…rst algorithm setting

…detection;

…rst algorithm setting

…detection;

…MORTAR into dev-Max-alkylfragmentation

…Fragmenter;

… duplicate rings;

… duplicate rings;

…Baensch/MORTAR into dev-Max-alkylfragmentation

…urn;

* master: (23 commits)
  Fix, calculateInitialHashMapCapacity() now accepts 0 as number of elements for fragmentations that generate no fragments;
  Preparations for v1.1.1.0 release and corrected some JavaDoc warnings;
  changed some variable names; added try catch block
  added comment
  changed EventHandler; correct casting
  Adjusted context menu label listener according to review comments;
  Removed commented out code;
  Adjustments according to review comments;
  Renamed ListUtil to CollectionUtil to hopefully resolve merge conflicts;
  Fixed a bug in OverviewView;
  Histogram and overview settings are now persisted within the same session and between sessions, calls to them are now managed through view tools manager;
  Carried on harmonising view tools, started working on overview view controller, added central parseSMILES method in ChemUtil;
  Corrected package path for fragmenter classes in tutorial;
  WIP, restructuring histogram view controller;
  Went on with reworking histogram tool, wip;
  Bugfix: if a fragmenter cannot be reloaded, the respective array position is not left empty anymore;
  Renamed TabNames enum constants; ad-hoc work on HistogramViewController; added some notes in HistogramViewController;
  WIP, does not compile! Refactoring and making sure the setting properties are used and updated correctly;
  WIP, does not compile! Started adjusting the overview view;
  WIP, does not compile! A few minor changes to variable names and documentation;
  ...

…ray not HashMap;

…es; fixed CPSF H-saturation bug; cleaned code;

…om chains;

…length;

* master:
  Added SonarCloud badges to readme;
  Removed unnecessary TODO block
  Added custom rule to spotless configuration to throw an error when wildcard imports are detected;
  Added spotless Gradle plugin for automatic code fomatting
  Added yml file for Gradle build in GitHub actions at push to master and pull request
  Added badges to readme

…ods (former implicit, now explicit usage);

* production: (143 commits)
  Satisfy the strict spotless and add a comment;
  Fix issue 72;
  First attempt to fix issue 72 but unsure whether everything is correct now, sometimes there seems to be one parent missing;
  Added note about new drag and drop feature to tutorial;
  MORTAR v1.2-beta
  Add missing dot to satisfy the Javadoc generator
  Add extension filter and supress multi file drop
  Check for file extension on export;
  Clean imports in MainViewController;
  Add drag'n'drop feature
  Preparations for v1.2, adjusted version numbers, updated gradle wrapper, fixed sorting of items tab again, re-introduced the always necessary preprocessing in the Ertl fragmenter, small fix in LogUtil, updated tutorial;
  Marked keepLastFragmentSetting for pipelines as deprecated and removed it from GUI; also removed it from tutorial text but not from the figures;
  New row added in pipeline settings view is now pre-set to selected fragmenter;
  Initial tutorial updates for v1.2, incomplete, but clarifies in more detail that and why MOL file bond orders higher than 4 are not parseable;
  started working on issue 59;
  adjusted widths of combo boxes and text fields in histogram view;
  Made + and - symbols on pipeline settings view bold;
  Added note about character replacement to tooltip;
  Renamed Fragment button in pipeline settings view Run and adjusted button layout of the view in general;
  Adjusted pref and max widths of text fields and combo boxes in settings view;
  ...

# Conflicts:
#	src/main/java/de/unijena/cheminf/mortar/model/fragmentation/FragmentationService.java
#	src/main/resources/de/unijena/cheminf/mortar/message/Message_en_GB.properties

…onjugatedPiSystemFragmenter classes; WIP: test coverage, not clear why Build fails;

…nted default fragmentation test for AlkylStructureFragmenter;

…nd expected fragments;

…ion;

…detection;