change open par CheckOpen

src/ordali_affiche.tcl

@@ -2541,7 +2541,10 @@ proc SauveLeLog {{fichier ""}} {
 	}
     }
 
-    set f [open $fichier w]
+    set f [CheckOpen $fichier]
+    if {$f eq ""} {
+	return
+    }
     global TexteDuLog
     if {[info exists TexteDuLog]} {
 	puts $f [OutputTLog Text $TexteDuLog]
@@ -5559,14 +5562,12 @@ proc DemandeEtSauveFichier {Extion {exc 0} {FichierParDefaut "Untitled"}} {
     update idletasks
 
     if {$file ne ""} {
-	if {[catch {set o [open $file w]}]} {
-	    FaireLire "Error !\n file is write-protected !"
-	    set file ""
-	} else {
-	    close $o
-	    file delete $file
+	set o [CheckOpen $file]
+	if {$o eq ""} {
+	    return
 	}
     }
+
     return $file
 }
 
@@ -6808,6 +6809,40 @@ proc ChangeConservation {} {
 }
 
 
+proc ExporteScoreConservation {} {
+    # Save conservation score as CSV file
+    global Cons TColScore Defauts
+
+    if {$Cons(ConsCou) eq "None"} {
+	return
+    }
+
+    set ft [SauveConservation]
+    puts "[join [array names TColScore *$ft*] \n]"
+
+    set file "[file rootname $Defauts(Fichier[TypeAli])]_$ft.csv" 
+    #puts "file= $file"
+    set o [CheckOpen $file]
+    if {$f eq ""} {
+	return
+    }
+    set Li {}
+    for {set i 1} {$i < [llength [lindex $TColScore($ft,Data) 0]]} {incr i} {
+	lappend Li $i
+    }
+    puts $o ",[join $Li ,]"
+    foreach gr $TColScore($ft,Owner) data $TColScore($ft,Data) {
+	set data [KirsleyData $data]
+	#puts "\ngrp= $gr [llength $data]"
+	#plist $data %6.3f
+	puts $o "$gr,[join $data ,]"
+    }
+    close $o
+    
+    return
+}
+
+
 proc SauveConservation {} {
     global TabSF ListeTypesDeFeatures ScoreMeth Cons ConsMeth TColScore LNDG
     
@@ -6815,7 +6850,7 @@ proc SauveConservation {} {
 	return
     }
     if {[regexp {^Cons\-} $Cons(ConsCou)]} {
-	return
+	return $Cons(ConsCou)
     }
     
     set ftold [lindex $Cons(ConsCou) 0]
@@ -6963,7 +6998,7 @@ proc InfosSurOrdali {} {
     wm iconname $w "Info"
     wm resizable $w 0 0
     wm protocol $w WM_DELETE_WINDOW KillParLaCroix
-
+    
     frame $w.f
     pack $w.f -side top -expand 1 -fill both
 
@@ -8695,7 +8730,7 @@ proc AfficheFrameFeatures {} {
     grid columnconfig $FrmBouton 0 -weight 0
     grid columnconfig $FrmBouton 1 -weight 1
     grid rowconfig    $FrmBouton 0 -weight 1
-
+    
     set wmac "$FrmBouton.fimg.limg"
     set Wdt [expr {[winfo reqwidth $NomNomSeq] - 10}]
     set fmacsim [file join $OrdEtcDir "MACSIM_50px_cut_transparent.gif"]

src/ordali_cluster.tcl

@@ -1238,7 +1238,10 @@ proc kir {{method ""}} {
     SauveConservation
 
     set file "[file rootname [set Defauts(Fichier[TypeAli])]].scores"
-    set o [open $file w]
+    set o [CheckOpen $file]
+    if {$o eq ""} {
+	return
+    }
     foreach g $LNDG {
 	set Lv [array names ScoreMeth "Cons-BILD,$g,*"]
 	puts "\ng= $g [llength $Lv]"

src/ordali_mode.tcl

@@ -1088,7 +1088,6 @@ proc AfficheBoutonsConservation {} {
 	-bg yellow \
 	-command [list LanceCalculConservation]
     set Cons(Show) [set ::Toggle(Scores)]
-    update
     checkbutton $wc.shh \
 	-text "Show scores " \
 	-anchor w -justify left \
@@ -1111,27 +1110,33 @@ proc AfficheBoutonsConservation {} {
 	-values $Cons(ListeCons)
     $wc.call current 0
     bind $wc.call <<ComboboxSelected>> [list ChangeConservation]
+    button $wc.save \
+	-text " Save " \
+	-bg green1 \
+	-command [list SauveConservation]
+    button $wc.expo \
+	-text " Export " \
+	-bg yellow \
+	-command [list ExporteScoreConservation]
     
     grid $wc.run  -row 0 -rowspan 2 -column 0 -sticky nsw -ipadx 5
     grid $wc.lal  -row 0 -column 1 -sticky nw 
     grid $wc.call -row 0 -column 2 -sticky new 
     grid $wc.shh  -row 1 -column 1 -columnspan 2 -sticky new -ipadx 5
+    grid $wc.save -row 0 -column 3 -sticky ew -padx 10
+    grid $wc.expo -row 1 -column 3 -sticky ew -padx 10
     grid rowconfig    $wc all -weight 1
 
