From 8c6d42712612f7885253b1b7ff300f516f9273e9 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 19 Dec 2018 08:49:56 +0100
Subject: [PATCH] variable name refactored
---
.../model/sbgnml/SbgnmlXmlExporter.java | 28 +++++++++----------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 1b536d4ee9..dc7eedc006 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/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);
}
--
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