package jalview.datamodel; import jalview.util.MapList; /** * Stores mapping between the columns of a protein alignment and a DNA alignment * and a list of individual codon to amino acid mappings between sequences. */ public class AlignedCodonFrame { /** * array of nucleotide positions for aligned codons at column of aligned proteins. */ public int[][] codons = null; /** * width of protein sequence alignement * implicit assertion that codons.length >= aaWidth */ public int aaWidth=0; /** * initialise codon frame with a nominal alignment width * @param aWidth */ public AlignedCodonFrame(int aWidth) { codons = new int[aWidth][]; for (int res = 0; res < aWidth; res++) codons[res] = null; } /** * ensure that codons array is at least as wide as aslen residues * @param aslen * @return (possibly newly expanded) codon array */ public int[][] checkCodonFrameWidth(int aslen) { if (codons.length <= aslen + 1) { // probably never have to do this ? int[][] c = new int[codons.length + 10][]; for (int i = 0; i < codons.length; i++) { c[i] = codons[i]; codons[i] = null; } codons = c; } return codons; } /** * @return width of aligned translated amino acid residues */ public int getaaWidth() { return aaWidth; } /** * increase aaWidth by one and insert a new aligned codon position space at aspos. * @param aspos */ public void insertAAGap(int aspos, char gapCharacter) { // this aa appears before the aligned codons at aspos - so shift them in each pair of mapped sequences aaWidth++; for (int sq=0;aaSeqs!=null && sq