Merge bugfix4.2 branch - #819

Merged

sbliven merged 66 commits into

biojava:masterfrom

sbliven:merge-bugfix

Jan 2, 2019

Commits on Nov 30, 2016

Added exception handler for out-of-bounds errors when parsing lines, usually indicative of misformated lines.
Matt Larson
committed
50c34d3

Commits on Feb 18, 2017

Catching empty coordinates earlier in quat sym detection
josemduarte
committed
0f322ee
[maven-release-plugin]prepare release biojava-4.2.6
Jenkins
committed
6624619
[maven-release-plugin]prepare for next development iteration
Jenkins
committed
2888f8f

Commits on Mar 2, 2017

Commits on Mar 7, 2017

Bugfix: chromosome mapping tool returns -1 if position falls outside coding region on the forward strand

Yana Valasatava
authored and
josemduarte
committed
331ac26
Chromosome mapping tool patch for converting a genomic position to the position on mRNA for the genes leaving on the forward strand

Yana Valasatava
authored and
josemduarte
committed
4e292b4
Unit tests for converting a genomic position to the position on mRNA for the genes leaving on the forward strand

Yana Valasatava
authored and
josemduarte
committed
73b56c3
Chromosome mapping tool: unit test to check handling multiple UTRs preceding the coding region

Yana Valasatava
authored and
josemduarte
committed
55639ac

Commits on Mar 8, 2017

[maven-release-plugin]prepare release biojava-4.2.7
Jenkins
committed
b369f5f
[maven-release-plugin]prepare for next development iteration
Jenkins
committed
714649c

Commits on Jul 5, 2017

Commits on Jul 6, 2017

Updating ligand URLs to latest RCSB convention
josemduarte
committed
dc7f3ea
Better http than https
josemduarte
committed
a38c8c8
Merge pull request #683 from josemduarte/bugfixes-4.2
josemduarte
authored
9291fab
Merge pull request #682 from valasatava/bugfixes-4.2
josemduarte
authored
1653b63
[maven-release-plugin] prepare release biojava-4.2.8
josemduarte
committed
9fb8fcc
[maven-release-plugin] prepare for next development iteration
josemduarte
committed
f7f5eec
[maven-release-plugin] rollback the release of biojava-4.2.8
josemduarte
committed
7c802e0
Fix for pom needed for release to be performed
josemduarte
committed
d7d7a28
[maven-release-plugin] prepare release biojava-4.2.8
josemduarte
committed
dee8b41
[maven-release-plugin] prepare for next development iteration
josemduarte
committed
bce39db

Commits on Jul 13, 2017

Fixing test after case change in RCSB rest service
josemduarte
committed
a24e23e

Commits on Oct 3, 2017

Updating genenames.org url to https
josemduarte
committed
97ca0c1

Commits on Oct 18, 2017

Changes for CONECT/LINK
larsonmattr
committed
e88637c
Fixing tests after PDB v5 remediation
josemduarte
committed
017df86

Commits on Oct 19, 2017

Fixing test issues related to v5 and changes in rcsb
josemduarte
committed
b840f05
Fixing another test problem related to v5
josemduarte
committed
5d753fd
Merge pull request #707 from edlunde-dnastar/linelength424
josemduarte
authored
58b00ff
Updating phosphosite urls to https
josemduarte
committed
103f8a1
[maven-release-plugin] prepare release biojava-4.2.9
josemduarte
committed
1a7244d
[maven-release-plugin] prepare for next development iteration
josemduarte
committed
d453215

Commits on Nov 16, 2017

Backporting bugfix from 5.0 branch
josemduarte
committed
56b9d07

Commits on Dec 8, 2017

Fix and unit test for #715
josemduarte
committed
fe8c716
Back porting fix and test for #716
josemduarte
committed
8f5d03d

Commits on Dec 12, 2017

Commits on Jan 11, 2018

Fixing hmmer scan web service and adding test for it
josemduarte
committed
9115b31

Commits on Jan 12, 2018

[maven-release-plugin] prepare release biojava-4.2.11
josemduarte
committed
fc0bb0b
[maven-release-plugin] prepare for next development iteration
josemduarte
committed
e9e69b0
Fix rcsb/symmetry#92: NullPointerException
sbliven
committed
0b24ceb

Commits on Jan 15, 2018

Merge pull request #723 from sbliven/fix92
sbliven
authored
b62c2e1

Commits on Jun 4, 2018

Improving CathInstallation logging
sbliven
committed
5c1a335
Add test for #703
sbliven
committed
4785d57

Commits on Jun 8, 2018

Commits on Jun 12, 2018

Incorporating suggestions from @josemduarte
sbliven
committed
f5b325f

Commits on Jun 14, 2018

Add GlobalsHelper class to manage our global state
sbliven
committed
13f267c
Fix NullPointer when restoring global state
sbliven
committed
c1c3c30

Commits on Jun 15, 2018

Fix test failure due to PDB change
sbliven
committed
0c10a2e

Commits on Jun 18, 2018

Revert fix for mmcif files without auth_seq_id column
sbliven
committed
08ab3e1
Merge pull request #774 from sbliven/fix703
sbliven
authored
5a4a68c

Commits on Jun 25, 2018

Add maven-deploy-plugin
sbliven
committed
211276d

Commits on Jun 27, 2018

Fix NonstandardProteinCompoundTest failure
sbliven
committed
99fda9d

Commits on Jan 2, 2019

Merge branch 'bugfixes-4.2'
sbliven
committed
0501615
Fix compilation errors from merge
sbliven
committed
893a391
Fix test failures from merge
sbliven
committed
1a2af22