CONECT/LINK line-length bug fix for the PDB Parser (already in BioJava Master branch).#707
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josemduarte merged 2 commits intobiojava:bugfixes-4.2from Oct 19, 2017
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…usually indicative of misformated lines. Added line length checks within the LINK and CONECT parsing blocks to allow for short lines to be parsed.
josemduarte
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Sep 12, 2017
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Looks good, thanks! Only 2 minor comments
| else if (recordName.equals("TURN")) pdb_TURN_Handler( line ) ; | ||
| } | ||
| } catch (StringIndexOutOfBoundsException ex) { | ||
| logger.info("Unable to parse [" + line + "]"); |
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This should be warn level
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| /** | ||
| * This class will test parsing short CONECT lines. | ||
| * <p>(c) 2016 DNASTAR, Inc.</p> |
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Please remove this for biojava code
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This solves #705, doesn't it? |
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@larsonmattr any chance to make the changes above before merging? |
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Jose,
My apologies that this fell off of my radar. I will make the fixes.
…On Wed, Oct 18, 2017 at 11:15 AM, Jose Manuel Duarte < ***@***.***> wrote:
@larsonmattr <https://github.com/larsonmattr> any chance to make the
changes above before merging?
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Thanks -
I've updated the change to fix the issues you highlighted.
…On Wed, Oct 18, 2017 at 12:13 PM, Matt Larson ***@***.***> wrote:
Jose,
My apologies that this fell off of my radar. I will make the fixes.
On Wed, Oct 18, 2017 at 11:15 AM, Jose Manuel Duarte <
***@***.***> wrote:
> @larsonmattr <https://github.com/larsonmattr> any chance to make the
> changes above before merging?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#707 (comment)>, or mute
> the thread
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>
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Matt Larson, PhD
Madison, WI 53705 U.S.A.
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Matt Larson, PhD
Madison, WI 53705 U.S.A.
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josemduarte
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Oct 19, 2017
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Thanks @larsonmattr. I'll release a new bugfix version today that will contain this and other small maintenance fixes. |
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These are line-length bug fixes which are in the Master BioJava branch but not in the bugfixes-4.2 (4.2.8 branch).