X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=7d6d519dca2cbbd6c0514e417851997092e9e9b0;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=45cd65156c3a022d6a1af2c0b265b89c2f91022d;hpb=ca9d31730ad0e4f617717fc3dc45daffb675aad2;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 45cd651..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 = ""; @@ -142,7 +142,7 @@ public class Jalview2XML } // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public void SaveAlignment(AlignFrame af, String jarFile, + public boolean SaveAlignment(AlignFrame af, String jarFile, String fileName) { try @@ -163,10 +163,12 @@ public class Jalview2XML out.close(); jout.close(); + return true; } catch (Exception ex) { ex.printStackTrace(); + return false; } } @@ -230,7 +232,7 @@ public class Jalview2XML vamsasSeq = new Sequence(); vamsasSeq.setId(id + ""); vamsasSeq.setName(jds.getName()); - vamsasSeq.setSequence(jds.getSequence()); + vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); if (jds.getDatasetSequence().getDBRef() != null) @@ -263,16 +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