
+    public OutDegreeRankingImpl(DirectedGraph graph, Interpolator interpolator) {
+        super(interpolator);
+        this.graph = graph;
+    }
+
+    @Override
+    public Number getValue(Element element) {
+        return graph.getOutDegree((Node) element);
+    }
+
+    @Override
+    protected void refresh() {
+        if (graph.getNodeCount() > 0) {
+            int minV = Integer.MAX_VALUE;
+            int maxV = Integer.MIN_VALUE;
+            for (Node n : graph.getNodes()) {
+                int degree = graph.getOutDegree(n);
+                minV = Math.min(degree, minV);
+                maxV = Math.max(degree, maxV);
+            }
+            min = minV;
+            max = maxV;
+        }
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/PartitionImpl.java

@@ -45,40 +45,19 @@ import java.awt.Color;
 import java.util.HashMap;
 import java.util.Map;
 import org.gephi.appearance.api.Partition;
-import org.gephi.graph.api.Column;
-import org.gephi.graph.api.Index;
 
 /**
  *
  * @author mbastian
  */
-public class PartitionImpl implements Partition {
+public abstract class PartitionImpl implements Partition {
 
-    private final Index index;
-    private final Column column;
-    private final Map<Object, Color> colorMap;
+    protected final Map<Object, Color> colorMap;
 
-    public PartitionImpl(Column column, Index index) {
-        this.column = column;
-        this.index = index;
+    protected PartitionImpl() {
         this.colorMap = new HashMap<Object, Color>();
     }
 
-    @Override
-    public Iterable getValues() {
-        return index.values(column);
-    }
-
-    @Override
-    public int getElementCount() {
-        return index.countElements(column);
-    }
-
-    @Override
-    public int count(Object value) {
-        return index.count(column, value);
-    }
-
     @Override
     public Color getColor(Object value) {
         return colorMap.get(value);
@@ -89,41 +68,4 @@ public class PartitionImpl implements Partition {
         colorMap.put(value, color);
     }
 
-    @Override
-    public float percentage(Object value) {
-        int count = index.count(column, value);
-        return (float) count / index.countElements(column);
-    }
-
-    @Override
-    public int size() {
-        return index.countValues(column);
-    }
-
-    @Override
-    public Column getColumn() {
-        return column;
-    }
-
-    @Override
-    public int hashCode() {
-        int hash = 3;
-        hash = 23 * hash + (this.column != null ? this.column.hashCode() : 0);
-        return hash;
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-        if (obj == null) {
-            return false;
-        }
-        if (getClass() != obj.getClass()) {
-            return false;
-        }
-        final PartitionImpl other = (PartitionImpl) obj;
-        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
-            return false;
-        }
-        return true;
-    }
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/RankingImpl.java

@@ -43,33 +43,31 @@ package org.gephi.appearance;
 
 import org.gephi.appearance.api.Interpolator;
 import org.gephi.appearance.api.Ranking;
-import org.gephi.graph.api.Column;
-import org.gephi.graph.api.Index;
 
 /**
  *
  * @author mbastian
  */
-public class RankingImpl implements Ranking {
+public abstract class RankingImpl implements Ranking {
 
-    private final Index index;
-    private final Column column;
-    private Interpolator interpolator;
+    protected Interpolator interpolator;
+    protected Number min;
+    protected Number max;
 
-    public RankingImpl(Column column, Index index, Interpolator interpolator) {
-        this.column = column;
-        this.index = index;
+    protected RankingImpl(Interpolator interpolator) {
         this.interpolator = interpolator;
     }
 
+    protected abstract void refresh();
+
     @Override
     public Number getMinValue() {
-        return index.getMinValue(column);
+        return min;
     }
 
     @Override
     public Number getMaxValue() {
-        return index.getMaxValue(column);
+        return max;
     }
 
     @Override
@@ -84,29 +82,7 @@ public class RankingImpl implements Ranking {
 
     @Override
     public float normalize(Number value) {
-        float normalizedValue = (float) (value.doubleValue() - getMinValue().doubleValue()) / (float) (getMaxValue().doubleValue() - getMinValue().doubleValue());
+        float normalizedValue = (float) (value.doubleValue() - min.doubleValue()) / (float) (max.doubleValue() - min.doubleValue());
         return interpolator.interpolate(normalizedValue);
     }
-
-    @Override
-    public int hashCode() {
-        int hash = 3;
-        hash = 67 * hash + (this.column != null ? this.column.hashCode() : 0);
-        return hash;
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-        if (obj == null) {
-            return false;
-        }
-        if (getClass() != obj.getClass()) {
-            return false;
-        }
-        final RankingImpl other = (RankingImpl) obj;
-        if (this.column != other.column && (this.column == null || !this.column.equals(other.column))) {
-            return false;
-        }
-        return true;
-    }
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/SimpleFunctionImpl.java

