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Use the new error reporting IO API
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Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
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@egonw @rajarshi
egonw authored and rajarshi committed Feb 3, 2010
1 parent ea5f0b7 commit fd81efc
Showing 1 changed file with 48 additions and 21 deletions.
69 changes: 48 additions & 21 deletions src/main/org/openscience/cdk/io/MDLV2000Reader.java
View file
@@ -1,6 +1,5 @@
/* $Revision$ $Author$ $Date$
*
* Copyright (C) 1997-2007 Christoph Steinbeck <steinbeck@users.sourceforge.net>
/* Copyright (C) 1997-2007 Christoph Steinbeck <steinbeck@users.sourceforge.net>
* 2010 Egon Willighagen <egonw@users.sourceforge.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
Expand Down Expand Up @@ -386,14 +385,14 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
}
}
}
if (mode == Mode.STRICT) {
if (line.contains("V3000") || line.contains("v3000")) {
throw new CDKException("This file must be read with the MDLV3000Reader.");
} else if (!line.contains("V2000") && !line.contains("v2000")) {
throw new CDKException("This file must be read with the MDLReader.");
}
}

// check the CT block version
if (line.contains("V3000") || line.contains("v3000")) {
handleError("This file must be read with the MDLV3000Reader.");
} else if (!line.contains("V2000") && !line.contains("v2000")) {
handleError("This file must be read with the MDLReader.");
}

atoms = Integer.parseInt(line.substring(0, 3).trim());
logger.debug("Atomcount: " + atoms);
bonds = Integer.parseInt(line.substring(3, 6).trim());
Expand Down Expand Up @@ -442,9 +441,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
}
atom = molecule.getBuilder().newPseudoAtom(element);
} else {
if (mode == ISimpleChemObjectReader.Mode.STRICT) {
throw new CDKException("Invalid element type. Must be an existing element, or one in: A, Q, L, LP, *.");
}
handleError(
"Invalid element type. Must be an existing " +
"element, or one in: A, Q, L, LP, *.",
linecount, 32, 35
);
atom = molecule.getBuilder().newPseudoAtom(element);
}

Expand All @@ -462,7 +463,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
atom.setMassNumber(major.getMassNumber() + massDiff);
}
} catch (Exception exception) {
logger.error("Could not parse mass difference field");
handleError(
"Could not parse mass difference field.",
linecount, 35, 37,
exception
);
}
} else {
logger.error("Cannot set mass difference for a non-element!");
Expand Down Expand Up @@ -572,7 +577,10 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
stereo = (IBond.Stereo)CDKConstants.UNSET;
}
} else {
logger.warn("Missing expected stereo field at line: " + line);
handleError(
"Missing expected stereo field at line: ",
linecount, 10, 12
);
}
if (logger.isDebugEnabled()) {
logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order);
Expand Down Expand Up @@ -609,7 +617,10 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
while (true) {
line = input.readLine(); linecount++;
if (line == null) {
throw new CDKException("The expected property block is missing!");
handleError(
"The expected property block is missing!",
linecount, 0, 0
);
}
if (line.startsWith("M END")) break;

Expand Down Expand Up @@ -678,7 +689,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
String error = "Error (" + exception.getMessage() + ") while parsing line "
+ linecount + ": " + line + " in property block.";
logger.error(error);
throw new CDKException("NumberFormatException in isotope information on line: " + line, exception);
handleError(
"NumberFormatException in isotope information.",
linecount, 7, 11,
exception
);
}
} else if (line.startsWith("M RAD")) {
try {
Expand All @@ -701,7 +716,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
String error = "Error (" + exception.getMessage() + ") while parsing line "
+ linecount + ": " + line + " in property block.";
logger.error(error);
throw new CDKException("NumberFormatException in radical information on line: " + line, exception);
handleError(
"NumberFormatException in radical information",
linecount, 7, 10,
exception
);
}
} else if (line.startsWith("G ")) {
try {
Expand All @@ -725,7 +744,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
String error = "Error (" + exception.toString() + ") while parsing line "
+ linecount + ": " + line + " in property block.";
logger.error(error);
throw new CDKException("NumberFormatException in group information on line: " + line, exception);
handleError(
"NumberFormatException in group information",
linecount, 4, 7,
exception
);
}
}
if (!lineRead) {
Expand All @@ -742,7 +765,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
handleError(
"Error while parsing line: " + line,
linecount, 0, 0,
exception
);
}
if (interpretHydrogenIsotopes.isSet()) {
fixHydrogenIsotopes(molecule);
Expand Down

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