X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=0750adf252ae1bccca1c854f0918377a80818fe6;hb=f52d7fc6ab9bf2c926f0208c225d3dc6e65c8ecf;hp=0c66da39af7776d9b728d95e8f81ac7349ea47f9;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 0c66da3..0750adf 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,18 +1,52 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import java.awt.*;
-import java.util.*;
-
-public interface ColourSchemeI
-{
-  public Color   findColour(String aa);
-  public Vector  getColours(SequenceI s, Vector aa);
-  public Color   getColour (SequenceI s, int pos, Vector aa);
-  public Vector  getColours(SequenceGroup sg, Vector aa);
-  public Color   findColour(SequenceI seq, String s,int j, Vector aa);
-
-  public boolean canThreshold();
-  public boolean isUserDefinable();
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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
+{
+  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);
+
+  public int getConservationInc();
+
+  public int getThreshold();
+
+  public void setThreshold(int ct, boolean ignoreGaps);
+
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps);
+
+}