Merge remote-tracking branch 'origin/master'

qPCR4vir · Aug 23, 2019 · e20f0c3 · e20f0c3
2 parents 79f2992 + 11375fe
commit e20f0c3
Show file tree

Hide file tree

Showing 34 changed files with 26,116 additions and 123 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
-project(ThDy_DNAHybrid VERSION      0.02.00
+project(ThDy_DNAHybrid VERSION      0.02.02
         DESCRIPTION "Thermo Dynamic DNA Hybridizations"
         HOMEPAGE_URL https://github.com/qPCR4vir/ThDySec
         LANGUAGES CXX         )
@@ -9,8 +9,8 @@ project(ThDy_DNAHybrid VERSION      0.02.00
 add_executable(   ThDy_DNAHybrid)
 
 target_include_directories(ThDy_DNAHybrid PUBLIC include)
-target_compile_features   (ThDy_DNAHybrid PUBLIC cxx_std_17)
-target_sources            (ThDy_DNAHybrid PRIVATE
+#target_compile_features   (ThDy_DNAHybrid PUBLIC cxx_std_17)
+target_sources (ThDy_DNAHybrid PRIVATE
         src/ThDySec/cod_deg.cpp
         src/ThDySec/sec.cpp
         src/ThDySec/sec_basic.cpp
@@ -35,7 +35,8 @@ target_sources            (ThDy_DNAHybrid PRIVATE
         src/ThDy_DNAHybrid.Nana/uArray.cpp)
 
 
-add_subdirectory(../ExtLib/nana.ext  ../ExtLib/cmake-nana_ext-build-${CMAKE_BUILD_TYPE} )
+add_subdirectory(../ExtLib/nana.ext  ../ExtLib/cmake-nana_ext-build-${CMAKE_BUILD_TYPE}
+                 EXCLUDE_FROM_ALL )
 target_link_libraries(ThDy_DNAHybrid PRIVATE nana_ext )
 
 

diff --git a/...family/Orthobunyavirus - genus/Simbu - serogroup -S.711.nt 140-420.export alignment.fasta b/...family/Orthobunyavirus - genus/Simbu - serogroup -S.711.nt 140-420.export alignment.fasta
diff --git a/...ribunyaviridae - family/Orthobunyavirus - genus/Simbu - serogroup -S.711.nt 140-420.fasta b/...ribunyaviridae - family/Orthobunyavirus - genus/Simbu - serogroup -S.711.nt 140-420.fasta
diff --git a/...iridae - family/Orthobunyavirus - genus/Simbu - serogroup -S.711.sequence alignment.fasta b/...iridae - family/Orthobunyavirus - genus/Simbu - serogroup -S.711.sequence alignment.fasta
diff --git a/...iridae - family/Orthobunyavirus - genus/Simbu - serogroup -S.713.sequence alignment.fasta b/...iridae - family/Orthobunyavirus - genus/Simbu - serogroup -S.713.sequence alignment.fasta
diff --git a/ThDy/sequences/primers/Bunyavirales - order/Lambert-Lanciotti-2009, Bunya-S.fasta b/ThDy/sequences/primers/Bunyavirales - order/Lambert-Lanciotti-2009, Bunya-S.fasta
@@ -1,40 +1,34 @@
->Cal_Bwa_group_forward Orthobunyavirus N ORF, 210nt	
+>Cal_Bwa_group_forward Orthobunyavirus N ORF, 210nt	. Lambert-Lanciotti-2009, Bunya-S	
 GCAAATGGATTTGATCCTGATGCAG
 
->Cal_Bwa_group_reverse Orthobunyavirus N ORF, 210nt	
+>Cal_Bwa_group_reverse Orthobunyavirus N ORF, 210nt. Lambert-Lanciotti-2009, Bunya-S		
 TTGTTCCTGTTTGCTGGAAAATGAT
 
->Bun_group_forward Orthobunyavirus N ORF, 250nt	
+>Bun_group_forward Orthobunyavirus N ORF, 250nt. Lambert-Lanciotti-2009, Bunya-S		
 CTGCTAACACCAGCAGTACTTTTGAC
 
->Bun_group_reverse Orthobunyavirus N ORF, 250nt	
+>Bun_group_reverse Orthobunyavirus N ORF, 250nt. Lambert-Lanciotti-2009, Bunya-S		
 TGGAGGGTAAGACCATCGTCAGGAACTG
 
