/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.analysis.Conservation;
+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
{
- public Color findColour(char c);
+ /**
+ * Returns the colour for the given character. For use when the colour depends
+ * only on the symbol.
+ *
+ * @param c
+ * @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 symbol
+ * @param position
+ * @param seq
+ * @return
+ */
+ Color findColour(char symbol, int position, SequenceI seq);
+
+ /**
+ * Assigns the given consensus profile for the colourscheme
+ */
+ void setConsensus(ProfilesI hconsensus);
+
+ /**
+ * Assigns the given conservation to the colourscheme
+ *
+ * @param c
+ */
+ void setConservation(Conservation c);
+
+ /**
+ * 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
+ */
+ boolean conservationApplied();
- public Color findColour(char c, int j);
+ /**
+ * Sets the scale factor for bleaching of colour in unconserved regions
+ *
+ * @param i
+ */
+ void setConservationInc(int i);
- public void setConsensus(java.util.Hashtable[] h);
+ /**
+ * Returns the scale factor for bleaching colour in unconserved regions
+ *
+ * @return
+ */
+ int getConservationInc();
- public void setConservation(jalview.analysis.Conservation c);
+ /**
+ * Returns the percentage identity threshold for applying colourscheme
+ *
+ * @return
+ */
+ int getThreshold();
- public boolean conservationApplied();
+ /**
+ * Sets the percentage identity threshold and type of %age identity
+ * calculation for shading
+ *
+ * @param pct
+ * 0..100 percentage identity for applying this colourscheme
+ * @param ignoreGaps
+ * when true, calculate PID without including gapped positions
+ */
+ void setThreshold(int pct, boolean ignoreGaps);
- public void setConservationInc(int i);
+ /**
+ * Recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
+ *
+ * @param alignment
+ * @param hiddenReps
+ */
+ void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps);
- public int getConservationInc();
+ /**
+ * 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.
+ *
+ * @param sg
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transferred
+ */
+ ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
- public int getThreshold();
+ /**
+ * 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);
- public void setThreshold(int ct, boolean ignoreGaps);
+ /**
+ * Answers the 'official' name of the colour scheme (as used, for example, as
+ * a Jalview startup parameter)
+ *
+ * @return
+ */
+ String getSchemeName();
+ /**
+ * 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.
+ *
+ * @return
+ */
+ boolean isSimple();
}
git://source.jalview.org / jalview.git / blobdiff