JAL-2371 remove ColourSchemeI.findColour(c), pure interface groovy

[jalview.git] / src / jalview / schemes / ColourSchemeI.java

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 9ebe791..f16ca21 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,47 +1,101 @@
 /*
- * 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.Color;
-
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Map;
+
 public interface ColourSchemeI
 {
-  public Color findColour(char c);
-
-  public Color findColour(char c, int j, SequenceI seq);
-
-  public void setConsensus(java.util.Hashtable[] h);
-
-  public void setConservation(jalview.analysis.Conservation c);
-
-  public boolean conservationApplied();
-
-  public void setConservationInc(int i);
+  /**
+   * 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
+   * @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
+   */
+  Color findColour(char symbol, int position, SequenceI seq,
+          String consensusResidue, float pid);
 
-  public int getConservationInc();
+  /**
+   * 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 getThreshold();
+  /**
+   * 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 void setThreshold(int ct, boolean ignoreGaps);
+  /**
+   * 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 alignmentChanged(AnnotatedCollectionI alignment);
+  /**
+   * 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();
 }