# .GDEmenus for Solaris-AMD64 
# This file was automatically generated by makemenus.py.
# Changes should be made to individual .item files,
# and the .GDEmenus file re-created using makemenus.py.
############################################################################
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#                                                                          #
#       .GDEmenus 1993 by Steven Smith                                     #
#       .GDEmenus Version   8/18/2004  by Brian Fristensky                 #
#                                                                          #
############################################################################


#
####################################################################
# This file creates menus for tgde, a pilot project aimed at 
# creating a client program for working with phylogenetic trees.
####################################################################


############################## File ##############################
menu:File

#-------------------------------- New tree ----------------------------
item:New tree   <meta N>
itemmethod:echo '"$NAME' > out1
itemmeta:n
itemhelp:doc/GDE/new_sequence.help
itemopen:gde_help_viewer.csh
 
arg:NAME 
argtype:text 
arglabel:New Tree name? 
argtext:New 
 

out:out1
outformat:flat

#------------------ Import Treefile  ( 10/ 1/09) -------------------

item:Import Treefile
itemmethod: python $birch/script/tree2flat.py $INPUTFILE out1; 
itemhelp:
itemopen:gde_help_viewer.csh

arg:INPUTFILE
argtype:text
#@argtype:file_chooser
arglabel:Name of tree file?

out:out1
outformat:flat


#-------------  Export Treefile  (10/ 1/09)   ---------------------
#

item:Export Treefile
itemmethod:(python $BIRCH/script/flat2tree.py in1 $OUTPUTFILE; $RM_CMD in1)
itemhelp:
itemopen:gde_help_viewer.csh

arg:OUTPUTFILE
argtype:text
#@argtype:file_chooser
arglabel:Save as?

in:in1
informat:flat
insave:

#-------------------------------- Save selection --------------------------
item:Save Selection
itemmethod: $SAVE_FUNC 
itemhelp:doc/GDE/save_selection.help
itemopen:gde_help_viewer.csh

arg:SAVE_FUNC
argtype:chooser
arglabel:File format
argchoice:Flat:cat in1 > $Name
argchoice:Phylip treefile:python $BIRCH/script/flat2tree.py in2 $Name
argchoice:GDE:cat in3 > $Name
argvalue:2

arg:Name
argtype:text
#@argtype:file_chooser
arglabel:File name?

in:in1
informat:flat

in:in2
informat:flat

in:in3
informat:gde


############################## Documentation ##############################
menu:Documentation

# ----------------------   DOCUMENTATION    ----------------------------


item:ViewDocumentation
itemmethod:($DOCUMENT)&

arg:DOCUMENT
arglabel:Documentation file
argtype:choice_menu
argchoice:bioLegato Documentation:$birch/script/browser.csh $tutorials/bioLegato/bioLegato.html
argchoice:tbiolegato Interface Documentation:$birch/script/browser.csh $tutorials/bioLegato/overview/bioLegato.interfaces.html#tbiolegato
argchoice:bioLegato Manual:$GDE_TEXTEDIT $DOC/bioLegato/bioLegato_man.txt
argchoice:GDE Documentation:$birch/script/browser.csh $tutorials/GDE/gde.html
argchoice:tGDE Documentation:$birch/script/browser.csh $tutorials/GDE/overview/GDE.interfaces.html#tGDE
argchoice:GDE Manual:$GDE_PDFVIEW $DOC/GDE/GDE2.2_manual.pdf
argchoice:Phylip Main Document:$birch/script/browser.csh $DOC/Phylip/main.html
argvalue:0


############################## Edit ##############################
menu:Edit

# -------------------------------   sort    --------------------------------
item:Sort
itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; tbiolegato in1.tmp;$RM_CMD -f in1*)&
itemhelp:heapsortHGL.help
itemopen:gde_help_viewer.csh

arg:PRIM_KEY
argtype:choice_menu
argchoice:Group:group-ID
argchoice:type:type
argchoice:name:name
argchoice:Sequence ID:sequence-ID
argchoice:creator:creator
argchoice:offset:offset
arglabel:Primary sort field?

arg:SEC_KEY
argtype:choice_menu
argchoice:None:
argchoice:Group:group-ID
argchoice:type:type
argchoice:name:name
argchoice:Sequence ID:sequence-ID
argchoice:creator:creator
argchoice:offset:offset
arglabel:Secondary sort field?

in:in1
informat:gde
insave:

