*/
package jalview.schemes;
+import jalview.analysis.Conservation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceCollectionI;
public interface ColourSchemeI
{
/**
+ * Returns the fixed colour for the colour scheme. For use when the colour
+ * does not vary.
+ *
+ * @return
+ */
+ Color findColour();
+
+ /**
+ * Returns the colour for the given character. For use when the colour depends
+ * only on the symbol.
*
* @param c
- * @return the colour for the given character
+ * @return
*/
Color findColour(char c);
/**
+ * Returns the possibly context dependent colour for the given symbol at the
+ * aligned position in the given sequence. For example, the colour may depend
+ * on the symbol's relationship to the consensus residue for the column.
*
- * @param c
- * - sequence symbol or gap
- * @param j
- * - position in seq
+ * @param symbol
+ * @param position
* @param seq
- * - sequence being coloured
- * @return context dependent colour for the given symbol at the position in
- * the given sequence
+ * @return
*/
- Color findColour(char c, int j, SequenceI seq);
+ Color findColour(char symbol, int position, SequenceI seq);
/**
- * assign the given consensus profile for the colourscheme
+ * Assigns the given consensus profile for the colourscheme
*/
void setConsensus(ProfilesI hconsensus);
/**
- * assign the given conservation to the colourscheme
+ * Assigns the given conservation to the colourscheme
*
* @param c
*/
- void setConservation(jalview.analysis.Conservation c);
+ void setConservation(Conservation c);
/**
- * enable or disable conservation shading for this colourscheme
+ * Enable or disable conservation shading for this colourscheme
*
* @param conservationApplied
*/
void setConservationApplied(boolean conservationApplied);
/**
+ * Answers true if conservation shading is enabled for this colourscheme
*
- * @return true if conservation shading is enabled for this colourscheme
+ * @return
*/
boolean conservationApplied();
/**
- * set scale factor for bleaching of colour in unconserved regions
+ * Sets the scale factor for bleaching of colour in unconserved regions
*
* @param i
*/
void setConservationInc(int i);
/**
+ * Returns the scale factor for bleaching colour in unconserved regions
*
- * @return scale factor for bleaching colour in unconserved regions
+ * @return
*/
int getConservationInc();
/**
+ * Returns the percentage identity threshold for applying colourscheme
*
- * @return percentage identity threshold for applying colourscheme
+ * @return
*/
int getThreshold();
/**
- * set percentage identity threshold and type of %age identity calculation for
- * shading
+ * Sets the percentage identity threshold and type of %age identity
+ * calculation for shading
*
- * @param ct
+ * @param pct
* 0..100 percentage identity for applying this colourscheme
* @param ignoreGaps
* when true, calculate PID without including gapped positions
*/
- void setThreshold(int ct, boolean ignoreGaps);
+ void setThreshold(int pct, boolean ignoreGaps);
/**
- * recalculate dependent data using the given sequence collection, taking
+ * Recalculate dependent data using the given sequence collection, taking
* account of hidden rows
*
* @param alignment
Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
- * create a new instance of the colourscheme configured to colour the given
- * connection
+ * Creates and returns a new instance of the colourscheme configured to colour
+ * the given connection
*
* @param sg
* @param hiddenRepSequences
*/
ColourSchemeI applyTo(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
+ /**
+ * Answers true if the colour scheme is suitable for the given data, else
+ * false. For example, some colour schemes are specific to either peptide or
+ * nucleotide, or only apply if certain kinds of annotation are present.
+ *
+ * @param ac
+ * @return
+ */
+ // TODO can make this method static in Java 8
+ boolean isApplicableTo(AnnotatedCollectionI ac);
+
+ /**
+ * Answers the 'official' name of the colour scheme (as used, for example, as
+ * a Jalview startup parameter)
+ *
+ * @return
+ */
+ String getSchemeName();
}