+ AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
+\r
+ af.setFileName(file, "Jalview");\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