From 3c063d717c07192b2a1b2870354586ec6ee456f4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 13 May 2019 19:15:58 +0200
Subject: [PATCH] center line is properly break between product operator and
reactant operator
---
.../sbml/reaction/SbmlReactionParser.java | 46 ++++++++-----------
1 file changed, 19 insertions(+), 27 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index d50f1c68a5..f9a80ab38f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -306,6 +306,10 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
operator = new AndOperator();
}
PolylineData line = extractCurve(reactionGlyph, reactionWithLayout, operator.getClass());
+ if (line.getPoints().size() == 0) {
+ line.addPoint(reactionWithLayout.getReactants().get(0).getLine().getEndPoint());
+ line.addPoint(reactionWithLayout.getReactants().get(0).getLine().getEndPoint());
+ }
operator.addInputs(reactionWithLayout.getReactants());
operator.setLine(line);
return operator;
@@ -344,7 +348,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
return new PolylineData();
}
- int requiredLines = 1;
+ int requiredLines = 0;
if (reaction.getReactants().size() > 1) {
requiredLines++;
}
@@ -353,20 +357,18 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
int existingLines = curve.getCurveSegmentCount();
- int reactantBreak;
- int productBreak;
- if (requiredLines == 3) {
- reactantBreak = (existingLines - 1) / 2;
- } else if (requiredLines == 2 && reaction.getReactants().size() > 1) {
- reactantBreak = existingLines - 1;
- } else if (requiredLines == 2 && reaction.getProducts().size() > 1) {
- reactantBreak = 0;
+ int breakPoint;
+ if (requiredLines == 2) {
+ breakPoint = existingLines / 2;
+ } else if (reaction.getReactants().size() > 1) {
+ breakPoint = existingLines;
+ } else if (reaction.getProducts().size() > 1) {
+ breakPoint = 0;
} else {
throw new InvalidArgumentException(
new ElementUtils().getElementTag(reaction) + "Reaction has no products and reactants");
}
- productBreak = reactantBreak + 1;
-
+
PolylineData result = new PolylineData();
if (operator == TruncationOperator.class ||
operator == DissociationOperator.class ||
@@ -374,22 +376,18 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
// Product operator
if (existingLines >= requiredLines) {
- CurveSegment segment = curve.getCurveSegment(productBreak);
+ CurveSegment segment = curve.getCurveSegment(breakPoint);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
- for (int i = productBreak; i < curve.getCurveSegmentCount(); i++) {
+ for (int i = breakPoint; i < curve.getCurveSegmentCount(); i++) {
segment = curve.getCurveSegment(i);
result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
- } else if (existingLines == 1) {
+ } else {
CurveSegment segment = curve.getCurveSegment(0);
- double startX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) * (requiredLines-1) / requiredLines;
- double startY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) * (requiredLines-1) / requiredLines;
+ double startX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) / 2;
+ double startY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) / 2;
result.addPoint(new Point2D.Double(startX, startY));
result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
- } else {
- CurveSegment segment = curve.getCurveSegment(1);
- result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
- result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
} else if (operator == AssociationOperator.class || operator == AndOperator.class) {
@@ -398,16 +396,10 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
if (existingLines >= requiredLines) {
CurveSegment segment = curve.getCurveSegment(0);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
- for (int i = 0; i < reactantBreak; i++) {
+ for (int i = 0; i < breakPoint; i++) {
segment = curve.getCurveSegment(i);
result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
- } else if (existingLines == 1) {
- CurveSegment segment = curve.getCurveSegment(0);
- result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
- double endX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) / requiredLines;
- double endY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) / requiredLines;
- result.addPoint(new Point2D.Double(endX, endY));
} else {
CurveSegment segment = curve.getCurveSegment(0);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
--
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