/// <summary> Read a Reaction from a file in MACiE RDF format.
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IChemObject readReactions(bool selectEntry)
{
ChemSequence entries = new ChemSequence();
currentEntry = null;
int entryCounter = 0;
currentReactionStepSet = null;
while (input.Peek() != -1)
{
//UPGRADE_WARNING: Method 'java.io.LineNumberReader.readLine' was converted to 'System.IO.StreamReader.ReadLine' which may throw an exception. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1101'"
System.String line = input.ReadLine();
if (line.StartsWith("$RDFILE"))
{
entries = new ChemSequence();
}
else if (line.StartsWith("$DATM"))
{
entries.setProperty(CreationDate, line.Substring(7));
}
else if (line.StartsWith("$RIREG"))
{
// new entry, store previous entry if any
if (currentEntry != null)
{
// store previous entry
currentEntry.SetOfReactions = currentReactionStepSet;
createNiceMACiETitle(currentEntry);
entries.addChemModel(currentEntry);
fireFrameRead();
if (selectEntry && (entryCounter == selectedEntry.SettingValue))
{
//logger.info("Starting reading wanted frame: ", selectedEntry);
return(currentEntry);
}
else
{
//logger.debug("Not reading unwanted frame: " + entryCounter);
}
}
currentEntry = new ChemModel();
entryCounter++;
if (!selectEntry || entryCounter == selectedEntry.SettingValue)
{
readThisEntry = true;
}
else
{
readThisEntry = false;
}
currentReactionStepSet = new SetOfReactions();
}
else if (line.StartsWith("$DTYPE"))
{
System.String[] tuple = readDtypeDatumTuple(line);
System.String dataType = tuple[0];
System.String datum = tuple[1];
// now some regular expression wizardry
Match subLevelMatcher = subLevelDatum.Match(dataType);
if (subLevelMatcher.Success)
{
// sub level field found
System.String field = subLevelMatcher.Groups[2].Value;
System.String fieldNumber = subLevelMatcher.Groups[3].Value;
System.String subfield = subLevelMatcher.Groups[4].Value;
processSubLevelField(field, fieldNumber, subfield, datum);
}
else
{
Match topLevelMatcher = topLevelDatum.Match(dataType);
if (topLevelMatcher.Success)
{
// top level field found
System.String field = topLevelMatcher.Groups[2].Value;
processTopLevelField(field, 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("Could not parse datum tuple of type ", dataType, " around line " + input.getLineNumber());
}
}
}
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.warn("Unrecognized command on line " + input.getLineNumber(), ": ", line);
}
}
if (currentEntry != null)
{
createNiceMACiETitle(currentEntry);
// store last entry
currentEntry.SetOfReactions = currentReactionStepSet;
entries.addChemModel(currentEntry);
fireFrameRead();
}
if (selectEntry)
{
// apparently selected last one, other already returned
return(currentEntry);
}
return(entries);
}
/// <summary> Read a Reaction from a file in MACiE RDF format.
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IChemObject readReactions(bool selectEntry)
{
ChemSequence entries = new ChemSequence();
currentEntry = null;
int entryCounter = 0;
currentReactionStepSet = null;
while (input.Peek() != -1)
{
//UPGRADE_WARNING: Method 'java.io.LineNumberReader.readLine' was converted to 'System.IO.StreamReader.ReadLine' which may throw an exception. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1101'"
System.String line = input.ReadLine();
if (line.StartsWith("$RDFILE"))
{
entries = new ChemSequence();
}
else if (line.StartsWith("$DATM"))
{
entries.setProperty(CreationDate, line.Substring(7));
}
else if (line.StartsWith("$RIREG"))
{
// new entry, store previous entry if any
if (currentEntry != null)
{
// store previous entry
currentEntry.SetOfReactions = currentReactionStepSet;
createNiceMACiETitle(currentEntry);
entries.addChemModel(currentEntry);
fireFrameRead();
if (selectEntry && (entryCounter == selectedEntry.SettingValue))
{
//logger.info("Starting reading wanted frame: ", selectedEntry);
return currentEntry;
}
else
{
//logger.debug("Not reading unwanted frame: " + entryCounter);
}
}
currentEntry = new ChemModel();
entryCounter++;
if (!selectEntry || entryCounter == selectedEntry.SettingValue)
{
readThisEntry = true;
}
else
{
readThisEntry = false;
}
currentReactionStepSet = new SetOfReactions();
}
else if (line.StartsWith("$DTYPE"))
{
System.String[] tuple = readDtypeDatumTuple(line);
System.String dataType = tuple[0];
System.String datum = tuple[1];
// now some regular expression wizardry
Match subLevelMatcher = subLevelDatum.Match(dataType);
if (subLevelMatcher.Success)
{
// sub level field found
System.String field = subLevelMatcher.Groups[2].Value;
System.String fieldNumber = subLevelMatcher.Groups[3].Value;
System.String subfield = subLevelMatcher.Groups[4].Value;
processSubLevelField(field, fieldNumber, subfield, datum);
}
else
{
Match topLevelMatcher = topLevelDatum.Match(dataType);
if (topLevelMatcher.Success)
{
// top level field found
System.String field = topLevelMatcher.Groups[2].Value;
processTopLevelField(field, 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("Could not parse datum tuple of type ", dataType, " around line " + input.getLineNumber());
}
}
}
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.warn("Unrecognized command on line " + input.getLineNumber(), ": ", line);
}
}
if (currentEntry != null)
{
createNiceMACiETitle(currentEntry);
// store last entry
currentEntry.SetOfReactions = currentReactionStepSet;
entries.addChemModel(currentEntry);
fireFrameRead();
}
if (selectEntry)
{
// apparently selected last one, other already returned
return currentEntry;
}
return entries;
}
