/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
public interface ColourSchemeI
{
+ /**
+ *
+ * @param c
+ * @return the colour for the given character
+ */
public Color findColour(char c);
- public Color findColour(char c, int j);
+ /**
+ *
+ * @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);
- public void setConsensus(java.util.Hashtable[] h);
+ /**
+ * 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
+ */
public boolean conservationApplied();
+ /**
+ * 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
+ */
public int getConservationInc();
+ /**
+ *
+ * @return percentage identity threshold for applying colourscheme
+ */
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
+ */
public void setThreshold(int ct, boolean ignoreGaps);
+ /**
+ * recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
+ *
+ * @param alignment
+ * @param hiddenReps
+ */
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps);
+
+ /**
+ * 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
+ */
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
}