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hivdb / sierra

HIVDB Genotypic Resistance Interpretation Program
GNU General Public License v3.0
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NGS (ongoing project, only for code review convenience) #19

Closed philiptzou closed 5 years ago

codecov-io commented 5 years ago

Codecov Report

Merging #19 into master will decrease coverage by 4.18%. The diff coverage is 69.23%.

Impacted file tree graph

@@             Coverage Diff              @@
##             master      #19      +/-   ##
============================================
- Coverage     80.85%   76.66%   -4.19%     
- Complexity     1305     1328      +23     
============================================
  Files            95      104       +9     
  Lines          6612     7269     +657     
  Branches        612      630      +18     
============================================
+ Hits           5346     5573     +227     
- Misses         1146     1579     +433     
+ Partials        120      117       -3
Impacted Files Coverage Δ Complexity Δ
...c/main/java/edu/stanford/hivdb/mutations/Tsms.java 24% <ø> (-3.28%) 3 <0> (ø)
...anford/hivdb/drugresistance/algorithm/AsiRega.java 100% <ø> (ø) 7 <0> (ø) :arrow_down:
...java/edu/stanford/hivdb/utilities/MyFileUtils.java 95.83% <ø> (ø) 4 <0> (ø) :arrow_down:
.../edu/stanford/hivdb/alignment/AlignedSequence.java 96.87% <ø> (ø) 38 <0> (ø) :arrow_down:
...c/main/java/edu/stanford/hivdb/mutations/Gene.java 93.33% <ø> (ø) 15 <0> (ø) :arrow_down:
...ugresistance/reports/TabularResistanceSummary.java 76.39% <ø> (ø) 21 <0> (ø) :arrow_down:
...ain/java/edu/stanford/hivdb/mutations/MutType.java 83.33% <ø> (-16.67%) 1 <0> (-1)
.../main/java/edu/stanford/hivdb/mutations/Sdrms.java 26.31% <ø> (ø) 3 <0> (ø) :arrow_down:
...anford/hivdb/alignment/TabularSequenceSummary.java 89.68% <ø> (ø) 28 <0> (ø) :arrow_down:
...u/stanford/hivdb/drugresistance/algorithm/Asi.java 24% <ø> (ø) 0 <0> (ø) :arrow_down:
... and 105 more

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arodcasanova commented 5 years ago

Overall, I agree that Mutation should be refactored into several classes. One question: why did you choose to use an interface as the root definition of what Mutation classes 'do' instead of an abstract class to define what a Mutation 'is'?

philiptzou commented 5 years ago

@arodcasanova To remove extra spaces:

find . -name "*.java" | xargs sed -i '' 's/[[:space:]]*$//g'
philiptzou commented 5 years ago

@arodcasanova I'm going to close this one. Please comment in #21 instead.