     # frame save/return
     set wb "$ws.sds"
     frame $wb
     grid $wb -row 0 -column 2 -sticky nse -padx 2 -pady 2
-    button $wb.save \
-	-text " Save " \
-	-bg green1 \
-	-command [list SauveConservation]
     button $wb.dis \
 	-text "Return" \
 	-background green1 \
 	-command [list QuitteModeConservation $ws]
-    grid $wb.save -row 0 -column 0 -sticky new
-    grid $wb.dis  -row 1 -column 0 -sticky new
+    #grid $wb.save -row 0 -column 0 -sticky new
+    grid $wb.dis  -row 0 -column 0 -sticky new
 
     update idletasks
     trace add variable Cons(PDB) write PrendPDBDansPilier

src/ordali_outils.tcl

+
+
 #
 # ordali_outils.tcl
 #
 
 
+proc CheckOpen {f} {
+    if {[catch {set o [open $f w]}]} {
+	if {[ModeI]} {
+	    FaireLire "Warning !\n The file >$f< can not be written ! Check permissions."
+	}
+	set o ""
+    }
+    
+    return $o
+}
+
+
 proc RepresentantDeTaxId {t} {
     global TDesTaxId TDesOrganismes LNOrdali
     

src/ordali_sequence.tcl

+
+
 #
 # ordali_sequence.tcl
 #
@@ -11,7 +13,7 @@ proc OuvrirFichierAlignementDansOrdali {{type "Unk"} {Fichier ""}} {
 	return
     }
 
-    if {[string tolower $type] eq "macsim"} {set type "XML"}
+    if {[string tolow]er $type] eq "macsim"} {set type "XML"}
     set tyfi $type
     if {$type eq "Unk"} {set tyfi "all"}
 
@@ -160,7 +162,7 @@ proc DecortiqueUnNEXUS {file aNom aSeq} {
     foreach l [lrange $Lignes 1 end] {
 	set l [string trim $l]
 	if {[regexp -nocase {^begin} $l]} {
-	    set what [lindex [split $l " "] 1]
+	    set hat [lindex [split $l " "] 1]
 	}
    }
 
@@ -510,11 +512,8 @@ proc CreeLeMSF {{outfile ""} {LNoms {}} {LSeqs {}}} {
     lappend Llg "\n\n"
 
     if {$outfile ne "OnRetourne"} {
-	if {[catch {set f [open $outfile w]}]} {
-	    if {[ModeI]} {
-		FaireLire "Warning !\nFile $outfile can not be open !"
-	    }
-
+	set f [CheckOpen $outfile]
+	if {$f eq ""} {
 	    return
 	}
 	puts $f [join $Llg \n]
@@ -558,7 +557,7 @@ proc CreeLAlignementDeLaFenetre {format {outfile ""}} {
     }
 
     set ftmp [file join $OrdTmpDir "[pid]_tfatmptfatmp.tfa"]
-    set f [open $ftmp w]
+    set f [CheckOpen $ftmp]
     set LongueurTotale [expr {$xx-$xm}]
     foreach Nm $noms Sq $seqs {
 	puts $f ">$Nm"
@@ -661,12 +660,9 @@ proc CreeLeAln {{FilOut ""}} {
     }
     if {$FilOut eq ""} {return}
 
-    if {[catch {set f [open $FilOut w]}]} {
-	    if {[ModeI]} {
-		FaireLire "Warning !\nFile $outfile can not be open !"
-	    }
-
-	    return
+    set f [CheckOpen $FilOut]
+    if {$f eq ""} {
+	return
     }
     puts $f "CLUSTAL W : Created by Ordalie [DonneDateEtHeure]"
     puts $f ""
@@ -711,13 +707,11 @@ proc EcritLeTfa {FilOut LesNoms LesSequences} {
     }
     if {$FilOut eq ""} {return}
 
