formatting

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 0cac9c1..7d6d519 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -463,9 +463,9 @@ public class Jalview2XML
 
                 an.setId(aa[i].annotationId);
 
-                if (aa[i].label.equals("Quality") ||
-                        aa[i].label.equals("Conservation") ||
-                        aa[i].label.equals("Consensus"))
+                if (aa[i]==av.quality ||
+                        aa[i]==av.conservation ||
+                        aa[i]==av.consensus)
                 {
                     an.setLabel(aa[i].label);
                     an.setGraph(true);
@@ -1313,9 +1313,16 @@ public class Jalview2XML
                 for (int s = 0; s < groups[i].getSeqCount(); s++)
                 {
                     String seqId = groups[i].getSeq(s)+"";
-                    seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
+                    jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
+                        seqRefIds.get(seqId);
+
+                    if (ts != null)
+                      seqs.addElement(ts);
                 }
 
+                if(seqs.size()<1)
+                  continue;
+
                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
                         groups[i].getDisplayText(), groups[i].getColourText(),