/*
- * 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.
*
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
}
int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
+ SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
ap.av.hideSequence(hseqs);
// refresh(); TODO: ? needed ?
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(),
sg.getEndRes() + 1);
String description;