# ----------------------- Copy out ( 1/4/06)  ----------------------------
item:Copy out
itemmethod:cat  in1 > $HOME/.tGDEclipboard

in:in1
informat:gde

# ----------------------- Paste in  1/4/06) ----------------------------
item:Paste in
itemmethod:cp $HOME/.tGDEclipboard out1

out:out1
outformat:gde

# -------------------------------- Extract --------------------------------
item:extract
#itemmethod:(tgde in1;$RM_CMD -f in1)&
itemmethod:(tbiolegato in1;$RM_CMD -f in1)&

in:in1
informat:gde
insave:



############################## Draw ##############################
menu:Draw

#------------------------- ATV ( 4/10/06) --------------------------
item:ATV - tree editor
itemmethod:(python $BIRCH/script/flat2tree.py in1 in1.treefile; rm in1; atv in1.treefile; rm in1.treefile)&
itemhelp:doc/forester/atv_documentation.pdf
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:



#------------------------- Drawtree ( 8/12/09) --------------------------
item:Drawtree - draw unrooted radial tree
itemmethod:(python $BIRCH/script/flat2tree.py in1 in1.treefile; rm in1; if test -s in1.treefile; then drawtree.csh in1.treefile $USELEN $LORIENT $LANGLE $ROTATION $ITERATE $ARCANGLE $REGULARIZATION $DAT/Phylip/$FONTFILE $CHARHEIGHT $OUTFORMAT in1.plotfile; rm in1.treefile; $WHERE fi)&
itemhelp:doc/Phylip/drawtree.html
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:USELEN
arglabel:use Branch Lengths?
argtype:chooser
argchoice:Yes:yes
argchoice:No:no
argvalue:0

arg:LORIENT
arglabel:LABEL ORIENTATION
argtype:chooser
argchoice:Fixed angle:f
argchoice:Radial:r
argchoice:Along branches:a
argchoice:branch points to middle of label:m
argvalue:0

arg:LANGLE
arglabel:Fixed label angle
argtype:chooser
argchoice:vertical:90
argchoice:horizontal:0
argchoice:downwards:-90
argvalue:1

arg:ROTATION
arglabel:ROTATION OF TREE (degrees)
argtype:slider
argmin:-360
argmax:360
argvalue:360

arg:ITERATE
arglabel:ITERATE TO IMPROVE TREE?
argtype:chooser
argchoice:Equal-Daylight algorithm:IE
argchoice:n-Body algorithm:In
argchoice:no iteration:No
argvalue:0

arg:ARCANGLE
arglabel:if no iteration: Angle of arc (degrees)
argtype:slider
argmin:0
argmax:360
argvalue:360

arg:REGULARIZATION
arglabel: if no iteration: regularize angles
argtype:chooser
argchoice:Yes:reg
argchoice:No:noreg
argvalue:0

arg:CHARHEIGHT
arglabel:RELATIVE CHARACTER HEIGHT
argtype:text
argtext:0.3333

arg:FONTFILE
arglabel:FONTFILE
argtype:choice_menu
argchoice:Roman (1 stroke):font1
argchoice:Roman (2 stroke):font2
argchoice:Roman (3 stroke):font3
argchoice:San Serif Italic (2 stroke):font4
argchoice:San Serif Italic (3 stroke):font5
argchoice:Cyrillic:font6
argvalue:0

arg:OUTFORMAT
arglabel:OUTPUT FORMAT
argtype:choice_menu
argchoice:PostScript:l
argchoice:MacDraw PICT:m
argchoice:Rayshade:r
argchoice:HP Laserjet:j
argchoice:Idraw:a
argchoice:VRML Virtual Reality Markup Lang.:z
argchoice:POVRAY 3D:v
argchoice:Houston Inst. plotter:b
argchoice:Epson MX-80:e
argchoice:Prowriter/Imagewriter:c
argchoice:Okidata:o
argchoice:Toshiba:t
argchoice:PC Paintbrush (PCX):p
argchoice:X bitmap (XBM):x
argchoice:FIG 2.0:f
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:PostScript viewer:($GDE_PSVIEW in1.plotfile; rm in1.plotfile)&
argchoice:Image viewer:($GDE_BITMAP_VIEWER in1.plotfile;rm in1.plotfile)&
argchoice:xfig:(mv in1.plotfile in1.fig; xfig in1.fig;rm in1.fig)&
argchoice:Output file:mv in1.plotfile $OUTNAME
argvalue:0

