Save featureGroup

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8406299..e387967 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -183,6 +183,7 @@ public class Jalview2XML
             vamsasSeq.setId(id + "");\r
             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
+            vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 \r
             jseq = new JSeq();\r
             jseq.setStart(jal.getSequenceAt(i).getStart());\r
@@ -206,6 +207,7 @@ public class Jalview2XML
                 features.setDescription(sf.getDescription());\r
                 features.setStatus(sf.getStatus());\r
                 features.setType(sf.getType());\r
+                features.setFeatureGroup(sf.getFeatureGroup());\r
                 jseq.addFeatures(features);\r
               }\r
             }\r
@@ -309,8 +311,10 @@ public class Jalview2XML
                 Annotation an = new Annotation();\r
                 an.setDescription(aa[i].description);\r
                 if(aa[i].graph>0)\r
+                {\r
                   an.setGraph(true);\r
-\r
+                  an.setGraphType(aa[i].graph);\r
+                }\r
                 an.setLabel(aa[i].label);\r
 \r
                 AnnotationElement ae;\r
@@ -652,6 +656,7 @@ public class Jalview2XML
         {\r
             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
                     vamsasSeq[i].getSequence());\r
+            jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 \r
             jseqs[i].setStart(JSEQ[i].getStart());\r
             jseqs[i].setEnd(JSEQ[i].getEnd());\r
@@ -678,6 +683,7 @@ public class Jalview2XML
                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
                   features[f].getDescription(), features[f].getStatus(),\r
                   features[f].getBegin(), features[f].getEnd());\r
+              sf.setFeatureGroup(features[f].getFeatureGroup());\r
               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
             }\r
           }\r
@@ -720,7 +726,7 @@ public class Jalview2XML
                 {\r
                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
                             an[i].getDescription(), anot, 0, 0,\r
-                            jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
+                            an[i].getGraphType());\r
                 }\r
                 else\r
                 {\r
@@ -875,9 +881,8 @@ public class Jalview2XML
 \r
         if (view.getShowSequenceFeatures())\r
         {\r
-           af.featureSettings.setEnabled(true);\r
            af.viewport.showSequenceFeatures = true;\r
-           af.sequenceFeatures.setSelected(true);\r
+           af.showSeqFeatures.setSelected(true);\r
         }\r
 \r
         if(jms.getFeatureSettings()!=null)\r