dssp 7-state to three state lookup

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

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 9cc74f1..96699c6 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -18,15 +18,26 @@
  */\r
 package jalview.schemes;\r
 \r
-import java.util.*;\r
-\r
 import java.awt.*;\r
 \r
 public interface ColourSchemeI\r
 {\r
-  public Color findColour(String aa);\r
+  public Color findColour(char c);\r
+\r
+  public Color findColour(char c, int j);\r
+\r
+  public void setConsensus(java.util.Hashtable[] h);\r
+\r
+  public void setConservation(jalview.analysis.Conservation c);\r
+\r
+  public boolean conservationApplied();\r
+\r
+  public void setConservationInc(int i);\r
+\r
+  public int getConservationInc();\r
+\r
+  public int getThreshold();\r
 \r
-  public Color findColour(String s, int j);\r
+  public void setThreshold(int ct, boolean ignoreGaps);\r
 \r
-  public void setConsensus(Vector v);\r
 }\r