1 package jalview.schemes;
3 import jalview.analysis.Conservation;
4 import jalview.datamodel.AnnotatedCollectionI;
5 import jalview.datamodel.ProfilesI;
6 import jalview.datamodel.SequenceCollectionI;
7 import jalview.datamodel.SequenceI;
12 public interface CollectionColourSchemeI
15 public abstract void setConsensus(ProfilesI cons);
17 public abstract boolean conservationApplied();
19 public abstract void setConservationApplied(boolean conservationApplied);
21 public abstract void setConservation(Conservation cons);
23 public abstract void alignmentChanged(AnnotatedCollectionI alignment,
24 Map<SequenceI, SequenceCollectionI> hiddenReps);
27 * Sets the percentage consensus threshold value, and whether gaps are ignored
28 * in percentage identity calculation
30 * @param consensusThreshold
33 public abstract void setThreshold(int consensusThreshold,
36 public abstract void setConservationInc(int i);
38 public abstract int getConservationInc();
41 * Get the percentage threshold for this colour scheme
43 * @return Returns the percentage threshold
45 public abstract int getThreshold();
48 * Returns the possibly context dependent colour for the given symbol at the
49 * aligned position in the given sequence. For example, the colour may depend
50 * on the symbol's relationship to the consensus residue for the column.
57 public abstract Color findColour(char symbol, int position, SequenceI seq);
59 public abstract ColourSchemeI getColourScheme();
61 public abstract void setColourScheme(ColourSchemeI cs);