X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=65c24c1ef6a8907624dea93705f3d89595bb8052;hb=9492f5b351797792472226ca975bb593653e8d94;hp=8f0f3c5c4dfc8cad9f76ed23dfefe5b76cc28c4f;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 8f0f3c5..65c24c1 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,44 +1,98 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-public interface ColourSchemeI
-{
-  public Color findColour(String aa);
-
-  public Color findColour(String s, int j);
-
-  public void setConsensus(java.util.Vector v);
-
-  public void setConservation(jalview.analysis.Conservation c);
-
-  public boolean conservationApplied();
-
-  public void setConservationInc(int i);
-
-  public int getConservationInc();
-
-  public int getThreshold();
-
-  public void setThreshold(int ct, boolean ignoreGaps);
-
-
-}
+/*
+ * 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;
+
+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;
+
+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);
+
+}