/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* @author jimp
*
*/
-public interface AlignViewportI
+public interface AlignViewportI extends ViewStyleI
{
int getCharWidth();
Hashtable[] getRnaStructureConsensusHash();
- boolean getIgnoreGapsConsensus();
-
- boolean getCentreColumnLabels();
+ boolean isIgnoreGapsConsensus();
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
* first column (inclusive, from 0)
* @param max
* last column (exclusive)
- * @return int[][] range of {start,end} visible positions TODO: change to list
- * of int ranges
+ * @return int[][] range of {start,end} visible positions
*/
- int[][] getVisibleRegionBoundaries(int min, int max);
+ List<int[]> getVisibleRegionBoundaries(int min, int max);
/**
* This method returns an array of new SequenceI objects derived from the
boolean hasHiddenRows();
+ /**
+ *
+ * @return a copy of this view's current display settings
+ */
+ public ViewStyleI getViewStyle();
+
+ /**
+ * update the view's display settings with the given style set
+ *
+ * @param settingsForView
+ */
+ public void setViewStyle(ViewStyleI settingsForView);
+
+ /**
+ * Returns a viewport which holds the cDna for this (protein), or vice versa,
+ * or null if none is set.
+ *
+ * @return
+ */
+ AlignViewportI getCodingComplement();
+
+ /**
+ * Sets the viewport which holds the cDna for this (protein), or vice versa.
+ * Implementation should guarantee that the reciprocal relationship is always
+ * set, i.e. each viewport is the complement of the other.
+ */
+ void setCodingComplement(AlignViewportI sl);
+
+ /**
+ * Answers true if viewport hosts DNA/RNA, else false.
+ *
+ * @return
+ */
+ boolean isNucleotide();
+
+ /**
+ * Returns an id guaranteed to be unique for this viewport.
+ *
+ * @return
+ */
+ String getViewId();
}