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source: trunk/gui/scripts/analyzer.tcl @ 4045

Last change on this file since 4045 was 3647, checked in by gah, 11 years ago
add string trim to inputs
File size: 53.5 KB

Rev	Line
[3330]	1	# -- mode: tcl; indent-tabs-mode: nil --
[1]	2	# ----------------------------------------------------------------------
	3	# COMPONENT: analyzer - output area for Rappture
	4	#
	5	# This widget acts as the output side of a Rappture application.
	6	# When the input has changed, it displays a Simulate button that
	7	# launches the simulation. When a simulation is running, this
	8	# area shows status. When it is finished, the results appear
	9	# in place of the button, according to the specs in the <analyze>
	10	# XML data.
	11	# ======================================================================
	12	# AUTHOR: Michael McLennan, Purdue University
[3177]	13	# Copyright (c) 2004-2012 HUBzero Foundation, LLC
[115]	14	#
	15	# See the file "license.terms" for information on usage and
	16	# redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES.
[1]	17	# ======================================================================
	18	package require Itk
	19
[173]	20	option add *Analyzer.width 3.5i widgetDefault
[69]	21	option add *Analyzer.height 4i widgetDefault
[11]	22	option add *Analyzer.simControl "auto" widgetDefault
	23	option add *Analyzer.simControlBackground "" widgetDefault
	24	option add *Analyzer.simControlOutline gray widgetDefault
	25	option add *Analyzer.simControlActiveBackground #ffffcc widgetDefault
	26	option add *Analyzer.simControlActiveOutline black widgetDefault
[1830]	27	option add *Analyzer.notebookpage "about" widgetDefault
[11]	28
	29	option add *Analyzer.font \
[676]	30	--helvetica-medium-r-normal--12-* widgetDefault
[170]	31	option add *Analyzer.codeFont \
[676]	32	--courier-medium-r-normal--12-* widgetDefault
[1]	33	option add *Analyzer.textFont \
[676]	34	--helvetica-medium-r-normal--12-* widgetDefault
[11]	35	option add *Analyzer.boldTextFont \
[676]	36	--helvetica-bold-r-normal--12-* widgetDefault
[1]	37
	38	itcl::class Rappture::Analyzer {
	39	inherit itk::Widget
	40
[170]	41	itk_option define -codefont codeFont Font ""
[11]	42	itk_option define -textfont textFont Font ""
	43	itk_option define -boldtextfont boldTextFont Font ""
	44	itk_option define -simcontrol simControl SimControl ""
	45	itk_option define -simcontroloutline simControlOutline Background ""
	46	itk_option define -simcontrolbackground simControlBackground Background ""
	47	itk_option define -simcontrolactiveoutline simControlActiveOutline Background ""
	48	itk_option define -simcontrolactivebackground simControlActiveBackground Background ""
[1]	49	itk_option define -holdwindow holdWindow HoldWindow ""
[1830]	50	itk_option define -notebookpage notebookPage NotebookPage ""
[1]	51
[3647]	52	constructor {tool args} {
	53	# defined below
	54	}
	55	destructor {
	56	# defined below
	57	}
[1]	58
[11]	59	public method simulate {args}
[745]	60	public method reset {{when -eventually}}
[903]	61	public method load {xmlobj}
[3024]	62	public method clear {{xmlobj "all"}}
[210]	63	public method download {option args}
[1]	64
[11]	65	protected method _plot {args}
	66	protected method _reorder {comps}
	67	protected method _autoLabel {xmlobj path title cntVar}
[1]	68	protected method _fixResult {}
[3024]	69	protected method _fixResultSet {args}
[11]	70	protected method _fixSize {}
	71	protected method _fixSimControl {}
[1159]	72	protected method _fixNotebook {}
[11]	73	protected method _simState {state args}
[23]	74	protected method _simOutput {message}
[413]	75	protected method _resultTooltip {}
[1797]	76	protected method _isPdbTrajectory {data}
	77	protected method _isLammpsTrajectory {data}
	78	protected method _pdbToSequence {xmlobj path id child data}
	79	protected method _lammpsToSequence {xmlobj path id child data}
	80	protected method _trajToSequence {xmlobj {path ""}}
[1]	81
[11]	82	private variable _tool "" ;# belongs to this tool
[1606]	83	private variable _appName "" ;# Name of application
[1]	84	private variable _control "manual" ;# start mode
[3024]	85	private variable _resultset "" ;# ResultSet object with all results
[11]	86	private variable _pages 0 ;# number of pages for result sets
	87	private variable _label2page ;# maps output label => result set
[413]	88	private variable _label2desc ;# maps output label => description
[3187]	89	private variable _label2item ;# maps output label => output.xxx item
[210]	90	private variable _lastlabel "" ;# label of last example loaded
[11]	91	private variable _plotlist "" ;# items currently being plotted
[3523]	92	private variable _lastPlot
[1]	93	private common job ;# array var used for blt::bgexec jobs
	94	}
[413]	95
[1]	96	itk::usual Analyzer {
	97	keep -background -cursor foreground -font
	98	}
	99
	100	# ----------------------------------------------------------------------
	101	# CONSTRUCTOR
	102	# ----------------------------------------------------------------------
[11]	103	itcl::body Rappture::Analyzer::constructor {tool args} {
	104	set _tool $tool
	105
[3024]	106	# use this to store all simulation results
[3647]	107	set _resultset [Rappture::ResultSet ::\#auto]
[3024]	108	$_resultset notify add $this [itcl::code $this _fixResultSet]
	109
	110	# widget settings...
[11]	111	itk_option add hull.width hull.height
	112	pack propagate $itk_component(hull) no
	113
	114	frame $itk_interior.simol -borderwidth 1 -relief flat
	115	pack $itk_interior.simol -fill x
	116
[1274]	117	itk_component add simbg {
[1663]	118	frame $itk_interior.simol.simbg -borderwidth 0
[1274]	119	} {
[1663]	120	usual
	121	rename -background -simcontrolcolor simControlColor Color
[1274]	122	}
	123	pack $itk_component(simbg) -expand yes -fill both
[11]	124
[3647]	125	set simtxt [string trim [$tool xml get tool.action.label]]
[1124]	126	if {"" == $simtxt} {
[1663]	127	set simtxt "Simulate"
[1124]	128	}
[11]	129	itk_component add simulate {
[1663]	130	button $itk_component(simbg).simulate -text $simtxt \
	131	-command [itcl::code $this simulate]
[1274]	132	} {
[1663]	133	usual
	134	rename -highlightbackground -simcontrolcolor simControlColor Color
[11]	135	}
	136	pack $itk_component(simulate) -side left -padx 4 -pady 4
	137
[3186]	138	# BE CAREFUL: Shift focus when we click on "Simulate".
	139	# This shifts focus away from input widgets and causes them to
	140	# finalize and log any pending changes. A better way would be
	141	# to have the "sync" operation finalize/sync, but this works
	142	# for now.