+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.gephi.appearance;
+
+import org.gephi.appearance.api.SimpleFunction;
+import org.gephi.appearance.spi.Transformer;
+import org.gephi.appearance.spi.TransformerUI;
+import org.gephi.graph.api.Graph;
+
+/**
+ *
+ * @author mbastian
+ */
+public class SimpleFunctionImpl extends FunctionImpl implements SimpleFunction {
+
+    public SimpleFunctionImpl(String id, Graph graph, Transformer transformer, TransformerUI transformerUI) {
+        super(id, null, graph, null, transformer, transformerUI, null, null);
+    }
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/AppearanceModel.java

@@ -41,6 +41,7 @@
  */
 package org.gephi.appearance.api;
 
+import org.gephi.graph.api.Graph;
 import org.gephi.project.api.Workspace;
 
 /**
@@ -57,18 +58,16 @@ public interface AppearanceModel {
     public Workspace getWorkspace();
 
     /**
-     * Returns
-     * <code>true</code> if rankings are using the currently visible graph as a
-     * scale. If
-     * <code>false</code> the complete graph is used to determine minimum and
-     * maximum values, the ranking scale.
+     * Returns <code>true</code> if rankings are using the currently visible
+     * graph as a scale. If <code>false</code> the complete graph is used to
+     * determine minimum and maximum values, the ranking scale.
      *
      * @return <code>true</code> if using a local scale, <code>false</code> if
      * global scale
      */
     public boolean isLocalScale();
 
-    public Function[] getNodeFunctions();
+    public Function[] getNodeFunctions(Graph graph);
 
-    public Function[] getEdgeFunctions();
+    public Function[] getEdgeFunctions(Graph graph);
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/Function.java

@@ -44,6 +44,7 @@ package org.gephi.appearance.api;
 import org.gephi.appearance.spi.Transformer;
 import org.gephi.appearance.spi.TransformerUI;
 import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Graph;
 
 /**
  *
@@ -64,4 +65,6 @@ public interface Function {
     public boolean isRanking();
 
     public boolean isPartition();
+
+    public Graph getGraph();
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/GraphFunction.java

+/*
+ Copyright 2008-2013 Gephi
+ Authors : Mathieu Bastian <mathieu.bastian@gephi.org>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2013 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2013 Gephi Consortium.
+ */
+package org.gephi.appearance.api;
+
+/**
+ *
+ * @author mbastian
+ */
+public interface GraphFunction extends Function {
+
+}

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/Interpolator.java

@@ -52,9 +52,7 @@ import java.awt.geom.Point2D;
 public abstract class Interpolator {
 
     /**
-     * Linear interpolation
-     * <code>x = interpolate(x)
-     * <code>
+     * Linear interpolation <code>x = interpolate(x)</code>
      */
     public static final Interpolator LINEAR = new Interpolator() {
         @Override

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/Partition.java

@@ -43,6 +43,7 @@ package org.gephi.appearance.api;
 
 import java.awt.Color;
 import org.gephi.graph.api.Column;
+import org.gephi.graph.api.Element;
 
 /**
  *
@@ -56,6 +57,8 @@ public interface Partition {
 
     public int count(Object value);
 
+    public Object getValue(Element element);
+
     public Color getColor(Object value);
 
     public void setColor(Object value, Color color);

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/PartitionFunction.java

@@ -45,7 +45,7 @@ package org.gephi.appearance.api;
  *
  * @author mbastian
  */
-public interface PartitionFunction extends AttributeFunction {
+public interface PartitionFunction extends Function {
 
     public Partition getPartition();
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/Ranking.java

@@ -41,6 +41,8 @@
  */
 package org.gephi.appearance.api;
 
+import org.gephi.graph.api.Element;
+
 /**
  *
  * @author mbastian
@@ -55,5 +57,7 @@ public interface Ranking {
 
     public void setInterpolator(Interpolator interpolator);
 
+    public Number getValue(Element element);
+
     public float normalize(Number value);
 }

