/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.schemes;
-import java.awt.Color;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import java.awt.Color;
+import java.util.Map;
+
public interface ColourSchemeI
{
/**
/**
*
- * @param c - sequence symbol or gap
- * @param j - position in seq
- * @param seq - sequence being coloured
- * @return context dependent colour for the given symbol at the position in the given sequence
+ * @param c
+ * - sequence symbol or gap
+ * @param j
+ * - position in seq
+ * @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(java.util.Hashtable[] h);
+ 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
+ *
+ * @param conservationApplied
*/
public void setConservationApplied(boolean conservationApplied);
+
/**
*
* @return true if conservation shading is enabled for this colourscheme
/**
* set scale factor for bleaching of colour in unconserved regions
+ *
* @param i
*/
public void setConservationInc(int i);
/**
*
- * @return scale factor for bleaching colour in unconserved regions
+ * @return scale factor for bleaching colour in unconserved regions
*/
public int getConservationInc();
public int getThreshold();
/**
- * set percentage identity threshold and type of %age identity calculation for shading
- * @param ct 0..100 percentage identity for applying this colourscheme
- * @param ignoreGaps when true, calculate PID without including gapped positions
+ * set percentage identity threshold and type of %age identity calculation for
+ * shading
+ *
+ * @param ct
+ * 0..100 percentage identity for applying this colourscheme
+ * @param ignoreGaps
+ * when true, calculate PID without including gapped positions
*/
public void setThreshold(int ct, boolean ignoreGaps);
/**
- * recalculate dependent data using the given sequence collection, taking account of hidden rows
+ * recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
+ *
* @param alignment
* @param hiddenReps
*/
Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
- * create a new instance of the colourscheme configured to colour the given connection
+ * create a new instance of the colourscheme configured to colour the given
+ * connection
+ *
* @param sg
* @param hiddenRepSequences
* @return copy of current scheme with any inherited settings transfered