showUnconserved view and group setting

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 115477d..db53d00 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -915,7 +915,7 @@ public class Jalview2XML
         groups[i].setTextCol1(sg.textColour.getRGB());
         groups[i].setTextCol2(sg.textColour2.getRGB());
         groups[i].setTextColThreshold(sg.thresholdTextColour);
-
+        groups[i].setShowUnconserved(sg.getShowunconserved());
         for (int s = 0; s < sg.getSize(); s++)
         {
           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
@@ -1022,6 +1022,7 @@ public class Jalview2XML
     view.setRightAlignIds(av.rightAlignIds);
     view.setShowSequenceFeatures(av.showSequenceFeatures);
     view.setShowText(av.getShowText());
+    view.setShowUnconserved(av.getShowUnconserved());
     view.setWrapAlignment(av.getWrapAlignment());
     view.setTextCol1(av.textColour.getRGB());
     view.setTextCol2(av.textColour2.getRGB());
@@ -2130,6 +2131,7 @@ public class Jalview2XML
 
         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+        sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false);
         sg.thresholdTextColour = groups[i].getTextColThreshold();
 
         if (groups[i].getConsThreshold() != 0)
@@ -2531,7 +2533,7 @@ public class Jalview2XML
     af.viewport.textColour = new java.awt.Color(view.getTextCol1());
     af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
     af.viewport.thresholdTextColour = view.getTextColThreshold();
-
+    af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view.isShowUnconserved() : false);
     af.viewport.setStartRes(view.getStartRes());
     af.viewport.setStartSeq(view.getStartSeq());