/*
- * 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.
*/
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
- if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
- .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+ if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
+ annotation, AppletFormatAdapter.PASTE))
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
param = applet.getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase("true"))
{
- newAlignFrame.viewport.showSequenceFeatures(true);
+ newAlignFrame.viewport.setShowSequenceFeatures(true);
new FeatureSettings(newAlignFrame.alignPanel);
}
{
param = setProtocolState(param);
- if (new AnnotationFile().readAnnotationFile(
- newAlignFrame.viewport.getAlignment(), param, protocol))
+ if (new AnnotationFile().annotateAlignmentView(
+ newAlignFrame.viewport, param, protocol))
{
newAlignFrame.alignPanel.fontChanged();
newAlignFrame.alignPanel.setScrollValues(0, 0);
param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
newAlignFrame.viewport.getAlignment(), 0, false); // false==do
+ SequenceI repseq = newAlignFrame.viewport.getAlignment()
+ .getSequenceAt(0);
+ newAlignFrame.viewport.getAlignment().setSeqrep(repseq);
+ ColumnSelection cs = new ColumnSelection();
+ cs.hideInsertionsFor(repseq);
+ newAlignFrame.viewport.setColumnSelection(cs);
// not
// add
// sequence