/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
import java.util.Hashtable;
import java.util.Map;
+import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
+ void setSequenceColour(SequenceI seq, Color col);
+
+ Color getSequenceColour(SequenceI seq);
+
+ void updateSequenceIdColours();
SequenceGroup getSelectionGroup();
SequenceI[] getSequenceSelection();
+ void clearSequenceColours();
CigarArray getViewAsCigars(boolean selectedRegionOnly);
char getGapCharacter();
+ void setColumnSelection(ColumnSelection cs);
+
+ void setConservation(Conservation cons);
}