Changes to test_align for changes to Clustalw object, and updates for…

… changes in how Gapped sequences are printed out.

Tests/output/test_align

@@ -95,19 +95,19 @@ gi|671626|emb|CAA85685.1|           -
 
 all_seqs...
 description: gi|6273285|gb|AF191659.1|AF191
-seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', IUPACUnambiguousDNA())
+seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', Gapped(IUPACUnambiguousDNA(), '-'))
 description: gi|6273284|gb|AF191658.1|AF191
-seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA-- ...', IUPACUnambiguousDNA())
+seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA-- ...', Gapped(IUPACUnambiguousDNA(), '-'))
 description: gi|6273287|gb|AF191661.1|AF191
-seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', IUPACUnambiguousDNA())
+seq: Seq('TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', Gapped(IUPACUnambiguousDNA(), '-'))
 description: gi|6273286|gb|AF191660.1|AF191
-seq: Seq('TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', IUPACUnambiguousDNA())
+seq: Seq('TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA---- ...', Gapped(IUPACUnambiguousDNA(), '-'))
 description: gi|6273290|gb|AF191664.1|AF191
-seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', IUPACUnambiguousDNA())
+seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', Gapped(IUPACUnambiguousDNA(), '-'))
 description: gi|6273289|gb|AF191663.1|AF191
-seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', IUPACUnambiguousDNA())
+seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', Gapped(IUPACUnambiguousDNA(), '-'))
 description: gi|6273291|gb|AF191665.1|AF191
-seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', IUPACUnambiguousDNA())
+seq: Seq('TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', Gapped(IUPACUnambiguousDNA(), '-'))
 length: 156
 Calculating summary information...
 consensus: Seq('TATACATTAAAGNAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA ...', IUPACAmbiguousDNA())
@@ -760,9 +760,9 @@ test print_info_content
 testing reading and writing fasta format...
 all_seqs...
 description: AK1H_ECOLI/1-378
-seq: Seq('CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE ...', IUPACProtein())
+seq: Seq('CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE ...', Gapped(IUPACProtein(), '-'))
 description: AKH_HAEIN/1-382
-seq: Seq('-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ ...', IUPACProtein())
+seq: Seq('-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ ...', Gapped(IUPACProtein(), '-'))
 length: 382
 consensus: Seq('CPDSINAALICRGEKMSXXXXXXXXXXXXXEXLSXXXXXXXXXXXXXGSHYXXXXXXXXX ...', IUPACProtein())
 >AK1H_ECOLI/1-378