/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.Color;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import java.awt.Color;
+import java.util.Map;
+
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
+ * @param symbol
+ * @param position
+ * @param seq
+ * @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 Color findColour(char c);
+ Color findColour(char symbol, int position, SequenceI seq,
+ String consensusResidue, float pid);
/**
+ * Recalculate dependent data using the given sequence collection, taking
+ * account of hidden rows
*
- * @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);
-
- /**
- * assign the given conservation to the colourscheme
- * @param c
+ * @param alignment
+ * @param hiddenReps
*/
- public void setConservation(jalview.analysis.Conservation c);
+ void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
- * enable or disable conservation shading for this colourscheme
- * @param conservationApplied
- */
- public void setConservationApplied(boolean conservationApplied);
- /**
+ * 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 true if conservation shading is enabled for this colourscheme
- */
- public boolean conservationApplied();
-
- /**
- * set scale factor for bleaching of colour in unconserved regions
- * @param i
+ * @param sg
+ * @param hiddenRepSequences
+ * @return copy of current scheme with any inherited settings transferred
*/
- public void setConservationInc(int i);
+ ColourSchemeI getInstance(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 scale factor for bleaching colour in unconserved regions
+ * @param ac
+ * @return
*/
- public int getConservationInc();
+ // 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 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
+ * @return
*/
- public void alignmentChanged(AnnotatedCollectionI alignment,
- Map<SequenceI, SequenceCollectionI> hiddenReps);
+ String getSchemeName();
/**
- * 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
+ * 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
*/
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
-
+ boolean isSimple();
}
git://source.jalview.org / jalview.git / blobdiff