Commit 10c674f4 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

import of structural state works with the new data structure

parent 47679cc5
......@@ -11,8 +11,7 @@ import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
......@@ -338,7 +337,7 @@ public class ModelContructor {
if (species instanceof Protein) {
Protein protein = ((Protein) species);
if (protein.getStructuralState() == null) {
protein.setStructuralState(state.getStructuralState());
protein.setStructuralState(createStructuralState(state, protein));
} else {
logger.warn(state.getWarningPrefix() + " tries to override another state: " + protein.getStructuralState());
}
......@@ -350,6 +349,18 @@ public class ModelContructor {
}
}
private StructuralState createStructuralState(State state, Species species) {
Double x = state.getRelX() * species.getWidth() + species.getX();
Double y = state.getRelY() * species.getHeight() + species.getY();
StructuralState structuralState= new StructuralState();
structuralState.setPosition(new Point2D.Double(x, y));
structuralState.setFontSize(10);
structuralState.setHeight(state.getHeight());
structuralState.setWidth(state.getWidth());
structuralState.setValue(state.getStructuralState());
return structuralState;
}
/**
* {@link ModificationResidue} in element might have slightly off coordinates
* (due to different symbol shapes). For that we need to align them to match our
......
......@@ -351,11 +351,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
Protein protein = (Protein) model1.getElementsByName("Protein").get(0);
assertEquals(0, protein.getModificationResidues().size());
assertEquals("GTP", protein.getStructuralState());
Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
assertNotNull(protein.getStructuralState());
}
}
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