Minor debug with graph visible

modules/DesktopContext/src/main/java/org/gephi/desktop/context/ContextPanel.java

@@ -97,14 +97,15 @@ public class ContextPanel extends javax.swing.JPanel {
 
         @Override
         public void run() {
-            Graph visibleGraph = model.getGraph(model.getVisibleView());
-            Graph fullGraph = model.getGraph(model.getVisibleView());
+            Graph visibleGraph = model.getGraphVisible();
+            Graph fullGraph = model.getGraph();
             final int nodesFull = fullGraph.getNodeCount();
             final int nodesVisible = visibleGraph.getNodeCount();
             final int edgesFull = fullGraph.getEdgeCount();
             final int edgesVisible = visibleGraph.getEdgeCount();
             final GraphType graphType = model.isDirected() ? GraphType.DIRECTED : model.isUndirected() ? GraphType.UNDIRECTED : GraphType.MIXED;
             SwingUtilities.invokeLater(new Runnable() {
+                @Override
                 public void run() {
                     String visible = NbBundle.getMessage(ContextPanel.class, "ContextPanel.visible");
                     String nodeText = String.valueOf(nodesVisible);

modules/DesktopContext/src/main/java/org/gephi/desktop/context/ContextRefreshThread.java

@@ -69,7 +69,7 @@ public class ContextRefreshThread extends TimerTask {
 
     private void initObserver() {
         if (observer == null || observer.isDestroyed()) {
-            observer = graphModel.getGraphObserver(graphModel.getGraph(graphModel.getVisibleView()), false);
+            observer = graphModel.getGraphObserver(graphModel.getGraphVisible(), false);
         }
     }
 

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/force/yifanHu/YifanHuLayout.java

@@ -228,7 +228,7 @@ public class YifanHuLayout extends AbstractLayout implements Layout {
         if (graphModel == null) {
             return;
         }
-        graph = graphModel.getGraph(graphModel.getVisibleView());
+        graph = graphModel.getGraphVisible();
         energy = Float.POSITIVE_INFINITY;
         for (Node n : graph.getNodes()) {
             n.setLayoutData(new ForceVector());
@@ -247,7 +247,7 @@ public class YifanHuLayout extends AbstractLayout implements Layout {
 
     @Override
     public void goAlgo() {
-        graph = graphModel.getGraph(graphModel.getVisibleView());
+        graph = graphModel.getGraphVisible();
         graph.readLock();
         Node[] nodes = graph.getNodes().toArray();
         for (Node n : nodes) {

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/forceAtlas/ForceAtlasLayout.java

@@ -46,10 +46,9 @@ import java.util.List;
 import org.gephi.graph.api.Edge;
 import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.Node;
-
 import org.gephi.layout.plugin.AbstractLayout;
-import org.gephi.layout.plugin.ForceVectorUtils;
 import org.gephi.layout.plugin.ForceVectorNodeLayoutData;
+import org.gephi.layout.plugin.ForceVectorUtils;
 import org.gephi.layout.spi.Layout;
 import org.gephi.layout.spi.LayoutBuilder;
 import org.gephi.layout.spi.LayoutProperty;
@@ -103,7 +102,7 @@ public class ForceAtlasLayout extends AbstractLayout implements Layout {
 
     @Override
     public void goAlgo() {
-        this.graph = graphModel.getGraph(graphModel.getVisibleView());
+        this.graph = graphModel.getGraphVisible();
         graph.readLock();
         Node[] nodes = graph.getNodes().toArray();
         Edge[] edges = graph.getEdges().toArray();

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/forceAtlas2/ForceAtlas2.java

@@ -95,7 +95,7 @@ public class ForceAtlas2 implements Layout {
     public void initAlgo() {
         speed = 1.;
 
-        graph = graphModel.getGraph(graphModel.getVisibleView());
+        graph = graphModel.getGraphVisible();
 
         graph.readLock();
         Node[] nodes = graph.getNodes().toArray();
@@ -124,7 +124,7 @@ public class ForceAtlas2 implements Layout {
         if (graphModel == null) {
             return;
         }
-        graph = graphModel.getGraph(graphModel.getVisibleView());
+        graph = graphModel.getGraphVisible();
 
         graph.readLock();
         Node[] nodes = graph.getNodes().toArray();
@@ -384,7 +384,7 @@ public class ForceAtlas2 implements Layout {
         int nodesCount = 0;
 
         if (graphModel != null) {
-            nodesCount = graphModel.getGraph(graphModel.getVisibleView()).getNodeCount();
+            nodesCount = graphModel.getGraphVisible().getNodeCount();
         }
 
         // Tuning

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/fruchterman/FruchtermanReingold.java

@@ -85,7 +85,7 @@ public class FruchtermanReingold extends AbstractLayout implements Layout {
 
