Output file generated on save is: Protein Sequence + Shape

The shape matching algorithm matches returns the phenotype after the first available perfect match. If on folding, the shape generates multiple hydrophobic cores, the shape matching algorithm will match the first in its path and return the corresponding phenotype.

The shape matching algorithm is done by brute force, matching coordinates of the template core with those generated by folding. Based on the success/failure the individual acids in the core are translated in six directions ie. E, SE, SW, W, NW, NE

The Default phenotype is determined prior to using the software. It is set manually by defining which phenotype ( or image ) befits the default and then naming that the phenotype as default.jpg. The current Species Editor application does not provide for a way for the user to choose a Default phenotype

 In Define Phenotype grid cell ( M0, M0 ) is non-editable. It is currently set to the predefined Default phenotype. 

In Define Phenotype grid all cells are editable and user may select any phenotype from the drop down.  No provision is made to avoid conflicting phenotypes for motif pairs. eg. If cell ( M1, M2) = blueTree.jpg, then cell (M2, M1) = redTree.jpg  should throw an exception. In all cases if the users set the cell ( M1, M2) = blueTree.jpg, then automatically cell (M2, M1) = blueTree.jpg  and vice versa.

 Usage via command prompt is not implemented.