JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index d82e5f5..effdf59 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,13 +1,128 @@
-package jalview.schemes;\r
-\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public interface ColourSchemeI\r
-{\r
-  public Color   findColour(String aa);\r
-  public Color   findColour(String s,int j, Vector aa);\r
-  public boolean canThreshold();\r
-  public boolean isUserDefinable();\r
-}\r
+/*
+ * 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.
+ *  
+ * 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;
+
+import jalview.datamodel.AnnotatedCollectionI;
+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);
+
+  /**
+   * 
+   * @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);
+
+  /**
+   * 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);
+
+}