Bugs item #3371962, was opened at 2011-07-20 12:41
Message generated for change (Tracker Item Submitted) made by cpudney
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Category: Algorithms
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Chris Pudney (cpudney)
Assigned to: Nobody/Anonymous (nobody)
Summary: FormulaUtils.ionizeFormula raises exception in CDK library
Initial Comment:
Revision 2421.
When running a peak identification task against an online database, e.g. KEGG,
the following exception is raised.
WARNING: Could not connect to KEGG Compound Database
java.lang.StringIndexOutOfBoundsException: String index out of range: 0
at java.lang.String.charAt(String.java:686)
at
org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator.getMolecularFormula(MolecularFormulaManipulator.java:427)
at
org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator.getMolecularFormula(MolecularFormulaManipulator.java:394)
at
org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator.getMolecularFormula(MolecularFormulaManipulator.java:370)
at net.sf.mzmine.util.FormulaUtils.ionizeFormula(FormulaUtils.java:72)
at net.sf.mzmine.util.FormulaUtils.ionizeFormula(FormulaUtils.java:108)
at
net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.SingleRowIdentificationTask.run(SingleRowIdentificationTask.java:162)
at net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60)
20/07/2011 12:34:58 PM net.sf.mzmine.taskcontrol.impl.WorkerThread run
SEVERE: Task error: Could not connect to KEGG Compound Database:
java.lang.StringIndexOutOfBoundsException: String index out of range: 0
(String.java:686)
It looks like ionizeFormula has changed in this revision - reverting to the
previous revision removes the bug.
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