+ sortby.addItem("No sort");\r
+ sortby.addItem("Id");\r
+ sortby.addItem("Pairwise Identity");\r
+ sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
+\r
+ epsRendering.addItem("Prompt each time");\r
+ epsRendering.addItem("Lineart");\r
+ epsRendering.addItem("Text");\r
+ epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
+\r
+ blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
+ clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
+ fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
+ msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
+ pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
+ pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
+ pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
+\r
+ modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
+\r
+ autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+ padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
+\r