Commit b4df7d8d authored by Piotr Gawron's avatar Piotr Gawron
Browse files

unused method removed

parent aea221fa
......@@ -826,45 +826,6 @@ public class SbgnmlXmlParser {
return rna;
}
/**
* Method used to parse state variable.
*
* @param unitOfInformationGlyph
* unit of information glyph from sbgn-ml file
* @param species
* species that the unit of information considers
* @throws Exception
* Exception is thrown if state variable is parsed for species other
* than Protein
*/
private void parseStateVariable(Glyph unitOfInformationGlyph, Species species) {
if (!(species instanceof Protein)) {
throw new InvalidArgumentException("Only macromolecule elements can have state variables.");
}
Protein protein = (Protein) species;
Residue mr = new Residue();
mr.setSpecies(protein);
mr.setIdModificationResidue(unitOfInformationGlyph.getId());
if (unitOfInformationGlyph.getState() != null) {
// If State variable consists of value and variable
mr.setName(unitOfInformationGlyph.getState().getVariable());
for (ModificationState ms : ModificationState.values()) {
if (ms.getAbbreviation().equals(unitOfInformationGlyph.getState().getValue())) {
mr.setState(ms);
}
}
}
// Compute the angle from coordinates and dimensions
double x = unitOfInformationGlyph.getBbox().getX() + unitOfInformationGlyph.getBbox().getW() / 2;
double y = unitOfInformationGlyph.getBbox().getY() + unitOfInformationGlyph.getBbox().getH() / 2;
mr.setPosition(new Point2D.Double(x, y));
protein.addResidue(mr);
}
/**
* Method used for parsing units of information.
*
......
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