annotation fin

src/ordali_affiche.tcl

@@ -2170,8 +2170,8 @@ proc BindModeNormal {} {
     bindtags $::NomNomSeq  $LNTags
     bindtags $::NomTextSeq $LSTags
 
-    # Sauvegarde
-    #bind . <Control-Key-s> [list SauveLAlignement]
+    # saving shortcut
+    bind . <Control-Key-s> [list SauveLAlignement]
 
     $::NomTextSeq tag delete Marque
     update idletasks
@@ -2798,6 +2798,9 @@ proc EtatSeqsOut {quoi} {
 
 
 proc EtatBouton {b} {
+    # returns :
+    #   - 0 if button is RAISED
+    #   - 1 if button is SUNKEN
 
     if {[$b cget -relief] eq "raised"} {
 	return 0
@@ -3956,39 +3959,41 @@ proc ChoixPDBReference {} {
 
 
 proc AfficheSnapshotAnnotations {} {
-    global NomTextSeq Anano WOrdali
+    global NomTextSeq Anno WOrdali
     
     if {[TypeAli] eq "pasdali"} {
 	return
     }
-    if {! [info exists Anno(Lanno)]} {
+    if {[QuelMode] eq "seqlab"} {
+	FaireLire "Not available in Editor mode yet !"
 	return
     }
-    
+    if {[QuelMode] eq "annotation"} {
+	return
+    }
+
+    unset -nocomplain Anno
+    LoadSnapAnnotations
+    parray Anno
+    update
+
     $NomTextSeq configure -state normal
+
     set bt $WOrdali(BoutAnno)
     if {! [EtatBouton $bt]} {
-	set Anno(Ltags) [list]
-	foreach ann $Anno(Lanno) {
-	    lassign $ann ian pka txt col zone
-	    set txt "$ian - $txt"
-	    set txtnsp [string map {_ @ " " "_"} $txt]
-	    set tag "FDisp_$txtnsp"
-	    $NomTextSeq tag configure $tag -background [CouleurO2Ordali $col] -foreground black
-	    $NomTextSeq tag add $tag {*}$zone
-	    lappend Anno(Ltags) "FDisp_$txtnsp"
-	}
+	# button is ON, show
+	ShowAnnotation All
 
 	$bt configure -relief sunken -background red -foreground white
     } else {
-	foreach tag $Anno(Ltags) {
-	    $NomTextSeq tag remove $tag 1.0 end
-	}
+	# Button is sunken, hide
+	ShowAnnotation None
+	
+	unset Anno
 	$bt configure -relief raised -background cyan -foreground black
     }
-
-    update idletasks
     $NomTextSeq configure -state disabled
+    update idletasks
 
     return
 }

src/ordali_db.tcl

@@ -76,7 +76,7 @@ proc DbProfile {sql time} {
 
 proc RemplitOrdaliDB {} {
     global OrdTmpDir LNOrdali LSOrdali
-    global {*}[info globals "TD*"] TabSF CompteurDeMac db Defauts LNDG SDG TColScore ListePDB
+    global {*}[info globals "TD*"] TabSF CompteurDeMac db Defauts LNDG SDG TColScore ListePDB ListeTypesDeFeatures
 
     #$db profile DbProfile
     $db eval {begin transaction}
@@ -122,25 +122,32 @@ proc RemplitOrdaliDB {} {
     # Met A Jour table des features
     # on a TabSF, copie conforme des features
     # du XML. On copie tel quel dans seqfeat
+    array set TAnno {}
     if {[info exists TabSF]} {
+	if {"SnapAnnotation" in $ListeTypesDeFeatures} {
+	    array set TAnno [array get TabSF "*,SnapAnnotation"]
+	    RemoveAnnotationFeatures
+	}
 	MetAJourTableFeatures
     } else {
 	set TabSF [list]
     }
+
     # Met A Jour table mac. 
     ##########a###########
     #
     # 1er MAC : initial mac, never be touched
     #
     #####################
-    $db eval {begin transaction}
-    set Lx [$db eval {select pk_seqali from seqali order by pk_seqali}]
-    set titre "M[NumeroNewMac] - original alignment"
     set pkm 1
-    $db eval {insert into snapshot values ($pkm, $titre,'original alignment')}
-
+    set titre "M[NumeroNewMac] - original alignment"
     LesDefauts IxMacCourant $pkm
     LesDefauts NmMacCourant $titre
+
+    $db eval {begin transaction}
+    set Lx [$db eval {select pk_seqali from seqali order by pk_seqali}]
+
+    $db eval {insert into snapshot values ($pkm, $titre,'original alignment')}
     
     set pos 0
     set i 1
@@ -163,6 +170,9 @@ proc RemplitOrdaliDB {} {
 	$db eval {insert into ln_seqali_cluster values ($i, $pk_Cst,$pos)}
 	incr pos
     }
+
+    # Add annotations
+    Features2Annotations [array get TAnno]
     
