first release clean up

src/org/pathvisio/complexviz/Activator.java

@@ -22,7 +22,6 @@
  */
 import org.osgi.framework.BundleActivator;
 import org.osgi.framework.BundleContext;
-import org.pathvisio.complexviz.plugins.ComplexVizPlugin;
 import org.pathvisio.desktop.plugin.Plugin;
 
 public class Activator implements BundleActivator {

src/org/pathvisio/complexviz/plugins/ComplexVizPlugin.java → src/org/pathvisio/complexviz/ComplexVizPlugin.java

@@ -1,4 +1,4 @@
-package org.pathvisio.complexviz.plugins;
+package org.pathvisio.complexviz;
 
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -20,6 +20,9 @@
 import org.bridgedb.Xref;
 import org.pathvisio.complexviz.gui.ComplexVizDialog;
 import org.pathvisio.complexviz.gui.ComplexVizTab;
+import org.pathvisio.complexviz.plugins.ColourComplexBorder;
+import org.pathvisio.complexviz.plugins.VisualisePercentScores;
+import org.pathvisio.complexviz.plugins.ComplexLabel;
 import org.pathvisio.core.ApplicationEvent;
 import org.pathvisio.core.Engine.ApplicationEventListener;
 import org.pathvisio.core.model.Pathway;
@@ -304,22 +307,22 @@ public void init(PvDesktop aDesktop) {
 		final VisualizationMethodRegistry reg = aDesktop
 				.getVisualizationManager().getVisualizationMethodRegistry();
 
-		reg.registerComplexMethod(ColourComplexes.class.toString(),
+		reg.registerComplexMethod(VisualisePercentScores.class.toString(),
 				new VisualizationMethodProvider() {
 					@Override
 					public VisualizationMethod create() {
-						return new ColourComplexes(desktop.getSwingEngine(), desktop
+						return new VisualisePercentScores(desktop.getSwingEngine(), desktop
 								.getGexManager(), desktop
 								.getVisualizationManager().getColorSetManager(), desktop.getVisualizationManager());
 					}
 				});
 
 		reg.registerComplexMethod(
-				ColourComplexComponentBorder.class.toString(),
+				ColourComplexBorder.class.toString(),
 				new VisualizationMethodProvider() {
 					@Override
 					public VisualizationMethod create() {
-						return new ColourComplexComponentBorder(desktop,
+						return new ColourComplexBorder(desktop,
 								desktop.getVisualizationManager()
 										.getColorSetManager());
 					}

src/org/pathvisio/complexviz/gui/ColorChooserDialog.java

@@ -19,15 +19,15 @@
 import javax.swing.table.TableColumn;
 import javax.swing.table.TableModel;
 
-import org.pathvisio.complexviz.plugins.ColorTableModel;
+import org.pathvisio.complexviz.plugins.BorderColorTableModel;
 
 public class ColorChooserDialog {
 
 	public JPanel colorChooserPanel() {
 		final JPanel newpanel = new JPanel();
 		final BorderLayout layout = new BorderLayout();
 		newpanel.setLayout(layout);
-		final TableModel model = new ColorTableModel();
+		final TableModel model = new BorderColorTableModel();
 		final JTable table = new JTable(model);
 		final TableColumn column = table.getColumnModel().getColumn(1);
 		final TableCellEditor editor = new ColorChooserEditor();

src/org/pathvisio/complexviz/plugins/ColourComplexesPanel.java → src/org/pathvisio/complexviz/gui/ColourComplexesPanel.java

@@ -14,7 +14,7 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 //
-package org.pathvisio.complexviz.plugins;
+package org.pathvisio.complexviz.gui;
 
 import java.awt.CardLayout;
 import java.awt.Color;
@@ -50,7 +50,7 @@
 import javax.swing.event.DocumentListener;
 
 import org.jdom.Element;
-import org.pathvisio.complexviz.gui.ComplexLegendPanel;
+import org.pathvisio.complexviz.plugins.VisualisePercentScores;
 import org.pathvisio.core.util.Resources;
 import org.pathvisio.desktop.util.TextFieldUtils;
 import org.pathvisio.desktop.visualization.ColorGradient;
@@ -64,13 +64,13 @@
 import com.jgoodies.forms.layout.FormLayout;
 
 /**
- * Configuration panel for the ColourComplexes visualization method
+ * Configuration panel for the VisualisePercentScores visualization method
  * 
  * @author anwesha
  */
 public class ColourComplexesPanel extends JPanel implements ActionListener {
 
-	private ComplexLegendPanel lp;
+//	private ComplexLegendPanel lp;
 
 	private class CriterionPanel extends JPanel {
 		/**
@@ -112,7 +112,7 @@ public void removeUpdate(final DocumentEvent e) {
 			});
 
 			add(txtExpr, cc.xyw(2, 4, 3));
-			final String[] OPERANDS = { "=", "<", ">", "<=", ">=", "<>" };
+			final String[] OPERANDS = { "<", ">", "<=", ">=","==", "!=" };
 			final JList lstOperators = new JList(OPERANDS);
 			add(new JScrollPane(lstOperators), cc.xy(2, 6));
 
@@ -315,8 +315,7 @@ public Rule() {
 
 			/**
 			 * Action Listeners for buttons, combo boxes and text boxes to set
-			 * colours, linethicknesses and values to be used for the
-			 * visualization
+			 * colours for the visualization
 			 */
 			rulecolourButton.addActionListener(new ActionListener() {
 				@Override
@@ -395,7 +394,7 @@ public void actionPerformed(ActionEvent e) {
 	static final Cursor COLOR_PICK_CURS = Toolkit.getDefaultToolkit()
 			.createCustomCursor(COLOR_PICK_ICON.getImage(), new Point(4, 19),
 					"Color picker");
-	private final ColourComplexes method;
+	private final VisualisePercentScores method;
 	private final Rule rule;
 	private final Gradient gradient;
 	private final CardLayout cardLayout;
@@ -414,7 +413,7 @@ public void actionPerformed(ActionEvent e) {
 	private boolean useRule = false;
 
 
-	public ColourComplexesPanel(final ColourComplexes method, ColorSetManager csm) {
+	public ColourComplexesPanel(final VisualisePercentScores method, ColorSetManager csm) {
 		this.method = method;
 		this.csm = csm;
 //		lp = new ComplexLegendPanel();

src/org/pathvisio/complexviz/plugins/ComplexColorRulePanel.java → src/org/pathvisio/complexviz/gui/ComplexColorRulePanel.java

@@ -1,7 +1,7 @@
 /**
  * 
  */
-package org.pathvisio.complexviz.plugins;
+package org.pathvisio.complexviz.gui;
 
 import java.awt.Color;
 import java.awt.event.ActionEvent;