X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=c56b1bbcd39bb55364ffb5e852602acb29ec12a4;hb=2d62dfc20ea72f47f3dfc44dfe78d6f451342716;hp=495947a16d61d553886d158da8ee2c36c98957f1;hpb=66b1bf1a6480b320ddaa00d4f5e70b2051041c11;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 495947a..c56b1bb 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,11 +1,51 @@
-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 (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 .
+ */
+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 hiddenReps);
+
+}