From 405da8d832cf8146ffd32f1e92aabb0109721c4c Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 3 Aug 2012 17:53:41 +0100 Subject: [PATCH] JAL-1136 Ensure asynchronously calculated autoannotation is also added to the alignment in the correct order --- src/jalview/gui/Jalview2XML.java | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 7fb7f0b..ea5d5a7 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -3413,22 +3413,25 @@ public class Jalview2XML // work through any autoCalculated annotation already on the view // removing it if it should be placed in a different location on the // annotation panel. + List remains=new ArrayList(visan.keySet()); for (int h = 0; h < hSize; h++) { jalview.datamodel.AlignmentAnnotation jalan = al .getAlignmentAnnotation()[h]; if (jalan.autoCalculated) { - JvAnnotRow valan = visan.get(jalan.label); + String k; + JvAnnotRow valan = visan.get(k=jalan.label); if (jalan.getCalcId()!=null) { - valan = visan.get(jalan.label+ "\t"+jalan.getCalcId()); + valan = visan.get(k=jalan.label+ "\t"+jalan.getCalcId()); } if (valan != null) { // delete the auto calculated row from the alignment al.deleteAnnotation(jalan, false); + remains.remove(k); hSize--; h--; if (valan != nullAnnot) @@ -3450,6 +3453,16 @@ public class Jalview2XML } } } + // Add any (possibly stale) autocalculated rows that were not appended to the view during construction + for (String other:remains) + { + JvAnnotRow othera=visan.get(other); + if (othera!=nullAnnot && othera.template.getCalcId()!=null && othera.template.getCalcId().length()>0) + { + reorder.add(othera); + } + } + // now put the automatic annotation in its correct place int s = 0, srt[] = new int[reorder.size()]; JvAnnotRow[] rws = new JvAnnotRow[reorder.size()]; for (JvAnnotRow jvar : reorder) -- 1.7.10.2