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|
From: <sar...@us...> - 2008-07-15 11:22:12
|
Revision: 7702
http://sbml.svn.sourceforge.net/sbml/?rev=7702&view=rev
Author: sarahkeating
Date: 2008-07-15 04:22:07 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
changed compartment id to C
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00104/00104-model.m
trunk/test-suite/cases/semantic/00104/00104-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00104/00104-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00104/00104-sbml-l2v3.xml
Modified: trunk/test-suite/cases/semantic/00104/00104-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00104/00104-model.m 2008-07-15 10:09:48 UTC (rev 7701)
+++ trunk/test-suite/cases/semantic/00104/00104-model.m 2008-07-15 11:22:07 UTC (rev 7702)
@@ -9,17 +9,17 @@
levels: 2.1, 2.2, 2.3
generatedBy: Numeric
-The model contains one varying compartment called "compartment". There are two
+The model contains one varying compartment called C. There are two
species called S1 and S2 and two parameters called k1 and p1. The model
contains one reaction defined as:
[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
-| S1 -> S2 | $compartment * multiply(k1,S1)$ |]
+| S1 -> S2 | $C * multiply(k1,S1)$ |]
The model contains one rule:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Rate | compartment | $-p1 * compartment$ |]
+ | Rate | C | $-p1 * C$ |]
The model contains one functionDefinition defined as:
@@ -35,7 +35,7 @@
|Initial amount of S2 |$1.5 \x 10^-15$ |mole |
|Value of parameter k1 |$ 1$ |second^-1^ |
|Value of parameter p1 |$0.1 \x 10^-12$ |second^-1^ |
-|Volume of compartment "compartment" |$ 1$ |litre |]
+|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
use the model in a discrete stochastic simulator, but (as per usual SBML
@@ -47,13 +47,13 @@
newcase[ "00104" ];
addFunction[ multiply, arguments -> {x, y}, math -> x * y];
-addCompartment[ compartment, size -> 1, constant -> False ];
+addCompartment[ C, size -> 1, constant -> False ];
addSpecies[ S1, initialAmount -> 1.5 10^-15 ];
addSpecies[ S2, initialAmount -> 1.5 10^-15 ];
addParameter[ k1, value -> 1 ];
-addParameter[ p1, value -> 0.1 10^-12 ];
-addRule[ type->RateRule, variable -> compartment, math -> -p1 * compartment];
+addParameter[ p1, value -> 0.01 ];
+addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 -> S2, reversible -> False,
- kineticLaw -> compartment * multiply[k1,S1] ];
+ kineticLaw -> C * multiply[k1,S1] ];
makemodel[]
Modified: trunk/test-suite/cases/semantic/00104/00104-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00104/00104-sbml-l2v1.xml 2008-07-15 10:09:48 UTC (rev 7701)
+++ trunk/test-suite/cases/semantic/00104/00104-sbml-l2v1.xml 2008-07-15 11:22:07 UTC (rev 7702)
@@ -21,23 +21,23 @@
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1.5e-015" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="1.5e-015" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1.5e-015" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="1.5e-015" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="1"/>
- <parameter id="p1" name="p1" value="1e-013"/>
+ <parameter id="p1" name="p1" value="0.01"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -55,7 +55,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
Modified: trunk/test-suite/cases/semantic/00104/00104-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00104/00104-sbml-l2v2.xml 2008-07-15 10:09:48 UTC (rev 7701)
+++ trunk/test-suite/cases/semantic/00104/00104-sbml-l2v2.xml 2008-07-15 11:22:07 UTC (rev 7702)
@@ -21,23 +21,23 @@
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1.5e-015" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="1.5e-015" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1.5e-015" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="1.5e-015" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="1"/>
- <parameter id="p1" name="p1" value="1e-013"/>
+ <parameter id="p1" name="p1" value="0.01"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -55,7 +55,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
Modified: trunk/test-suite/cases/semantic/00104/00104-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00104/00104-sbml-l2v3.xml 2008-07-15 10:09:48 UTC (rev 7701)
+++ trunk/test-suite/cases/semantic/00104/00104-sbml-l2v3.xml 2008-07-15 11:22:07 UTC (rev 7702)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 12-February-2008 12:48:13.0468750 -->
-<!-- Generated by MathSBML 2.7.2b -->
+<!-- Generated 15-July-2008 12:19:53.7968750 -->
+<!-- Generated by MathSBML 2.7.5 [2-May-2008] -->
<!-- Generated using Mathematica Version 5.2 for Microsoft Windows (June 20, 2005) -->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3"
level="2"
@@ -32,17 +32,17 @@
<!-- <listOfCompartmentTypes/> -->
<!-- <listOfSpeciesTypes/> -->
<listOfCompartments>
- <compartment id="compartment"
- name="compartment"
+ <compartment id="C"
+ name="C"
spatialDimensions="3"
units="volume"
- size="1"
+ size="1."
constant="false"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1"
name="S1"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.5000000000000001e-15"
@@ -50,7 +50,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S2"
name="S2"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.5000000000000001e-15"
@@ -60,14 +60,14 @@
<listOfParameters>
<parameter id="k1"
name="k1"
- value="1"/>
+ value="1."/>
<parameter id="p1"
name="p1"
- value="1.e-13"/>
+ value="0.01"/>
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
- <rateRule variable="compartment"
+ <rateRule variable="C"
metaid="rule1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
@@ -75,7 +75,7 @@
<apply>
<times/>
<cn type="integer">-1</cn>
- <ci>compartment</ci>
+ <ci>C</ci>
</apply>
<ci>p1</ci>
</apply>
@@ -99,7 +99,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<apply>
<ci>multiply</ci>
<ci>k1</ci>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-15 10:09:51
|
Revision: 7701
http://sbml.svn.sourceforge.net/sbml/?rev=7701&view=rev
Author: sarahkeating
Date: 2008-07-15 03:09:48 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
corrected data to actually vary the compartment volume
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00052/00052-results.csv
trunk/test-suite/cases/semantic/00052/00052-settings.txt
Modified: trunk/test-suite/cases/semantic/00052/00052-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00052/00052-results.csv 2008-07-15 10:08:38 UTC (rev 7700)
+++ trunk/test-suite/cases/semantic/00052/00052-results.csv 2008-07-15 10:09:48 UTC (rev 7701)
@@ -1,52 +1,52 @@
-time,case00052`S1,case00052`S2,case00052`S3
-0,1.,2.,1.
-0.2,0.8198171312539935,1.819817131253993,1.220182868746005
-0.4,0.7080742604066437,1.708074260406643,1.371925739593355
-0.6,0.6364489785291186,1.636448978529118,1.48355102147088
-0.8,0.5898324665032921,1.589832466503291,1.570167533496707
-1.,0.5594811869428185,1.559481186942818,1.640518813057181
-1.2,0.540032542111409,1.540032542111408,1.69996745788859
-1.4,0.5280550927004409,1.52805509270044,1.751944907299558
-1.6,0.5212829017980629,1.521282901798062,1.798717098201936
-1.8,0.518183693509497,1.518183693509496,1.841816306490502
-2.,0.5177022644029617,1.517702264402961,1.882297735597037
-2.2,0.5191015236497389,1.519101523649738,1.92089847635026
-2.4,0.5218607130475412,1.52186071304754,1.958139286952457
-2.6,0.5256084953228837,1.525608495322882,1.994391504677115
-2.8,0.5300780381385013,1.5300780381385,2.029921961861498
-3.,0.5350763383352658,1.535076338335264,2.064923661664734
-3.2,0.5404630102576957,1.540463010257694,2.099536989742303
-3.4,0.5461354282858664,1.546135428285865,2.133864571714132
-3.6,0.5520182436519066,1.552018243651905,2.167981756348092
-3.8,0.5580559170011699,1.558055917001169,2.201944082998829
-4.,0.5642073723447471,1.564207372344746,2.235792627655252
-4.2,0.5704421424519646,1.570442142451964,2.269557857548034
-4.4,0.5767375716616708,1.57673757166167,2.303262428338328
-4.6,0.583076783759119,1.583076783759118,2.33692321624088
-4.8,0.58944719412231,1.589447194122308,2.370552805877689
-5.,0.5958394148630277,1.595839414863026,2.404160585136971
-5.2,0.6022464509222383,1.602246450922237,2.43775354907776
-5.4,0.6086631012855388,1.608663101285537,2.47133689871446
-5.6,0.6150855169587584,1.615085516958757,2.504914483041239
-5.8,0.6215108699276832,1.621510869927682,2.538489130072315
-6.,0.6279371058820977,1.627937105882096,2.5720628941179
-6.2,0.6343627581571291,1.634362758157128,2.605637241842869
-6.4,0.640786808286666,1.640786808286665,2.639213191713332
-6.6,0.6472085802646421,1.647208580264641,2.672791419735356
-6.8,0.6536276603760372,1.653627660376036,2.706372339623961
-7.,0.6600438363752626,1.660043836375262,2.739956163624736
-7.2,0.6664570508363642,1.666457050836363,2.773542949163635
-7.4,0.6728673661024906,1.67286736610249,2.807132633897508
-7.6,0.6792749365463965,1.679274936546396,2.840725063453602
-7.8,0.6856799881431922,1.685679988143191,2.874320011856807
-8.,0.6920828019038647,1.692082801903864,2.907917198096134
