Major changes in the pia core.

[ypriverol]

• [ ] We have updated the pom file with new versionf for most of the dependencies that relies in xxindex.
• [ ] We have included some inor changes arelated with code style for example String encode of single characters. replace all "c" -> c
• [ ] I have removed the visualization part of PIA. You can update you version if you want and then merge this PR and fix the errors.

thanks @julianu

[julianu]

There seems to be an dependency problem with org.mozillla.chardet: it cannot be downloaded (neither by travis, nor by myself) using the current POM file. It is a dependency of xxindex, though.

[julianu]

My last comment is probably directly related to this one: https://github.com/PRIDE-Utilities/jmzml/issues/22

[codecov-io]

Codecov Report

Merging #141 into master will increase coverage by 2.56%. The diff coverage is 38.31%.

@@             Coverage Diff              @@
##             master     #141      +/-   ##
============================================
+ Coverage      52.8%   55.37%   +2.56%     
- Complexity     2316     2331      +15     
============================================
  Files           174      161      -13     
  Lines         17488    16529     -959     
  Branches       2879     2744     -135     
============================================
- Hits           9235     9153      -82     
+ Misses         7290     6376     -914     
- Partials        963     1000      +37

Impacted Files	Coverage Δ	Complexity Δ
.../protein/inference/SpectrumExtractorInference.java	84.61% <ø> (-0.05%)	65 <0> (ø)
...c/pia/modeller/protein/ProteinExecuteCommands.java	0% <ø> (ø)	0 <0> (ø)	:arrow_down:
.../de/mpc/pia/tools/openms/jaxb/DigestionEnzyme.java	44% <ø> (+1.69%)	3 <0> (ø)	:arrow_down:
...ler/protein/inference/OccamsRazorWorkerThread.java	0% <0%> (ø)	0 <0> (ø)	:arrow_down:
...mpc/pia/modeller/report/filter/AbstractFilter.java	28.39% <0%> (ø)	28 <0> (ø)	:arrow_down:
...ava/de/mpc/pia/modeller/peptide/ReportPeptide.java	57.25% <0%> (ø)	69 <0> (ø)	:arrow_down:
.../java/de/mpc/pia/intermediate/piaxml/ScoreXML.java	78.57% <0%> (ø)	8 <0> (ø)	:arrow_down:
...c/pia/modeller/report/filter/FilterComparator.java	21.12% <0%> (ø)	1 <0> (ø)	:arrow_down:
...c/pia/intermediate/compiler/PIACachedCompiler.java	71.15% <0%> (ø)	28 <0> (ø)	:arrow_down:
...java/de/mpc/pia/tools/matomo/PIAMatomoTracker.java	0% <0%> (ø)	0 <0> (ø)	:arrow_down:
... and 43 more

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