Figure 1.

Java code for the method getSelectedAminoacids( ). A. Initialize the local variable vers with the current version of the amino acid sequence. This value is changed whenever the residue sequence changes. Before the analysis is performed, the value of selectedResidues is null, so that the code following these lines will always be executed when the plugin is initialized; B. If the residues have not been changed since the last analysis, just return the previously selected residues; C. We use the private class method setSequence to alter the class variable seq, which holds the current amino acid sequence. The method getResidueType of the class StrapProtein is used to retrieve the current amino acid sequence from the STRAP GUI; D. pred_coils performs the analysis for coiled coil regions, and places the results of its analysis in the array selectedResidues; E. Finally, we return the array selectedResidues to the STRAP GUI, which uses this information in order to mark the residues in amino acid sequences or protein structures.