diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
index f558c3d7f1ead56135c366f2a461978a2fa981ae..f94f91807ddf8c5db8f002e394d9182c32079fa3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
@@ -19,97 +19,104 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected AntisenseRnaCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected AntisenseRnaCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
- /**
- * How big should be the arc in rectangle for nucleic acid feature
- * representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (isSbgn()) {
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
- ArrayList<Point2D> points = getPoints(alias);
- return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- }
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (isSbgn()) {
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), anchor);
+ }
+ ArrayList<Point2D> points = getPoints(alias);
+ return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ }
- @Override
- protected PathIterator getBoundPathIterator(Species alias) {
- return getAntisebseRnaPath(alias).getPathIterator(new AffineTransform());
- }
+ @Override
+ protected PathIterator getBoundPathIterator(Species alias) {
+ return getAntisebseRnaPath(alias).getPathIterator(new AffineTransform());
+ }
- /**
- * Returns shape of the AntisenseRna as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPoints(Element alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
+ /**
+ * Returns shape of the AntisenseRna as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x + width / 8, y + height / 2));
- points.add(new Point2D.Double(x, y));
- points.add(new Point2D.Double(x + width * 3 / 8, y));
- points.add(new Point2D.Double(x + width * 3 / 4, y));
- points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
- points.add(new Point2D.Double(x + width, y + height));
- points.add(new Point2D.Double(x + width * 5 / 8, y + height));
- points.add(new Point2D.Double(x + width / 4, y + height));
- // CHECKSTYLE:ON
- return points;
- }
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x + width / 8, y + height / 2));
+ points.add(new Point2D.Double(x, y));
+ points.add(new Point2D.Double(x + width * 3 / 8, y));
+ points.add(new Point2D.Double(x + width * 3 / 4, y));
+ points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width, y + height));
+ points.add(new Point2D.Double(x + width * 5 / 8, y + height));
+ points.add(new Point2D.Double(x + width / 4, y + height));
+ // CHECKSTYLE:ON
+ return points;
+ }
- /**
- * Returns shape of the AntisenseRna as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getAntisebseRnaPath(Element alias) {
- // CHECKSTYLE:OFF
- GeneralPath path;
- if (!isSbgn()) {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + alias.getWidth() / 4, alias.getY() + alias.getHeight());
- path.closePath();
- } else {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+ /**
+ * Returns shape of the AntisenseRna as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getAntisebseRnaPath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path;
+ if (!isSbgn()) {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
+ path.moveTo(alias.getX(), alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + alias.getWidth() / 4, alias.getY() + alias.getHeight());
+ path.closePath();
+ } else {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- }
- // CHECKSTYLE:ON
- return path;
- }
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width,
+ y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ }
+ // CHECKSTYLE:ON
+ return path;
+ }
+
+ @Override
+ public Point2D getResidueCoordinates(Species element, double angle) {
+ return new Point2D.Double(element.getX() + element.getWidth() * 3.0 / 4.0 * angle, element.getY());
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
index 0cee48a0e63f19509fc0dc46c7ea5b004cea319d..7116bb1f8a3b17aadf41e8d1b13cdcd39a2b1b90 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
@@ -1,118 +1,122 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for Rna.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected RnaCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (isSbgn()) {
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
- alias.getWidth(), alias.getHeight(), anchor);
- }
- ArrayList<Point2D> points = getPoints(alias);
- return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- }
-
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- return getRnaPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the Rna as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPoints(Element alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x + width / 8, y + height / 2));
- points.add(new Point2D.Double(x + width / 4, y));
- points.add(new Point2D.Double(x + width * 5 / 8, y));
- points.add(new Point2D.Double(x + width, y));
- points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
- points.add(new Point2D.Double(x + width * 3 / 4, y + height));
- points.add(new Point2D.Double(x + width * 3 / 8, y + height));
- // CHECKSTYLE:ON
- points.add(new Point2D.Double(x, y + height));
- return points;
- }
-
- /**
- * Returns shape of the Rna as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getRnaPath(Element alias) {
- // CHECKSTYLE:OFF
- GeneralPath path;
- if (!isSbgn()) {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight());
- path.closePath();
- } else {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- }
- // CHECKSTYLE:ON
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Rna. It's
+ * used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected RnaCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (isSbgn()) {
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), anchor);
+ }
+ ArrayList<Point2D> points = getPoints(alias);
+ return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ return getRnaPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the Rna as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x + width / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width / 4, y));
+ points.add(new Point2D.Double(x + width * 5 / 8, y));