	143	bind $itk_component(simulate) <ButtonPress> {focus %W}
	144
[1274]	145	# if there's a hub url, then add "About" and "Questions" links
[1606]	146	set _appName [$_tool xml get tool.id]
[1274]	147	set url [Rappture::Tool::resources -huburl]
[1606]	148	if {"" != $url && "" != $_appName} {
[1663]	149	itk_component add hubcntls {
	150	frame $itk_component(simbg).hubcntls
	151	} {
	152	usual
	153	rename -background -simcontrolcolor simControlColor Color
	154	}
	155	pack $itk_component(hubcntls) -side right -padx 4
[1274]	156
[1663]	157	itk_component add icon {
	158	label $itk_component(hubcntls).icon -image [Rappture::icon ask] \
	159	-highlightthickness 0
	160	} {
	161	usual
	162	ignore -highlightthickness
	163	rename -background -simcontrolcolor simControlColor Color
	164	}
	165	pack $itk_component(icon) -side left
[1274]	166
[1663]	167	itk_component add about {
	168	button $itk_component(hubcntls).about -text "About this tool" \
	169	-command [list Rappture::filexfer::webpage \
	170	"$url/tools/$_appName"]
	171	} {
	172	usual
	173	ignore -font
	174	rename -background -simcontrolcolor simControlColor Color
	175	rename -highlightbackground -simcontrolcolor simControlColor Color
	176	}
	177	pack $itk_component(about) -side top -anchor w
[1274]	178
[1663]	179	itk_component add questions {
	180	button $itk_component(hubcntls).questions -text Questions? \
	181	-command [list Rappture::filexfer::webpage \
	182	"$url/resources/$_appName/questions"]
	183	} {
	184	usual
	185	ignore -font
	186	rename -background -simcontrolcolor simControlColor Color
	187	rename -highlightbackground -simcontrolcolor simControlColor Color
	188	}
	189	pack $itk_component(questions) -side top -anchor w
[1274]	190	}
	191
[11]	192	itk_component add simstatus {
[1663]	193	text $itk_component(simbg).simstatus -borderwidth 0 \
	194	-highlightthickness 0 -height 1 -width 1 -wrap none \
	195	-state disabled
[11]	196	} {
[1663]	197	usual
	198	ignore -highlightthickness
	199	rename -background -simcontrolcolor simControlColor Color
	200	rename -font -textfont textFont Font
[11]	201	}
	202	pack $itk_component(simstatus) -side left -expand yes -fill x
	203
	204	$itk_component(simstatus) tag configure popup \
[1663]	205	-underline 1 -foreground blue
[11]	206
	207	$itk_component(simstatus) tag bind popup \
[1663]	208	<Enter> {%W configure -cursor center_ptr}
[11]	209	$itk_component(simstatus) tag bind popup \
[1663]	210	<Leave> {%W configure -cursor ""}
[11]	211	$itk_component(simstatus) tag bind popup \
[1663]	212	<ButtonPress> {after idle {Rappture::Tooltip::tooltip show %W}}
[11]	213
	214
[1]	215	itk_component add notebook {
[1663]	216	Rappture::Notebook $itk_interior.nb
[1]	217	}
	218	pack $itk_interior.nb -expand yes -fill both
	219
	220	# ------------------------------------------------------------------
[11]	221	# ABOUT PAGE
	222	# ------------------------------------------------------------------
	223	set w [$itk_component(notebook) insert end about]
	224
	225	Rappture::Scroller $w.info -xscrollmode off -yscrollmode auto
	226	pack $w.info -expand yes -fill both -padx 4 -pady 20
	227	itk_component add toolinfo {
[1663]	228	text $w.info.text -width 1 -height 1 -wrap word \
	229	-borderwidth 0 -highlightthickness 0
[11]	230	} {
[1663]	231	usual
	232	ignore -borderwidth -relief
	233	rename -font -textfont textFont Font
[11]	234	}
	235	$w.info contents $w.info.text
	236
	237	# ------------------------------------------------------------------
[1]	238	# SIMULATION PAGE
	239	# ------------------------------------------------------------------
	240	set w [$itk_component(notebook) insert end simulate]
	241	frame $w.cntls
[11]	242	pack $w.cntls -side bottom -fill x -pady 12
	243	frame $w.cntls.sep -background black -height 1
	244	pack $w.cntls.sep -side top -fill x
[1]	245
[11]	246	itk_component add abort {
[1663]	247	button $w.cntls.abort -text "Abort" \
	248	-command [itcl::code $_tool abort]
[1]	249	}
[11]	250	pack $itk_component(abort) -side left -expand yes -padx 4 -pady 4
[1]	251
[168]	252	Rappture::Scroller $w.info -xscrollmode auto -yscrollmode auto
[11]	253	pack $w.info -expand yes -fill both -padx 4 -pady 4
	254	itk_component add runinfo {
[1663]	255	text $w.info.text -width 1 -height 1 -wrap none \
	256	-borderwidth 0 -highlightthickness 0 \
	257	-state disabled
[1]	258	} {
[1663]	259	usual
	260	ignore -borderwidth -relief
	261	rename -font -codefont codeFont Font
[1]	262	}
	263	$w.info contents $w.info.text
	264
[23]	265	itk_component add progress {
[1663]	266	Rappture::Progress $w.progress
[23]	267	}
	268
[1]	269	# ------------------------------------------------------------------
	270	# ANALYZE PAGE
	271	# ------------------------------------------------------------------
	272	set w [$itk_component(notebook) insert end analyze]
	273
[11]	274	frame $w.top
	275	pack $w.top -side top -fill x -pady 8
	276	label $w.top.l -text "Result:" -font $itk_option(-font)
	277	pack $w.top.l -side left
	278
[3024]	279	itk_component add viewselector {
[1663]	280	Rappture::Combobox $w.top.sel -width 10 -editable no
[172]	281	} {
[1663]	282	usual
	283	rename -font -textfont textFont Font
[172]	284	}
[3024]	285	pack $itk_component(viewselector) -side left -expand yes -fill x
	286	bind $itk_component(viewselector) <<Value>> [itcl::code $this _fixResult]
	287	bind $itk_component(viewselector) <Enter> \
[1663]	288	[itcl::code $this download coming]
[172]	289
[3024]	290	Rappture::Tooltip::for $itk_component(viewselector) \
[1663]	291	"@[itcl::code $this _resultTooltip]"
[413]	292
[3024]	293	$itk_component(viewselector) choices insert end \
[1663]	294	--- "---"
[1077]	295
	296	itk_component add download {
[1663]	297	button $w.top.dl -image [Rappture::icon download] -anchor e \
	298	-borderwidth 1 -relief flat -overrelief raised \
	299	-command [itcl::code $this download start $w.top.dl]
[1077]	300	}
	301	pack $itk_component(download) -side right -padx {4 0}
	302	bind $itk_component(download) <Enter> \
[1663]	303	[itcl::code $this download coming]
[1077]	304
[3024]	305	$itk_component(viewselector) choices insert end \
[1663]	306	@download [Rappture::filexfer::label download]
[1077]	307
[171]	308	if {[Rappture::filexfer::enabled]} {
[1663]	309	Rappture::Tooltip::for $itk_component(download) "Downloads the current result to a new web browser window on your desktop. From there, you can easily print or save results.
[171]	310
	311	NOTE: Your web browser must allow pop-ups from this site. If your output does not appear, look for a 'pop-up blocked' message and enable pop-ups."
[1077]	312	} else {
[1663]	313	Rappture::Tooltip::for $itk_component(download) "Saves the current result to a file on your desktop."
