-package jalview.schemes;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public interface ColourSchemeI\r
-{\r
- public Color findColour(String aa);\r
- public Vector getColours(SequenceI s, Vector aa);\r
- public Color getColour (SequenceI s, int pos, Vector aa);\r
- public Vector getColours(SequenceGroup sg, Vector aa);\r
- public Color findColour(SequenceI seq, String s,int j, Vector aa);\r
-\r
- public boolean canThreshold();\r
- public boolean isUserDefinable();\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 jalview.datamodel.AnnotatedCollectionI;
+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);
+
+}