-8.2,0.6984837017771915,1.698483701777191,2.941516298222807
-8.4,0.7048830447057761,1.704883044705775,2.975116955294223
-8.6,0.7112812132727242,1.711281213272724,3.008718786727275
-8.8,0.7176786098968143,1.717678609896814,3.042321390103185
-9.,0.7240756521783606,1.72407565217836,3.075924347821639
-9.2,0.7304727694234842,1.730472769423484,3.109527230576515
-9.4,0.7368703998747928,1.736870399874792,3.143129600125206
-9.6,0.7432689884916879,1.743268988491687,3.176731011508311
-9.8,0.7496689852733291,1.749668985273328,3.210331014726669
-10.,0.7560708439291842,1.756070843929184,3.243929156070814
\ No newline at end of file
+time,S1,S2,S3,C
+0,1,2,1,1
+0.1,0.8720905993141901,1.852289272620888,1.088306747299207,0.9900498337491392
+0.2,0.771872391304281,1.732661830456543,1.149706487000244,0.9801986733067243
+0.3,0.6920534227362242,1.633817956320375,1.191475644432076,0.9704455335484573
+0.4,0.6275999975559922,1.550716343942454,1.218632695216932,0.9607894391522328
+0.5,0.574931893672325,1.479769311708035,1.234742942399094,0.9512294245005826
+0.6,0.5314390246445934,1.418359461361569,1.242401848789358,0.941764533584152
+0.7,0.4951787642395512,1.364536999638363,1.243537706558072,0.9323938199059512
+0.8,0.4646799026527765,1.31682369161876,1.239607675279191,0.9231163463865125
+0.9,0.4388119815401887,1.274082192950872,1.231728441281178,0.913931185270906
+1,0.4166952993826794,1.235426052460548,1.220766206773057,0.9048374180358968
+1.1,0.3976374695732236,1.200156267535371,1.207400126351071,0.8958341352963433
+1.2,0.3810889919914187,1.167716853057005,1.192166730139753,0.886920436716612
+1.3,0.3666101675606017,1.137661753364188,1.175493004046571,0.8780954309205726
+1.4,0.3538462207478511,1.109629962202333,1.157721262161114,0.8693582353980909
+1.5,0.3425099579877606,1.08332817866917,1.139126483375057,0.8607079764248784
+1.6,0.3323668486583851,1.058515885730806,1.119931225486456,0.8521437889654661
+1.7,0.3232251138116145,1.034995436573328,1.100315531711813,0.8436648165958526
+1.8,0.3149268313788531,1.012603157448339,1.080425820760117,0.8352702114103466
+1.9,0.3073417839909456,0.9912031932022068,1.060381034431576,0.8269591339427004
+2,0.3003619965769201,0.9706820426100942,1.040278095489427,0.818730753076476
+2.1,0.2938979381466251,0.9509447579612337,1.020195701482591,0.8105842459699104
+2.2,0.2878748049939303,0.9319112260727828,1.000198037163775,0.8025187979598065
+2.3,0.2822304329698567,0.913514078476851,0.9803368580441324,0.7945336025033772
+2.4,0.2769124384785779,0.8956958302788455,0.9606543451219579,0.7866278610628205
+2.5,0.2718772248139735,0.8784078845243117,0.9411840946067027,0.7788007830699312
+2.6,0.2670878913322374,0.8616084392995438,0.9219532046023754,0.7710515858016934
+2.7,0.2625134380008799,0.8452616903663707,0.9029830667301023,0.7633794943312867
+2.8,0.2581278127313087,0.8293368765796394,0.8842903149653515,0.7557837414554048
+2.9,0.2539087597886561,0.8138071263455303,0.8658879733250914,0.7482635675728665
+3,0.2498376300357185,0.7986492661186848,0.8477856421302139,0.740818220674253
+3.1,0.2458985497012152,0.7838429872957705,0.8299903254878948,0.7334469562242078
+3.2,0.2420778896258066,0.7693703136560738,0.8125069584347284,0.7261490370648903
+3.3,0.2383642043013423,0.755215538774943,0.7953384646458596,0.718923733419339
+3.4,0.2347476827873493,0.7413646751506148,0.778486301939181,0.7117703227609769
+3.5,0.2312198259919921,0.7278051297729947,0.7619507815700134,0.7046880897113296
+3.6,0.2277734369246687,0.714525692852702,0.7457310749313969,0.6976763260481418
+3.7,0.2244023658229215,0.7015162813275577,0.7298254651863513,0.6907343306254846
+3.8,0.2211012244039902,0.6887676514152085,0.7142316296184452,0.6838614092133126
+3.9,0.2178653493252614,0.6762713605961557,0.6989466732165272,0.6770568744728129
+4,0.2146907832563641,0.6640197473188864,0.6839671448686804,0.6703200459948384
+4.1,0.2115740577124211,0.6520057121928927,0.6692892512485222,0.6636502501170866
+4.2,0.2085121061982865,0.6402226296293854,0.654908940663911,0.6570468198165933
+4.3,0.2055022486114161,0.6286643308780682,0.6408219159218879,0.6505090946840421
+4.4,0.2025421738466227,0.6173250854180141,0.6270236492961601,0.644036420997595
+4.5,0.1996298313907578,0.6061994910431814,0.6135094879140891,0.6376281515526299
+4.6,0.1967633831900826,0.5952824242509911,0.6002746989317345,0.6312836454882295
+4.7,0.1939411946430201,0.584569030006024,0.5873144760829875,0.6250022682862869
+4.8,0.1911618188035898,0.5740547047715604,0.5746239531323515,0.6187833918003703
+4.9,0.1884239517900568,0.5637350506385631,0.5621982459069557,0.6126263941820547
+5,0.1857264142904868,0.5536058554667562,0.5500324680620518,0.6065306597166126
Modified: trunk/test-suite/cases/semantic/00052/00052-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/00052/00052-settings.txt 2008-07-15 10:08:38 UTC (rev 7700)
+++ trunk/test-suite/cases/semantic/00052/00052-settings.txt 2008-07-15 10:09:48 UTC (rev 7701)
@@ -1,5 +1,5 @@
start: 0
-duration: 10.0
+duration: 5.0
steps: 50
variables: S1, S2, S3
absolute: 1.000000e-003
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-15 10:08:40
|
Revision: 7700
http://sbml.svn.sourceforge.net/sbml/?rev=7700&view=rev
Author: sarahkeating
Date: 2008-07-15 03:08:38 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
changed compartment id to C
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00052/00052-model.m
trunk/test-suite/cases/semantic/00052/00052-sbml-l1v2.xml
trunk/test-suite/cases/semantic/00052/00052-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00052/00052-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00052/00052-sbml-l2v3.xml
Modified: trunk/test-suite/cases/semantic/00052/00052-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00052/00052-model.m 2008-07-15 08:45:04 UTC (rev 7699)
+++ trunk/test-suite/cases/semantic/00052/00052-model.m 2008-07-15 10:08:38 UTC (rev 7700)
@@ -9,19 +9,19 @@
levels: 1.2, 2.1, 2.2, 2.3
generatedBy: Numeric
-The model contains one varying compartment called "compartment". There are three
+The model contains one varying compartment called C. There are three
species called S1, S2 and S3 and three parameters called k1, k2 and p1. The
model contains two reactions defined as:
[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
-| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |
-| S3 -> S1 + S2 | $k2 * S3 * compartment$ |]
+| S1 + S2 -> S3 | $k1 * S1 * S2 * C$ |
+| S3 -> S1 + S2 | $k2 * S3 * C$ |]
The model contains one rule which defines the rate at which the volume of
the compartment is changing:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Rate | compartment | $-p1 * compartment$ |]
+ | Rate | C | $-p1 * C$ |]
The initial conditions are as follows:
@@ -32,7 +32,7 @@
|Value of parameter k1 |$ 0.75$ |litre mole^-1^ second^-1^ |
|Value of parameter k2 |$ 0.25$ |second^-1^ |
|Value of parameter p1 |$ 0.1$ |second^-1^ |
-|Volume of compartment "compartment" |$ 1$ |litre |]
+|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
use the model in a discrete stochastic simulator, but (as per usual SBML
@@ -43,17 +43,17 @@
newcase[ "00052" ];
-addCompartment[ compartment, constant->False, size -> 1 ];
+addCompartment[ C, constant->False, size -> 1 ];
addSpecies[ S1, initialAmount -> 1.0];
addSpecies[ S2, initialAmount -> 2.0];
addSpecies[ S3, initialAmount -> 1.0];
addParameter[ k1, value -> 0.75 ];
addParameter[ k2, value -> 0.25 ];
addParameter[ p1, value -> 0.1 ];
-addRule[ type->RateRule, variable -> compartment, math -> -p1 * compartment];
+addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 + S2 -> S3, reversible -> False,
- kineticLaw -> k1 * S1 * S2 * compartment ];
+ kineticLaw -> k1 * S1 * S2 * C ];
addReaction[ S3 -> S1 + S2, reversible -> False,
- kineticLaw -> k2 * S3 * compartment ];
+ kineticLaw -> k2 * S3 * C ];
makemodel[]
Modified: trunk/test-suite/cases/semantic/00052/00052-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00052/00052-sbml-l1v2.xml 2008-07-15 08:45:04 UTC (rev 7699)
+++ trunk/test-suite/cases/semantic/00052/00052-sbml-l1v2.xml 2008-07-15 10:08:38 UTC (rev 7700)
@@ -2,12 +2,12 @@
<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
<model name="case00052">
<listOfCompartments>
- <compartment name="compartment" volume="1" units="volume"/>
+ <compartment name="C" volume="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
- <species name="S1" compartment="compartment" initialAmount="1" units="substance"/>
- <species name="S2" compartment="compartment" initialAmount="2" units="substance"/>
- <species name="S3" compartment="compartment" initialAmount="1" units="substance"/>
+ <species name="S1" compartment="C" initialAmount="1" units="substance"/>
+ <species name="S2" compartment="C" initialAmount="2" units="substance"/>
+ <species name="S3" compartment="C" initialAmount="1" units="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter name="k1" value="0.75"/>
@@ -15,7 +15,7 @@
<parameter name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <compartmentVolumeRule formula="-1 * compartment * p1" type="rate" compartment="compartment"/>