[171]	314	}
	315
[1]	316	itk_component add results {
[1663]	317	Rappture::Panes $w.pane -sashwidth 1 -sashrelief solid -sashpadding {4 0}
[1]	318	}
[11]	319	pack $itk_component(results) -expand yes -fill both
	320	set f [$itk_component(results) pane 0]
[1]	321
[11]	322	itk_component add resultpages {
[1663]	323	Rappture::Notebook $f.nb
[11]	324	}
	325	pack $itk_component(resultpages) -expand yes -fill both
	326
	327	set f [$itk_component(results) insert end -fraction 0.1]
[3024]	328	itk_component add resultselector {
	329	Rappture::ResultSelector $f.rsel -resultset $_resultset \
	330	-settingscommand [itcl::code $this _plot]
[11]	331	}
[3024]	332	pack $itk_component(resultselector) -expand yes -fill both
	333	bind $itk_component(resultselector) <<Layout>> [itcl::code $this _fixSize]
[413]	334	bind $itk_component(results) <Configure> [itcl::code $this _fixSize]
[11]	335
[1]	336	eval itk_initialize $args
[11]	337
[170]	338	$itk_component(runinfo) tag configure ERROR -foreground red
	339	$itk_component(runinfo) tag configure text -font $itk_option(-textfont)
	340
[11]	341	#
	342	# Load up tool info on the first page.
	343	#
	344	$itk_component(toolinfo) tag configure title \
[1663]	345	-font $itk_option(-boldtextfont)
[11]	346
[3647]	347	set mesg [string trim [$tool xml get tool.title]]
[11]	348	if {"" != $mesg} {
[1663]	349	$itk_component(toolinfo) insert end $mesg title
	350	$itk_component(toolinfo) insert end "\n\n"
[11]	351	}
	352
[3647]	353	set mesg [string trim [$tool xml get tool.about]]
[11]	354	if {"" != $mesg} {
[1663]	355	$itk_component(toolinfo) insert end $mesg
[11]	356	}
	357	$itk_component(toolinfo) configure -state disabled
	358	$itk_component(notebook) current about
	359
	360	# tool can run on "manual" (default) or "auto"
[3513]	361	set cntl [string trim [$tool xml get tool.control]]
[22]	362	if {"" == $cntl} {
[3513]	363	set cntl [string trim [$tool xml get tool.control.type]]
[22]	364	}
[11]	365	if {"" != $cntl} {
[1663]	366	set _control $cntl
[11]	367	}
[12]	368
	369	# reset everything to a clean state
	370	reset
[1]	371	}
	372
	373	# ----------------------------------------------------------------------
	374	# DESTRUCTOR
	375	# ----------------------------------------------------------------------
	376	itcl::body Rappture::Analyzer::destructor {} {
[11]	377	after cancel [itcl::code $this simulate]
[3030]	378	$_resultset notify remove $this
[3024]	379	itcl::delete object $_resultset
[1]	380	}
	381
	382	# ----------------------------------------------------------------------
[11]	383	# USAGE: simulate ?-ifneeded?
	384	# USAGE: simulate ?<path1> <value1> <path2> <value2> ...?
[1]	385	#
[11]	386	# Kicks off the simulator by executing the tool.command associated
	387	# with the tool. If any arguments are specified, they are used to
	388	# set parameters for the simulation. While the simulation is running,
	389	# it shows status. When the simulation is finished, it switches
	390	# automatically to "analyze" mode and shows the results.
[1]	391	# ----------------------------------------------------------------------
[11]	392	itcl::body Rappture::Analyzer::simulate {args} {
	393	if {$args == "-ifneeded"} {
[1663]	394	# check to see if simulation is really needed
	395	$_tool sync
[3024]	396	if {[$_resultset contains [$_tool xml object]]
[1663]	397	&& ![string equal $_control "manual-resim"]} {
	398	# not needed -- show results and return
	399	$itk_component(notebook) current analyze
	400	return
	401	}
	402	set args ""
[1442]	403	}
[1]	404
[11]	405	# simulation is needed -- go to simulation page
	406	$itk_component(notebook) current simulate
[1]	407
[23]	408	# no progress messages yet
	409	pack forget $itk_component(progress)
	410	lappend args -output [itcl::code $this _simOutput]
	411
[11]	412	_simState off
	413	$itk_component(runinfo) configure -state normal
	414	$itk_component(runinfo) delete 1.0 end
[170]	415	$itk_component(runinfo) insert end "Running simulation...\n\n" text
[11]	416	$itk_component(runinfo) configure -state disabled
[1]	417
[11]	418	# if the hold window is set, then put up a busy cursor
	419	if {$itk_option(-holdwindow) != ""} {
[1663]	420	blt::busy hold $itk_option(-holdwindow)
	421	raise $itk_component(hull)
[11]	422	}
[1]	423
[11]	424	# execute the job
	425	foreach {status result} [eval $_tool run $args] break
[1]	426
[11]	427	# if job was aborted, then allow simulation again
	428	if {$result == "ABORT"} {
[1663]	429	_simState on "Aborted"
[11]	430	}
[1]	431
[903]	432	# load results from run.xml into analyzer
[11]	433	if {$status == 0 && $result != "ABORT"} {
[1663]	434	set status [catch {load $result} result]
[1]	435	}
[11]	436
	437	# back to normal
	438	if {$itk_option(-holdwindow) != ""} {
[1663]	439	blt::busy release $itk_option(-holdwindow)
[11]	440	}
	441	$itk_component(abort) configure -state disabled
	442
	443	if {$status != 0} {
[1663]	444	$itk_component(runinfo) configure -state normal
	445	$itk_component(runinfo) delete 1.0 end
	446	$itk_component(runinfo) insert end "Problem launching job:\n\n" text
	447	_simOutput $result
	448	$itk_component(runinfo) configure -state disabled
	449	$itk_component(runinfo) see 1.0
[724]	450
[1663]	451	# Try to create a support ticket for this error.
	452	# It may be a real problem.
	453	if {[Rappture::bugreport::shouldReport for jobs]} {
[2611]	454	set ::errorInfo "\n\n== RAPPTURE INPUT ==\n[$_tool xml xml]"
[1861]	455	Rappture::bugreport::register "Problem launching job:\n$result"
[2744]	456	Rappture::bugreport::attachment [$_tool xml xml]
[1861]	457	Rappture::bugreport::send
[1663]	458	}
[11]	459	} else {
[1663]	460	$itk_component(notebook) current analyze
[11]	461	}
[168]	462
	463	# do this last -- after _simOutput above
	464	pack forget $itk_component(progress)
[1]	465	}
	466
	467	# ----------------------------------------------------------------------
[745]	468	# USAGE: reset ?-eventually\|-now?
[1]	469	#
	470	# Used to reset the analyzer whenever the input to a simulation has
	471	# changed. Sets the mode back to "simulate", so the user has to
	472	# simulate again to see the output. If the <start> option is set
	473	# to "auto", the simulation is invoked immediately.
	474	# ----------------------------------------------------------------------
[745]	475	itcl::body Rappture::Analyzer::reset {{when -eventually}} {
	476	if {$when == "-eventually"} {
[1663]	477	after cancel [list catch [itcl::code $this reset -now]]
	478	after idle [list catch [itcl::code $this reset -now]]
	479	return
[745]	480	}
	481
[11]	482	# check to see if simulation is really needed
	483	$_tool sync
[3024]	484	if {![$_resultset contains [$_tool xml object]]
[1663]	485	\|\| [string equal $_control "manual-resim"]} {
	486	# if control mode is "auto", then simulate right away
	487	if {[string match auto* $_control]} {
	488	# auto control -- don't need button
	489	pack forget $itk_interior.simol
[1]	490
[1663]	491	after cancel [itcl::code $this simulate]
	492	after idle [itcl::code $this simulate]
	493	} else {
	494	_simState on "new input parameters"
	495	}
[11]	496	} else {
[1663]	497	_simState off
[1]	498	}
	499	}
	500
	501	# ----------------------------------------------------------------------
[903]	502	# USAGE: load <xmlobj>
[1]	503	#
[903]	504	# Loads the data from the given <xmlobj> into the appropriate results
[11]	505	# sets. If necessary, new results sets are created to store the data.