-    if {[catch {set f [open $FilOut w]}]} {
-	if {[ModeI]} {
-	    FaireLire "Warning !\nFile $fileOut can not be open !"
-	}
-	
+    set f [CheckOpen $FilOut]
+    if {$f eq ""} {
 	return
     }
+    
     foreach Nm $LesNoms s $LesSequences {
 	if {[string trim $Nm] eq ""} {continue}
 	puts $f ">$Nm"

src/ordali_services.tcl

@@ -668,7 +668,7 @@ proc IDMapping_help {{args ""}} {
     if {$args eq ""} {
 	puts "Usage : idmapping <from> <to> <ids list>"
 	puts ""
-	puts " <from> should be one of ACC ID ACC+DI"
+	puts " <from> should be one of ACC ID ACC+ID"
 	puts "    OR "
 	puts " <to>   should be one of ACC ID"
 	puts ""
@@ -718,7 +718,7 @@ proc CheckIDMappingInputParam {args} {
     set to   [string toupper $to]
 	
     set LidmDBs [lsort [LesLignesDuFichier [file join [IDMappingDir] id_dbs.txt]]]
-    lappend LidmDBs "ACC+ID" ACC
+    lappend LidmDBs "ACC+ID" ACC ID
     if {$from ni $LidmDBs || $to ni $LidmDBs} {
 	puts "\nError :\nBad <FROM_db> and/or <TO_db> names !"
 	IDMapping_help
@@ -786,12 +786,19 @@ proc DbIDMappingSQL {bank what} {
 
 proc IDMapping_sql {from to Lids {taxid ""}} {
     set Lacc {}
+    if {$from eq $to} {
+	puts ">$from> == <$to> !!"
+	IDMapping_Help
+
+	return
+    } 
+    
     if {$from ni {ACC ID ACC+ID} && $to ni {ACC ID}} {
 	set jointure 1
     } else {
 	set jointure 0
     }
-    
+
     switch $from {
 	"ACC" {
 	    set source acc
@@ -802,7 +809,11 @@ proc IDMapping_sql {from to Lids {taxid ""}} {
 	"ID" -
 	"ACC+ID" {
 	    set source acc
-	    set bank $to
+	    if {$to eq "ACC"} {
+		set bank ""
+	    } else {
+		set bank $to
+	    }
 	    set target id
 	    
 	    # get everything as an ACC
@@ -833,7 +844,12 @@ proc IDMapping_sql {from to Lids {taxid ""}} {
 	    set Lacc $Lids
 	}
     }
-    
+
+    # idmapping inside UniProt itself
+    if {$bank eq ""} {
+	return $Lacc
+    }
+
     if {! $jointure} {
 	set db [DbIDMappingSQL $bank open]
 	if {$taxid eq ""} {
@@ -1190,9 +1206,9 @@ proc InfosFromUniProt {Lids {Lsqn ""}} {
 	}
 	
 	unset -nocomplain TInf
-	Espionne $em
+	#Espionne $em
 	array set TInf [DecortiqueLesLignesEMBL $em ID AC DE GN OS OC OX Seq LaDETotal GNTotal]
-	Espionne [string range $em 0 11]=$AC
+	#Espionne [string range $em 0 11]=$AC
 	# access: take all of them, if we have an obsolete one
 	set AC [string map {";" ""} [join $TInf(AC)]]
 	regsub -all { +} [string trim $AC] " " AC

src/ordali_setup.tcl

+
 #
 # ordali_setup.tcl
 #
@@ -957,7 +958,8 @@ proc SauveOrdalieDefauts {{fout ""}} {
 	}
     }
 
-    if {[catch {set foo [open $fout w]} Msg]} {
+    set foo [CheckOpen $fout]
+    if {$foo eq ""} {
 	return
     }
     foreach e [set Defauts(UserDef)] {

src/ordali_tree.tcl

+
 #
 # ordali_tree.tcl
 #
@@ -366,7 +367,10 @@ proc NettoieArbre {a} {
     }
     set a [string map [list " " ""] $a]
 
-    set o [open treenet w]
+    set o [CheckOpen treenet]
+    if {$o eq ""} {
+	return
+    }
     puts $o $a
     close $o
 
@@ -554,7 +558,10 @@ proc SaveTree {AId {file ""}} {
     }
     if {$file eq ""} {return}
 
-    set fo [open $file w]
+    set fo [CheckOpen $file]
+    if {$fo eq ""} {
+	return
+    }
     puts $fo $::Abr($AId,TextePH)
     close $fo
 
@@ -3601,7 +3608,10 @@ proc EcritUnArbre {AId {fout ""}} {
     EcritUnNoeud $AId root
     append Abr($AId,OutPH) ";"
 
-    set o [open $fout w]
+    set o [CheckOpen $fout]
+    if {$o eq ""} {
+	return
+    }
     puts $o $Abr($AId,OutPH)
     close $o