+ <compartmentVolumeRule formula="-1 * C * p1" type="rate" compartment="C"/>
</listOfRules>
<listOfReactions>
<reaction name="reaction1" reversible="false">
@@ -26,7 +26,7 @@
<listOfProducts>
<speciesReference species="S3"/>
</listOfProducts>
- <kineticLaw formula="compartment * k1 * S1 * S2"/>
+ <kineticLaw formula="C * k1 * S1 * S2"/>
</reaction>
<reaction name="reaction2" reversible="false">
<listOfReactants>
@@ -36,7 +36,7 @@
<speciesReference species="S1"/>
<speciesReference species="S2"/>
</listOfProducts>
- <kineticLaw formula="compartment * k2 * S3"/>
+ <kineticLaw formula="C * k2 * S3"/>
</reaction>
</listOfReactions>
</model>
Modified: trunk/test-suite/cases/semantic/00052/00052-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00052/00052-sbml-l2v1.xml 2008-07-15 08:45:04 UTC (rev 7699)
+++ trunk/test-suite/cases/semantic/00052/00052-sbml-l2v1.xml 2008-07-15 10:08:38 UTC (rev 7700)
@@ -2,12 +2,12 @@
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model metaid="_case00052" id="case00052" name="case00052">
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="2" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="2" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="1" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
@@ -15,12 +15,12 @@
<parameter id="p1" name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -39,7 +39,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k1 </ci>
<ci> S1 </ci>
<ci> S2 </ci>
@@ -59,7 +59,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
</apply>
Modified: trunk/test-suite/cases/semantic/00052/00052-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00052/00052-sbml-l2v2.xml 2008-07-15 08:45:04 UTC (rev 7699)
+++ trunk/test-suite/cases/semantic/00052/00052-sbml-l2v2.xml 2008-07-15 10:08:38 UTC (rev 7700)
@@ -2,12 +2,12 @@
<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
<model metaid="_case00052" id="case00052" name="case00052">
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="2" substanceUnits="substance"/>
- <species id="S3" name="S3" compartment="compartment" initialAmount="1" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="2" substanceUnits="substance"/>
+ <species id="S3" name="S3" compartment="C" initialAmount="1" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.75"/>
@@ -15,12 +15,12 @@
<parameter id="p1" name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -39,7 +39,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k1 </ci>
<ci> S1 </ci>
<ci> S2 </ci>
@@ -59,7 +59,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k2 </ci>
<ci> S3 </ci>
</apply>
Modified: trunk/test-suite/cases/semantic/00052/00052-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00052/00052-sbml-l2v3.xml 2008-07-15 08:45:04 UTC (rev 7699)
+++ trunk/test-suite/cases/semantic/00052/00052-sbml-l2v3.xml 2008-07-15 10:08:38 UTC (rev 7700)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 7-February-2008 14:42:13.7031250 -->
-<!-- Generated by MathSBML 2.7.1 (7 December 2007) -->
+<!-- Generated 15-July-2008 10:16:02.3125000 -->
+<!-- Generated by MathSBML 2.7.5 [2-May-2008] -->
<!-- Generated using Mathematica Version 5.2 for Microsoft Windows (June 20, 2005) -->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3"
level="2"
@@ -13,17 +13,17 @@
<!-- <listOfCompartmentTypes/> -->
<!-- <listOfSpeciesTypes/> -->
<listOfCompartments>
- <compartment id="compartment"
- name="compartment"
+ <compartment id="C"
+ name="C"
spatialDimensions="3"
units="volume"
- size="1"
+ size="1."
constant="false"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1"
name="S1"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1."
@@ -31,7 +31,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S2"
name="S2"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="2."
@@ -39,7 +39,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S3"
name="S3"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1."
@@ -59,7 +59,7 @@
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
- <rateRule variable="compartment"
+ <rateRule variable="C"
metaid="rule1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
@@ -67,7 +67,7 @@
<apply>
<times/>
<cn type="integer">-1</cn>
- <ci>compartment</ci>
+ <ci>C</ci>
</apply>
<ci>p1</ci>
</apply>
@@ -92,7 +92,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<ci>k1</ci>
<ci>S1</ci>
<ci>S2</ci>
@@ -117,7 +117,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<ci>k2</ci>
<ci>S3</ci>
</apply>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-15 08:45:07
|
Revision: 7699
http://sbml.svn.sourceforge.net/sbml/?rev=7699&view=rev
Author: sarahkeating
Date: 2008-07-15 01:45:04 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
corrected data to actually vary the compartment volume
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00051/00051-results.csv
trunk/test-suite/cases/semantic/00051/00051-settings.txt
Modified: trunk/test-suite/cases/semantic/00051/00051-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00051/00051-results.csv 2008-07-15 08:43:56 UTC (rev 7698)
+++ trunk/test-suite/cases/semantic/00051/00051-results.csv 2008-07-15 08:45:04 UTC (rev 7699)
@@ -1,52 +1,52 @@
-time,case00051`S1,case00051`S2
-0,1.5,0
-0.1,1.381077796244329,0.1389222037556713
-0.2,1.273472221128284,0.2665277788717167
-0.3,1.176029035107873,0.3839709648921268
-0.4,1.08771993734494,0.4922800626550608
-0.5,1.007628051416898,0.5923719485831026
-0.6,0.9349350517808335,0.6850649482191675
-0.7,0.8689099691131446,0.7710900308868563
-0.8,0.8088992393442802,0.8511007606557208
-0.9,0.7543182264426419,0.9256817735573591
-1.,0.7046430865005352,0.9953569134994657
-1.1,0.65940444316524,1.060595556834761
-1.2,0.6181811590295173,1.121818840970483
-1.3,0.5805951427948712,1.179404857205129
-1.4,0.5463066396954213,1.233693360304579
-1.5,0.5150100878903114,1.284989912109689
-1.6,0.4864305295419281,1.333569470458072
-1.7,0.4603201929182076,1.379679807081793
-1.8,0.4364558206331177,1.423544179366883
-1.9,0.4146359071259086,1.465364092874092
-2.,0.3946785839253513,1.505321416074649
-2.1,0.3764194699906899,1.543580530009311
-2.2,0.3597099510577693,1.580290048942231
-2.3,0.3444155252465535,1.615584474753447
-2.4,0.3304143838312421,1.649585616168759
-2.5,0.3175961442157208,1.68240385578428
-2.6,0.3058606737729306,1.71413932622707
-2.7,0.2951171169091404,1.74488288309086
-2.8,0.2852829235140605,1.77471707648594
-2.9,0.2762830930674662,1.803716906932534
-3.,0.2680493805320687,1.831950619467932
-3.1,0.2605196962419291,1.859480303758071
-3.2,0.2536374677176586,1.886362532282342
-3.3,0.247351145976213,1.912648854023787
-3.4,0.241613717555681,1.938386282444319
-3.5,0.236382264194835,1.963617735805165
-3.6,0.2316175995086596,1.988382400491341
-3.7,0.2272839164322783,2.012716083567723
-3.8,0.2233484626617502,2.036651537338251
-3.9,0.2197812711384953,2.060218728861505
-4.,0.2165549154160136,2.083445084583987
-4.1,0.213644256519339,2.106355743480662
-4.2,0.2110262527568561,2.128973747243144
-4.3,0.2086797684150067,2.151320231584994
-4.4,0.2065854044469326,2.173414595553068
-4.5,0.2047253452050569,2.195274654794944
-4.6,0.2030832196075954,2.216916780392406
-4.7,0.2016439752989696,2.238356024701031
-4.8,0.2003937645154883,2.259606235484513
-4.9,0.1993198418809065,2.280680158119095
-5.,0.1984104651179985,2.301589534882003
\ No newline at end of file
+time,S1,S2,C
+0,1.5,0,1
+0.12,1.346441378191859,0.1695827388756832,0.9880717128616042
+0.24,1.208602935566175,0.3197820363376107,0.9762857097575088
+0.36,1.08487535627685,0.4526063549344016,0.9646402934829141
+0.48,0.9738139905104121,0.5698583626286757,0.9531337870755688
+0.6,0.8741223880639144,0.6731555153906105,0.9417645335842687
+0.72,0.7846362797841228,0.7639500799105792,0.9305308958083909
+0.84,0.704311265320773,0.8435445235268111,0.9194312560948148
+0.96,0.6322091190733082,0.9131086312796949,0.9084640160647094
+1.08,0.5674884667136961,0.9736911599148176,0.8976275964303671
+1.2,0.5093931807266163,1.0262343429264,0.8869204367118242
+1.32,0.4572455072101137,1.071582481761474,0.876340995079529
+1.44,0.4104360796533791,1.11049442803438,0.8658877480539221
+1.56,0.3684188486010753,1.143649921194021,0.8555591903708611
+1.68,0.3307028546391529,1.17165987172579,0.845353834679857
+1.8,0.2968480678896983,1.195071561532526,0.8352702114104798
+1.92,0.2664589827916952,1.214376649924959,0.8253068684877751
+2.04,0.2391809616046024,1.230015743967386,0.8154623711856743
+2.16,0.2146954270149293,1.242384407239036,0.8057353018707726
+2.28,0.1927165391427043,1.251837313258424,0.7961242598329626
+2.4,0.1729877004005492,1.258692613996506,0.7866278610651699
+2.52,0.1552785156785195,1.263235739274994,0.7772447380656768
+2.64,0.1393823088183196,1.265722500833054,0.7679735396565088
+2.76,0.125113380819378,1.266382519145926,0.7588129307574127
+2.88,0.1123052536315224,1.265421418409754,0.7497615922395507
+3,0.1008082688125307,1.263023827754917,0.7408182206776433
+3.12,0.09048830968152437,1.259354978327136,0.7319815282288221
+3.24,0.08122478357335515,1.2545632249881,0.7232502423758903