->Wyeomyia_forward Orthobunyavirus N ORF, 230nt	
+>Wyeomyia_forward Orthobunyavirus N ORF, 230nt. Lambert-Lanciotti-2009, Bunya-S		
 ATGTCTGAAATTGTATTTGATGATATTGG
 
->Wyeomyia_reverse Orthobunyavirus N ORF, 230nt	
+>Wyeomyia_reverse Orthobunyavirus N ORF, 230nt. Lambert-Lanciotti-2009, Bunya-S		
 TATTTCGATTCCCCGGAAAGT
 
->Oropouche_forward Orthobunyavirus N ORF, 300nt	
+>Oropouche_forward Orthobunyavirus N ORF, 300nt. Lambert-Lanciotti-2009, Bunya-S		
 GGCCCATGGTTGACCTTACTTT
 
->Oropouche_reverse Orthobunyavirus N ORF, 300nt	
+>Oropouche_reverse Orthobunyavirus N ORF, 300nt. Lambert-Lanciotti-2009, Bunya-S		
 ACCAAAGGGAAGAAAGTGAAT
 
->Nairo_forward Nairovirus S - N ORF, 400 nt	
-TCTCAAAGAAACACGTGCCGC
-
->Nairo_reverse Nairovirus S - N ORF, 400 nt	
-GTCCTTCCTCCACTTGWGRGCAGCCTGCTGGTA
-
->Phlebo_forward_1 Phlebovirus N ORF, 370 nt	
+>Phlebo_forward_1 Phlebovirus N ORF, 370 nt. Lambert-Lanciotti-2009, Bunya-S		
 TTTGCTTATCAAGGATTTGATGC
 
->Phlebo_reverse Phlebovirus N ORF, 370 nt	
+>Phlebo_reverse Phlebovirus N ORF, 370 nt. Lambert-Lanciotti-2009, Bunya-S		
 TCAATCAGTCCAGCAAAGCTGGGATGCATCAT
 
->Phlebo_forward_2 Phlebovirus N ORF, 370 nt	
+>Phlebo_forward_2 Phlebovirus N ORF, 370 nt. Lambert-Lanciotti-2009, Bunya-S		
 TTTGCTTATCAAGGATTTGACC
 
 
diff --git a/...s/primers/Bunyavirales - order/Nairoviridae - family/Nairovirus_sL. Villinger, 2017.fasta b/...s/primers/Bunyavirales - order/Nairoviridae - family/Nairovirus_sL. Villinger, 2017.fasta
@@ -0,0 +1,14 @@
+>Nairo_L_1a_F	Nairovirus_RdRp_(L_segment)_NC_005301_1–28_56.2_375	
+TCTCAAAGATATCAATCCCCCCITTACCC
+>Nairo_L_1b_F	Nairovirus_RdRp_(L_segment)_1–28_375	Villinger, 2017
+TCTCAAAGACATCAATCCCCCTTWTCCC
+>Nairo_L_1a_R	Nairovirus_RdRp_(L_segment)_187–214_150		Villinger, 2017
+CTATRCTGTGRTAGAAGCAGTTCCCATC
+>Nairo_L_1b_R	Nairovirus_RdRp_(L_segment)_185–215_150		Villinger, 2017
+GCAATACTATGATAAAAACAATTMCCATCAC
+>Nairo_L_1c_R	Nairovirus_RdRp_(L_segment)_187–214_150		Villinger, 2017
+CAATGCTGTGRTARAARCAGTTGCCATC
+>Nairo_L_1d_R	Nairovirus_RdRp_(L_segment)_187–215_150		Villinger, 2017
+GCAATGCTATGGTAGAAACAGTTTCCATC
+>Nairo_L_1e_R	Nairovirus_RdRp_(L_segment)_187–214_150		Villinger, 2017
+CRAKGCTGTGGTAAAAGCAGTTRCCATC
diff --git a/...GV-Sp.184–293. Vina-Rodrigues, 2019.fasta → ...GV-Sp.184-293. Vina-Rodrigues, 2019.fasta b/...GV-Sp.184–293. Vina-Rodrigues, 2019.fasta → ...GV-Sp.184-293. Vina-Rodrigues, 2019.fasta
diff --git a/...airoviridae - family/Orthonairovirus - genus/Nairo. Lambert-Lanciotti-2009. Bunya-S.fasta b/...airoviridae - family/Orthonairovirus - genus/Nairo. Lambert-Lanciotti-2009. Bunya-S.fasta
@@ -0,0 +1,5 @@
+>Nairo_forward #530. Nairovirus S - N ORF, 400 nt. Lambert-Lanciotti-2009, Bunya-S		
+TCTCAAAGAAACACGTGCCGC
+
+>Nairo_reverse #527. Nairovirus S - N ORF, 400 nt. Lambert-Lanciotti-2009, Bunya-S	
+GTCCTTCCTCCACTTGWGRGCAGCCTGCTGGTA
diff --git a/...es/primers/Bunyavirales - order/Nairoviridae - family/Orthonairovirus - genus/Nairo.fasta b/...es/primers/Bunyavirales - order/Nairoviridae - family/Orthonairovirus - genus/Nairo.fasta
diff --git a/...ovirus - genus/Nairobi sheep disease orthonairovirus - specie/NSDV_GV_sS Tarif,2012.fasta b/...ovirus - genus/Nairobi sheep disease orthonairovirus - specie/NSDV_GV_sS Tarif,2012.fasta
@@ -7,6 +7,9 @@ TGACCATGCAGAACCAGATYG
 >NSDV_GV_R1A Tarif,2012. Pos S~193-215
 GAAACAAGCCTCATGCTAACCT
 
