+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.schemes;\r
\r
-import jalview.datamodel.*;\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
+ 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 void setThreshold(int ct, boolean ignoreGaps);\r
+\r
}\r