From 3640aa8bd3308650c499f631fb2922cde429c43b Mon Sep 17 00:00:00 2001 From: "j.procter@dundee.ac.uk" Date: Fri, 12 Sep 2014 17:04:03 +0100 Subject: [PATCH] JAL-1486 fix: pass selected region to jalview.io via alignment view and align viewport annotation methods --- src/jalview/gui/PopupMenu.java | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 44860a1..25cad0a 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -2071,23 +2071,21 @@ public class PopupMenu extends JPopupMenu System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens // or we simply trust the user wants // wysiwig behaviour - SequenceGroup sg = ap.av.getSelectionGroup(); - ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); - omitHidden = ap.av.getViewAsString(true); - Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.getAlignment() - .getAlignmentAnnotation(); - if (nala != null) + + AlignmentView selvew = ap.av.getAlignmentView(true, false); + AlignmentI aselview = selvew.getVisibleAlignment(ap.av + .getGapCharacter()); + List ala = (ap.av + .getVisibleAlignmentAnnotation(true)); + if (ala != null) { - for (int i = 0; i < nala.length; i++) + for (AlignmentAnnotation aa : ala) { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); + aselview.addAnnotation(aa); } } cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - oal, omitHidden, csel, sg)); - oal = null; + aselview, null, null, null)); } public void pdbFromFile_actionPerformed() -- 1.7.10.2