[FEATURE] change file format of cached files

- write spectra and chromatogram number at the end of the file
- allows to start writing spectra without knowledge of the number of
  data to write
- [DOC] fix output
[DOC] clearer documentation
[API] simplify API of MSDataCachedConsumer

- it is now longer necessary to know the number of spectra and
  chromatograms beforehand
[FIX #806] ConsensusID

TOPP ConsensusID FileType idXML:
- after reading a peptide identification, sort their peptide hits with assignRanks()
- set the score type and the higherScoreBetter flag in the final peptide identifications before apply consensus

ConsensusID:
- ranked:
	- read the score_type information to write it into the output file
	- set higherScoreBetter = true, to recognize it easier that it should be true
	- setScoreType with Consensus_ranked instead of Consensus_average

- PEPMatrix_, PEPIons_: raise error if higher_better == true instead of false

Check if score type and higherScoreBetter are equal in all peptide identifications (average_, PEPMatrix_, PEPIons_):
move the check to the peptide identifications loop instead of the peptide hits loop, because only peptide information is needed for the check.

Test:
- ConsensusID_1: instead of average is ranked
- ConsensusID_4 (algorithm "PEPMatrix_"): test if the peptide hits are sorted

modified:   ../src/openms/source/ANALYSIS/ID/ConsensusID.cpp
modified:   ../src/tests/topp/CMakeLists.txt
modified:   ../src/tests/topp/ConsensusID_1_output.idXML
new file:   ../src/tests/topp/ConsensusID_4_input.idXML
new file:   ../src/tests/topp/ConsensusID_4_output.idXML
new file:   ../src/tests/topp/ConsensusID_4_parameters.ini
modified:   ../src/topp/ConsensusID.cpp
[FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists
[FIX] fix error from 5b5bb90673145db3dd21927c591f2b925ca55a6a
[FIX] cleanup, add documentation
Implemented feedback from hroest
Merge pull request #1 from hroest/fix/small_fix

[FIX] fix error from 5b5bb90673145db3dd21927c591f2b925ca55a6a
Implemented further feedback
[BUILD] do not warn about unused functions

- Wunused-function is a concept with very limited utility and it will
  warn about all files that include a header with static functions but
  does not use _all_ of them.
- for example: ITRAQLabeler.cpp includes MatrixUtils.h and uses the
  function convertOpenMSMatrix2EigenMatrixXd but does not use
  matrixIsIdentityMatrix -> a warning will be emitted about the unused
  matrixIsIdentityMatrix function.
[FIX] removed unused typedefs
[FIX] add static cast (no narrowing conversion)
[FIX] add DLLAPI to two functions

- these two explicit template initializations are only ever included in
  BaseModel.cpp and are thus part of the library. To be visible to the
  client, they need to be exported explicitly (they are used in
  CONCEPT/Factory.h)
[FIX] add DLLAPI to assignment operator

- since the assignment operator of ToolDescription is available through
  the API, it also needs to able to assign ToolExternalDetails which
  contains a MappingParam object.
[FIX] add DLLAPI to two functions
[BUILD] turn on -fvisibility=hidden for gcc
made SplineSpectrum::Navigator public (not usable otherwise); fix compile error (VS2013) due to missing include; fixed interface(names); fixed intendation
fixed segfault (>=0 issue)
hide default Ctor; add missing tests (no content)