Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / datamodel / GroupSetI.java

diff --git a/src/jalview/datamodel/GroupSetI.java b/src/jalview/datamodel/GroupSetI.java
new file mode 100644 (file)
index 0000000..003101b
--- /dev/null
+++ b/src/jalview/datamodel/GroupSetI.java
@@ -0,0 +1,54 @@
+/*
+ * 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.datamodel;
+
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
+public interface GroupSetI
+{
+  boolean hasGroups();
+
+  String getNewick();
+
+  boolean hasTree();
+
+  void updateGroups(List<BitSet> colGroups);
+
+  BitSet getGroupsFor(int column);
+
+  Color getColourForGroup(BitSet bs);
+
+  void setColorForGroup(BitSet bs, Color color);
+
+  void restoreGroups(List<BitSet> newgroups, String treeMethod, String tree,
+          double thresh2);
+
+  boolean hasCutHeight();
+
+  double getCutHeight();
+
+  String getTreeMethod();
+
+  List<BitSet> getGroups();
+
+}