[1]	506	# ----------------------------------------------------------------------
[903]	507	itcl::body Rappture::Analyzer::load {xmlobj} {
[43]	508	# only show the last result? then clear first
[3513]	509	if {[string trim [$_tool xml get tool.analyzer]] == "last"} {
[1663]	510	clear
[43]	511	}
[3024]	512	$_resultset add $xmlobj
[11]	513
[3024]	514	# NOTE: Adding will trigger a !change event on the ResultSet
	515	# object, which will trigger calls to _fixResultSet to add
	516	# the results to display.
[1]	517	}
	518
	519	# ----------------------------------------------------------------------
[2943]	520	# USAGE: clear ?<xmlobj>?
[1]	521	#
[2943]	522	# Discards one or more results previously loaded into the analyzer.
	523	# If an <xmlobj> is specified, then that one result is cleared.
	524	# Otherwise, all results are cleared.
[1]	525	# ----------------------------------------------------------------------
[3024]	526	itcl::body Rappture::Analyzer::clear {{xmlobj "all"}} {
	527	if {$xmlobj eq "" \|\| $xmlobj eq "all"} {
	528	$_resultset clear
[2943]	529	} else {
[3024]	530	$_resultset clear $xmlobj
[11]	531	}
	532
[3024]	533	# NOTE: Clearing will trigger a !change event on the ResultSet
	534	# object, which will trigger calls to _fixResultSet to clean up
	535	# the results being displayed.
[11]	536	}
	537
	538	# ----------------------------------------------------------------------
[193]	539	# USAGE: download coming
[464]	540	# USAGE: download controls <downloadCommand>
	541	# USAGE: download start ?widget?
[210]	542	# USAGE: download now ?widget?
[50]	543	#
	544	# Spools the current result so the user can download it.
	545	# ----------------------------------------------------------------------
[210]	546	itcl::body Rappture::Analyzer::download {option args} {
[3024]	547	set title [$itk_component(viewselector) value]
	548	set page [$itk_component(viewselector) translate $title]
[193]	549
[1077]	550	switch -- $option {
[1663]	551	coming {
	552	#
	553	# Warn result that a download is coming, in case
	554	# it needs to take a screen snap.
	555	#
	556	if {![regexp {^(\|@download\|---)$} $page]} {
	557	set f [$itk_component(resultpages) page $page]
	558	$f.rviewer download coming
	559	}
	560	}
	561	controls {
	562	# no controls for this download yet
	563	return ""
	564	}
	565	start {
	566	set widget $itk_component(download)
	567	if {[llength $args] > 0} {
	568	set widget [lindex $args 0]
	569	if {[catch {winfo class $widget}]} {
	570	set widget $itk_component(download)
	571	}
	572	}
	573	#
	574	# See if this download has any controls. If so, then
	575	# post them now and let the user continue the download
	576	# after selecting a file format.
	577	#
	578	if {$page != ""} {
	579	set ext ""
	580	set f [$itk_component(resultpages) page $page]
	581	set arg [itcl::code $this download now $widget]
	582	set popup [$f.rviewer download controls $arg]
	583	if {"" != $popup} {
	584	$popup activate $widget below
	585	} else {
	586	download now $widget
	587	}
	588	} else {
	589	# this shouldn't happen
	590	set file error.html
	591	set data "<h1>Not Found</h1>There is no result selected."
	592	}
	593	}
	594	now {
	595	set widget $itk_component(download)
	596	if {[llength $args] > 0} {
	597	set widget [lindex $args 0]
	598	if {[catch {winfo class $widget}]} {
	599	set widget $itk_component(download)
	600	}
	601	}
	602	#
	603	# Perform the actual download.
	604	#
	605	if {$page != ""} {
	606	set ext ""
	607	set f [$itk_component(resultpages) page $page]
[3024]	608	set item [$itk_component(viewselector) value]
[1663]	609	set result [$f.rviewer download now $widget $_appName $item]
	610	if { $result == "" } {
	611	return; # User cancelled the download.
	612	}
	613	foreach {ext data} $result break
	614	if {"" == $ext} {
	615	if {"" != $widget} {
	616	Rappture::Tooltip::cue $widget \
	617	"Can't download this result."
	618	}
	619	return
	620	}
	621	regsub -all {[\ -\/\:-\@\{-\~]} $title {} title
	622	set file "$title$ext"
	623	} else {
	624	# this shouldn't happen
	625	set file error.html
	626	set data "<h1>Not Found</h1>There is no result selected."
	627	}
[50]	628
[3186]	629	Rappture::Logger::log download [$itk_component(viewselector) value]
[1663]	630	set mesg [Rappture::filexfer::download $data $file]
	631	if {[string length $mesg] > 0} {
	632	Rappture::Tooltip::cue $widget $mesg
	633	}
	634	}
	635	default {
	636	error "bad option \"$option\": should be coming, controls, now, start"
	637	}
[50]	638	}
	639	}
	640
	641	# ----------------------------------------------------------------------
[11]	642	# USAGE: _plot ?<index> <options> <index> <options>...?
	643	#
	644	# Used internally to update the plot shown in the current result
[3024]	645	# viewer whenever the resultselector settings have changed. Causes the
[11]	646	# desired results to show up on screen.
	647	# ----------------------------------------------------------------------
	648	itcl::body Rappture::Analyzer::_plot {args} {
	649	set _plotlist $args
	650
[3024]	651	set page [$itk_component(viewselector) value]
	652	set page [$itk_component(viewselector) translate $page]
[43]	653	if {"" != $page} {
[1663]	654	set f [$itk_component(resultpages) page $page]
	655	$f.rviewer plot clear
	656	foreach {index opts} $_plotlist {
	657	$f.rviewer plot add $index $opts
	658	}
[11]	659	}
[1]	660	}
	661
	662	# ----------------------------------------------------------------------
[13]	663	# USAGE: _reorder <compList>
[1]	664	#
[11]	665	# Used internally to change the order of a series of output components
	666	# found in the <output> section. Moves the <log> elements to the end
	667	# and returns the updated list.
[1]	668	# ----------------------------------------------------------------------
[11]	669	itcl::body Rappture::Analyzer::_reorder {comps} {
	670	set i 0
	671	set max [llength $comps]
	672	while {$i < $max} {
[1663]	673	set c [lindex $comps $i]
	674	if {[string match log* $c]} {
	675	set comps [lreplace $comps $i $i]
	676	lappend comps $c
	677	incr max -1
	678	} else {
	679	incr i
	680	}
[1]	681	}
[11]	682	return $comps
[1]	683	}
	684
	685	# ----------------------------------------------------------------------
[11]	686	# USAGE: _autoLabel <xmlobj> <path> <title> <cntVar>
[1]	687	#
[11]	688	# Used internally to check for an about.label property at the <path>
	689	# in <xmlobj>. If this object doesn't have a label, then one is
	690	# supplied using the given <title>. The <cntVar> is an array of
	691	# counters in the calling scopes for titles that have been used
	692	# in the past. This is used to create titles like "Plot #2" the
	693	# second time it is encountered.
	694	#
	695	# The <xmlobj> is updated so that the label is inserted directly in
	696	# the tree.
