javadoc

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

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index e4e6ebe..65c24c1 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
@@ -28,24 +29,69 @@ import jalview.datamodel.SequenceI;
 
 public interface ColourSchemeI
 {
+  /**
+   * 
+   * @param c
+   * @return the colour for the given character
+   */
   public Color findColour(char c);
 
+  /**
+   * 
+   * @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
+   */
   public void setConservation(jalview.analysis.Conservation c);
 
+  /**
+   * 
+   * @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);