+ points.add(new Point2D.Double(x + width, y));
+ points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width * 3 / 4, y + height));
+ points.add(new Point2D.Double(x + width * 3 / 8, y + height));
+ // CHECKSTYLE:ON
+ points.add(new Point2D.Double(x, y + height));
+ return points;
+ }
+
+ /**
+ * Returns shape of the Rna as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getRnaPath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path;
+ if (!isSbgn()) {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
+ path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX(), alias.getY() + alias.getHeight());
+ path.closePath();
+ } else {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width,
+ y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ }
+ // CHECKSTYLE:ON
+ return path;
+ }
+
+ @Override
+ public Point2D getResidueCoordinates(Species element, double angle) {
+ return new Point2D.Double(element.getX() + element.getWidth() / 4.0 + element.getWidth() * 3.0 / 4.0 * angle,
+ element.getY());
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
index be71b282d64dee36a9dde2b5bbb91832cd130e9f..dd6373dc2985071908e814fc55a3e17d50581a51 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
@@ -146,7 +146,7 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
@Override
public void updateModelElementAfterLayoutAdded(Species element) {
for (CellDesignerModificationResidue region : regions) {
- ((AntisenseRna) element).addRegion(region.createAntisenseRegionAlias(element));
+ ((AntisenseRna) element).addRegion(region.createModificationResidue(element));
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
index db286beee208268c42f18a0d3dba3c6130b81b5a..7e485de81648c9a341e7c26f21983230751d4d40 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
@@ -115,7 +115,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
@Override
public void updateModelElementAfterLayoutAdded(Species element) {
for (CellDesignerModificationResidue region : modificationResidues) {
- ((Gene) element).addModificationResidue(region.createGeneModification(element));
+ ((Gene) element).addModificationResidue(region.createModificationResidue(element));
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index 12892adc56594de9cd3c6082b03480833004090c..9fa15ca0dff3c18c82d4db90de02094f23bda405 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -152,7 +152,7 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
@Override
public void updateModelElementAfterLayoutAdded(Species element) {
for (CellDesignerModificationResidue mr : modificationResidues) {
- ((Protein) element).addModificationResidue(mr.createProteinModification(element));
+ ((Protein) element).addModificationResidue(mr.createModificationResidue(element));
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index 2c0bc90eea43b79ea1f4b477b870d75f2a354f39..745cc58d1b03b876e25bfafafdaa57c364a66248 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -145,7 +145,7 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
public void updateModelElementAfterLayoutAdded(Species element) {
for (CellDesignerModificationResidue region : regions) {
Rna rna = (Rna) element;
- rna.addRegion(region.createRnaRegionAlias(rna));
+ rna.addRegion(region.createModificationResidue(rna));
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
index 20eeb4f4276348a6596c1476dbdd805c84c0a12f..49a4e24703a9d937a74ff7abf251da2d5f5e6d68 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-import java.awt.geom.Point2D;
import java.io.Serializable;
import org.apache.log4j.Logger;
@@ -348,19 +347,46 @@ public class CellDesignerModificationResidue implements Serializable {
*
* @return {@link ModificationResidue} representing this object in a model
*/
- public ModificationResidue createProteinModification(Element element) {
+ public ModificationResidue createModificationResidue(Element element) {
CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, false);
- ModificationResidue result = null;
if (modificationType == null) {
throw new InvalidArgumentException("No type information for modification: " + idModificationResidue);
} else if (modificationType.equals("RESIDUE")) {
- result = new Residue();
- ((Residue) result).setState(this.getState());
+ return createResidue(element, converter);
+ } else if (modificationType.equals("MODIFICATION_SITE")) {
+ return createModificationSite(element, converter);
+ } else if (modificationType.equals("CODING_REGION")) {
+ return createCodingRegion(element, converter);
+ } else if (modificationType.equals("PROTEIN_BINDING_DOMAIN")) {
+ return createProteinBindingDomain(element, converter);
} else {
- throw new InvalidArgumentException("Unknown protein modification type: " + modificationType);
+ throw new InvalidArgumentException("Unknown modification type: " + modificationType);
}
+ }
+
+ private ProteinBindingDomain createProteinBindingDomain(Element element, CellDesignerAliasConverter converter) {
+ ProteinBindingDomain result = new ProteinBindingDomain();
+ result.setWidth(element.getWidth() * size);
+ result.setIdModificationResidue(idModificationResidue);
+ result.setName(name);
+ result.setPosition(converter.getResidueCoordinates(element, angle));
+ return result;
+ }
+
+ private CodingRegion createCodingRegion(Element element, CellDesignerAliasConverter converter) {
+ CodingRegion result = new CodingRegion();
+ result.setWidth(element.getWidth() * size);
+ result.setIdModificationResidue(idModificationResidue);
+ result.setName(name);
+ result.setPosition(converter.getResidueCoordinates(element, angle));
+ return result;
+ }
+
+ private ModificationSite createModificationSite(Element element, CellDesignerAliasConverter converter) {
+ ModificationSite result = new ModificationSite();
+ result.setState(this.getState());
result.setIdModificationResidue(this.getIdModificationResidue());
result.setName(this.getName());
if (angle == null) {
@@ -371,26 +397,9 @@ public class CellDesignerModificationResidue implements Serializable {
return result;
}
- /**
- * Creates model representation of {@link ModificationResidue}.
