X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=7d6d519dca2cbbd6c0514e417851997092e9e9b0;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=a9763d3ae34dd7a69b1e98cf98171bc876434f84;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index a9763d3..7d6d519 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -21,8 +21,6 @@ package jalview.gui; import jalview.schemes.*; -import jalview.gui.*; - import java.io.*; import java.net.*; @@ -58,6 +56,8 @@ public class Jalview2XML */ Hashtable viewportsAdded; + Hashtable annotationIds = new Hashtable(); + String uniqueSetSuffix = ""; @@ -265,16 +265,20 @@ public class Jalview2XML { jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); - if(jal.getSequenceAt(i).getHiddenSequences()!=null) + if(av.hiddenRepSequences!=null + && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i))) { - jalview.datamodel.SequenceI [] reps = - jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal); + jalview.datamodel.SequenceI[] reps = + ( (jalview.datamodel.SequenceGroup) + av.hiddenRepSequences.get( + jal.getSequenceAt(i))).getSequencesInOrder(jal); for(int h=0; h