private void processSubLevelField(System.String field, System.String fieldNumber, System.String subfield, System.String datum)
{
//logger.debug("Processing sub level field");
if (field.Equals("OVERALL REACTION"))
{
if (subfield.Equals("REACTION_ID"))
{
if (readSecondaryFiles.Set && readThisEntry)
{
// parse referenced file
System.String filename = readSecondaryDir.getSetting() + datum + ".rxn";
System.IO.FileInfo file = new System.IO.FileInfo(filename);
bool tmpBool;
if (System.IO.File.Exists(file.FullName))
tmpBool = true;
else
tmpBool = System.IO.Directory.Exists(file.FullName);
if (tmpBool)
{
//logger.info("Reading overall reaction from: ", filename);
//UPGRADE_TODO: Constructor 'java.io.FileReader.FileReader' was converted to 'System.IO.StreamReader' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
System.IO.StreamReader reader = new System.IO.StreamReader(file.FullName, System.Text.Encoding.Default);
IChemObjectReader rxnReader = new ReaderFactory().createReader(reader);
currentReaction = (Reaction)rxnReader.read(new Reaction());
currentReaction.ID = datum;
currentReaction.setProperty(CDKConstants.TITLE, "Overall Reaction");
// don't add it now, wait until annotation is parsed
}
else
{
System.String error = "Cannot find secondary file: " + filename;
//logger.error(error);
throw new CDKException(error);
}
}
else
{
//logger.warn("Not reading overall reaction for this entry");
}
}
else if (subfield.Equals("OVERALL REACTION ANNOTATION"))
{
parseReactionAnnotation(datum, currentReaction);
currentReactionStepSet.addReaction(currentReaction);
}
}
else if (field.Equals("REACTION STAGES"))
{
if (subfield.Equals("REACTION STAGES"))
{
// new reaction step
// cannot create one, because CDK io does not
// allow that (yet)
reactionStepAnnotation = null;
reactionStepComments = null;
}
else if (subfield.Equals("ANNOTATION"))
{
reactionStepAnnotation = datum;
}
else if (subfield.Equals("COMMENTS"))
{
reactionStepComments = datum;
}
else if (subfield.Equals("STEP_ID"))
{
// read secondary RXN files?
if (readSecondaryFiles.Set && readThisEntry)
{
// parse referenced file
System.String filename = readSecondaryDir.getSetting() + datum + ".rxn";
System.IO.FileInfo file = new System.IO.FileInfo(filename);
bool tmpBool2;
if (System.IO.File.Exists(file.FullName))
tmpBool2 = true;
else
tmpBool2 = System.IO.Directory.Exists(file.FullName);
if (tmpBool2)
{
//logger.info("Reading reaction step from: ", filename);
//UPGRADE_TODO: Constructor 'java.io.FileReader.FileReader' was converted to 'System.IO.StreamReader' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
System.IO.StreamReader reader = new System.IO.StreamReader(file.FullName, System.Text.Encoding.Default);
IChemObjectReader rxnReader = new ReaderFactory().createReader(reader);
currentReaction = (Reaction)rxnReader.read(new Reaction());
currentReaction.ID = datum;
currentReaction.setProperty(CDKConstants.TITLE, "Step " + fieldNumber);
}
else
{
//logger.error("Cannot find secondary file: ", filename);
}
// convert PseudoAtom's in EnzymeResidueLocator's if appropriate
markEnzymeResidueLocatorAtoms(currentReaction);
// now parse annotation
if (reactionStepAnnotation != null)
{
parseReactionAnnotation(reactionStepAnnotation, currentReaction);
}
// and set comments
if (reactionStepComments != null)
{
currentReaction.setProperty(CDKConstants.COMMENT, reactionStepComments);
}
// now, I'm ready to add reaction
currentReactionStepSet.addReaction(currentReaction);
}
else
{
//logger.warn("Not reading reactions of this entry.");
}
}
}
else if (field.Equals("SUBSTRATES"))
{
//logger.warn("Ignoring top level definition of substrates");
}
else if (field.Equals("PRODUCTS"))
{
//logger.warn("Ignoring top level definition of products");
}
else if (field.Equals("REFERENCES"))
{
if (subfield.Equals("MEDLINE_ID"))
{
currentEntry.setProperty(MedlineID, datum);
}
}
else
{
//UPGRADE_ISSUE: Method 'java.io.LineNumberReader.getLineNumber' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioLineNumberReadergetLineNumber'"
//logger.error("Unrecognized sub level field ", field, " around line " + input.getLineNumber());
}
}