[Phylobase-commits] r816 - in pkg/inst: nexusfiles unitTests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 27 20:05:40 CEST 2010
Author: bbolker
Date: 2010-10-27 20:05:40 +0200 (Wed, 27 Oct 2010)
New Revision: 816
Added:
pkg/inst/nexusfiles/badnex.nex
pkg/inst/unitTests/runit.badnex.R
Log:
add unit tests for bad nexus file
Added: pkg/inst/nexusfiles/badnex.nex
===================================================================
--- pkg/inst/nexusfiles/badnex.nex (rev 0)
+++ pkg/inst/nexusfiles/badnex.nex 2010-10-27 18:05:40 UTC (rev 816)
@@ -0,0 +1,101 @@
+#NEXUS
+[written Sat Oct 23 12:11:18 PDT 2010 by Mesquite version 2.6 (build 486)
+at Macintosh-101.local/10.0.1.6]
+
+BEGIN TAXA;
+ TITLE Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ S1FS3_S3FS1_&_S2LS4 Desulfodehalobacter_spongiphilus_strain_
+Desulfobacterium_indolicum_strain_DSM_33
+Desulfobacter_postgatei_strain_DSM_2034_ Geobacter_sulfurreducens_#U13928
+S2HS1_&_S3HS1 Geobacter_chapelleii_strain_172_#NR_0259 F2HS1b
+Shewanella_putrefaciens_strain_Hac334_#D Shewanella_aquimarina_#AY485225
+Pseudomonas_meridiana_strain_CMS_38T_AJ5 F2FS1_&_F3FS2 F2HS1_&_F2HS3
+Pseudomonas_stutzeri_strain_LS401_#U2641 F2FS2_&_F3HS2
+Marinobacter_hydrocarbonoclasticus_strai S3FS4_S3FS5_&_S3FS6
+Marinobacter_guineae_strain_LMG_24048_#A Marinobacter_lipolyticus_strain_SM
+S1HS1 Desulfopila_aestuarii_#AB110542 S3FS2
+S1HS2_S1HS3_S1HS4_S1HS5_S3HS4_&_F2HA2a F3FS1
+Desulfovibrio_putealis_#AY574979 Desulfovibrio_desulfuricans_subsp._desul
+S2LS1 Desulfovibrio_bizertensis_strain_MB3_#DQ S1FS1
+Desulfovibrio_marinisediminis_#AB353727 S2LS3_S3LS1_S3FS3_&_F2HA2b
+Acidobacterium_capsulatum_#D26171
+ ;
+
+END;
+
+
+BEGIN TREES;
+ Title Imported_trees;
+ LINK Taxa = Taxa;
+ TRANSLATE
+ 1 S1FS3_S3FS1_&_S2LS4,
+ 2 D_s_strain_,
+ 3 D_i_strain_DSM_3,
+ 4 D_p_strain_DSM_2_,
+ 5 G_s_#,
+ 6 S2HS1_&_S3HS1,
+ 7 G_c_strain_1_#NR_0,
+ 8 F2HS1b,
+ 9 S_p_strain_H_#D,
+ 10 S_a_#,
+ 11 P_m_strain_C_3_A,
+ 12 F2FS1_&_F3FS2,
+ 13 F2HS1_&_F2HS3,
+ 14 P_s_strain_L_#,
+ 15 F2FS2_&_F3HS2,
+ 16 M_h_s,
+ 17 S3FS4_S3FS5_&_S3FS6,
+ 18 M_g_s_L_2_#A,
+ 19 M_l_s_S,
+ 20 S1HS1,
+ 21 D_a_#A,
+ 22 S3FS2,
+ 23 S1HS2_S1HS3_S1HS4_S1HS5_S3HS4_&_F2HA2a,
+ 24 F3FS1,
+ 25 D_p_#,
+ 26 D_d_s._d,
+ 27 S2LS1,
+ 28 D_b_s_M_#D,
+ 29 S1FS1,
+ 30 D_m_#A,
+ 31 S2LS3_S3LS1_S3FS3_&_F2HA2b,
+ 32 A_c_#;
+ TREE Imported_tree_0 =
+(((1:0.014294865658239897,2:0.016346131753724284)100:0.04531876862101268,(3:0.07787046050007705,(4:0.1575116382471088,((((5:0.04822215084893891,(6:0.0271216303442505,7:0.02007948214228989)100:0.03528659400373911)99:0.05981681725589428,(((8:1.12919178858362E-6,9:1.12919178858362E-6)100:0.057530109591399765,10:0.037691124354788864)100:0.08304244998885398,((11:0.030702696010829537,((12:8.544451267088965E-4,13:1.12919178858362E-6)100:0.020184245020285173,(14:1.12919178858362E-6,15:0.0034181003601162514)85:0.012235337246177081)93:0.01895791066948832)100:0.047681348350900744,(16:0.020642180955472003,(17:0.0033048657512852178,(18:0.005988936129628456,(19:0.005010797883775309,20:0.01691780810184798)67:0.007663605184147101)74:0.006198749083268308)74:0.014460306032529943)100:0.06150881986749245)96:0.03607879771546074)100:0.1898411550405616)61:0.05839829698184673,((21:0.03207541431435525,22:0.03529636469585623)86:0.014049212961742451,23:0.015891647611896632)100:0.12157794121374672)43:
+
+ 0!
+.025419418511636843,((24:0.008361788925720447,25:8.737200748323158E-4)100:0.12954900469798472,(26:0.12890159096837994,((27:1.12919178858362E-6,28:0.004140667057671182)100:0.07459471196756032,(29:1.12919178858362E-6,(30:1.12919178858362E-6,31:0.0033956963116614446)89:0.002536358334238893)100:0.14144374970927193)77:0.030026874274203138)83:0.03329468873634148)98:0.09177164340960056)45:0.034517167840112765)51:0.04130953485123759)27:0.02140636921130952)100:0.21688189318012785,32:0.21688189318012785)100:0.23;
+
+END;
+
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 4448951287512167596;
+ endTell;
+ getWindow;
+ tell It;
+ suppress;
+ setResourcesState true false 100;
+ setPopoutState 400;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 700 464;
+ setLocation 8 8;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ desuppress;
+ endTell;
+ endTell;
+end;
Added: pkg/inst/unitTests/runit.badnex.R
===================================================================
--- pkg/inst/unitTests/runit.badnex.R (rev 0)
+++ pkg/inst/unitTests/runit.badnex.R 2010-10-27 18:05:40 UTC (rev 816)
@@ -0,0 +1,16 @@
+#
+# --- Test badnex.R ---
+#
+
+if (Sys.getenv("RCMDCHECK") == FALSE) {
+ pth <- file.path(getwd(), "..", "inst", "nexusfiles")
+} else {
+ pth <- system.file(package="phylobase", "nexusfiles")
+}
+
+badFile <- file.path(pth, "badnex.nex")
+
+test.checkTree <- function() {
+ checkException(readNexus(file=badFile))
+}
+
More information about the Phylobase-commits
mailing list