     @Override
     public void goAlgo() {
-        this.graph = graphModel.getGraph(graphModel.getVisibleView());
+        this.graph = graphModel.getGraphVisible();
         graph.readLock();
         Node[] nodes = graph.getNodes().toArray();
         Edge[] edges = graph.getEdges().toArray();

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/labelAdjust/LabelAdjust.java

@@ -87,7 +87,7 @@ public class LabelAdjust extends AbstractLayout implements Layout {
 
     @Override
     public void goAlgo() {
-        this.graph = graphModel.getGraph(graphModel.getVisibleView());
+        this.graph = graphModel.getGraphVisible();
         graph.readLock();
         Node[] nodes = graph.getNodes().toArray();
 

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/random/RandomLayout.java

@@ -76,7 +76,7 @@ public class RandomLayout extends AbstractLayout implements Layout {
 
     @Override
     public void goAlgo() {
-        graph = graphModel.getGraph(graphModel.getVisibleView());
+        graph = graphModel.getGraphVisible();
         for (Node n : graph.getNodes()) {
             n.setX((float) (-size / 2 + size * random.nextDouble()));
             n.setY((float) (-size / 2 + size * random.nextDouble()));

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/rotate/RotateLayout.java

@@ -73,7 +73,7 @@ public class RotateLayout extends AbstractLayout implements Layout {
 
     @Override
     public void goAlgo() {
-        graph = graphModel.getGraph(graphModel.getVisibleView());
+        graph = graphModel.getGraphVisible();
         double sin = Math.sin(getAngle() * Math.PI / 180);
         double cos = Math.cos(getAngle() * Math.PI / 180);
         double px = 0f;

modules/LayoutPlugin/src/main/java/org/gephi/layout/plugin/scale/ScaleLayout.java

@@ -73,7 +73,7 @@ public class ScaleLayout extends AbstractLayout implements Layout {
 
     @Override
     public void goAlgo() {
-        graph = graphModel.getGraph(graphModel.getVisibleView());
+        graph = graphModel.getGraphVisible();
         double xMean = 0, yMean = 0;
         for (Node n : graph.getNodes()) {
             xMean += n.x();

modules/VisualizationImpl/src/main/java/org/gephi/visualization/component/ActionsToolbar.java

@@ -113,7 +113,7 @@ public class ActionsToolbar extends JToolBar {
                 color = resetColorButton.getColor();
                 GraphController gc = Lookup.getDefault().lookup(GraphController.class);
                 GraphModel gm = gc.getGraphModel();
-                Graph graph = gm.getGraph(gm.getVisibleView());
+                Graph graph = gm.getGraphVisible();
                 for (Node n : graph.getNodes()) {
                     n.setR(color.getRed() / 255f);
                     n.setG(color.getGreen() / 255f);
@@ -139,7 +139,7 @@ public class ActionsToolbar extends JToolBar {
             public void actionPerformed(ActionEvent e) {
                 GraphController gc = Lookup.getDefault().lookup(GraphController.class);
                 GraphModel gm = gc.getGraphModel();
-                Graph graph = gm.getGraph(gm.getVisibleView());
+                Graph graph = gm.getGraphVisible();
                 for (Node n : graph.getNodes()) {
                     n.setSize(size);
                 }
@@ -171,7 +171,7 @@ public class ActionsToolbar extends JToolBar {
             public void actionPerformed(ActionEvent evt) {
                 GraphController gc = Lookup.getDefault().lookup(GraphController.class);
                 GraphModel gm = gc.getGraphModel();
-                Graph graph = gm.getGraph(gm.getVisibleView());
+                Graph graph = gm.getGraphVisible();
                 for (Node n : graph.getNodes().toArray()) {
                     n.getTextProperties().setColor(null);
                 }
@@ -191,7 +191,7 @@ public class ActionsToolbar extends JToolBar {
             public void actionPerformed(ActionEvent evt) {
                 GraphController gc = Lookup.getDefault().lookup(GraphController.class);
                 GraphModel gm = gc.getGraphModel();
-                Graph graph = gm.getGraph(gm.getVisibleView());
+                Graph graph = gm.getGraphVisible();
                 for (Node n : graph.getNodes()) {
                     n.getTextProperties().setVisible(true);
                 }
@@ -211,7 +211,7 @@ public class ActionsToolbar extends JToolBar {
             public void actionPerformed(ActionEvent e) {
                 GraphController gc = Lookup.getDefault().lookup(GraphController.class);
                 GraphModel gm = gc.getGraphModel();
-                Graph graph = gm.getGraph(gm.getVisibleView());
+                Graph graph = gm.getGraphVisible();
                 for (Node n : graph.getNodes()) {
                     n.getTextProperties().setSize(1f);
                 }