[1]	697	# ----------------------------------------------------------------------
[11]	698	itcl::body Rappture::Analyzer::_autoLabel {xmlobj path title cntVar} {
	699	upvar $cntVar counters
	700
[13]	701	set group [$xmlobj get $path.about.group]
[11]	702	set label [$xmlobj get $path.about.label]
	703	if {"" == $label} {
[1663]	704	# no label -- make one up using the title specified
	705	if {![info exists counters($group-$title)]} {
	706	set counters($group-$title) 1
	707	set label $title
	708	} else {
	709	set label "$title (#[incr counters($group-$title)])"
	710	}
	711	$xmlobj put $path.about.label $label
[11]	712	} else {
[1663]	713	# handle the case of two identical labels in <output>
	714	if {![info exists counters($group-$label)]} {
	715	set counters($group-$label) 1
	716	} else {
	717	set label "$label (#[incr counters($group-$label)])"
	718	$xmlobj put $path.about.label $label
	719	}
[1]	720	}
[11]	721	return $label
[1]	722	}
	723
	724	# ----------------------------------------------------------------------
[11]	725	# USAGE: _fixResult
[1]	726	#
[11]	727	# Used internally to change the result page being displayed whenever
	728	# the user selects a page from the results combobox.
[1]	729	# ----------------------------------------------------------------------
[11]	730	itcl::body Rappture::Analyzer::_fixResult {} {
[3024]	731	set name [$itk_component(viewselector) value]
[210]	732	set page ""
	733	if {"" != $name} {
[3024]	734	set page [$itk_component(viewselector) translate $name]
[210]	735	}
	736	if {$page == "@download"} {
[1663]	737	# put the combobox back to its last value
[3024]	738	$itk_component(viewselector) component entry configure -state normal
	739	$itk_component(viewselector) component entry delete 0 end
	740	$itk_component(viewselector) component entry insert end $_lastlabel
	741	$itk_component(viewselector) component entry configure -state disabled
[1663]	742	# perform the actual download
	743	download start $itk_component(download)
[210]	744	} elseif {$page == "---"} {
[1663]	745	# put the combobox back to its last value
[3024]	746	$itk_component(viewselector) component entry configure -state normal
	747	$itk_component(viewselector) component entry delete 0 end
	748	$itk_component(viewselector) component entry insert end $_lastlabel
	749	$itk_component(viewselector) component entry configure -state disabled
[216]	750	} elseif {$page != ""} {
[1663]	751	set _lastlabel $name
	752	set win [winfo toplevel $itk_component(hull)]
	753	$itk_component(resultpages) current $page
[3523]	754	set f [$itk_component(resultpages) page $page]
[11]	755
[3523]	756	# We don't want to replot if we're using an existing viewer with the
	757	# the same list of objects to plot. So track the viewer and the list.
	758	if { ![info exists _lastPlot($f)] \|\| $_plotlist != $_lastPlot($f) } {
	759	set _lastPlot($f) $_plotlist
	760	blt::busy hold $win
	761	$f.rviewer plot clear
	762	eval $f.rviewer plot add $_plotlist
	763	blt::busy release [winfo toplevel $itk_component(hull)]
	764	}
[3187]	765	Rappture::Logger::log output $_label2item($name)
	766	Rappture::Tooltip::for $itk_component(viewselector) \
	767	"@[itcl::code $this _resultTooltip]" -log $_label2item($name)
[13]	768	}
[11]	769	}
	770
	771	# ----------------------------------------------------------------------
[3024]	772	# USAGE: _fixResultSet ?<eventData>...?
	773	#
	774	# Used internally to react to changes within the ResultSet. When a
	775	# result is added, a new result viewer is created for the object.
	776	# When all results are cleared, the viewers are deleted.
	777	# ----------------------------------------------------------------------
	778	itcl::body Rappture::Analyzer::_fixResultSet {args} {
	779	array set eventData $args
	780	switch -- $eventData(op) {
	781	add {
	782	set xmlobj $eventData(what)
	783
	784	# Detect molecule elements that contain trajectory data
	785	# and convert to sequences.
	786	_trajToSequence $xmlobj output
	787
	788	# Go through the analysis and find all result sets.
	789	set haveresults 0
	790	foreach item [_reorder [$xmlobj children output]] {
	791	switch -glob -- $item {
	792	log* {
	793	_autoLabel $xmlobj output.$item "Output Log" counters
	794	}
	795	number* {
	796	_autoLabel $xmlobj output.$item "Number" counters
	797	}
	798	integer* {
	799	_autoLabel $xmlobj output.$item "Integer" counters
	800	}
	801	string* {
	802	_autoLabel $xmlobj output.$item "String" counters
	803	}
	804	histogram* - curve* - field* {
	805	_autoLabel $xmlobj output.$item "Plot" counters
	806	}
	807	drawing* {
	808	_autoLabel $xmlobj output.$item "Drawing" counters
	809	}
	810	structure* {
	811	_autoLabel $xmlobj output.$item "Structure" counters
	812	}
	813	table* {
	814	_autoLabel $xmlobj output.$item "Energy Levels" counters
	815	}
	816	sequence* {
	817	_autoLabel $xmlobj output.$item "Sequence" counters
	818	}
	819	}
	820	set label [$xmlobj get output.$item.about.group]
	821	if {"" == $label} {
	822	set label [$xmlobj get output.$item.about.label]
	823	}
	824
	825	set hidden [$xmlobj get output.$item.hide]
	826	set hidden [expr {"" != $hidden && $hidden}]
	827
	828	if {"" != $label && !$hidden} {
	829	set haveresults 1
	830	}
	831	}
	832
	833	# if there are any valid results, add them to the resultset
	834	if {$haveresults} {
	835	set index [$_resultset get simnum $xmlobj]
	836
	837	# add each result to a result viewer
	838	foreach item [_reorder [$xmlobj children output]] {
	839	set label [$xmlobj get output.$item.about.group]
	840	if {"" == $label} {
	841	set label [$xmlobj get output.$item.about.label]
	842	}
	843	set hidden [$xmlobj get output.$item.hide]
	844	if { $hidden == "" } {
	845	set hidden 0
	846	}
	847	if {"" != $label && !$hidden} {
	848	if {![info exists _label2page($label)]} {
	849	set name "page[incr _pages]"
	850	set page [$itk_component(resultpages) \
	851	insert end $name]
	852	set _label2page($label) $page
[3187]	853	set _label2item($label) output.$item
[3024]	854	set _label2desc($label) \
	855	[$xmlobj get output.$item.about.description]
	856	Rappture::ResultViewer $page.rviewer
	857	pack $page.rviewer -expand yes -fill both -pady 4
	858
	859	set end [$itk_component(viewselector) \
	860	choices index -value ---]
	861	if {$end < 0} {
	862	set end "end"
	863	}
	864	$itk_component(viewselector) choices insert $end \
	865	$name $label
	866	}
	867
	868	# add/replace the latest result into this viewer
	869	set page $_label2page($label)
	870
	871	if {![info exists reset($page)]} {
	872	$page.rviewer clear $index
	873	set reset($page) 1
	874	}
	875	$page.rviewer add $index $xmlobj output.$item
	876	}
	877	}
	878	}
	879
	880	# show the first page by default
	881	set max [$itk_component(viewselector) choices size]
	882	for {set i 0} {$i < $max} {incr i} {
	883	set first [$itk_component(viewselector) choices get -label $i]
	884	if {$first != ""} {
	885	set page [$itk_component(viewselector) choices get -value $i]
	886	set char [string index $page 0]
	887	if {$char != "@" && $char != "-"} {
	888	$itk_component(resultpages) current $page
	889	$itk_component(viewselector) value $first
	890	set _lastlabel $first
	891	break
	892	}
	893	}
	894	}
	895	}
	896	clear {
[3078]	897	if {$eventData(what) ne "all"} {
[3024]	898	# delete this result from all viewers
[3078]	899	array set params $eventData(what)
[3024]	900	foreach label [array names _label2page] {
	901	set page $_label2page($label)
[3078]	902	$page.rviewer clear $params(simnum)
[3024]	903	}
	904	}
	905
	906	if {[$_resultset size] == 0} {
	907	# reset the size of the controls area
	908	set ht [winfo height $itk_component(results)]
	909	set cntlht [$itk_component(resultselector) size -controlarea]
	910	set frac [expr {double($cntlht)/$ht}]
	911	$itk_component(results) fraction end $frac
	912
	913	foreach label [array names _label2page] {
	914	set page $_label2page($label)
	915	destroy $page.rviewer
	916	}
	917	$itk_component(resultpages) delete -all
	918	set _pages 0
	919
	920	$itk_component(viewselector) value ""
	921	$itk_component(viewselector) choices delete 0 end
	922	catch {unset _label2page}
[3187]	923	catch {unset _label2item}
[3024]	924	catch {unset _label2desc}
	925	set _plotlist ""
	926
	927	$itk_component(viewselector) choices insert end --- "---"
	928	$itk_component(viewselector) choices insert end \
	929	@download [Rappture::filexfer::label download]
	930	set _lastlabel ""
	931	}
	932
	933	# fix Simulate button state
	934	reset
	935	}
	936	default {
	937	error "don't know how to handle op \"$eventData(op)\""
	938	}
	939	}
	940	}
	941
	942	# ----------------------------------------------------------------------
[11]	943	# USAGE: _fixSize
	944	#
	945	# Used internally to change the size of the result set area whenever
	946	# a new control appears. Adjusts the size available for the result
	947	# set up to some maximum.