+3.36,0.07290962541397146,1.248781291637924,0.7146231058162076
+3.48,0.06544567909323017,1.242128294028958,0.7060988762109308
+3.6,0.05874585796342578,1.234710788928056,0.6976763260705806
+3.72,0.05273189789833509,1.226624332355073,0.6893542425215955
+3.84,0.04733361035081941,1.217954413020918,0.6811314271783691
+3.96,0.04248795537191667,1.208777610664742,0.6730066959358068
+4.08,0.03813835984287378,1.199162447984829,0.6649788788204913
+4.2,0.03423404864707434,1.189170226343483,0.6570468198145737
+4.32,0.03072942235040061,1.178855803341903,0.6492093766826156
+4.44,0.02758358373439113,1.16826818438403,0.6414654208277438
+4.56,0.02475978033659235,1.157451219133519,0.6338138370956052
+4.68,0.02222506832108114,1.146444021458131,0.6262535236583907
+4.8,0.0199498294279225,1.135281572845845,0.6187833918030657
+4.92,0.01790752242122131,1.123995032910589,0.6114023658331282
+5.04,0.01607428246505253,1.112612239768011,0.6041093828529744
+5.16,0.01442872288172454,1.101157957662908,0.5969033926747011
+5.28,0.01295161761830956,1.089654273496716,0.589783357610455
+5.4,0.0116257311364911,1.078120809280222,0.5827482523737791
+5.52,0.01043557634946406,1.066575024354707,0.5757970638888198
+5.64,0.009367261733284267,1.055032406292669,0.56892879117828
+5.76,0.008408313010303006,1.04350669347977,0.5621424451960793
+5.88,0.007547533278479937,1.032010049707968,0.5554370486965697
+6,0.006774875606374476,1.020553223170142,0.5488116360949922
Modified: trunk/test-suite/cases/semantic/00051/00051-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/00051/00051-settings.txt 2008-07-15 08:43:56 UTC (rev 7698)
+++ trunk/test-suite/cases/semantic/00051/00051-settings.txt 2008-07-15 08:45:04 UTC (rev 7699)
@@ -1,5 +1,5 @@
start: 0
-duration: 5.0
+duration: 6.0
steps: 50
variables: S1, S2
absolute: 1.000000e-003
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|
|
From: <sar...@us...> - 2008-07-15 08:43:59
|
Revision: 7698
http://sbml.svn.sourceforge.net/sbml/?rev=7698&view=rev
Author: sarahkeating
Date: 2008-07-15 01:43:56 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
changed compartment id to C
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00051/00051-model.m
trunk/test-suite/cases/semantic/00051/00051-sbml-l1v2.xml
trunk/test-suite/cases/semantic/00051/00051-sbml-l2v1.xml
trunk/test-suite/cases/semantic/00051/00051-sbml-l2v2.xml
trunk/test-suite/cases/semantic/00051/00051-sbml-l2v3.xml
Modified: trunk/test-suite/cases/semantic/00051/00051-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00051/00051-model.m 2008-07-14 03:14:30 UTC (rev 7697)
+++ trunk/test-suite/cases/semantic/00051/00051-model.m 2008-07-15 08:43:56 UTC (rev 7698)
@@ -9,18 +9,18 @@
levels: 1.2, 2.1, 2.2, 2.3
generatedBy: Numeric
-The model contains one varying compartment called "compartment". There are two
+The model contains one varying compartment called C. There are two
species called S1 and S2 and two parameters called k1 and p1. The model
contains one reaction defined as:
[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
-| S1 -> S2 | $k1 * S1 * compartment$ |]
+| S1 -> S2 | $k1 * S1 * C$ |]
The model contains one rule which defines the rate at which the volume of
the compartment is changing:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Rate | compartment | $-p1 * compartment$ |]
+ | Rate | C | $-p1 * C$ |]
The initial conditions are as follows:
@@ -29,7 +29,7 @@
|Initial amount of S2 |$ 0$ |mole |
|Value of parameter k1 |$ 0.9$ |second^-1^ |
|Value of parameter p1 |$ 0.1$ |second^-1^ |
-|Volume of compartment "compartment" |$ 1$ |litre |]
+|Volume of compartment C |$ 1$ |litre |]
The species values are given as amounts of substance to make it easier to
use the model in a discrete stochastic simulator, but (as per usual SBML
@@ -40,13 +40,13 @@
newcase[ "00051" ];
-addCompartment[ compartment, size->1, constant->False ];
+addCompartment[ C, size->1, constant->False ];
addSpecies[ S1, initialAmount -> 1.5 ];
addSpecies[ S2, initialAmount -> 0 ];
addParameter[ k1, value -> 0.9 ];
addParameter[ p1, value -> 0.1 ];
-addRule[ type->RateRule, variable -> compartment, math -> -p1 * compartment];
+addRule[ type->RateRule, variable -> C, math -> -p1 * C];
addReaction[ S1 -> S2, reversible -> False,
- kineticLaw -> k1 * S1 * compartment ];
+ kineticLaw -> k1 * S1 * C ];
makemodel[]
Modified: trunk/test-suite/cases/semantic/00051/00051-sbml-l1v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00051/00051-sbml-l1v2.xml 2008-07-14 03:14:30 UTC (rev 7697)
+++ trunk/test-suite/cases/semantic/00051/00051-sbml-l1v2.xml 2008-07-15 08:43:56 UTC (rev 7698)
@@ -2,18 +2,18 @@
<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
<model name="case00051">
<listOfCompartments>
- <compartment name="compartment" volume="1" units="volume"/>
+ <compartment name="C" volume="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
- <species name="S1" compartment="compartment" initialAmount="1.5" units="substance"/>
- <species name="S2" compartment="compartment" initialAmount="0" units="substance"/>
+ <species name="S1" compartment="C" initialAmount="1.5" units="substance"/>
+ <species name="S2" compartment="C" initialAmount="0" units="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter name="k1" value="0.9"/>
<parameter name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <compartmentVolumeRule formula="-1 * compartment * p1" type="rate" compartment="compartment"/>
+ <compartmentVolumeRule formula="-1 * C * p1" type="rate" compartment="C"/>
</listOfRules>
<listOfReactions>
<reaction name="reaction1" reversible="false">
@@ -23,7 +23,7 @@
<listOfProducts>
<speciesReference species="S2"/>
</listOfProducts>
- <kineticLaw formula="compartment * k1 * S1"/>
+ <kineticLaw formula="C * k1 * S1"/>
</reaction>
</listOfReactions>
</model>
Modified: trunk/test-suite/cases/semantic/00051/00051-sbml-l2v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00051/00051-sbml-l2v1.xml 2008-07-14 03:14:30 UTC (rev 7697)
+++ trunk/test-suite/cases/semantic/00051/00051-sbml-l2v1.xml 2008-07-15 08:43:56 UTC (rev 7698)
@@ -2,23 +2,23 @@
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model metaid="_case00051" id="case00051" name="case00051">
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1.5" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1.5" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="0" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.9"/>
<parameter id="p1" name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -36,7 +36,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k1 </ci>
<ci> S1 </ci>
</apply>
Modified: trunk/test-suite/cases/semantic/00051/00051-sbml-l2v2.xml
===================================================================
--- trunk/test-suite/cases/semantic/00051/00051-sbml-l2v2.xml 2008-07-14 03:14:30 UTC (rev 7697)
+++ trunk/test-suite/cases/semantic/00051/00051-sbml-l2v2.xml 2008-07-15 08:43:56 UTC (rev 7698)
@@ -2,23 +2,23 @@
<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
<model metaid="_case00051" id="case00051" name="case00051">
<listOfCompartments>
- <compartment id="compartment" name="compartment" size="1" units="volume" constant="false"/>
+ <compartment id="C" name="C" size="1" units="volume" constant="false"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S1" name="S1" compartment="compartment" initialAmount="1.5" substanceUnits="substance"/>
- <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance"/>
+ <species id="S1" name="S1" compartment="C" initialAmount="1.5" substanceUnits="substance"/>
+ <species id="S2" name="S2" compartment="C" initialAmount="0" substanceUnits="substance"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="0.9"/>
<parameter id="p1" name="p1" value="0.1"/>
</listOfParameters>
<listOfRules>
- <rateRule metaid="rule1" variable="compartment">
+ <rateRule metaid="rule1" variable="C">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> p1 </ci>
</apply>
</math>
@@ -36,7 +36,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci> compartment </ci>
+ <ci> C </ci>
<ci> k1 </ci>
<ci> S1 </ci>
</apply>
Modified: trunk/test-suite/cases/semantic/00051/00051-sbml-l2v3.xml
===================================================================
--- trunk/test-suite/cases/semantic/00051/00051-sbml-l2v3.xml 2008-07-14 03:14:30 UTC (rev 7697)
+++ trunk/test-suite/cases/semantic/00051/00051-sbml-l2v3.xml 2008-07-15 08:43:56 UTC (rev 7698)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated 7-February-2008 14:26:58.7656250 -->
-<!-- Generated by MathSBML 2.7.1 (7 December 2007) -->
+<!-- Generated 15-July-2008 08:50:47.7500000 -->
+<!-- Generated by MathSBML 2.7.5 [2-May-2008] -->
<!-- Generated using Mathematica Version 5.2 for Microsoft Windows (June 20, 2005) -->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3"
level="2"
@@ -13,17 +13,17 @@
<!-- <listOfCompartmentTypes/> -->
<!-- <listOfSpeciesTypes/> -->
<listOfCompartments>
- <compartment id="compartment"
- name="compartment"
+ <compartment id="C"
+ name="C"
spatialDimensions="3"
units="volume"
- size="1"
+ size="1."