- *
- * @return {@link ModificationResidue} representing this object in a model
- */
- public ModificationResidue createGeneModification(Element element) {
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, false);
- ModificationResidue result;
-
- if (modificationType == null) {
- logger.debug(this);
- throw new InvalidArgumentException("Unknown gene modification type");
- } else if (modificationType.equals("MODIFICATION_SITE")) {
- result = new ModificationSite();
- ((ModificationSite) result).setState(this.getState());
- } else {
- logger.debug(this);
- throw new InvalidArgumentException("Unknown gene modification type: " + modificationType);
- }
-
+ private Residue createResidue(Element element, CellDesignerAliasConverter converter) {
+ Residue result = new Residue();
+ result.setState(this.getState());
result.setIdModificationResidue(this.getIdModificationResidue());
result.setName(this.getName());
if (angle == null) {
@@ -401,61 +410,6 @@ public class CellDesignerModificationResidue implements Serializable {
return result;
}
- /**
- * Creates model representation of {@link AntisenseRnaRegion}.
- *
- * @return {@link AntisenseRnaRegion} representing this object in a model
- */
- public ModificationResidue createAntisenseRegionAlias(Element element) {
- ModificationResidue result;
- if (modificationType.equals("MODIFICATION_SITE")) {
- result = new ModificationSite();
- } else if (modificationType.equals("CODING_REGION")) {
- result = new CodingRegion();
- ((CodingRegion) result).setWidth(element.getWidth() * size);
- } else if (modificationType.equals("PROTEIN_BINDING_DOMAIN")) {
- result = new ProteinBindingDomain();
- ((ProteinBindingDomain) result).setWidth(element.getWidth() * size);
- } else {
- throw new InvalidArgumentException("Unknown antisense rna modification type: " + modificationType);
-
- }
- result.setIdModificationResidue(idModificationResidue);
- result.setName(name);
-
- result.setPosition(new Point2D.Double(element.getX() + element.getWidth() * 3.0 / 4.0 * pos, element.getY()));
- return result;
- }
-
- /**
- * Creates model representation of {@link RnaRegion}.
- *
- * @return {@link RnaRegion} representing this object in a model
- */
- public ModificationResidue createRnaRegionAlias(Element element) {
- ModificationResidue result;
- if (modificationType == null) {
- throw new InvalidArgumentException("No type information for modification: " + idModificationResidue);
- } else if (modificationType.equals("MODIFICATION_SITE")) {
- result = new ModificationSite();
- ((ModificationSite) result).setState(this.state);
- } else if (modificationType.equals("CODING_REGION")) {
- result = new CodingRegion();
- ((CodingRegion) result).setWidth(element.getWidth() * size);
- } else if (modificationType.equals("PROTEIN_BINDING_DOMAIN")) {
- result = new ProteinBindingDomain();
- ((ProteinBindingDomain) result).setWidth(element.getWidth() * size);
- } else {
- throw new InvalidArgumentException("Unknown antisense rna modification type: " + modificationType);
-
- }
- result.setIdModificationResidue(this.idModificationResidue);
- result.setPosition(new Point2D.Double(
- element.getX() + element.getWidth() / 4.0 + element.getWidth() * 3.0 / 4.0 * pos, element.getY()));
- result.setName(this.name);
- return result;
- }
-
public String getModificationType() {
return modificationType;
}