Commit 4b6b4c90 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

information about reaction line added that connects products and reactants

parent 8df588b4
Pipeline #4405 passed with stage
in 1 minute and 26 seconds
package lcsb.mapviewer.converter.model.sbml.reaction;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
......@@ -34,6 +35,7 @@ import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.modifier.Trigger;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
......@@ -170,20 +172,57 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
protected void assignLayoutToGlyph(Reaction reaction, AbstractReferenceGlyph compartmentGlyph) {
ReactionGlyph reactionGlyph = (ReactionGlyph) compartmentGlyph;
boolean firstReactant = true;
reactionGlyph.setCurve(new Curve());
Point2D reactantEndPoint = null;
for (Reactant reactant : reaction.getReactants()) {
SpeciesReferenceGlyph reactantGlyph = createNodeGlyph(reactionGlyph, reactant);
if (firstReactant) {
reactantGlyph.setRole(SpeciesReferenceRole.SUBSTRATE);
for (NodeOperator operator : reaction.getOperators()) {
if (operator.isReactantOperator()) {
addOperatorLineToGlyph(reactionGlyph, operator, true);
if (reactantEndPoint == null) {
reactantEndPoint = operator.getLine().getEndPoint();
}
}
}
if (reactantEndPoint == null) {
reactantEndPoint = reactant.getLine().getEndPoint();
}
} else {
reactantGlyph.setRole(SpeciesReferenceRole.SIDESUBSTRATE);
}
firstReactant = false;
}
boolean firstProduct = true;
Point2D productStartPoint = null;
for (Product product : reaction.getProducts()) {
SpeciesReferenceGlyph productGlyph = createNodeGlyph(reactionGlyph, product);
if (firstProduct) {
productGlyph.setRole(SpeciesReferenceRole.PRODUCT);
for (NodeOperator operator : reaction.getOperators()) {
if (operator.isProductOperator()) {
if (productStartPoint == null) {
productStartPoint = operator.getLine().getBeginPoint();
LineSegment segment = new LineSegment();
segment.setStart(new Point(reactantEndPoint.getX(), reactantEndPoint.getY()));
segment.setEnd(new Point(productStartPoint.getX(), productStartPoint.getY()));
reactionGlyph.getCurve().addCurveSegment(segment);
}
addOperatorLineToGlyph(reactionGlyph, operator, false);
}
}
if (productStartPoint == null) {
productStartPoint = product.getLine().getBeginPoint();
LineSegment segment = new LineSegment();
segment.setStart(new Point(reactantEndPoint.getX(), reactantEndPoint.getY()));
segment.setEnd(new Point(productStartPoint.getX(), productStartPoint.getY()));
reactionGlyph.getCurve().addCurveSegment(segment);
}
} else {
productGlyph.setRole(SpeciesReferenceRole.SIDEPRODUCT);
}
......@@ -201,6 +240,23 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
}
private void addOperatorLineToGlyph(ReactionGlyph reactantGlyph, NodeOperator operator, boolean reverse) {
Curve curve = reactantGlyph.getCurve();
List<Line2D> lines = operator.getLine().getLines();
if (reverse) {
lines = operator.getLine().reverse().getLines();
}
for (Line2D line : lines) {
if (line.getP1().distance(line.getP2()) > Configuration.EPSILON) {
LineSegment segment = new LineSegment();
segment.setStart(new Point(line.getX1(), line.getY1()));
segment.setEnd(new Point(line.getX2(), line.getY2()));
curve.addCurveSegment(segment);
}
}
}
private SpeciesReferenceGlyph createNodeGlyph(ReactionGlyph reactionGlyph, ReactionNode node) {
SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
reactantGlyph.setSpeciesGlyph(speciesExporter.getSbmlGlyphByElementId(node.getElement().getElementId()).getId());
......@@ -209,11 +265,11 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
return reactantGlyph;
}
private Curve createCurve(ReactionNode reactant, boolean reverse) {
private Curve createCurve(ReactionNode node, boolean reverse) {
Curve curve = new Curve();
List<Line2D> lines = reactant.getLine().getLines();
List<Line2D> lines = node.getLine().getLines();
if (reverse) {
lines = reactant.getLine().reverse().getLines();
lines = node.getLine().reverse().getLines();
}
for (Line2D line : lines) {
if (line.getP1().distance(line.getP2()) > Configuration.EPSILON) {
......
......@@ -45,30 +45,38 @@
"litemol": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
},
"dependencies": {
"ProtVista": {
"version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
"dev": true,
"requires": {
"d3": "3.5.17",
"file-saver": "1.3.3",
"jquery": "2.2.4",
"jszip": "3.1.4",
"underscore": "1.8.3"
},
"dependencies": {
"jquery": {
"version": "2.2.4",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
"integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
"dev": true
}
}
},
"jquery": {
"version": "3.3.1",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
"integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
"dev": true
}
}
},
"ProtVista": {
"version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
"dev": true,
"requires": {
"d3": "3.5.17",
"file-saver": "1.3.3",
"jquery": "2.2.4",
"jszip": "3.1.4",
"underscore": "1.8.3"
},
"dependencies": {
"jquery": {
"version": "2.2.4",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
"integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
"dev": true
},
"litemol": {
"version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
"dev": true,
"requires": {
"@types/react": "15.6.14",
"@types/react-dom": "15.5.7"
}
}
}
},
......@@ -2050,14 +2058,6 @@
"immediate": "3.0.6"
}
},
"litemol": {
"version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
"dev": true,
"requires": {
"@types/react": "15.6.14",
"@types/react-dom": "15.5.7"
}
},
"lodash": {
"version": "4.17.4",
"resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz",
......
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