sequences are private in SequenceGroup

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index f79a158..ca6e9f4 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -429,7 +429,7 @@ public class Jalview2XML
                 groups[i].setDisplayText(sg.getDisplayText());\r
                 groups[i].setColourText(sg.getColourText());\r
 \r
-                for (int s = 0; s < sg.getSize(); s++)\r
+                for (int s = 0; s < sg.getSize(false); s++)\r
                 {\r
                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
                     int index = seqids.indexOf(seq);\r
@@ -915,7 +915,7 @@ public class Jalview2XML
                 if (groups[i].getConsThreshold() != 0)\r
                 {\r
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
-                            ResidueProperties.propHash, 3, sg.sequences, 0,\r
+                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
                             sg.getWidth() - 1);\r
                     c.calculate();\r
                     c.verdict(false, 25);\r