+>NSDV_GV_P1 Vina-Rodriguez, 2019. Pos S~90-103
+CAAGGATGCCATCCTTGCATGGCA
+
 >NSDV_GV_F2  Tarif,2012. F2xR2=313 pb. Pos S~874-894 inespecific: S~352-372,553-573, 
 GGAGAATGGCAAAGAGGTTGT 
 

diff --git a/...nus/Nairobi sheep disease orthonairovirus - specie/Nairo_S Vina-Rodriguez,2019. 1000-1200 b/...nus/Nairobi sheep disease orthonairovirus - specie/Nairo_S Vina-Rodriguez,2019. 1000-1200
@@ -0,0 +1,8 @@
+>Nairo_S_f Vina-Rodriguez,2019. 1014-1038
+CAGGTGTGACWGCAGAGATGTTYCC
+
+>Nairo_S_p Vina-Rodriguez,2019. 1039-1065
+GACAGTCTCACAGTTYCTYTTTGAGCT
+
+>Nairo_S_r Vina-Rodriguez,2019. 1165-1189
+CATGTAAATCCGATTRGCAGTGAAG
diff --git a/...avirales - order/Peribunyaviridae - family/Orthobunyavirus - genus/Simbu group.fasta..txt b/...avirales - order/Peribunyaviridae - family/Orthobunyavirus - genus/Simbu group.fasta..txt
@@ -0,0 +1,23 @@
+>Simbu_F Camarao, 2019. NC018477  120-145
+TAGAGTCTTCTTCCTCAAYCAGAAGA
+
+>Simbu_R Camarao, 2019. NC018477  218-242
+TAYTGGGGAAAATGGTTATTAACCA
+
+>Simbu_CladeAP Camarao, 2019. NC018477  161-177 VIC-MGB 
+TACGTMAGACGYCGAGG
+
+>Simbu_CladeBP Camarao, 2019. NC018477  166-181 FAM-MGB
+TYGGTTGTGSCGTCTT
+
+
+
+>Uni-S-59F Golender-Wernike, 2018
+GATGTWCCWCAACGGAAT
+
+>Uni-S-254R Golender-Wernike, 2018
+TGGGGAAAATGGTTATTAAC
+
+>Uni-S-probe FAM--MGB-NFQ Golender-Wernike, 2018
+GAGTCTTCTTCCTCAA
+
diff --git a/...yavirales - order/Peribunyaviridae - family/Orthobunyavirus - genus/pan-Simbu group.fasta b/...yavirales - order/Peribunyaviridae - family/Orthobunyavirus - genus/pan-Simbu group.fasta
@@ -0,0 +1,51 @@
+>Simbu.A.18
+TTTGGAGGGGTCAAA--TTTACACTG
+
+>Simbu.s.17
+TGGTCGGTATGGGCAACAA---CTTAACTTCAGTGTTGT
+
+>Akabane.s.16
+CAGTAAGTATGGGCAGCAG---CTCAACTTTACTGTTGC
+
+>Shuni.s.15
+TGCTAAAYATGGGGCCCAA---CTCAATTTCGATACCGT
+
+>Shuni.A.14
+TTTGGTGGCATCAAA--TTTACACTG
+
+>Akabane.A.13
+TTTGCAGGGGTCAAA--TTYACAGTG
+
+>Akabane.a.11
+TATGGGCAGCAG---CTCAACTTT
+
+>B.b.10
+GGGTATGTGGCATTTAT
+
+>B.h.9
+TAAGACGSCACAACCAAGTGTYGATCTTAC
+
+>B.h.8
+TAAGACGGCACAACCRAGTGTYGATCTTAC
+
+>h.7
+TAAGACGGCACAACCRAGTGT
+
+>p.6
+TCTTCTTCCTCAACCARAAGAAGGCCAA
+
+>p.5
+TAGAGTCTTCTTCCTCAACCARAAGAAGGC
+
+>p.4
+TAGAGTCTTCTTCCTCAACCARAAGA
+
+>p.2
+TAGAGTCTTCTTCCTCAACCA
+
+>f.1
+GATGTWCCWGCAACGGAAT
+
+
+>r.3_c