arg:OUTNAME
arglabel:Output filename
argtype:text
argtext:none

#------------------------- Drawgram ( 4/10/06) --------------------------
item:Drawgram - draw cladogram
itemmethod:(python $BIRCH/script/flat2tree.py in1 in1.treefile; rm in1; if test -s in1.treefile; then (drawgram.csh in1.treefile $TORIENT $TSTYLE $USELEN $LANGLE $DBRATIO $LDRATIO $DAT/Phylip/$FONTFILE $CHARHEIGHT $ANCESTNODE $OUTFORMAT in1.plotfile; rm in1.treefile; $WHERE ) & fi)
itemhelp:doc/Phylip/drawgram.html
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:TORIENT
arglabel:TREE GROWS
argtype:chooser
argchoice:Vertically:v
argchoice:Horizontally:h
argvalue:1

arg:TSTYLE
arglabel:TREE STYLE
argtype:choice_menu
argchoice:Cladogram:c
argchoice:Phenogram:p
argchoice:Curvogram:v
argchoice:Eurogram:e
argchoice:Swoopogram:s
argchoice:Circular:o
argvalue:1

arg:USELEN
arglabel:USE BRANCH LENGTHS?
argtype:chooser
argchoice:Yes:yes
argchoice:No:no
argvalue:0

arg:LANGLE
arglabel:Angle of labels (as if tree grew vertically)
argtype:chooser
argchoice:vertical:90
argchoice:horizontal:0
argchoice:diagonal:45
argvalue:0

arg:DBRATIO
arglabel:DEPTH/BREADTH OF TREE
argtype:text
argtext:0.53

arg:LDRATIO
arglabel:STEM LENGTH/TREE DEPTH
argtype:text
argtext:0.05

arg:CHARHEIGHT
arglabel:RELATIVE CHARACTER HEIGHT
argtype:text
argtext:0.3333

arg:ANCESTNODE
arglabel:ANCESTRAL NODES
argtype:choice_menu
argchoice:intermediate bet. immed. descendants:i
argchoice:wt. avg. of tip positions:w
argchoice:centered among descendants:c
argchoice:innermost of immed. descendants:n
argchoice:V-shaped tree:v
argvalue:0

arg:FONTFILE
arglabel:FONTFILE
argtype:choice_menu
argchoice:Roman (1 stroke):font1
argchoice:Roman (2 stroke):font2
argchoice:Roman (3 stroke):font3
argchoice:San Serif Italic (2 stroke):font4
argchoice:San Serif Italic (3 stroke):font5
argchoice:Cyrillic:font6
argvalue:0

arg:OUTFORMAT
arglabel:OUTPUT FORMAT
argtype:choice_menu
argchoice:PostScript:l
argchoice:MacDraw PICT:m
argchoice:Rayshade:r
argchoice:HP Laserjet:j
argchoice:Idraw:a
argchoice:VRML Virtual Reality Markup Lang.:z
argchoice:POVRAY 3D:v
argchoice:Houston Inst. plotter:b
argchoice:Epson MX-80:e
argchoice:Prowriter/Imagewriter:c
argchoice:Okidata:o
argchoice:Toshiba:t
argchoice:PC Paintbrush (PCX):p
argchoice:X bitmap (XBM):x
argchoice:FIG 2.0:f
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:PostScript viewer:($GDE_PSVIEW in1.plotfile; rm in1.plotfile)&
argchoice:Image viewer:($GDE_BITMAP_VIEWER in1.plotfile;rm in1.plotfile)&
argchoice:xfig:(xfig in1.plotfile;rm in1.plotfile)&
argchoice:Output file:mv in1.plotfile $OUTNAME
argvalue:0

arg:OUTNAME
arglabel:Output filename
argtype:text
argtext:none

#------------------------- TreeTool (1/13/06) --------------------------
item:TreeTool - tree editor 
itemmethod:(python $BIRCH/script/flat2tree.py in1 in1.treefile; rm in1; treetool in1.treefile; rm in1.treefile) &

in:in1
informat:flat
insave:


############################## Evaluate ##############################
menu:Evaluate

#------------------------- CONSENSUS ( 4/10/06) --------------------------
item:consense - consensus trees
itemmethod:(python $BIRCH/script/flat2tree.py in1 in1.intree; rm in1; consense.csh in1.intree $METHOD $FRACTION $OUTGROUP $ROOTED in1.outfile in1.outtree; rm in1.intree; $WHERE)&
itemhelp:doc/Phylip/consense.html
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:METHOD
argtype:choice_menu
arglabel:Consensus method
argchoice:Majority rule (extended):e
argchoice:Strict consensus (100%):s
argchoice:Ml(> F%):l
argchoice:Majority rule (>50%):m
argvalue:0   

arg:FRACTION
argtype:slider
arglabel:_____fraction F (Ml only)
argmin:51
argmax:99
argvalue:51

