1 package jalview.renderer;
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;
8 import jalview.schemes.ColourSchemeI;
10 import java.awt.Color;
13 public interface ResidueShaderI
16 public abstract void setConsensus(ProfilesI cons);
18 public abstract boolean conservationApplied();
20 public abstract void setConservationApplied(boolean conservationApplied);
22 public abstract void setConservation(Conservation cons);
24 public abstract void alignmentChanged(AnnotatedCollectionI alignment,
25 Map<SequenceI, SequenceCollectionI> hiddenReps);
28 * Sets the percentage consensus threshold value, and whether gaps are ignored
29 * in percentage identity calculation
31 * @param consensusThreshold
34 public abstract void setThreshold(int consensusThreshold,
37 public abstract void setConservationInc(int i);
39 public abstract int getConservationInc();
42 * Get the percentage threshold for this colour scheme
44 * @return Returns the percentage threshold
46 public abstract int getThreshold();
49 * Returns the possibly context dependent colour for the given symbol at the
50 * aligned position in the given sequence. For example, the colour may depend
51 * on the symbol's relationship to the consensus residue for the column.
58 public abstract Color findColour(char symbol, int position, SequenceI seq);
60 public abstract ColourSchemeI getColourScheme();
62 public abstract void setColourScheme(ColourSchemeI cs);