+TGGGGAAAATGGTTATTAAC
diff --git a/...nces/primers/Bunyavirales - order/Phenuiviridae - family/Phlebovirus - genus/Phlebo.fasta b/...nces/primers/Bunyavirales - order/Phenuiviridae - family/Phlebovirus - genus/Phlebo.fasta
diff --git a/...r/Phenuiviridae - family/Phlebovirus - genus/Phlebovirus_sS. Lambert-Lanciotti-2009.fasta b/...r/Phenuiviridae - family/Phlebovirus - genus/Phlebovirus_sS. Lambert-Lanciotti-2009.fasta
@@ -0,0 +1,9 @@
+>Phlebo_reverse #526 Phlebovirus N ORF, 370 nt. Lambert-Lanciotti-2009, Bunya-S	
+TCAATCAGTCCAGCAAAGCTGGGATGCATCAT
+
+>Phlebo_forward_1 #528 Phlebovirus N ORF, 370 nt. Lambert-Lanciotti-2009, Bunya-S
+TTTGCTTATCAAGGATTTGATGC
+
+>Phlebo_forward_2 #529 Phlebovirus N ORF, 370 nt. Lambert-Lanciotti-2009, Bunya-S	
+TTTGCTTATCAAGGATTTGACC
+
diff --git a/... - order/Phenuiviridae - family/Phlebovirus - genus/Phlebovirus_sS. Villinger, 2017.fasta b/... - order/Phenuiviridae - family/Phlebovirus - genus/Phlebovirus_sS. Villinger, 2017.fasta
@@ -0,0 +1,6 @@
+>Phlebo_JV3a_F	Phlebovirus_NP_(S_segment)_NC_014395_1549–1573_59.86_500	Villinger, 2017	
+AGTTTGCTTATCAAGGGTTTGATGC
+>Phlebo_JV3b_F	Phlebovirus_NP_(S_segment)_1550–1574_500		Villinger, 2017
+GAGTTTGCTTATCAAGGGTTTGACC
+>Phlebo_JV3_R	Phlebovirus_NP_(S_segment)_1201–1220_500		Villinger, 2017
+CCGGCAAAGCTGGGGTGCAT
diff --git a/...mers/Togaviridae - Family/Alphavirus - genus/SindbisV/Sindbis virus. Lundstrom-2010.fasta b/...mers/Togaviridae - Family/Alphavirus - genus/SindbisV/Sindbis virus. Lundstrom-2010.fasta
@@ -1,17 +1,24 @@
 >A1a		+ RT-PCR (527 bp) & Sequencing. Lundstrom-2010
 AAAGGATACTTTCTCCTCGC 
+
 >A2a - RT-PCR (527?bp) & Sequencing. Lundstrom-2010
 TGGGCAACAGGGACCATGCA
+
 >Alpha8187	+ RT-PCR (2075 bp) & Sequencing. Lundstrom-2010
-tggcaycayggngcngtncarta				
+tggcaycayggngcngtncarta		
+
 >cAlpha10262 - RT-PCR (2075 bp) & Sequencing. Lundstrom-2010
 RTCRCARAARCANTRNGCNCCNCCCCACAT
+
 >Sin_AU_639c	+ RT-PCR (2418 bp) & Sequencing. Lundstrom-2010
 AAAAGGSGACAGTGGAMGAC		
+
 >Sin_AU_c3057c - RT-PCR (2418 bp) & Sequencing. Lundstrom-2010
 GCTACTGGTAAGGGATGTTGCTTGTATGTC	
+
 >Sin_AU_2423c	+ Sequencing. Lundstrom-2010
 CCTTCGAACATGCGACCACTGTCCC
+
 >Sin_AU_c2575c - Sequencing. Lundstrom-2010
 ACTTGCATGTGACGTACTCCAGGTTCG
 
