+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.io.DataSourceType;
+
+import java.util.List;
+
/**
* prototype abstract controller for a Jalview alignment view
+ *
* @author jimp
*
- * All operations should return true if the view has changed as a result of the operation
- * @param <ViewportI>
- *
+ * All operations should return true if the view has changed as a result
+ * of the operation
+ *
+ * The controller holds methods that operate on an alignment view,
+ * modifying its state in some way that may result in side effects
+ * reflected in an associated GUI
+ *
*/
-public interface AlignViewControllerI<ViewportI>
+public interface AlignViewControllerI
{
public boolean makeGroupsFromSelection();
public boolean deleteGroups();
- public void setViewportAndAlignmentPanel(AlignViewportI viewport, AlignmentViewPanel alignPanel);
+ public void setViewportAndAlignmentPanel(AlignViewportI viewport,
+ AlignmentViewPanel alignPanel);
+
+ /**
+ * Mark columns in the current column selection according to positions of
+ * sequence features
+ *
+ * @param invert
+ * - when set, mark all but columns containing given type
+ * @param extendCurrent
+ * - when set, do not clear existing column selection
+ * @param toggle
+ * - rather than explicitly set, toggle selection state
+ * @param featureType
+ * - feature type string
+ * @return true if operation affected state
+ */
+ boolean markColumnsContainingFeatures(boolean invert,
+ boolean extendCurrent, boolean toggle, String featureType);
+
+ /**
+ * sort the alignment or current selection by average score over the given set
+ * of features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
+ */
+ void sortAlignmentByFeatureScore(List<String> typ);
+
+ /**
+ * sort the alignment or current selection by distribution of the given set of
+ * features
+ *
+ * @param typ
+ * list of feature names or null to use currently displayed features
+ */
+ void sortAlignmentByFeatureDensity(List<String> typ);
+
+ /**
+ * add a features file of some kind to the current view
+ *
+ * @param file
+ * @param sourceType
+ * @param relaxedIdMatching
+ * if true, try harder to match up IDs with local sequence data
+ * @return true if parsing resulted in something being imported to the view or
+ * dataset
+ */
+ public boolean parseFeaturesFile(Object file, DataSourceType sourceType,
+ boolean relaxedIdMatching);
+
+ /**
+ * mark columns containing highlighted regions (e.g. from search, structure
+ * highlight, or a mouse over event in another viewer)
+ *
+ * @param invert
+ * @param extendCurrent
+ * @param toggle
+ * @return
+ */
+ boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
+ boolean toggle);
}