quit saves screen size

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b8977c5..addba63 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -580,21 +580,24 @@ public class Jalview2XML
           }\r
         }\r
 \r
+        Vector seqs = new Vector();\r
+        int[] ids = groups[i].getSeq();\r
+\r
+        for (int s = 0; s < ids.length; s++)\r
+        {\r
+          seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(\r
+              ids[s]));\r
+        }\r
+\r
         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.\r
-            SequenceGroup(groups[i].getName(),\r
+            SequenceGroup(seqs, groups[i].getName(),\r
                           cs, groups[i].getDisplayBoxes(),\r
                           groups[i].getDisplayText(), groups[i].getColourText(),\r
                           groups[i].getStart(), groups[i].getEnd());\r
+\r
         sg.setOutlineColour(new java.awt.Color(\r
             groups[i].getOutlineColour()));\r
 \r
-        int[] ids = groups[i].getSeq();\r
-\r
-        for (int s = 0; s < ids.length; s++)\r
-        {\r
-          sg.addSequence( (jalview.datamodel.SequenceI) seqids.elementAt(\r
-              ids[s]));\r
-        }\r
 \r
         if (groups[i].getConsThreshold() != 0)\r
         {\r
@@ -623,17 +626,24 @@ public class Jalview2XML
     af.viewport.showQuality = view.getShowQuality();\r
     af.viewport.showIdentity = view.getShowIdentity();\r
     af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
+    af.abovePIDThreshold.setSelected(view.getPidSelected());\r
     af.viewport.setColourText(view.getShowColourText());\r
+    af.colourTextMenuItem.setSelected(view.getShowColourText());\r
     af.viewport.setConservationSelected(view.getConservationSelected());\r
+    af.conservationMenuItem.setSelected(view.getConservationSelected());\r
+\r
     af.viewport.setShowFullId(view.getShowFullId());\r
+    af.fullSeqId.setSelected(view.getShowFullId());\r
+\r
     af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
                                           view.getFontStyle(), view.getFontSize()));\r
     af.alignPanel.fontChanged();\r
 \r
-    af.sequenceFeatures_actionPerformed(null);\r
     af.viewport.setRenderGaps(view.getRenderGaps());\r
+    af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 \r
     af.viewport.setWrapAlignment(view.getWrapAlignment());\r
+    af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 \r
     if (view.getWrapAlignment())\r
     {\r
@@ -646,7 +656,9 @@ public class Jalview2XML
     }\r
 \r
     af.viewport.setShowBoxes(view.getShowBoxes());\r
+    af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
     af.viewport.setShowText(view.getShowText());\r
+    af.viewTextMenuItem.setSelected(view.getShowText());\r
 \r
     ColourSchemeI cs = null;\r
 \r
@@ -685,8 +697,8 @@ public class Jalview2XML
     if (view.getShowSequenceFeatures())\r
     {\r
       af.viewport.showSequenceFeatures = true;\r
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,\r
-          af.alignPanel);\r
+      af.sequenceFeatures.setSelected(true);\r
+      new SequenceFeatureFetcher(al, af.alignPanel);\r
        al.featuresAdded = true;\r
     }\r
 \r