diff --git a/ThDy/sequences/primers/Togaviridae - Family/Alphavirus - genus/VEEV/VEEV-PCR.paper.fasta b/ThDy/sequences/primers/Togaviridae - Family/Alphavirus - genus/VEEV/VEEV-PCR.paper.fasta
@@ -2,11 +2,11 @@
 >A_VIR966_f   Vina-Rodriguez et al. 2015. Modif Eshoo. PanAlpha (58-62°C)
 TCCATGCTAATGCYAGAGCGTTTTCGCA
 
->V_p          Vina-Rodriguez et al. 2015. Modif Eshoo. VEEV (25-63°C)
+>V_p          Vina-Rodriguez et al. 2015. VEEV (25-63°C)
 TGATCGARACGGAGGTRGAMCCATCC
 
 >A_VIR966.R   Vina-Rodriguez et al. 2015. Modif Eshoo. PanAlpha (28-49°C)
 TGGCGCACTTCCAATGTCHAGGAT
 
->A_VIR966.Rc   Vina-Rodriguez et al. 2015. Modif Eshoo. PanAlpha (28-49°C)
+>A_VIR966.R(c)   Vina-Rodriguez et al. 2015. Modif Eshoo. PanAlpha (28-49°C)
 ATCCTDGACATTGGAAGTGCGCCA
diff --git a/ThDy/sequences/primers/Togaviridae - Family/Alphavirus - genus/WEEV/WEEV.fasta b/ThDy/sequences/primers/Togaviridae - Family/Alphavirus - genus/WEEV/WEEV.fasta
diff --git a/ThDy/sequences/primers/Villinger, 2017.txt b/ThDy/sequences/primers/Villinger, 2017.txt
@@ -0,0 +1,35 @@
+
+
+>Bunya_group_F	Orthobunyavirus_NP_(S_segment)_NC_001927_114–139_58.92_167		Villinger, 2017
+CTGCTAACACCAGCAGTACTTTTGAC
+>Bunya_group_R	Orthobunyavirus_336–363_167		Villinger, 2017
+TGGAGGGTAAGACCATCGTCAGGAACTG
+
+>AlphaVir_2052_F	Alphavirus_nsP4_NC_001449_6971–6997_58.39_400		Villinger, 2017
+TGGCGCTATGATGAAATCTGGAATGTT
+>AlphaVir_2052_R	Alphavirus_7086–7109_400		Villinger, 2017
+TACGATGTTGTCGTCGCCGATGAA
+
+>Flavi_JV2a_F	Flavivirus_nsP5_NC_009942_9097–9120_58.63_200		Villinger, 2017
+AGYMGHGCCATHTGGTWCATGTGG
+>Flavi_JV2b_F	Flavivirus_9097–9120_125		Villinger, 2017
+AGCCGYGCCATHTGGTATATGTGG
+>Flavi_JV2c_F	Flavivirus_9097–9120_125		Villinger, 2017
+AGYCGMGCAATHTGGTACATGTGG
+>Flavi_JV2d_F	Flavivirus_9097–9120_50		Villinger, 2017
+AGTAGAGCTATATGGTACATGTGG
+>Flavi_JV2a_R	Flavivirus_9283–9305_400		Villinger, 2017
+GTRTCCCADCCDGCDGTRTCATC
+>Flavi_JV2b_R	Flavivirus_9283–9305_100		Villinger, 2017
+GTRTCCCAKCCWGCTGTGTCGTC
+
+>Thogoto_S6_F	Thogotovirus_M_(segment_6)_NC_006504_486–510_60.28_300		Villinger, 2017
+GATGACAGYCCTTCTGCAGTGGTGT
+>Thogoto_S6_R	Thogotovirus_771–797_300		Villinger, 2017
+RACTTTRTTGCTGACGTTCTTGAGGAC
+
+>Dhori_S5F_	Dhori_NP(segment_5)_M17435_1024–1042_56.51_800		Villinger, 2017
+CGAGGAAGAGCAAAGGAAAG
+>Dhori_S5_R	Dhori 1107–1125 800		Villinger, 2017
+GTGCGCCCCTCTGGGGTTT
+
diff --git a/ThDy/sequences/probes/pan-Simbu group.fasta b/ThDy/sequences/probes/pan-Simbu group.fasta
@@ -0,0 +1,51 @@
+>Simbu18 nt 190. Tm: 49-54 C (no 42 C)
+TTTGGAGGGGTCAAATTTACACTG
+
+>Simbu17 nt 74. Tm: 66 C (no 53 C)
+TGGTCGGTATGGGCAACAACTTAACTTCAGTGTTGT
+
+>Akabane16 nt 74. Tm: 55-66 C