arg:OUTGROUP
argtype:slider
arglabel:OUTGROUP
argmin:1
argmax:1000
argvalue:1

arg:ROOTED
argtype:chooser
arglabel:Output consensus tree
argchoice:Rooted:y
argchoice:Unrooted:n
argvalue:1
  
arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0

#arg:WHERE
#arglabel:WHERE TO SEND OUTPUT
#argtype:chooser
#argchoice:tGDE: ($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (python $birch/script/tree2flat.py in1.outtree in1.flat; tgde in1.flat; rm in1.flat)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree)&  
#argchoice:ATV: ($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (atv in1.outtree)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree)&  
#argchoice:Drawtree:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)&  (drawtree.csh in1.outtree yes f 0 360 IE 360 reg $DAT/Phylip/font1 0.333 l in1.plotfile; $GDE_PSVIEW in1.plotfile; rm in1.plotfile)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree) &
#argchoice:Output files:mv in1.outfile $OUTNAME.outfile; mv in1.outtree $OUTNAME.treefile
#argvalue:0
  
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:consense

#------------------------- TREEDIST ( 8/12/09) --------------------------
item:treedist - distances between trees
itemmethod:(python $BIRCH/script/flat2tree.py in1 in1.intree; rm in1; treedist.csh in1.intree $DISTTYPE $OUTGROUP $ROOTED $WHICHDIST $OUTSTYLE in1.outfile; rm in1.intree; $WHERE)&
itemhelp:doc/Phylip/treedist.html
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:DISTTYPE
argtype:choice_menu
arglabel:Distance method
argchoice:Branch score distance (default):b
argchoice:Symmetric Difference (no branch lengths):s
argvalue:0   

arg:OUTGROUP
argtype:slider
arglabel:OUTGROUP
argmin:1
argmax:1000
argvalue:1

arg:ROOTED
argtype:chooser
arglabel:Are trees rooted?
argchoice:Rooted:y
argchoice:Unrooted:n
argvalue:1

arg:WHICHDIST
argtype:chooser
arglabel:Which distances?
argchoice:Dist. between adjacent pairs:a
argchoice:All pairwise distances:p
argvalue:1

arg:OUTSTYLE
argtype:choice_menu
arglabel:Output style
argchoice:Full matrix (only with All pairwise distances):f
argchoice:One pair per line, verbose:v
argchoice:One pair per line, numbers only:s
argvalue:0
  
arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Text editor:($GDE_TEXTEDIT in1.outfile; $RM_CMD in1*)&
argchoice:Output files:mv in1.outfile $OUTNAME.outfile
argvalue:0
  
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:treedist


############################## Help ##############################
menu:Help

#--------------------- Help - Overview  ( 9 August 2009) -----------------------
item:Overview
itemlabel:Overview
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/Overview.html)&

#--------------------- Help - Windows and Menus  ( 9 August 2009) -----------------------
item:Windows_And_Menus
itemlabel:Windows and Menus
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/WindowsAndMenus.html)&

#--------------------- Help - Open and Import Files  ( 9 August 2009) -----------------------
item:Open_And_Import
itemlabel:Open, Import, Save Export
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/OpenAndImport.html)&

#--------------------- Help - Selecting Data  ( 9 August 2009) -----------------------
item:Selecting_Data
itemlabel:Selecting Data
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/Selection.html)&

#--------------------- Group/Ungroup - work on groups of sequences  (20 February 2010) -----------------------
item:Group/Ungroup
itemlabel:Group/Ungroup
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/Group.html)&

#--------------------- Help - Properties  ( 9 August 2009) -----------------------
item:Properties
itemlabel:Properties
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/Properties.html)&

#--------------------- Help - Edit Menu  ( 9 August 2009) -----------------------
item:Edit_Menu
itemlabel:Edit Menu
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/Edit.html)&

#--------------------- Help - New Sequence  ( 9 August 2009) -----------------------
item:New_Sequence
itemlabel:New Sequence
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/NewSequence.html)&

#--------------------- Help - Editing Data  ( 9 August 2009) -----------------------
item:Editing_Data
itemlabel:Editing Data
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/Editing.html)&

#--------------------- Help - FAQ  ( 9 August 2009) -----------------------
item:Frequently_Asked_Questions
itemlabel:Frequently Asked Questions
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/FAQ.html)&

#--------------------- Help - Index  (19 July 2009) -----------------------
item:Index
itemlabel:Index
itemmethod:($birch/script/browser.csh $doc/bioLegato/Help/bioLegatoHelp.html)&

