From 8a5564b7645e73b98bcc1338b4d58937b43e5133 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Fri, 21 Aug 2015 10:50:35 +0100 Subject: [PATCH] JAL-1831 updated json schema doc --- src/jalview/io/HtmlSvgOutput.java | 7 ++++--- src/jalview/json/binding/biojson/v1/AlignmentPojo.java | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index 16b2647..6612db3 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -98,7 +98,8 @@ public class HtmlSvgOutput .getDefault("EXPORT_EMBBED_BIOJSON", "true")); if (isEmbbedBioJSON) { - AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport( + AlignmentExportData exportData = jalview.gui.AlignFrame + .getAlignmentForExport( JSONFile.FILE_DESC, av); if (exportData.getSettings().isCancelled()) { @@ -107,8 +108,8 @@ public class HtmlSvgOutput jsonData = new FormatAdapter(ap, exportData.getSettings()) .formatSequences(JSONFile.FILE_DESC, exportData .getAlignment(), exportData.getOmitHidden(), - exportData.getStartEndPostions(), ap - .getAlignViewport().getColumnSelection()); + exportData.getStartEndPostions(), + av.getColumnSelection()); } String htmlData = getHtml(titleSvgData, alignSvgData, jsonData); FileOutputStream out = new FileOutputStream(file); diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java index dfb60bc..f7f20bb 100644 --- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java +++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java @@ -33,7 +33,7 @@ public class AlignmentPojo required = false, minItems = 0, maxItems = 2147483647, - description = "A sequence group is a bracket of alignment residues spanning
across multiple columns and rows. These can be treated as a
sub-alignments.") + description = "A sequence group is a bracket of alignment residues which
could span across multiple columns and/or rows. These can be
treated as a sub-alignments.") private List seqGroups = new ArrayList(); @Attributes( -- 1.7.10.2