constant="false"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1"
name="S1"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="1.5"
@@ -31,7 +31,7 @@
hasOnlySubstanceUnits="false"/>
<species id="S2"
name="S2"
- compartment="compartment"
+ compartment="C"
boundaryCondition="false"
constant="false"
initialAmount="0"
@@ -48,7 +48,7 @@
</listOfParameters>
<!-- <listOfInitialAssignments/> -->
<listOfRules>
- <rateRule variable="compartment"
+ <rateRule variable="C"
metaid="rule1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
@@ -56,7 +56,7 @@
<apply>
<times/>
<cn type="integer">-1</cn>
- <ci>compartment</ci>
+ <ci>C</ci>
</apply>
<ci>p1</ci>
</apply>
@@ -80,7 +80,7 @@
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
- <ci>compartment</ci>
+ <ci>C</ci>
<ci>k1</ci>
<ci>S1</ci>
</apply>
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|
|
From: <mh...@us...> - 2008-07-14 03:14:34
|
Revision: 7697
http://sbml.svn.sourceforge.net/sbml/?rev=7697&view=rev
Author: mhucka
Date: 2008-07-13 20:14:30 -0700 (Sun, 13 Jul 2008)
Log Message:
-----------
Replaced CVS's Source keyword with SVN's HeadURL
Modified Paths:
--------------
trunk/specifications/sbml-level-2/version-4/spec/Makefile
Modified: trunk/specifications/sbml-level-2/version-4/spec/Makefile
===================================================================
--- trunk/specifications/sbml-level-2/version-4/spec/Makefile 2008-07-11 14:43:21 UTC (rev 7696)
+++ trunk/specifications/sbml-level-2/version-4/spec/Makefile 2008-07-14 03:14:30 UTC (rev 7697)
@@ -5,7 +5,7 @@
## @author Michael Hucka
##
## $Id$
-## $Source$
+## $HeadURL$
##
##<!---------------------------------------------------------------------------
## This file is part of the SBML project. Please visit http://sbml.org for
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|
|
From: <ajo...@us...> - 2008-07-11 14:54:30
|
Revision: 7696
http://sbml.svn.sourceforge.net/sbml/?rev=7696&view=rev
Author: ajouraku
Date: 2008-07-11 07:43:21 -0700 (Fri, 11 Jul 2008)
Log Message:
-----------
Fixed to return true when mModel is NULL.
Modified Paths:
--------------
trunk/libsbml/src/sbml/SBMLDocument.cpp
Modified: trunk/libsbml/src/sbml/SBMLDocument.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.cpp 2008-07-11 14:28:38 UTC (rev 7695)
+++ trunk/libsbml/src/sbml/SBMLDocument.cpp 2008-07-11 14:43:21 UTC (rev 7696)
@@ -323,6 +323,10 @@
}
}
+ else
+ {
+ conversionSuccess = true;
+ }
/* commented out addition of note on conversion - it seemed like a good idea
* at the time but needs to located differently :-)
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|
|
From: <ajo...@us...> - 2008-07-11 14:28:41
|
Revision: 7695
http://sbml.svn.sourceforge.net/sbml/?rev=7695&view=rev
Author: ajouraku
Date: 2008-07-11 07:28:38 -0700 (Fri, 11 Jul 2008)
Log Message:
-----------
Added a missing check code for the compatibility check result.
Previously, the conversion was wrongly peformed even if the result is error.
Modified Paths:
--------------
trunk/libsbml/src/sbml/SBMLDocument.cpp
Modified: trunk/libsbml/src/sbml/SBMLDocument.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.cpp 2008-07-11 02:38:44 UTC (rev 7694)
+++ trunk/libsbml/src/sbml/SBMLDocument.cpp 2008-07-11 14:28:38 UTC (rev 7695)
@@ -286,10 +286,8 @@
if (version == 1)
{
mErrorLog.add(CannotConvertToL1V1);
- return conversionSuccess;
}
-
- if (!conversion_errors(checkL1Compatibility()))
+ else if (!conversion_errors(checkL1Compatibility()))
{
mModel->convertToL1();
conversionSuccess = true;
@@ -317,6 +315,12 @@
conversionSuccess = true;
}
}
+
+ if (!conversionSuccess)
+ {
+ return conversionSuccess;
+ }
+
}
}
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|
|
From: <bes...@us...> - 2008-07-11 02:38:54
|
Revision: 7694
http://sbml.svn.sourceforge.net/sbml/?rev=7694&view=rev
Author: beshapiro
Date: 2008-07-10 19:38:44 -0700 (Thu, 10 Jul 2008)
Log Message:
-----------
Update version compatibility list and news file for 2.8.0
Modified Paths:
--------------
trunk/mathsbml/NEWS.txt
trunk/mathsbml/Version-Compatibility.txt
Modified: trunk/mathsbml/NEWS.txt
===================================================================
--- trunk/mathsbml/NEWS.txt 2008-07-10 10:37:09 UTC (rev 7693)
+++ trunk/mathsbml/NEWS.txt 2008-07-11 02:38:44 UTC (rev 7694)
@@ -1,9 +1,13 @@
This file provides a summary of Major Changes in Recent File Releases.
-This file was last updated 2 May 2008
+This file was last updated 10 July 2008
For detailed release notes, please see
http://sbml.org/software/mathsbml/release-notes.html
+Version 2.8.xx
+=========================================================
+2.8.0 - Compatibility with Mathematica 6.0.2 & 6.0.3 [re bug 2014380]
+
Version 2.7.xx
===========================================================================
2.7.5 - Allow rational numbers and small exponents in value fields (modelbuilder) [bug 1956215]
Modified: trunk/mathsbml/Version-Compatibility.txt
===================================================================
--- trunk/mathsbml/Version-Compatibility.txt 2008-07-10 10:37:09 UTC (rev 7693)
+++ trunk/mathsbml/Version-Compatibility.txt 2008-07-11 02:38:44 UTC (rev 7694)
@@ -1,7 +1,13 @@
+Always use the highest version of MathSBML that is
+compatible with your version of Mathematica.
+
If you are using Mathematica 6.0
=========================================================
-Use MathSBML 2.7.x
-Make sure to upgrade to at least 6.0.1 or 6.0.2
+Use MathSBML 2.7.x or higher for 6.0.1
+Use MathSMBL 2.8.0 or higher for 6.0.2 or 6.0.3
+(MathSBML 2.7.x will not work with 6.0.2 or 6.0.3)
+
+Make sure to upgrade to at least Mathematica 6.0.1
Mathematica 6.0.0 is unstable and has bugs in the XML Libraries.
If you are using Mathematica 5.1 or 5.2
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|
|
From: <ajo...@us...> - 2008-07-10 10:37:11
|
Revision: 7693
http://sbml.svn.sourceforge.net/sbml/?rev=7693&view=rev
Author: ajouraku
Date: 2008-07-10 03:37:09 -0700 (Thu, 10 Jul 2008)
Log Message:
-----------
Fixed a bug which could happen when reading an SBML L2V1 file with
an empty math element.
For exmaple, when reading an SBML L2V1 file which contains the following
three reactions (a kineticlaw in the reaction "r1" contains an empty math
element which consist of a start and end 'math' tag pair),
the reaction "r2" and "r3" (i.e. all reactions after the reaction "r1") are
ignored due to the bug and only "r1" is stored in an listOfReactions object.
<listOfReactions>
<reaction id="r1" ... >
...
<kineticLaw>
<math ...>
</math>
</kineticLaw>
</reaction>
<reaction id="r2" ... >
...
</reaction>
<reaction id="r3" ... >
...
</reaction>
</listOfReactions>
An empty math element which consists of single tag ( <math ... /> ) doesn't cause
the problem.
Modified Paths:
--------------
trunk/libsbml/src/math/MathML.cpp
Modified: trunk/libsbml/src/math/MathML.cpp
===================================================================
--- trunk/libsbml/src/math/MathML.cpp 2008-07-10 04:18:33 UTC (rev 7692)
+++ trunk/libsbml/src/math/MathML.cpp 2008-07-10 10:37:09 UTC (rev 7693)
@@ -506,6 +506,13 @@
readMathML (ASTNode& node, XMLInputStream& stream)
{
stream.skipText();
+
+ // catch case where user has an empty math tags ( <math ...></math> )
+ if( stream.peek().getName() == "math" && stream.peek().isEnd() )
+ {
+ stream.skipPastEnd(stream.peek());
+ return;
+ }
const XMLToken elem = stream.next ();
const string& name = elem.getName();
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|
|
From: <kb...@us...> - 2008-07-10 04:18:35
|
Revision: 7692
http://sbml.svn.sourceforge.net/sbml/?rev=7692&view=rev
Author: kbegley
Date: 2008-07-09 21:18:33 -0700 (Wed, 09 Jul 2008)
Log Message:
-----------
updated standalone version root jar file
Modified Paths:
--------------
trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite.jar
Modified: trunk/test-suite/src/StandAloneTestSuite/SBMLTestSuite.jar
===================================================================
(Binary files differ)
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|
|
From: <bes...@us...> - 2008-07-10 02:45:32
|
Revision: 7691
http://sbml.svn.sourceforge.net/sbml/?rev=7691&view=rev
Author: beshapiro
Date: 2008-07-09 19:45:01 -0700 (Wed, 09 Jul 2008)
Log Message:
-----------
Workaround the change in calling sequence for
XML`MathML`ExpressionToSymbolicMathML
which in Mathematica 6.0.2 reverted back to the version 5 syntax from
the new syntax they introduced in 6.0.0 and 6.0.1. Also works in 6.0.3.
