X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=db4ab8b1d2593a45da03f374dbfc90d910007be5;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=495947a16d61d553886d158da8ee2c36c98957f1;hpb=66b1bf1a6480b320ddaa00d4f5e70b2051041c11;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 495947a..db4ab8b 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,11 +1,44 @@
-package jalview.schemes;
-
-import java.awt.*;
-import java.util.*;
-
-public interface ColourSchemeI
-{
-  public Color   findColour(String aa);
-  public Color   findColour(String s,int j);
-  public void    setConsensus(Vector v);
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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);
+
+
+}