updated imports

1. Some classes were moved in libGPML- updated import name 2. Added Static Property get methods to libGPML
PathVisio · Nov 29, 2021 · b9b46bd · b9b46bd
1 parent e88aca5
commit b9b46bd
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Showing 42 changed files with 892 additions and 762 deletions.
diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/Engine.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/Engine.java
@@ -31,7 +31,7 @@
 import javax.swing.SwingUtilities;
 
 import org.pathvisio.debug.Logger;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.model.PathwayModel;
 import org.pathvisio.event.PathwayModelExporter;
 import org.pathvisio.event.PathwayModelImporter;

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/data/GdbManager.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/data/GdbManager.java
@@ -39,11 +39,12 @@
  * This gene database could be a SimpleGdb, DoubleGdb or aggregateGdb or
  * otherwise.
  *
- * This class is not needed in headless mode. 
+ * This class is not needed in headless mode.
  * 
  * @author unknown
  */
 public class GdbManager extends AbstractListModel {
+
 	private final IDMapperStack currentGdb = new IDMapperStack();
 	private IDMapper metabolites;
 	private IDMapper genes;

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/gui/PathwayTransferable.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/gui/PathwayTransferable.java
@@ -38,8 +38,8 @@
 import org.jdom2.output.XMLOutputter;
 import org.pathvisio.core.Engine;
 import org.pathvisio.debug.Logger;
-import org.pathvisio.io.ConverterException;
-import org.pathvisio.io.GpmlFormat;
+import org.pathvisio.model.ConverterException;
+import org.pathvisio.model.GpmlFormat;
 import org.pathvisio.model.PathwayModel;
 import org.pathvisio.model.PathwayObject;
 import org.pathvisio.model.Pathway;

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/model/BatikImageExporter.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/model/BatikImageExporter.java
@@ -38,7 +38,7 @@
 import org.pathvisio.core.preferences.GlobalPreference;
 import org.pathvisio.core.preferences.PreferenceManager;
 import org.pathvisio.core.view.model.VPathwayModel;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.model.PathwayModel;
 import org.w3c.dom.DOMImplementation;
 import org.w3c.dom.Document;

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/model/DataNodeListExporter.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/model/DataNodeListExporter.java
@@ -31,7 +31,7 @@
 import org.bridgedb.Xref;
 import org.pathvisio.core.data.GdbManager;
 import org.pathvisio.event.PathwayModelExporter;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.model.DataNode;
 import org.pathvisio.model.PathwayModel;
 

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/model/EUGeneExporter.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/model/EUGeneExporter.java
@@ -29,7 +29,7 @@
 import org.bridgedb.Xref;
 import org.pathvisio.debug.Logger;
 import org.pathvisio.event.PathwayModelExporter;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.model.DataNode;
 import org.pathvisio.model.PathwayModel;
 import org.pathvisio.model.PathwayObject;

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/model/ImageExporter.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/model/ImageExporter.java
@@ -21,7 +21,7 @@
 import java.util.List;
 
 import org.pathvisio.event.PathwayModelExporter;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.model.PathwayModel;
 
 /**

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/model/RasterImageExporter.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/model/RasterImageExporter.java
@@ -26,7 +26,7 @@
 import javax.imageio.ImageIO;
 
 import org.pathvisio.core.view.model.VPathwayModel;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.model.PathwayModel;
 
 /**

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/util/ColorExporter.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/util/ColorExporter.java
@@ -29,7 +29,7 @@
 
 import org.pathvisio.debug.Logger;
 import org.pathvisio.core.model.BatikImageExporter;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.core.model.ImageExporter;
 import org.pathvisio.model.PathwayModel;
 import org.pathvisio.model.PathwayObject;

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/util/Converter.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/util/Converter.java
@@ -22,9 +22,9 @@
 import org.pathvisio.core.Engine;
 import org.pathvisio.debug.Logger;
 import org.pathvisio.core.model.BatikImageExporter;
-import org.pathvisio.io.ConverterException;
+import org.pathvisio.model.ConverterException;
 import org.pathvisio.core.model.EUGeneExporter;
-import org.pathvisio.io.GpmlFormat;
+import org.pathvisio.model.GpmlFormat;
 import org.pathvisio.core.model.ImageExporter;
 import org.pathvisio.model.PathwayModel;
 import org.pathvisio.event.PathwayModelExporter;

diff --git a/org.pathvisio.core/src/main/java/org/pathvisio/core/view/model/DefaultTemplates.java b/org.pathvisio.core/src/main/java/org/pathvisio/core/view/model/DefaultTemplates.java
@@ -35,6 +35,7 @@
 import org.pathvisio.model.Interaction;
 import org.pathvisio.model.DataNode;
 import org.pathvisio.model.Shape;
+import org.pathvisio.model.shape.IShape;
 import org.pathvisio.model.LineElement;
 import org.pathvisio.model.LineElement.LinePoint;
 import org.pathvisio.model.LineElement.Anchor;
@@ -102,7 +103,7 @@ public abstract class DefaultTemplates {
 	public static void setInitialSize(PathwayObject o) {
 		// set size for Shape (depends on shape type)
 		if (o.getClass() == Shape.class) {
-			ShapeType type = ((Shape) o).getShapeType();
+			IShape type = ((Shape) o).getShapeType();
 			if (type.equals(ShapeType.BRACE)) {
 				((Shape) o).setWidth(BRACE_WIDTH);
 				((Shape) o).setHeight(BRACE_HEIGHT);
@@ -322,7 +323,7 @@ public String getName() {
 		}
 
 		public void setInitialBorderStyle(Shape shape) {
-			ShapeType type = shape.getShapeType();
+			IShape type = shape.getShapeType();
 			// set borderStyle depending on shape type
 			if (type.equals(ShapeType.CELL) || type.equals(ShapeType.NUCLEUS) || type.equals(ShapeType.ORGANELLE)) {
 				shape.setBorderStyle(LineStyleType.DOUBLE);