/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
+ Stack<CommandI> historyList = new Stack<CommandI>();
- Stack redoList = new Stack();
+ Stack<CommandI> redoList = new Stack<CommandI>();
int thresholdTextColour = 0;
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
sortByTree = Cache.getDefault("SORT_BY_TREE", false);
followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- "SORT_ANNOTATIONS", SequenceAnnotationOrder.SEQUENCE_AND_LABEL.name()));
- showAutocalculatedAbove = Cache
- .getDefault("SHOW_AUTOCALC_ABOVE", false);
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
}
/**