X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=96699c6f572874f610b594c127951ca149baf986;hb=0eca27bca577e774acd5aefb165e7c6396a1995e;hp=0c66da39af7776d9b728d95e8f81ac7349ea47f9;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 0c66da3..96699c6 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,18 +1,43 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 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();
+  public Color findColour(char c);
+
+  public Color findColour(char c, int j);
+
+  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);
+
 }