Save text colours

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index a036988..1e479fb 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -182,7 +182,6 @@ public class Jalview2XML_V1
                     vamsasSeq[i].getSequence());\r
             jseqs[i].setStart(JSEQ[i].getStart());\r
             jseqs[i].setEnd(JSEQ[i].getEnd());\r
-            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
             seqids.add(jseqs[i]);\r
         }\r
 \r
@@ -269,6 +268,15 @@ public class Jalview2XML_V1
 \r
         AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
 \r
+        for (int i = 0; i < JSEQ.length; i++)\r
+        {\r
+          af.viewport.setSequenceColour(\r
+              af.viewport.alignment.getSequenceAt(i),\r
+              new java.awt.Color(\r
+                  JSEQ[i].getColour()));\r
+        }\r
+\r
+\r
 \r
         //  af.changeColour() );\r
         /////////////////////////\r