Class XMLFileFilter should be declared as final.

Comment matches to-do format 'TODO:'.

Comment matches to-do format 'TODO:'.

Comment matches to-do format 'TODO:'.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Line is longer than 120 characters (found 140).

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'.

Expected @PARAM tag for 'daughterProspero'.

Expected @PARAM tag for 'daughterDeadpan'.

Conditional logic can be removed.

Missing a Javadoc comment.

Expected @PARAM tag for 'daughterProspero'.

Expected @PARAM tag for 'daughterDeadpan'.

First sentence should end with a period.

Expected @PARAM tag for 'daughterProspero'.

Expected @PARAM tag for 'daughterDeadpan'.

First sentence should end with a period.

More than 7 parameters (found 8).

Expected @PARAM tag for 'daughterProspero'.

Expected @PARAM tag for 'daughterDeadpan'.

Expected @PARAM tag for 'daughterProspero'.

Expected @PARAM tag for 'daughterDeadpan'.

Line is longer than 120 characters (found 131).

Line is longer than 120 characters (found 131).

Comment matches to-do format 'TODO:'.

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.

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]*|_)$'.

Using the '.*' form of import should be avoided - arcade.potts.agent.cell.*.

Missing a Javadoc comment.

Missing a Javadoc comment.

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.

Comment matches to-do format 'TODO:'.

Missing a Javadoc comment.

Missing a Javadoc comment.

First sentence should end with a period.

Missing a Javadoc comment.

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.

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

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Missing a Javadoc comment.

Comment matches to-do format 'TODO:'.

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

Comment matches to-do format 'TODO:'.

'module' hides a field.

'module' hides a field.

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

'VARIABLE_DEF' should be separated from previous line.

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

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

';' is followed by whitespace.

Avoid nested blocks.

Line is longer than 100 characters (found 101).

Line is longer than 100 characters (found 140).

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 151).

Line is longer than 100 characters (found 110).