From: <no...@so...> - 2002-10-08 14:08:30
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Bugs item #620242, was opened at 2002-10-08 14:08 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 Category: org.openscience.cdk.io Group: None Status: Open Resolution: None Priority: 5 Submitted By: Hans Vanderzijl (hansvdz) Assigned to: Nobody/Anonymous (nobody) Summary: MDLReader : nullpointerexception Initial Comment: When reading a SDF file with several molecules, each molecule is seperated with $$$$. At the end of the file is also a $$$$. There will be a nullpointerexception on this. I changed the code with the following lines : String line = input.readLine(); if (line == null) return null; So there is no exception anymore. MDLReader. private Molecule readMolecule() { int atoms = 0, bonds = 0, atom1 = 0, atom2 = 0, order = 0, stereo = 0; double x=0, y=0, z=0; int[][] conMat = new int[0][0]; String help; Molecule molecule = new Molecule(); Bond bond; Atom atom; try { String title = new String(input.readLine() + "\n" + input.readLine() + "\n" + input.readLine()); molecule.setTitle(title); // added 30.09 hvanderz - reading last empty line (nullpointer exception) String line = input.readLine(); if (line == null) return null; StringBuffer strBuff = new StringBuffer(line); ... ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 |
From: <no...@so...> - 2002-10-08 14:30:10
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Bugs item #620242, was opened at 2002-10-08 14:08 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 Category: org.openscience.cdk.io Group: None Status: Open Resolution: None Priority: 5 Submitted By: Hans Vanderzijl (hansvdz) Assigned to: Nobody/Anonymous (nobody) Summary: MDLReader : nullpointerexception Initial Comment: When reading a SDF file with several molecules, each molecule is seperated with $$$$. At the end of the file is also a $$$$. There will be a nullpointerexception on this. I changed the code with the following lines : String line = input.readLine(); if (line == null) return null; So there is no exception anymore. MDLReader. private Molecule readMolecule() { int atoms = 0, bonds = 0, atom1 = 0, atom2 = 0, order = 0, stereo = 0; double x=0, y=0, z=0; int[][] conMat = new int[0][0]; String help; Molecule molecule = new Molecule(); Bond bond; Atom atom; try { String title = new String(input.readLine() + "\n" + input.readLine() + "\n" + input.readLine()); molecule.setTitle(title); // added 30.09 hvanderz - reading last empty line (nullpointer exception) String line = input.readLine(); if (line == null) return null; StringBuffer strBuff = new StringBuffer(line); ... ---------------------------------------------------------------------- >Comment By: Hans Vanderzijl (hansvdz) Date: 2002-10-08 14:30 Message: Logged In: YES user_id=625197 I made a ViewerFrame. This frame reads a sdf file and shows every molecule in a seperate panel. A NullPointerException occurs, but it still shows the frame. I shall upload the sdf file. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2002-10-08 14:20 Message: Logged In: YES user_id=25678 What is the exact error you get? The Exception should be catched, and not result in any problem. I agree that the reader has a strange design. The program does not really fail does it? Can you contribute a test SDF file that we can use for testing purposes (it will be distributed)? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 |
From: <no...@so...> - 2002-10-08 14:43:24
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Bugs item #620242, was opened at 2002-10-08 16:08 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 Category: org.openscience.cdk.io Group: None >Status: Pending >Resolution: Postponed Priority: 5 Submitted By: Hans Vanderzijl (hansvdz) Assigned to: Nobody/Anonymous (nobody) Summary: MDLReader : nullpointerexception Initial Comment: When reading a SDF file with several molecules, each molecule is seperated with $$$$. At the end of the file is also a $$$$. There will be a nullpointerexception on this. I changed the code with the following lines : String line = input.readLine(); if (line == null) return null; So there is no exception anymore. MDLReader. private Molecule readMolecule() { int atoms = 0, bonds = 0, atom1 = 0, atom2 = 0, order = 0, stereo = 0; double x=0, y=0, z=0; int[][] conMat = new int[0][0]; String help; Molecule molecule = new Molecule(); Bond bond; Atom atom; try { String title = new String(input.readLine() + "\n" + input.readLine() + "\n" + input.readLine()); molecule.setTitle(title); // added 30.09 hvanderz - reading last empty line (nullpointer exception) String line = input.readLine(); if (line == null) return null; StringBuffer strBuff = new StringBuffer(line); ... ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2002-10-08 16:43 Message: Logged In: YES user_id=25678 This bug will be fixed when the MDLReader gets a redesign. ---------------------------------------------------------------------- Comment By: Hans Vanderzijl (hansvdz) Date: 2002-10-08 16:30 Message: Logged In: YES user_id=625197 I made a ViewerFrame. This frame reads a sdf file and shows every molecule in a seperate panel. A NullPointerException occurs, but it still shows the frame. I shall upload the sdf file. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2002-10-08 16:20 Message: Logged In: YES user_id=25678 What is the exact error you get? The Exception should be catched, and not result in any problem. I agree that the reader has a strange design. The program does not really fail does it? Can you contribute a test SDF file that we can use for testing purposes (it will be distributed)? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 |
From: <no...@so...> - 2002-10-08 14:20:33
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Bugs item #620242, was opened at 2002-10-08 16:08 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 Category: org.openscience.cdk.io Group: None Status: Open Resolution: None Priority: 5 Submitted By: Hans Vanderzijl (hansvdz) Assigned to: Nobody/Anonymous (nobody) Summary: MDLReader : nullpointerexception Initial Comment: When reading a SDF file with several molecules, each molecule is seperated with $$$$. At the end of the file is also a $$$$. There will be a nullpointerexception on this. I changed the code with the following lines : String line = input.readLine(); if (line == null) return null; So there is no exception anymore. MDLReader. private Molecule readMolecule() { int atoms = 0, bonds = 0, atom1 = 0, atom2 = 0, order = 0, stereo = 0; double x=0, y=0, z=0; int[][] conMat = new int[0][0]; String help; Molecule molecule = new Molecule(); Bond bond; Atom atom; try { String title = new String(input.readLine() + "\n" + input.readLine() + "\n" + input.readLine()); molecule.setTitle(title); // added 30.09 hvanderz - reading last empty line (nullpointer exception) String line = input.readLine(); if (line == null) return null; StringBuffer strBuff = new StringBuffer(line); ... ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2002-10-08 16:20 Message: Logged In: YES user_id=25678 What is the exact error you get? The Exception should be catched, and not result in any problem. I agree that the reader has a strange design. The program does not really fail does it? Can you contribute a test SDF file that we can use for testing purposes (it will be distributed)? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=620242&group_id=20024 |