	948	# ----------------------------------------------------------------------
	949	itcl::body Rappture::Analyzer::_fixSize {} {
[413]	950	set ht [winfo height $itk_component(results)]
	951	if {$ht <= 1} { set ht [winfo reqheight $itk_component(results)] }
[3024]	952	set cntlht [$itk_component(resultselector) size -controlarea]
[413]	953	set frac [expr {double($cntlht)/$ht}]
	954
	955	if {$frac < 0.4} {
[1663]	956	$itk_component(results) fraction end $frac
[1]	957	}
[11]	958	_fixSimControl
	959	}
[1]	960
[11]	961	# ----------------------------------------------------------------------
	962	# USAGE: _simState <boolean> ?<message>? ?<settings>?
	963	#
	964	# Used internally to change the "Simulation" button on or off.
	965	# If the <boolean> is on, then any <message> and <settings> are
[1159]	966	# displayed as well. If the <boolean> is off, then only display
	967	# the message. The <message> is a note to the user about
[11]	968	# what will be simulated, and the <settings> are a list of
	969	# tool parameter settings of the form {path1 val1 path2 val2 ...}.
	970	# When these are in place, the next Simulate operation will use
	971	# these settings. This helps fill in missing data values.
	972	# ----------------------------------------------------------------------
	973	itcl::body Rappture::Analyzer::_simState {state args} {
	974	if {$state} {
[1663]	975	$itk_interior.simol configure \
	976	-background $itk_option(-simcontrolactiveoutline)
	977	configure -simcontrolcolor $itk_option(-simcontrolactivebackground)
[1]	978
[1663]	979	$itk_component(abort) configure -state disabled
	980	$itk_component(simulate) configure -state normal \
	981	-command [itcl::code $this simulate]
[1]	982
[1663]	983	#
	984	# If there's a special message, then put it up next to the button.
	985	#
	986	set mesg [lindex $args 0]
	987	if {"" != $mesg} {
	988	$itk_component(simstatus) configure -state normal
	989	$itk_component(simstatus) delete 1.0 end
	990	$itk_component(simstatus) insert end $mesg
[1]	991
[1663]	992	#
	993	# If there are any settings, then install them in the
	994	# "Simulate" button. Also, pop them up as a tooltip
	995	# for the message.
	996	#
	997	set settings [lindex $args 1]
	998	if {[llength $settings] > 0} {
	999	$itk_component(simulate) configure \
	1000	-command [eval itcl::code $this simulate $settings]
[8]	1001
[1663]	1002	set details ""
	1003	foreach {path val} $settings {
[3647]	1004	set str [string trim [$_tool xml get $path.about.label]]
[1663]	1005	if {"" == $str} {
[2241]	1006	set str [$_tool xml element -as id $path]
[1663]	1007	}
	1008	append details "$str = $val\n"
	1009	}
	1010	set details [string trim $details]
[8]	1011
[1663]	1012	Rappture::Tooltip::for $itk_component(simstatus) $details
	1013	$itk_component(simstatus) insert end " "
	1014	$itk_component(simstatus) insert end "(details...)" popup
	1015	}
	1016	$itk_component(simstatus) configure -state disabled
	1017	}
[11]	1018	} else {
[1663]	1019	if {"" != $itk_option(-simcontrolbackground)} {
	1020	set simcbg $itk_option(-simcontrolbackground)
	1021	} else {
	1022	set simcbg $itk_option(-background)
	1023	}
	1024	$itk_interior.simol configure \
	1025	-background $itk_option(-simcontroloutline)
	1026	configure -simcontrolcolor $simcbg
[1]	1027
[1663]	1028	$itk_component(simulate) configure -state disabled
	1029	$itk_component(abort) configure -state normal
[11]	1030
[1663]	1031	$itk_component(simstatus) configure -state normal
	1032	$itk_component(simstatus) delete 1.0 end
	1033	set mesg [lindex $args 0]
	1034	if {"" != $mesg} {
	1035	$itk_component(simstatus) insert end $mesg
	1036	}
	1037	$itk_component(simstatus) configure -state disabled
[1]	1038	}
[11]	1039	}
[1]	1040
[11]	1041	# ----------------------------------------------------------------------
[23]	1042	# USAGE: _simOutput <message>
	1043	#
	1044	# Invoked automatically whenever output comes in while running the
	1045	# tool. Extracts any =RAPPTURE-???=> messages from the output and
	1046	# sends the output to the display. For example, any
	1047	# =RAPPTURE-PROGRESS=> message pops up the progress meter and updates
	1048	# it to show the latest progress message. This is useful for
	1049	# long-running tools, to let the user know how much longer the
	1050	# simulation will take.
	1051	# ----------------------------------------------------------------------
	1052	itcl::body Rappture::Analyzer::_simOutput {message} {
	1053	#
	1054	# Scan through and pick out any =RAPPTURE-PROGRESS=> messages first.
	1055	#
	1056	while {[regexp -indices \
[1663]	1057	{=RAPPTURE-PROGRESS=> ([-+]?[0-9]+) +([^\n])(\n\|$)} $message \
	1058	match percent mesg]} {
[23]	1059
[1663]	1060	foreach {i0 i1} $percent break
	1061	set percent [string range $message $i0 $i1]
[23]	1062
[1663]	1063	foreach {i0 i1} $mesg break
	1064	set mesg [string range $message $i0 $i1]
[23]	1065
[1663]	1066	pack $itk_component(progress) -fill x -padx 10 -pady 10
	1067	$itk_component(progress) settings -percent $percent -message $mesg
[23]	1068
[1663]	1069	foreach {i0 i1} $match break
	1070	set message [string replace $message $i0 $i1]
[23]	1071	}
	1072
	1073	#
	1074	# Break up the remaining lines according to =RAPPTURE-ERROR=> messages.
	1075	# Show errors in a special color.