Modified Paths:
--------------
trunk/mathsbml/MathSBML.m
trunk/mathsbml/MathSBML.nb
trunk/mathsbml/VERSION.txt
Modified: trunk/mathsbml/MathSBML.m
===================================================================
--- trunk/mathsbml/MathSBML.m 2008-07-09 22:49:20 UTC (rev 7690)
+++ trunk/mathsbml/MathSBML.m 2008-07-10 02:45:01 UTC (rev 7691)
@@ -57,7 +57,7 @@
TEMP$FIRST=True];
Remove[versions];
-$MathSBML$Version = "2.7.5 [2-May-2008]";
+$MathSBML$Version = "2.8.0 [9-July-2008]";
bulletize[mystring$$$_?StringQ,bullet$$$_?StringQ]:="\n\n"<>bullet$$$<>" "<>mystring$$$;
@@ -1187,7 +1187,13 @@
If[$VersionNumber<6,
Xpression2SymbolicMathML[x_]:= XML`MathML`ExpressionToSymbolicMathML[x,"Formats"-> {"ContentMathML"}],
-Xpression2SymbolicMathML[x_]:= XML`MathML`ExpressionToSymbolicMathML[x, "Semantics"-> True, "Presentation"-> False];
+If[$ReleaseNumber<2,
+(* Version 6.0.1 introducted a different syntax *)
+Xpression2SymbolicMathML[x_]:= XML`MathML`ExpressionToSymbolicMathML[x, "Semantics"-> True, "Presentation"-> False],
+
+(* the version 5 syntax was used in 6.0.2 + 6.0.3 *)
+Xpression2SymbolicMathML[x_]:= XML`MathML`ExpressionToSymbolicMathML[x,"Formats"-> {"ContentMathML"}]
+];
];
@@ -18758,11 +18764,14 @@
msgflag=True;
];
+VR=" (Version "<>ToString[$VersionNumber]<>", Release "<>ToString[$ReleaseNumber]<>")";
+rightnow=DateString[{"Day"," ","MonthName", " ", "Year", " at ", "Hour24",":", "Minute", " ", "TimeZone"}];
+
If[msgflag,
If[TEMP$FIRST \[Or] (!TEMP$FIRST \[And] !Equal[ToString[$MathSBML$Version], TEMP$OLDVERSION]),
-Print[MyStyleForm["MathSBML Version "<>ToString[$MathSBML$Version]<>" using Mathematica Version "<>$Version<>" loaded "<>now[], FontWeight-> Bold, FontColor-> Black]];,
+Print[MyStyleForm["MathSBML Version "<>ToString[$MathSBML$Version]<>" using Mathematica Version "<>$Version<>VR<>" loaded "<>rightnow<>"\nGNU Lesser General Public License (LGPL) Terms Apply. ", FontWeight-> Bold, FontColor-> Black]];,
-Print[MyStyleForm["MathSBML Version "<>ToString[$MathSBML$Version]<>" using Mathematica Version "<>$Version<>" reloaded "<>now[], FontWeight-> Bold, FontColor-> Black]];
+Print[MyStyleForm["MathSBML Version "<>ToString[$MathSBML$Version]<>" using Mathematica Version "<>$Version<>VR<>" reloaded "<>rightnow<>"\nGNU Lesser General Public License (LGPL) Terms Apply. ", FontWeight-> Bold, FontColor-> Black]];
];
@@ -18780,6 +18789,7 @@
Remove[TEMP$OLDVERSION];
Remove[TEMP$FIRST];
+Remove[rightnow];
FLAGS`ECHOLOAD=True;
EndPackage[];
Modified: trunk/mathsbml/MathSBML.nb
===================================================================
--- trunk/mathsbml/MathSBML.nb 2008-07-09 22:49:20 UTC (rev 7690)
+++ trunk/mathsbml/MathSBML.nb 2008-07-10 02:45:01 UTC (rev 7691)
@@ -10,11 +10,11 @@
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 145, 7]
-NotebookDataLength[ 4229052, 93279]
-NotebookOptionsPosition[ 4153140, 90876]
-NotebookOutlinePosition[ 4156067, 90959]
-CellTagsIndexPosition[ 4155348, 90940]
-WindowFrame->ThinFrame
+NotebookDataLength[ 4230631, 93330]
+NotebookOptionsPosition[ 4155169, 90927]
+NotebookOutlinePosition[ 4158093, 91010]
+CellTagsIndexPosition[ 4157374, 90991]
+WindowFrame->Normal
ContainsDynamic->False*)
(* Beginning of Notebook Content *)
@@ -10976,36 +10976,35 @@
FontSlant->"Italic"],
StyleBox["\n Author(s):\tSBML Team\n Organization: \tCaltech Biological \
Network Modeling Center\n Created :\t2007-08-29\n Revision:\t$ld$\n Source:\t\
-$Source$\n\nCopyright 2004-2007 \
-California Institute of Technology and Japan Science and Technology \
-Corporation.\n \nThis package is free software; you can redistribute it \
-and/or modify it under the terms of the GNU Lesser General Public License as \
-published by the Free Software Foundation; either version 2.1 of the License, \
-or any later version.\n \nThis package is distributed in the hope that it \
-will be useful, but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY \
-OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and \
-documentation provided hereunder is on an \"as is\" basis, and the \
-California Institute of Technology and Japan Science and Technology \
-Corporation have no obligations to provide maintenance, support, updates, \
-enhancements or modifications. In no event shall the California Institute of \
-Technology or the Japan Science and Technology Corporation be liable to any \
-party for direct, indirect, special, incidental or consequential damages, \
-including lost profits, arising out of the use of this software and its \
-documentation, even if the California Institute of Technology and/or Japan \
-Science and Technology Corporation have been advised of the possibility of \
-such damage. See the GNU Lesser General Public License for more details.\n\n\
-You should have received a copy of the GNU Lesser General Public License \
-along with this library; if not, write to the Free Software Foundation, Inc., \
-59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.\n\n The original code \
-contained here was initially developed by:\n\n \tBruce E. Shapiro\n \t\
-Biological Network Modeling Center\n \tThe Beckman Institute at Caltech\n \t\
-Mail Code 139-74\n \tCalifornia Institute of Technology\n \tPasadena, CA, \
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-Foundation, the US National Institutes of Health, DARPA, and the Beckman \
-Institute at Caltech..",
+$Source$\n\nCopyright 2004-2007 California Institute of Technology and Japan \
+Science and Technology Corporation.\n \nThis package is free software; you \
+can redistribute it and/or modify it under the terms of the GNU Lesser \
+General Public License as published by the Free Software Foundation; either \
+version 2.1 of the License, or any later version.\n \nThis package is \
+distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY, \
+WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A \
+PARTICULAR PURPOSE. The software and documentation provided hereunder is on \
+an \"as is\" basis, and the California Institute of Technology and Japan \
+Science and Technology Corporation have no obligations to provide \
+maintenance, support, updates, enhancements or modifications. In no event \
+shall the California Institute of Technology or the Japan Science and \
+Technology Corporation be liable to any party for direct, indirect, special, \
+incidental or consequential damages, including lost profits, arising out of \
+the use of this software and its documentation, even if the California \
+Institute of Technology and/or Japan Science and Technology Corporation have \
+been advised of the possibility of such damage. See the GNU Lesser General \
+Public License for more details.\n\nYou should have received a copy of the \
+GNU Lesser General Public License along with this library; if not, write to \
+the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA \
+02111-1307 USA.\n\n The original code contained here was initially developed \
+by:\n\n \tBruce E. Shapiro\n \tBiological Network Modeling Center\n \tThe \
+Beckman Institute at Caltech\n \tMail Code 139-74\n \tCalifornia Institute of \
+Technology\n \tPasadena, CA, 91125-7400, USA\n \t\nThe conservation matrix \
+code was developed Joanna Murakami.\n\nThe SBML Validator was developed by \
+Ben Bornstein.\n\nThe inverse eigenvalue plug-in was developed by James Lu.\n\
+\nSupport was provided by the Japan Science and Technology Corporation, the \
+US National Science Foundation, the US National Institutes of Health, DARPA, \
+and the Beckman Institute at Caltech..",
FontSize->12],
StyleBox["\n \n",
FontFamily->"Helvetica",
@@ -11144,8 +11143,8 @@
RowBox[{"Remove", "[", "versions", "]"}], ";"}],
"\[IndentingNewLine]"}], "\[IndentingNewLine]",
RowBox[{
- RowBox[{"$MathSBML$Version", " ", "=", " ", "\"\<2.7.5 [2-May-2008]\>\""}],
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+ RowBox[{"$MathSBML$Version", " ", "=", " ", "\"\<2.8.0 [9-July-2008]\>\""}],
+ ";"}]}], "Input",
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Cell[CellGroupData[{
@@ -11195,9 +11196,14 @@
Cell["Revision Log", "Section"],
Cell[TextData[{
- StyleBox["May 2 08 - 2.7.5 - allow rational numbers and mathematica \
-scientific notation in value fields, such as value->1/400000, value-> \
-\"3/270000\", 3*10^-23, 3.5*10^-23, 3.5*^-14 re bug ",
+ StyleBox["July 9 08 - 2.8 - fix use of different calling sequence in version \
+6.0.2/6.0.3 compared to 6.0.1 for ExpressionToSymbolicMathML. Version 6.0.1 \
+used a different syntax; 6.02 appears to revert to the version 5 syntax, An \
+increase in major version number was needed for automated version number \
+checking by other programs (if 6.02 or 6.03 must have version 2.8 or higher)\n\
+May 2 08 - 2.7.5 - allow rational numbers and mathematica scientific notation \
+in value fields, such as value->1/400000, value-> \"3/270000\", 3*10^-23, \
+3.5*10^-23, 3.5*^-14 re bug ",
FontSize->12],
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StyleBox["\n\nApril 1 08 - 2.7.4 - fixed bug 1887544 - Initial assignments \
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@@ -13370,10 +13377,10 @@
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+\!\(\*FractionBox[\(SubscriptBox[V, f] \((S - P/\*SubscriptBox[\(K\), \
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-\(mp\)])\))\)]\).\>\""}]], "Input",
+SubscriptBox[K, ms] \((1 + P/\*SubscriptBox[\(K\), \(mp\)])\))\)]\).\>\""}]], \
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Cell[BoxData["\<\"isouur[S, P, \\!\\(V\\_f\\), \\!\\(K\\_ms\\), \
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- RowBox[{"\"\<Presentation\>\"", "\[Rule]", " ", "False"}]}], "]"}]}],
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+ RowBox[{
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+ RowBox[{
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+ RowBox[{"(*", " ",
+ RowBox[{
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+ RowBox[{
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+ RowBox[{"x", ",",
