Avoid nested blocks.

Name 'EPSILON' must match pattern '^[a-z][a-zA-Z0-9]*$'.

'module' hides a field.

'module' hides a field.

Comment matches to-do format 'TODO:'.

'module' hides a field.

'module' hides a field.

'VARIABLE_DEF' should be separated from previous line.

File length is 2,371 lines (max allowed is 2,000).

';' is followed by whitespace.

Comment matches to-do format 'TODO:'.

Comment matches to-do format 'TODO:'.

Comment matches to-do format 'TODO:'.

Class XMLFileFilter should be declared as final.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Expression can be simplified.

Expression can be simplified.

Class 'PottsModuleFlyStemProliferation' looks like designed for extension (can be subclassed), but the method 'updateVolumeBasedGrowthRate' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PottsModuleFlyStemProliferation' final or making the method 'updateVolumeBasedGrowthRate' static/final/abstract/empty, or adding allowed annotation for the method.

Missing a Javadoc comment.

Expression can be simplified.

Class 'PottsModuleFlyStemProliferation' looks like designed for extension (can be subclassed), but the method 'updateGrowthRateBasedOnOtherNBs' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PottsModuleFlyStemProliferation' final or making the method 'updateGrowthRateBasedOnOtherNBs' static/final/abstract/empty, or adding allowed annotation for the method.

Missing a Javadoc comment.

Name 'Kn' must match pattern '^([a-z][a-zA-Z0-9]*|_)$'.

Name 'Npn' must match pattern '^([a-z][a-zA-Z0-9]*|_)$'.

Name 'apical_axis' must match pattern '^([a-z][a-zA-Z0-9]*|_)$'.

Expected @param tag for 'stemType'.

Expected @param tag for 'rotatedNormalVector'.

Conditional logic can be removed.

Missing a Javadoc comment.

First sentence should end with a period.

First sentence should end with a period.

Line is longer than 120 characters (found 131).

Line is longer than 120 characters (found 131).

First sentence should end with a period.

Class 'PottsModuleFlyStemProliferation' looks like designed for extension (can be subclassed), but the method 'getNBsInSimulation' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PottsModuleFlyStemProliferation' final or making the method 'getNBsInSimulation' static/final/abstract/empty, or adding allowed annotation for the method.

Missing a Javadoc comment.

'if' construct must use '{}'s.

Missing a Javadoc comment.

Class 'PottsModuleFlyGMCDifferentiation' looks like designed for extension (can be subclassed), but the method 'updateGrowthRate' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PottsModuleFlyGMCDifferentiation' final or making the method 'updateGrowthRate' static/final/abstract/empty, or adding allowed annotation for the method.

Missing a Javadoc comment.

'if' construct must use '{}'s.

'if' construct must use '{}'s.

Unused import - arcade.potts.agent.cell.PottsCellFlyNeuron.

Class 'PottsModuleProliferationVolumeBasedDivision' looks like designed for extension (can be subclassed), but the method 'updateCellVolumeBasedGrowthRate' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PottsModuleProliferationVolumeBasedDivision' final or making the method 'updateCellVolumeBasedGrowthRate' static/final/abstract/empty, or adding allowed annotation for the method.

Missing a Javadoc comment.

Name 'Ka' must match pattern '^([a-z][a-zA-Z0-9]*|_)$'.

Wrong order for 'sim.engine.SimState' import.

Extra separation in import group before 'arcade.potts.util.PottsEnums.State'

Missing a Javadoc comment.

Missing a Javadoc comment.

Variable 'prosperoCounter' must be private and have accessor methods.

Class 'PottsCellFlyStem' looks like designed for extension (can be subclassed), but the method 'setApicalAxis' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PottsCellFlyStem' final or making the method 'setApicalAxis' static/final/abstract/empty, or adding allowed annotation for the method.

Missing a Javadoc comment.

Line is longer than 120 characters (found 151).

Class 'PottsCellFlyStem' looks like designed for extension (can be subclassed), but the method 'make' does not have javadoc that explains how to do that safely. If class is not designed for extension consider making the class 'PottsCellFlyStem' final or making the method 'make' static/final/abstract/empty, or adding allowed annotation for the method.

Missing a Javadoc comment.

Comment matches to-do format 'TODO:'.

Method create3DDrawers length is 277 lines (max allowed is 150).

Process completed with exit code 1.

Line is longer than 100 characters (found 101).

Line is longer than 100 characters (found 105).

Line is longer than 100 characters (found 113).

Line is longer than 100 characters (found 131).

Line is longer than 100 characters (found 131).

Line is longer than 100 characters (found 110).

Line is longer than 100 characters (found 151).