*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public interface ColourSchemeI
{
/**
+ * 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
- * @return the colour for the given character
- */
- public Color findColour(char c);
-
- /**
- *
- * @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
- */
- public Color findColour(char c, int j, SequenceI seq);
-
- /**
- * assign the given consensus profile for the colourscheme
- */
- public void setConsensus(ProfilesI hconsensus);
-
- /**
- * assign the given conservation to the colourscheme
- *
- * @param c
- */
- public void setConservation(jalview.analysis.Conservation c);
-
- /**
- * enable or disable conservation shading for this colourscheme
- *
- * @param conservationApplied
- */
- public void setConservationApplied(boolean conservationApplied);
-
- /**
- *
- * @return true if conservation shading is enabled for this colourscheme
+ * @param consensusResidue
+ * the modal symbol (e.g. K) or symbols (e.g. KF) for the column
+ * @param pid
+ * the percentage identity of the column's consensus (if known)
+ * @return
*/
- public boolean conservationApplied();
+ Color findColour(char symbol, int position, SequenceI seq,
+ String consensusResidue, float pid);
/**
- * set scale factor for bleaching of colour in unconserved regions
+ * Recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
*
- * @param i
+ * @param alignment
+ * @param hiddenReps
*/
- public void setConservationInc(int i);
+ void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
+ * Creates and returns a new instance of the colourscheme configured to colour
+ * the given collection. Note that even simple colour schemes should return a
+ * new instance for each call to this method, as different instances may have
+ * differing shading by consensus or percentage identity applied.
*
- * @return scale factor for bleaching colour in unconserved regions
+ * @param viewport
+ * - the parent viewport
+ * @param sg
+ * - the collection of sequences to be coloured
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transferred
*/
- public int getConservationInc();
+ ColourSchemeI getInstance(AlignViewportI viewport,
+ 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.
*
- * @return percentage identity threshold for applying colourscheme
+ * @param ac
+ * @return
*/
- public int getThreshold();
+ // TODO can make this method static in Java 8
+ boolean isApplicableTo(AnnotatedCollectionI ac);
/**
- * set percentage identity threshold and type of %age identity calculation for
- * shading
+ * Answers the 'official' name of the colour scheme (as used, for example, as
+ * a Jalview startup parameter)
*
- * @param ct
- * 0..100 percentage identity for applying this colourscheme
- * @param ignoreGaps
- * when true, calculate PID without including gapped positions
+ * @return
*/
- public void setThreshold(int ct, boolean ignoreGaps);
+ String getSchemeName();
/**
- * recalculate dependent data using the given sequence collection, taking
- * account of hidden rows
+ * Answers true if the colour scheme depends only on the sequence symbol, and
+ * not on other information such as alignment consensus or annotation. (Note
+ * that simple colour schemes may have a fading by percentage identity or
+ * conservation overlaid.) Simple colour schemes can be propagated to
+ * structure viewers.
*
- * @param alignment
- * @param hiddenReps
+ * @return
*/
- public void alignmentChanged(AnnotatedCollectionI alignment,
- Map<SequenceI, SequenceCollectionI> hiddenReps);
+ boolean isSimple();
/**
- * create a new instance of the colourscheme configured to colour the given
- * connection
+ * Answers true if the colour scheme has a colour specified for gaps.
*
- * @param sg
- * @param hiddenRepSequences
- * @return copy of current scheme with any inherited settings transfered
+ * @return
*/
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
-
+ boolean hasGapColour();
}