+ RowBox[{"\"\<Formats\>\"", "\[Rule]", " ",
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3.389720786677952*^9}, {3.3897217372062483`*^9, 3.389721804977943*^9}, {
3.389722343812415*^9, 3.389722404203517*^9}, {3.389722552946127*^9,
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+ 3.3897225561074963`*^9}, {3.418732582873226*^9, 3.418732590736833*^9}, {
+ 3.424633728899529*^9, 3.424633836364608*^9}, {3.424633973029078*^9,
+ 3.424633974418697*^9}}]
}, Closed]],
Cell[CellGroupData[{
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- "\[IndentingNewLine]"}],
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- ";"}]}], "]"}]}], ";"}], "\n"}], "\[IndentingNewLine]",
+ ";"}]}], "]"}]}], ";"}], "\[IndentingNewLine]"}], "\n",
RowBox[{
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",", "z"}], "]"}], "\[IndentingNewLine]", "]"}], ";"}]}],
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+ "\[IndentingNewLine]", "]"}]}], ";"}], "\n"}], "\[IndentingNewLine]",
RowBox[{
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RowBox[{
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"]"}]}]}], "\[IndentingNewLine]", "]"}]}], ";"}],
- "\n"}], "\[IndentingNewLine]",
+ "\[IndentingNewLine]"}], "\n",
RowBox[{
RowBox[{
RowBox[{
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"]"}]}]}], "\[IndentingNewLine]", "]"}]}], ";"}],
- "\n"}], "\[IndentingNewLine]",
+ "\[IndentingNewLine]"}], "\n",
RowBox[{
RowBox[{
RowBox[{
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"]"}]}]}], "\[IndentingNewLine]", "]"}]}], ";"}],
- "\[IndentingNewLine]"}], "\n",
+ "\n"}], "\[IndentingNewLine]",
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RowBox[{"{",
RowBox[{"t1", ",", "t2"}], "}"}], ",", "opt"}], "]"}]}]}],
- "\[IndentingNewLine]", "]"}]}], ";"}], "\[IndentingNewLine]"}], "\n",
+ "\[IndentingNewLine]", "]"}]}], ";"}], "\n"}], "\[IndentingNewLine]",
RowBox[{
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- RowBox[{"type1", "//", "boldBlue"}], ",", " ",
- RowBox[{
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- ",", " ", "\[IndentingNewLine]",
- RowBox[{
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RowBox[{
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- "\[IndentingNewLine]", "]"}]}], ";"}], "\[IndentingNewLine]",
- "\[IndentingNewLine]", "\[IndentingNewLine]",
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+ "\[IndentingNewLine]", "]"}], ";"}]}], "\[IndentingNewLine]",
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}, Closed]],
@@ -79779,94 +79805,93 @@
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- "boldBlack"}], ",",
- RowBox[{
- "\"\<\\n\\tparametricScan[filname, p, pmin, pmax, deltap, V, time] \
+ "\"\<\\n\\tparametricScan[filname, p, pmin, pmax, deltap, V, time] \
or\\n\\tparametricScan[model, p, pmin, pmax, deltap, V, time]\\n\>\"", "//",
- "boldBlack"}]}], "]"}]}], ";"}]}], " "}]], "Input",
+ "boldBlack"}]}], "]"}]}], ";"}], " "}]}], "Input",
InitializationCell->True]
}, Closed]],
@@ -79874,94 +79899,93 @@
Cell["icScan", "Subsection"],
-Cell[BoxData[
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[truncated message content] |
|
From: <ajo...@us...> - 2008-07-09 22:49:23
|
Revision: 7690
http://sbml.svn.sourceforge.net/sbml/?rev=7690&view=rev
Author: ajouraku
Date: 2008-07-09 15:49:20 -0700 (Wed, 09 Jul 2008)
Log Message:
-----------
Added a setUp function in which a missing initialization for
SBMLDocument variable ($D) is added.
(Most of test functions that include '$D->setLevelAndVersion(1,1)'
fail without the initialization.
Actually, this problem was detected by the recent fix for
SBMLDocument::setLevelAndVersion function.)
setUp function was inserted into the top of each test function.
Modified Paths:
--------------
trunk/libsbml/src/bindings/perl/t/06__TestWriteSBML.t
Modified: trunk/libsbml/src/bindings/perl/t/06__TestWriteSBML.t
===================================================================
--- trunk/libsbml/src/bindings/perl/t/06__TestWriteSBML.t 2008-07-09 12:28:32 UTC (rev 7689)
+++ trunk/libsbml/src/bindings/perl/t/06__TestWriteSBML.t 2008-07-09 22:49:20 UTC (rev 7690)
@@ -88,7 +88,8 @@
# some global(s)
#---
-sub clear_OStringStream {
+sub setUp {
+ $D = new LibSBML::SBMLDocument();
$OSS = new LibSBML::OStringStream();
$XOS = new LibSBML::XMLOutputStream($OSS->get_ostream());
}
@@ -195,6 +196,7 @@
#---
sub test_WriteSBML_SBMLDocument_L1v1 {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level1\" " .
"level=\"1\" version=\"1\"/>\n");
@@ -204,6 +206,7 @@
#---
sub test_WriteSBML_SBMLDocument_L1v2 {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level1\" " .
"level=\"1\" version=\"2\"/>\n");
@@ -213,6 +216,7 @@
#---
sub test_WriteSBML_SBMLDocument_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2\" " .
"level=\"2\" version=\"1\"/>\n");
@@ -222,6 +226,7 @@
#---
sub test_WriteSBML_SBMLDocument_L2v2 {
+ setUp();
$D->setLevelAndVersion(2, 2);
my $expected = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version2\" " .
"level=\"2\" version=\"2\"/>\n");
@@ -231,6 +236,7 @@
#---
sub test_WriteSBML_Model {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapSBML_L1v1(" <model name=\"Branch\"/>\n");
$D->createModel("Branch");
@@ -240,6 +246,7 @@
#---
sub test_WriteSBML_Model_skipOptional {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapSBML_L1v2(" <model/>\n");
$D->createModel();
@@ -249,6 +256,7 @@
#---
sub test_WriteSBML_Model_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapSBML_L2v1(" <model id=\"Branch\"/>\n");
$D->createModel("Branch");
@@ -258,6 +266,7 @@
#---
sub test_WriteSBML_Model_L2v1_skipOptional {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapSBML_L2v1(" <model/>\n");
$D->createModel();
@@ -267,6 +276,7 @@
#---
sub test_WriteSBML_FunctionDefinition {
+ setUp();
my $expected = wrapXML("<functionDefinition id=\"pow3\">\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
" <lambda>\n" .
@@ -282,70 +292,70 @@
" </math>\n" .
"</functionDefinition>");
my $fd = new LibSBML::FunctionDefinition("pow3", "lambda(x, x^3)");
- clear_OStringStream();
$fd->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Unit {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<unit kind=\"kilogram\" exponent=\"2\" scale=\"-3\"/>");
my $u = new LibSBML::Unit("kilogram", 2, -3);
$u->setSBMLDocument($D);
- clear_OStringStream();
$u->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Unit_l2v3 {
+ setUp();
$D->setLevelAndVersion(2, 3);
my $expected = wrapXML("<unit kind=\"kilogram\" exponent=\"2\" scale=\"-3\"/>");
my $u = new LibSBML::Unit("kilogram", 2, -3);
$u->setOffset(32);
$u->setSBMLDocument($D);
- clear_OStringStream();
$u->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Unit_defaults {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<unit kind=\"kilogram\"/>");
my $u = new LibSBML::Unit("kilogram", 1, 0);
$u->setSBMLDocument($D);
- clear_OStringStream();
$u->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Unit_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<unit kind=\"Celsius\" multiplier=\"1.8\" offset=\"32\"/>");
my $u = new LibSBML::Unit("Celsius", 1, 0, 1.8);
$u->setOffset(32);
$u->setSBMLDocument($D);
- clear_OStringStream();
$u->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_UnitDefinition {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<unitDefinition name=\"mmls\"/>");
my $ud = new LibSBML::UnitDefinition("mmls");
$ud->setSBMLDocument($D);
- clear_OStringStream();
$ud->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_UnitDefinition_full {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<unitDefinition name=\"mmls\">\n" .
" <listOfUnits>\n" .
@@ -362,24 +372,24 @@
$ud->addUnit($u2);
$ud->addUnit($u3);
$ud->setSBMLDocument($D);
- clear_OStringStream();
$ud->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_UnitDefinition_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<unitDefinition id=\"mmls\"/>");
my $ud = new LibSBML::UnitDefinition("mmls");
$ud->setSBMLDocument($D);
- clear_OStringStream();
$ud->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_UnitDefinition_L2v1_full {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<unitDefinition id=\"Fahrenheit\">\n" .
" <listOfUnits>\n" .
@@ -391,76 +401,76 @@
my $ud = new LibSBML::UnitDefinition("Fahrenheit");
$ud->addUnit($u1);
$ud->setSBMLDocument($D);
- clear_OStringStream();
$ud->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Compartment {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<compartment name=\"A\" volume=\"2.1\" outside=\"B\"/>");
my $c = new LibSBML::Compartment("A");
$c->setSize(2.1);
$c->setOutside("B");
$c->setSBMLDocument($D);
- clear_OStringStream();
$c->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Compartment_unsetVolume {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<compartment name=\"A\"/>");
my $c = new LibSBML::Compartment();
$c->setId("A");
$c->setSBMLDocument($D);
- clear_OStringStream();
$c->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Compartment_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<compartment id=\"M\" spatialDimensions=\"2\" size=\"2.5\"/>");
my $c = new LibSBML::Compartment("M");
$c->setSize(2.5);
$c->setSpatialDimensions(2);
$c->setSBMLDocument($D);
- clear_OStringStream();
$c->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Compartment_L2v1_constant {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<compartment id=\"cell\" size=\"1.2\" constant=\"false\"/>");
my $c = new LibSBML::Compartment("cell");
$c->setSize(1.2);
$c->setConstant(0);
$c->setSBMLDocument($D);
- clear_OStringStream();
$c->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Compartment_L2v1_unsetSize {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<compartment id=\"A\"/>");
my $c = new LibSBML::Compartment();
$c->setId("A");
$c->setSBMLDocument($D);
- clear_OStringStream();
$c->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Species {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<species name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"" .
