-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
+import java.awt.Color;
import java.util.Hashtable;
import java.util.Map;
+import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.RNAHelicesColour;
/**
* @author jimp
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);
+
+ AlignmentView getAlignmentView(boolean selectedOnly);
+
+ AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+
+ String[] getViewAsString(boolean selectedRegionOnly);
+
+ void setSelectionGroup(SequenceGroup sg);
+
+ char getGapCharacter();
+
+ void setColumnSelection(ColumnSelection cs);
+
+ void setConservation(Conservation cons);
+
+
}