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/RankingFunction.java

@@ -45,7 +45,7 @@ package org.gephi.appearance.api;
  *
  * @author mbastian
  */
-public interface RankingFunction extends AttributeFunction {
+public interface RankingFunction extends Function {
 
     public Ranking getRanking();
 }

modules/AppearanceAPI/src/main/resources/org/gephi/appearance/Bundle.properties

+NodeGraphFunction.Degree.name = Degree
+NodeGraphFunction.InDegree.name = In-Degree
+NodeGraphFunction.OutDegree.name = Out-Degree
+EdgeGraphFunction.Weight.name = Weight
+EdgeGraphFunction.Type.name = Type

modules/DesktopAppearance/src/main/java/org/gephi/desktop/appearance/AppearanceUIModel.java

@@ -56,6 +56,9 @@ import org.gephi.appearance.spi.Transformer;
 import org.gephi.appearance.spi.TransformerCategory;
 import org.gephi.appearance.spi.TransformerUI;
 import static org.gephi.desktop.appearance.AppearanceUIController.ELEMENT_CLASSES;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphController;
+import org.openide.util.Lookup;
 
 /**
  *
@@ -65,6 +68,7 @@ public class AppearanceUIModel {
 
     protected final AppearanceUIController controller;
     protected final AppearanceModel appearanceModel;
+    protected final GraphController graphController;
     protected final Map<String, Map<TransformerCategory, TransformerUI>> selectedTransformerUI;
     protected final Map<String, Map<TransformerUI, Function>> selectedFunction;
     protected final Map<String, TransformerCategory> selectedCategory;
@@ -75,6 +79,7 @@ public class AppearanceUIModel {
     public AppearanceUIModel(AppearanceUIController controller, AppearanceModel model) {
         this.controller = controller;
         this.appearanceModel = model;
+        this.graphController = Lookup.getDefault().lookup(GraphController.class);
 
         //Init maps
         selectedCategory = new HashMap<String, TransformerCategory>();
@@ -90,8 +95,9 @@ public class AppearanceUIModel {
     }
 
     private void initSelectedTransformerUIs(String elementClass) {
+        Graph graph = graphController.getGraphModel(appearanceModel.getWorkspace()).getGraph();
         Map<TransformerCategory, TransformerUI> newMap = new HashMap<TransformerCategory, TransformerUI>();
-        for (Function func : elementClass.equals(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions() : appearanceModel.getEdgeFunctions()) {
+        for (Function func : elementClass.equals(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions(graph) : appearanceModel.getEdgeFunctions(graph)) {
             TransformerUI ui = func.getUI();
             if (ui != null) {
                 TransformerCategory cat = ui.getCategory();
@@ -111,7 +117,8 @@ public class AppearanceUIModel {
 
     private void refreshSelectedFunctions(String elementClass) {
         Set<Function> functionSet = new HashSet<Function>();
-        for (Function func : elementClass.equals(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions() : appearanceModel.getEdgeFunctions()) {
+        Graph graph = graphController.getGraphModel(appearanceModel.getWorkspace()).getGraph();
+        for (Function func : elementClass.equals(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions(graph) : appearanceModel.getEdgeFunctions(graph)) {
             TransformerUI ui = func.getUI();
             if (ui != null) {
                 functionSet.add(func);
@@ -127,9 +134,10 @@ public class AppearanceUIModel {
     }
 
     public boolean refreshSelectedFunction() {
+        Graph graph = graphController.getGraphModel(appearanceModel.getWorkspace()).getGraph();
         Function sFunction = getSelectedFunction();
         if (sFunction != null && sFunction.isAttribute()) {
-            for (Function func : getSelectedElementClass().equals(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions() : appearanceModel.getEdgeFunctions()) {
+            for (Function func : getSelectedElementClass().equals(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions(graph) : appearanceModel.getEdgeFunctions(graph)) {
                 if (func.equals(sFunction)) {
                     return false;
                 }
@@ -170,8 +178,9 @@ public class AppearanceUIModel {
     }
 
     public Collection<Function> getFunctions() {
+        Graph graph = graphController.getGraphModel(appearanceModel.getWorkspace()).getGraph();
         List<Function> functions = new ArrayList<Function>();
-        for (Function func : selectedElementClass.equalsIgnoreCase(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions() : appearanceModel.getEdgeFunctions()) {
+        for (Function func : selectedElementClass.equalsIgnoreCase(AppearanceUIController.NODE_ELEMENT) ? appearanceModel.getNodeFunctions(graph) : appearanceModel.getEdgeFunctions(graph)) {
             TransformerUI ui = func.getUI();
             if (ui != null && ui.getDisplayName().equals(getSelectedTransformerUI().getDisplayName())) {
                 if (ui.getCategory().equals(selectedCategory.get(selectedElementClass))) {