1 package jalview.datamodel;
3 public interface ProfileI
7 * Set the full profile of counts
11 public abstract void setCounts(ResidueCount residueCounts);
14 * Returns the percentage identity of the profile, i.e. the highest proportion
15 * of conserved (equal) symbols. The percentage is as a fraction of all
16 * sequences, or only ungapped sequences if flag ignoreGaps is set true.
21 public abstract float getPercentageIdentity(boolean ignoreGaps);
24 * Returns the full symbol counts for this profile
28 public abstract ResidueCount getCounts();
31 * Returns the number of sequences in the profile
35 public abstract int getHeight();
38 * Returns the number of sequences in the profile which had a gap character
39 * (or were too short to be included in this column's profile)
43 public abstract int getGapped();
46 * Returns the highest count for any symbol(s) in the profile
50 public abstract int getMaxCount();
53 * Returns the symbol (or concatenated symbols) which have the highest count
54 * in the profile, or an empty string if there were no symbols counted
58 public abstract String getModalResidue();
61 * Answers the number of non-gapped sequences in the profile
65 public abstract int getNonGapped();