	1076	#
	1077	$itk_component(runinfo) configure -state normal
	1078
	1079	while {[regexp -indices \
[1663]	1080	{=RAPPTURE-([a-zA-Z]+)=>([^\n]*)(\n\|$)} $message \
	1081	match type mesg]} {
[23]	1082
[1663]	1083	foreach {i0 i1} $match break
	1084	set first [string range $message 0 [expr {$i0-1}]]
	1085	if {[string length $first] > 0} {
	1086	$itk_component(runinfo) insert end $first
	1087	$itk_component(runinfo) insert end \n
	1088	}
[23]	1089
[1663]	1090	foreach {t0 t1} $type break
	1091	set type [string range $message $t0 $t1]
	1092	foreach {m0 m1} $mesg break
	1093	set mesg [string range $message $m0 $m1]
	1094	if {[string length $mesg] > 0 && $type != "RUN"} {
	1095	$itk_component(runinfo) insert end $mesg $type
	1096	$itk_component(runinfo) insert end \n $type
	1097	}
[23]	1098
[1663]	1099	set message [string range $message [expr {$i1+1}] end]
[23]	1100	}
	1101
	1102	if {[string length $message] > 0} {
[1663]	1103	$itk_component(runinfo) insert end $message
	1104	if {[$itk_component(runinfo) get end-2char] != "\n"} {
	1105	$itk_component(runinfo) insert end "\n"
	1106	}
	1107	$itk_component(runinfo) see end
[23]	1108	}
	1109	$itk_component(runinfo) configure -state disabled
	1110	}
	1111
	1112	# ----------------------------------------------------------------------
[413]	1113	# USAGE: _resultTooltip
	1114	#
	1115	# Used internally to build the tooltip string displayed for the
	1116	# result selector. If the current page has an associated description,
	1117	# then it is displayed beneath the result.
	1118	#
	1119	# Returns the string for the tooltip.
	1120	# ----------------------------------------------------------------------
	1121	itcl::body Rappture::Analyzer::_resultTooltip {} {
	1122	set tip ""
[3024]	1123	set name [$itk_component(viewselector) value]
[413]	1124	if {[info exists _label2desc($name)] &&
[1663]	1125	[string length $_label2desc($name)] > 0} {
	1126	append tip "$_label2desc($name)\n\n"
[413]	1127	}
	1128	if {[array size _label2page] > 1} {
[1663]	1129	append tip "Use this control to display other output results."
[413]	1130	}
	1131	return $tip
	1132	}
	1133
	1134	# ----------------------------------------------------------------------
[11]	1135	# USAGE: _fixSimControl
	1136	#
	1137	# Used internally to add or remove the simulation control at the
	1138	# top of the analysis area. This is controlled by the -simcontrol
	1139	# option.
	1140	# ----------------------------------------------------------------------
	1141	itcl::body Rappture::Analyzer::_fixSimControl {} {
	1142	switch -- $itk_option(-simcontrol) {
[1663]	1143	on {
	1144	pack $itk_interior.simol -fill x -before $itk_interior.nb
	1145	}
	1146	off {
	1147	pack forget $itk_interior.simol
	1148	}
	1149	auto {
	1150	#
	1151	# If we have two or more radiodials, then there is a
	1152	# chance of encountering a combination of parameters
	1153	# with no data, requiring simulation.
	1154	#
[3024]	1155	if {[$itk_component(resultselector) size -controls] >= 2} {
[1663]	1156	pack $itk_interior.simol -fill x -before $itk_interior.nb
	1157	} else {
	1158	pack forget $itk_interior.simol
	1159	}
	1160	}
	1161	default {
	1162	error "bad value \"$itk_option(-simcontrol)\": should be on, off, auto"
	1163	}
[1]	1164	}
	1165	}
[11]	1166
	1167	# ----------------------------------------------------------------------
[1159]	1168	# USAGE: _fixNotebook
	1169	#
	1170	# Used internally to switch the active notebook page
	1171	# ----------------------------------------------------------------------
	1172	itcl::body Rappture::Analyzer::_fixNotebook {} {
	1173	switch -- $itk_option(-notebookpage) {
[1663]	1174	about {
	1175	$itk_component(notebook) current about
	1176	}
	1177	simulate {
	1178	$itk_component(notebook) current simulate
	1179	}
	1180	analyze {
	1181	$itk_component(notebook) current analyze
	1182	}
	1183	default {
	1184	error "bad value \"$itk_option(-notebookpage)\": should be about, simulate, analyze"
	1185	}
[1159]	1186	}
	1187	}
	1188
	1189	# ----------------------------------------------------------------------
[1797]	1190	# USAGE: _isPdbTrajectory <data>
[1791]	1191	#
	1192	# Used internally to determine whether pdb or lammps data represents a
[2175]	1193	# trajectory rather than a single frame
[1791]	1194	# ----------------------------------------------------------------------
[1797]	1195	itcl::body Rappture::Analyzer::_isPdbTrajectory {data} {
[3330]	1196	if { [llength $data] == 0 } {
[1929]	1197	return 0
[1791]	1198	}
[1797]	1199	set nModels 0
	1200	foreach line $data {
[1929]	1201	if { [string match "MODEL*" $line] } {
	1202	incr nModels
	1203	if { $nModels > 1 } {
	1204	# Stop if more than one model found. No need to count them
	1205	# all.
	1206	return 1
	1207	}
	1208	}
[1797]	1209	}
	1210	return 0
	1211	}
[1791]	1212
[1797]	1213	# ----------------------------------------------------------------------
	1214	# USAGE: _isLammpsTrajectory <data>
	1215	#
	1216	# Used internally to determine whether pdb or lammps data represents a
[2175]	1217	# trajectory rather than a single frame
[1797]	1218	# ----------------------------------------------------------------------
	1219	itcl::body Rappture::Analyzer::_isLammpsTrajectory { data } {
[3330]	1220	if { [llength $data] == 0 } {
[1929]	1221	return 0
[1797]	1222	}
	1223	set nModels 0
	1224	foreach line $data {
[1929]	1225	if { [regexp {^[\t ]*ITEM:[ \t]+TIMESTEP} $line] } {
	1226	incr nModels
	1227	if { $nModels > 1 } {
	1228	# Stop if more than one model found. No need to count them
	1229	# all.
	1230	return 1
	1231	}
	1232	}
[1797]	1233	}
	1234	return 0
[1791]	1235	}
	1236
	1237	# ----------------------------------------------------------------------
[1830]	1238	# USAGE: _pdbToSequence <xmlobj> ?<path>?
[1791]	1239	#
[1830]	1240	# If the molecule element is a trajectory, delete the original
	1241	# and create a sequence of individual molecules.
[1791]	1242	# Used internally to detect any molecule output elements that contain
	1243	# trajectory data. Trajectories will be converted into sequences of
	1244	# individual molecules. All other elements will be unaffected. Scans
	1245	# the entire xml tree if a starting path is not specified.
	1246	# ----------------------------------------------------------------------
[1797]	1247	itcl::body Rappture::Analyzer::_pdbToSequence {xmlobj path id child data} {
[1791]	1248
[1797]	1249	set seqLabel [$xmlobj get ${child}.about.label]
	1250	set descr [$xmlobj get ${child}.about.description]
	1251	set formula [$xmlobj get ${child}.components.molecule.formula]
	1252	$xmlobj remove $child
[1791]	1253
[1830]	1254	set sequence $path.sequence($id)
	1255	$xmlobj put ${sequence}.about.label $seqLabel
	1256	$xmlobj put ${sequence}.about.description $descr
[2175]	1257	$xmlobj put ${sequence}.index.label "Frame"
[1791]	1258
[2175]	1259	set frameNum 0
[1830]	1260	set numLines [llength $data]
	1261	for { set i 0 } { $i < $numLines } { incr i } {
[1929]	1262	set line [lindex $data $i]
	1263	set line [string trim $line]
	1264	set contents {}
	1265	if { [string match "MODEL*" $line] } {
	1266	# Save the contents until we get an ENDMDL record.
