variable name refactored

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -469,32 +469,32 @@ public class SbgnmlXmlExporter {
    * Returns glyph with unit of information extracted from the alias or null if no
    * unit of information was found.
    * 
-   * @param alias
+   * @param element
    *          input alias
    * @return glyph with unit of information extracted from the alias or null if no
    *         unit of information was found
    */
-  private Glyph getUnitOfInformationGlyph(Element alias) {
+  private Glyph getUnitOfInformationGlyph(Element element) {
     Glyph uoiGlyph = null;
 
     String uoiText = "";
-    if (alias instanceof Species) {
-      Species species = (Species) alias;
+    if (element instanceof Species) {
+      Species species = (Species) element;
       int homodir = species.getHomodimer();
       if (homodir > 1) {
         uoiText = "N:".concat(Integer.toString(homodir));
       }
     }
 
-    if (alias instanceof TruncatedProtein) {
+    if (element instanceof TruncatedProtein) {
       if (!uoiText.equals("")) {
         uoiText = uoiText.concat("; ");
       }
       uoiText = uoiText.concat("ct:truncatedProtein");
     }
 
-    if (alias instanceof Species) {
-      Species speciesAlias = (Species) alias;
+    if (element instanceof Species) {
+      Species speciesAlias = (Species) element;
       if ((speciesAlias.getStateLabel() != null) && (speciesAlias.getStatePrefix() != null)) {
         if (!uoiText.equals("")) {
           uoiText = uoiText.concat("; ");
@@ -507,19 +507,19 @@ public class SbgnmlXmlExporter {
     }
 
     if (!uoiText.contains("ct:")) {
-      if (alias instanceof Rna) {
+      if (element instanceof Rna) {
         if (!uoiText.equals("")) {
           uoiText = uoiText.concat("; ");
         }
         uoiText = uoiText.concat("ct:RNA");
       }
-      if (alias instanceof AntisenseRna) {
+      if (element instanceof AntisenseRna) {
         if (!uoiText.equals("")) {
           uoiText = uoiText.concat("; ");
         }
         uoiText = uoiText.concat("ct:antisenseRNA");
       }
-      if (alias instanceof Gene) {
+      if (element instanceof Gene) {
         if (!uoiText.equals("")) {
           uoiText = uoiText.concat("; ");
         }
@@ -530,17 +530,17 @@ public class SbgnmlXmlExporter {
     if (!uoiText.equals("")) {
       uoiGlyph = new Glyph();
       uoiGlyph.setClazz(GlyphClazz.UNIT_OF_INFORMATION.getClazz());
-      uoiGlyph.setId(alias.getElementId().concat("uoi"));
+      uoiGlyph.setId(element.getElementId().concat("uoi"));
 
       Label label = new Label();
       label.setText(uoiText);
       uoiGlyph.setLabel(label);
 
       Bbox bbox = new Bbox();
-      bbox.setX((float) (alias.getX() + UNIT_OF_INFORMATION_MARGIN));
-      bbox.setY((float) (alias.getY() - UNIT_OF_INFORMATION_HEIGHT / 2));
+      bbox.setX((float) (element.getX() + UNIT_OF_INFORMATION_MARGIN));
+      bbox.setY((float) (element.getY() - UNIT_OF_INFORMATION_HEIGHT / 2));
       bbox.setH((float) UNIT_OF_INFORMATION_HEIGHT);
-      bbox.setW((float) (alias.getWidth() - 2 * UNIT_OF_INFORMATION_MARGIN));
+      bbox.setW((float) (element.getWidth() - 2 * UNIT_OF_INFORMATION_MARGIN));
       uoiGlyph.setBbox(bbox);
     }