Commit 79e345e9 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

import of structural state check if data is not null

parent ef19828d
......@@ -11,6 +11,8 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
exporter violates SBGN specification (#707)
* Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are
visualized with proper line type across all included modifiers (#957)
* Bug fix: dimension of the modifications is the same as in minerva when
exporting to SBGNML-PD (#554)
minerva (15.0.0~alpha.0) stable; urgency=medium
* Improvement: logs provided for validation data model are structurized (#325)
......
......@@ -4,15 +4,14 @@ import java.awt.Color;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.sbgn.*;
import org.sbgn.bindings.*;
import org.sbgn.bindings.Arc.*;
import org.sbgn.bindings.Map;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
......@@ -80,6 +79,8 @@ public class SbgnmlXmlParser {
*/
private List<Arc> logicArcs = new ArrayList<Arc>();
Model model;
/**
* Method used to create a model from SBGN-ML file.
*
......@@ -94,7 +95,7 @@ public class SbgnmlXmlParser {
*/
public Model createModel(String filename, File inputSbgnmlFile) throws InvalidInputDataExecption {
Model model = new ModelFullIndexed(null);
model = new ModelFullIndexed(null);
model.setIdModel(filename);
Sbgn sbgnData;
......@@ -598,7 +599,7 @@ public class SbgnmlXmlParser {
logger.warn("Only macromolecule elements can have state variables.");
}
} else {
StructuralState state = stateVariableToStructuralState(child);
StructuralState state = createStructuralState(child);
if (newSpecies instanceof Protein) {
((Protein) newSpecies).setStructuralState(state);
} else {
......@@ -625,21 +626,12 @@ public class SbgnmlXmlParser {
}
private StructuralState stateVariableToStructuralState(Glyph glyph) {
StructuralState state = new StructuralState();
state.setFontSize(10);
state.setPosition(new Point2D.Double(glyph.getBbox().getX(), glyph.getBbox().getY()));
state.setHeight((double) glyph.getBbox().getH());
state.setWidth((double) glyph.getBbox().getW());
if (glyph.getState() != null) {
state.setValue(glyph.getState().getValue());
}
return state;
}
private StructuralState createStructuralState(Glyph glyph) {
if (glyph.getState() == null || glyph.getState().getValue() == null) {
logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, glyph.getId(), "state", model.getName()),
"Invalid structural state");
return null;
}
StructuralState structuralState = new StructuralState();
double height = new Double(glyph.getBbox().getH());
......
<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
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<glyph id="s_id_sa1894_sa1894" class="macromolecule">
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