+CAGTAAGTATGGGCAGCAGCTCAACTTTACTGTTGC
+
+>Shuni15 nt 74. Tm: 59-67 C
+TGCTAAAYATGGGGCCCAACTCAATTTCGATACCGT
+
+>Shuni14 nt 190. Tm: 49-54 C
+TTTGGTGGCATCAAATTTACACTG
+
+>Akabane13 nt 190. Tm: 48-56 C
+TTTGCAGGGGTCAAATTYACAGTG
+
+>Akabane11 nt 81. Tm: 40-55 C
+TATGGGCAGCAGCTCAACTTT
+
+>cladeB10 nt 57. Tm: 36-47 C
+GGGTATGTGGCATTTAT
+
+>cladeB9 nt 159. Tm: 46-61 C
+TAAGACGSCACAACCAAGTGTYGATCTTAC
+
+>cladeB8 nt 159. Tm: 52-60 C
+TAAGACGGCACAACCRAGTGTYGATCTTAC
+
+>cladeB7 nt 159. Tm: 42-56 C
+TAAGACGGCACAACCRAGTGT
+
+>panSimbu6 modify Simbu_F Camarao, 2019. NC018477 nt 125. Tm: 33-49 C
+TCTTCTTCCTCAACCARAAGAAGGCCAA
+
+>panSimbu5 modify Simbu_F Camarao, 2019. NC018477 nt 120. Tm: 55-60 C
+TAGAGTCTTCTTCCTCAACCARAAGAAGGC
+
+>panSimbu4 modify Simbu_F Camarao, 2019. NC018477 nt 120. Tm: 48-55 C
+TAGAGTCTTCTTCCTCAACCARAAGA
+
+>panSimbu2 modify Simbu_F Camarao, 2019. NC018477 120. Tm: 40-50 C 
+TAGAGTCTTCTTCCTCAACCA
+
+>Uni-S-59F Golender-Wernike, 2018. Very low Tm: 20-40 C
+GATGTWCCWGCAACGGAAT
+
+
+>Uni-S-254R(c) Golender-Wernike, 2018 -r.3_c
+GTTAATAACCATTTTCCCCA
diff --git a/include/ThDySec/sec_mult.h b/include/ThDySec/sec_mult.h
@@ -52,7 +52,7 @@ class CMultSec
 		CMultSec			*_parentMS {nullptr};		///< std::weak_ptr<CMultSec> _parentMS	;
         CSec				*_Consenso {nullptr};
         bool                 _selected { true };
-		std::string			 _Path ;				///< file path of the original sequence source
+		std::string			 _orig_file_path ;				///< file path of the original sequence source
 
 
      //explicit CMultSec (const std::string &Name  )                 : _name		(trim_string(Name))  {	}
@@ -111,7 +111,7 @@ class CMultSec
 			return path;
         }
 
-        /// Construct a filesystem path acording to the current tree, which can be different from the original path saved in member variable ._Path
+        /// Construct a filesystem path acording to the current tree, which can be different from the original path saved in member variable ._orig_file_path
 		std::string	path( )
 		{
 			std::string sep(std::string(1, std::filesystem::path::preferred_separator));// ::slash<std::filesystem::path>().value));
@@ -238,7 +238,7 @@ class CMultSec
         /// (will try all child of base to set the base dir and export)
         /// To decide the name of the file it need the path of the base node that do not form part of the file name
         /// That is for example: "all_seq/Primers for Multiplex PCR/"...
-        bool    Export_from   ( CMultSec& base, bool only_selected)  ;
+        bool    Export_from   ( CMultSec& tree_base, bool only_selected)  ;
 
 		/// Export local sequences to a new file in fasta format with filters applied