	1267	for {} { $i < $numLines } { incr i } {
	1268	set line [lindex $data $i]
	1269	set line [string trim $line]
	1270	if { $line == "" } {
[2744]	1271	continue; # Skip blank lines.
[1929]	1272	}
	1273	if { [string match "ENDMDL*" $line] } {
	1274	break;
	1275	}
	1276	append contents $line\n
	1277	}
[2175]	1278	set frame ${sequence}.element($frameNum)
	1279	$xmlobj put ${frame}.index $frameNum
[1929]	1280
[2175]	1281	set molecule ${frame}.structure.components.molecule
[1929]	1282	$xmlobj put ${molecule}.pdb $contents
	1283	$xmlobj put ${molecule}.formula $formula
[2175]	1284	incr frameNum
[1929]	1285	}
[1797]	1286	}
	1287	}
[1791]	1288
[1830]	1289	# ----------------------------------------------------------------------
	1290	# USAGE: _lammpsToSequence <xmlobj> ?<path>?
	1291	#
	1292	# If the molecule element is a trajectory, delete the original
	1293	# and create a sequence of individual molecules.
	1294	# Used internally to detect any molecule output elements that contain
	1295	# trajectory data. Trajectories will be converted into sequences of
	1296	# individual molecules. All other elements will be unaffected. Scans
	1297	# the entire xml tree if a starting path is not specified.
	1298	# ----------------------------------------------------------------------
[1797]	1299	itcl::body Rappture::Analyzer::_lammpsToSequence {xmlobj path id child data} {
	1300
	1301	set seqLabel [$xmlobj get ${child}.about.label]
	1302	set descr [$xmlobj get ${child}.about.description]
	1303	set typemap [$xmlobj get ${child}.components.molecule.lammpstypemap]
	1304	$xmlobj remove $child
	1305
[1830]	1306	set sequence ${path}.sequence($id)
	1307	$xmlobj put ${sequence}.about.label $seqLabel
	1308	$xmlobj put ${sequence}.about.description $descr
[2175]	1309	$xmlobj put ${sequence}.index.label "Frame"
[1797]	1310
[2175]	1311	set frameNum 0
	1312	set frameContents ""
[1797]	1313	set inModel 0
	1314	foreach line $data {
[1929]	1315	set line [string trim $line]
	1316	if { $line == "" } {
[2744]	1317	continue; # Skip blank lines
[1929]	1318	}
	1319	if {[regexp {^[\t ]*ITEM:[ \t]+ATOMS} $line] } {
[2175]	1320	if { $inModel && $frameContents != "" } {
	1321	set frame ${sequence}.element($frameNum)
	1322	$xmlobj put ${frame}.index $frameNum
[1929]	1323
[2175]	1324	set molecule ${frame}.structure.components.molecule
	1325	$xmlobj put ${molecule}.lammps $frameContents
[1929]	1326	$xmlobj put ${molecule}.lammpstypemap $typemap
	1327
[2175]	1328	incr frameNum
	1329	set frameContents ""
[1929]	1330	}
	1331	set inModel 1
	1332	} elseif { [scan $line "%d %d %f %f %f" a b c d e] == 5 } {
	1333	if { !$inModel } {
	1334	puts stderr "found \"$line\" without previous \"ITEM: ATOMS\""
	1335	set inModel 1
	1336	}
[2175]	1337	append frameContents $line\n
[1929]	1338	}
[1797]	1339	}
[2175]	1340	if { $frameContents != "" } {
	1341	set frame ${sequence}.element($frameNum)
	1342	$xmlobj put ${frame}.index $frameNum
[1929]	1343
[2175]	1344	set molecule ${frame}.structure.components.molecule
	1345	$xmlobj put ${molecule}.lammps $frameContents
[1929]	1346	$xmlobj put ${molecule}.lammpstypemap $typemap
[1797]	1347	}
[1791]	1348	}
	1349
	1350	# ----------------------------------------------------------------------
[1830]	1351	# USAGE: _trajToSequence <xmlobj> ?<path>?
[1797]	1352	#
[2744]	1353	# Check for PDB and LAMMPS trajectories in molecule data and rewrite
	1354	# the individual models as a sequence of molecules. Used internally
	1355	# to detect any molecule output elements that contain trajectory data.
	1356	# Trajectories will be converted into sequences of individual molecules.
	1357	# All other elements will be unaffected. Scans the entire xml tree if a
	1358	# starting path is not specified.
[1797]	1359	#
	1360	# ----------------------------------------------------------------------
	1361	itcl::body Rappture::Analyzer::_trajToSequence {xmlobj {path ""}} {
	1362	# Remove leading dot from path, if present.
	1363	if { [string index $path 0] == "." } {
[1929]	1364	set path [string range $path 1 end]
[1797]	1365	}
	1366	# Otherwise check each child.
	1367	foreach child [$xmlobj children $path] {
[1929]	1368	set current ${path}.${child}
	1369	if { [string match "structure*" $child] } {
	1370	set isTraj [$xmlobj get ${current}.components.molecule.trajectory]
	1371	if { $isTraj == "" \|\| !$isTraj } {
[2744]	1372	continue; # Not a trajectory.
[1929]	1373	}
	1374	# Look for trajectory if molecule element found. Check both pdb
	1375	# data and lammps data.
	1376	set type [$xmlobj element -as type $current]
	1377	set id [$xmlobj element -as id $current]
	1378	set pdbdata [$xmlobj get ${current}.components.molecule.pdb]
	1379	set lammpsdata [$xmlobj get ${current}.components.molecule.lammps]
	1380	if { $pdbdata != "" && $lammpsdata != "" } {
	1381	puts stderr \
	1382	"found both <pdb> and <lammps> elements: picking pdb"
	1383	}
	1384	set pdbdata [split $pdbdata \n]
	1385	set lammpsdata [split $lammpsdata \n]
	1386	if { [_isPdbTrajectory $pdbdata] } {
	1387	_pdbToSequence $xmlobj $path $id $current $pdbdata
	1388	} elseif { [_isLammpsTrajectory $lammpsdata] } {
	1389	_lammpsToSequence $xmlobj $path $id $current $lammpsdata
	1390	}
	1391	continue
	1392	}
	1393	if 0 {
	1394	# Recurse over all child nodes.
	1395	_trajToSequence $xmlobj $current
	1396	}
[1797]	1397	}
	1398	}
	1399
	1400	# ----------------------------------------------------------------------
[11]	1401	# CONFIGURATION OPTION: -simcontrol
	1402	#
	1403	# Controls whether or not the Simulate button is showing. In some
	1404	# cases, it is not needed.
	1405	# ----------------------------------------------------------------------
	1406	itcl::configbody Rappture::Analyzer::simcontrol {
	1407	_fixSimControl
	1408	}
[1159]	1409
	1410	# ----------------------------------------------------------------------
	1411	# CONFIGURATION OPTION: -notebookpage
	1412	#
	1413	# Controls which page of the analyzer notebook is shown. It is
	1414	# particularly needed when using rerun, when you don't want to
	1415	# "simulate -ifneeded" because an actual simulation might be
	1416	# kicked off due to differences between tool.xml and run.xml
	1417	# ----------------------------------------------------------------------
	1418	itcl::configbody Rappture::Analyzer::notebookpage {
	1419	_fixNotebook
	1420	}

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