     ################
     #
@@ -179,7 +189,9 @@ proc RemplitOrdaliDB {} {
 	set titre "M$pkm - working alignment"
 	set name "working alignment"
     }
-
+    LesDefauts IxMacCourant $pkm
+    LesDefauts NmMacCourant $titre
+    
     $db eval {insert into snapshot values ($pkm, $titre,$name)}
     set pos 0
     foreach s $Lx {
@@ -187,9 +199,6 @@ proc RemplitOrdaliDB {} {
 	incr pos
     }
     
-    LesDefauts IxMacCourant $pkm
-    LesDefauts NmMacCourant $titre
-    
     incr pk_Clg ; # clustering
     incr pk_Cst ; # cluster
     if {[TypeAli] eq "XML"} {
@@ -217,6 +226,9 @@ proc RemplitOrdaliDB {} {
     set pk_snap [$db eval {select max(pk_snap) from snapshot}]
     set CompteurDeMac $pk_snap
 
+    # Add annotations if any
+    Features2Annotations [array get TAnno]
+    
     # Met A Jour conservation/colscores
     if {[info exists TColScore]} {
 	foreach name $TColScore(Names) {
@@ -254,7 +266,7 @@ proc RemplitOrdaliDB {} {
 	    }
 	}
     }
-
+    
     # Creation des Index
     $db eval {create index idx_seqinfo on seqinfo (pk_seqinfo, seqname, access)}
     $db eval {create index idx_seqali on seqali (pk_seqali, pk_seqinfo, seqname, seq)}

src/ordali_mode.tcl

@@ -253,13 +253,16 @@ proc AfficheModeFeatures {} {
 
 
 proc AfficheModeAnnotation {} {
+    # hide annotations through snapshot button
+    set on 0
     if {! [EtatBouton $::WOrdali(BoutAnno)]} {
 	AfficheSnapshotAnnotations
+	set on 1
     }
 
     AfficheBoutonsAnnotation
 
-    if {[EtatBouton $::WOrdali(BoutAnno)]} {
+    if {$on} {
 	AfficheSnapshotAnnotations
     }
 
@@ -300,10 +303,9 @@ proc AfficheBoutonsOrdali {} {
 proc AfficheBoutonsAnnotation {} {
     global FrmBouton Anno NomTextSeq WOrdali
     
-    if {[TypeAli] eq "pasdali"} {return}
-    
+    unset -nocomplain Anno
     LoadSnapAnnotations
-
+    
     # gui	
     grid columnconfig $FrmBouton 1 -weight 1
     set wp "${FrmBouton}.fanno"

src/ordali_setup.tcl

-
+#
+# ordali_setup.tcl
+#
 
 
 proc InitLesDefauts {} {
@@ -718,7 +720,9 @@ proc DefinitionPreferences {} {
 
     ValsDeCouleurs
 
-    set Couleurs(Stock) {red blue yellow green1 magenta orange cyan brown forest_green pink goldenrod sea_green coral violet khaki navy_blue salmon sienna turquoise lime_green maroon spring_green medium_blue indian_red dim_gray light_gray gray}
+    #  Following colors are Tk colors
+    set Couleurs(Stock) {red blue yellow green1 magenta orange cyan brown ForestGreen pink goldenrod SeaGreen coral violet khaki NavyBlue salmon sienna turquoise LimeGreen maroon SpringGreen MediumBlue IndianRed DimGray LightGray gray}
+    #set Couleurs(Stock) {red blue yellow green1 magenta orange cyan brown forest_green pink goldenrod sea_green coral violet khaki navy_blue salmon sienna turquoise lime_green maroon spring_green medium_blue indian_red dim_gray light_gray gray}
 
     return
 }

src/ordali_visu3d.tcl

@@ -807,9 +807,3 @@ proc TestCoupeMainChain {type Lca {Lcol {}} {Lc {}} {Lo {}}} {
 }
 
 
-
-
-
-
-
-

src/ordali_xml.tcl

-
+#
+# ordali_xml.tcl
+#
 
 
 proc CreeLeMacsim {{out "dehors"} {LNoms ""} {LSeqs ""}} {
@@ -1043,12 +1045,18 @@ proc CreeLeXml {{filout ""}} {
     if {$filout eq ""} {
 	set filout [DemandeEtSauveFichier xml 1]
     }
-    if {$filout eq ""} {return}
+    if {$filout eq ""} {
+	return
+    }
 
     lassign [SequencesASauver] LNoms LSeqs
-    if {$LNoms == {} || $LSeqs == {}} {return}
+    if {$LNoms == {} || $LSeqs == {}} {
+	return
+    }
 
+    Annotations2Features
     CreeLeMacsim $filout $LNoms $LSeqs
+    RemoveAnnotationFeatures
 
     return
 }