" units=\"mole\" boundaryCondition=\"true\" charge=\"2\"/>");
@@ -471,13 +481,13 @@
$s->setBoundaryCondition(1);
$s->setCharge(2);
$s->setSBMLDocument($D);
- clear_OStringStream();
$s->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Species_L1v1 {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<specie name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"" .
" units=\"mole\" boundaryCondition=\"true\" charge=\"2\"/>");
@@ -488,13 +498,13 @@
$s->setBoundaryCondition(1);
$s->setCharge(2);
$s->setSBMLDocument($D);
- clear_OStringStream();
$s->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Species_defaults {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<species name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"" .
" units=\"mole\" charge=\"2\"/>");
@@ -504,26 +514,26 @@
$s->setUnits("mole");
$s->setCharge(2);
$s->setSBMLDocument($D);
- clear_OStringStream();
$s->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Species_skipOptional {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<species name=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\"/>");
my $s = new LibSBML::Species("Ca2");
$s->setCompartment("cell");
$s->setInitialAmount(0.7);
$s->setSBMLDocument($D);
- clear_OStringStream();
$s->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Species_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<species id=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\" " .
"substanceUnits=\"mole\" constant=\"true\"/>");
@@ -533,106 +543,106 @@
$s->setSubstanceUnits("mole");
$s->setConstant(1);
$s->setSBMLDocument($D);
- clear_OStringStream();
$s->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Species_L2v1_skipOptional {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<species id=\"Ca2\" compartment=\"cell\"/>");
my $s = new LibSBML::Species("Ca2");
$s->setCompartment("cell");
$s->setSBMLDocument($D);
- clear_OStringStream();
$s->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Parameter {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<parameter name=\"Km1\" value=\"2.3\" units=\"second\"/>");
my $p = new LibSBML::Parameter("Km1", 2.3, "second");
$p->setSBMLDocument($D);
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Parameter_L1v1_required {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<parameter name=\"Km1\" value=\"NaN\"/>");
my $p = new LibSBML::Parameter();
$p->setId("Km1");
$p->unsetValue();
$p->setSBMLDocument($D);
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Parameter_L1v2_skipOptional {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<parameter name=\"Km1\"/>");
my $p = new LibSBML::Parameter();
$p->setId("Km1");
$p->setSBMLDocument($D);
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Parameter_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<parameter id=\"Km1\" value=\"2.3\" units=\"second\"/>");
my $p = new LibSBML::Parameter("Km1", 2.3, "second");
$p->setSBMLDocument($D);
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Parameter_L2v1_skipOptional {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<parameter id=\"Km1\"/>");
my $p = new LibSBML::Parameter("Km1");
$p->setSBMLDocument($D);
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Parameter_L2v1_constant {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<parameter id=\"x\" constant=\"false\"/>");
my $p = new LibSBML::Parameter("x");
$p->setConstant(0);
$p->setSBMLDocument($D);
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_AlgebraicRule {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<algebraicRule formula=\"x + 1\"/>");
my $r = new LibSBML::AlgebraicRule("x + 1");
$r->setSBMLDocument($D);
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_AlgebraicRule_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<algebraicRule>\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -645,13 +655,13 @@
"</algebraicRule>");
my $r = new LibSBML::AlgebraicRule("x + 1");
$r->setSBMLDocument($D);
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesConcentrationRule {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<speciesConcentrationRule " .
"formula=\"t * s\" type=\"rate\" species=\"s\"/>");
@@ -660,13 +670,13 @@
my $r = $D->getModel()->createRateRule();
$r->setVariable("s");
$r->setFormula("t * s");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesConcentrationRule_defaults {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<speciesConcentrationRule formula=\"t * s\" species=\"s\"/>");
$D->createModel();
@@ -674,13 +684,13 @@
my $r = $D->getModel()->createAssignmentRule();
$r->setVariable("s");
$r->setFormula("t * s");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesConcentrationRule_L1v1 {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<specieConcentrationRule formula=\"t * s\" specie=\"s\"/>");
$D->createModel();
@@ -688,13 +698,13 @@
my $r = $D->getModel()->createAssignmentRule();
$r->setVariable("s");
$r->setFormula("t * s");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesConcentrationRule_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<assignmentRule variable=\"s\">\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -710,13 +720,13 @@
my $r = $D->getModel()->createAssignmentRule();
$r->setVariable("s");
$r->setFormula("t * s");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_CompartmentVolumeRule {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<compartmentVolumeRule " .
"formula=\"v + c\" type=\"rate\" compartment=\"c\"/>");
@@ -725,13 +735,13 @@
my $r = $D->getModel()->createRateRule();
$r->setVariable("c");
$r->setFormula("v + c");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_CompartmentVolumeRule_defaults {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<compartmentVolumeRule formula=\"v + c\" compartment=\"c\"/>");
$D->createModel();
@@ -739,13 +749,13 @@
my $r = $D->getModel()->createAssignmentRule();
$r->setVariable("c");
$r->setFormula("v + c");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_CompartmentVolumeRule_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<assignmentRule variable=\"c\">\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -761,13 +771,13 @@
my $r = $D->getModel()->createAssignmentRule();
$r->setVariable("c");
$r->setFormula("v + c");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_ParameterRule {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<parameterRule " .
"formula=\"p * t\" type=\"rate\" name=\"p\"/>");
@@ -776,13 +786,13 @@
my $r = $D->getModel()->createRateRule();
$r->setVariable("p");
$r->setFormula("p * t");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_ParameterRule_defaults {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<parameterRule formula=\"p * t\" name=\"p\"/>");
$D->createModel();
@@ -790,13 +800,13 @@
my $r = $D->getModel()->createAssignmentRule();
$r->setVariable("p");
$r->setFormula("p * t");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_ParameterRule_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<rateRule variable=\"p\">\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -812,37 +822,37 @@
my $r = $D->getModel()->createRateRule();
$r->setVariable("p");
$r->setFormula("p * t");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Reaction {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<reaction name=\"r\" reversible=\"false\" fast=\"true\"/>");
my $r = new LibSBML::Reaction("r", "", undef, 0);
$r->setFast(1);
$r->setSBMLDocument($D);
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Reaction_defaults {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<reaction name=\"r\"/>");
my $r = new LibSBML::Reaction();
$r->setId("r");
$r->setSBMLDocument($D);
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Reaction_full {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<reaction name=\"v1\">\n" .
" <listOfReactants>\n" .
@@ -860,24 +870,24 @@
$r->createReactant()->setSpecies("x0");
$r->createProduct()->setSpecies("s1");
$r->createKineticLaw()->setFormula("(vm * s1)/(km + s1)");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Reaction_L2v1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<reaction id=\"r\" reversible=\"false\"/>");
my $r = new LibSBML::Reaction("r", "", undef, 0);
$r->setSBMLDocument($D);
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Reaction_L2v1_full {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<reaction id=\"v1\">\n" .
" <listOfReactants>\n" .
@@ -915,46 +925,46 @@
$r->createProduct()->setSpecies("s1");;
$r->createModifier()->setSpecies("m1");
$r->createKineticLaw()->setFormula("(vm * s1)/(km + s1)");
- clear_OStringStream();
$r->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesReference {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<speciesReference species=\"s\" stoichiometry=\"3\" denominator=\"2\"/>");
my $sr = new LibSBML::SpeciesReference("s", 3, 2);
$sr->setSBMLDocument($D);
- clear_OStringStream();
$sr->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesReference_L1v1 {
+ setUp();
$D->setLevelAndVersion(1, 1);
my $expected = wrapXML("<specieReference specie=\"s\" stoichiometry=\"3\" denominator=\"2\"/>");
my $sr = new LibSBML::SpeciesReference("s", 3, 2);
$sr->setSBMLDocument($D);
- clear_OStringStream();
$sr->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesReference_defaults {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<speciesReference species=\"s\"/>");
my $sr = new LibSBML::SpeciesReference("s");
$sr->setSBMLDocument($D);
- clear_OStringStream();
$sr->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesReference_L2v1_1 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<speciesReference species=\"s\">\n" .
" <stoichiometryMath>\n" .
@@ -965,24 +975,24 @@
"</speciesReference>");
my $sr = new LibSBML::SpeciesReference("s", 3, 2);
$sr->setSBMLDocument($D);
- clear_OStringStream();
$sr->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesReference_L2v1_2 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<speciesReference species=\"s\" stoichiometry=\"3.2\"/>");
my $sr = new LibSBML::SpeciesReference("s", 3.2);
$sr->setSBMLDocument($D);
- clear_OStringStream();
$sr->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_SpeciesReference_L2v1_3 {
+ setUp();
$D->setLevelAndVersion(2, 1);
my $expected = wrapXML("<speciesReference species=\"s\">\n" .
" <stoichiometryMath>\n" .
@@ -1001,36 +1011,36 @@
$stoich->setMath($math);
$sr->setStoichiometryMath($stoich);
$sr->setSBMLDocument($D);
- clear_OStringStream();
$sr->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_KineticLaw {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<kineticLaw formula=\"k * e\" timeUnits=\"second\" " .
"substanceUnits=\"item\"/>");
my $kl = new LibSBML::KineticLaw("k * e", "second", "item");
$kl->setSBMLDocument($D);
- clear_OStringStream();
$kl->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_KineticLaw_skipOptional {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<kineticLaw formula=\"k * e\"/>");
my $kl = new LibSBML::KineticLaw("k * e");
$kl->setSBMLDocument($D);
- clear_OStringStream();
$kl->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_KineticLaw_ListOfParameters {
+ setUp();
$D->setLevelAndVersion(1, 2);
my $expected = wrapXML("<kineticLaw formula=\"nk * e\" timeUnits=\"second\" " .
"substanceUnits=\"item\">\n" .
@@ -1042,23 +1052,23 @@
$kl->setSBMLDocument($D);
my $p = new LibSBML::Parameter("n", 1.2);
$kl->addParameter($p);
- clear_OStringStream();
$kl->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Event {
+ setUp();
my $expected = wrapXML("<event id=\"e\"/>");
my $e = new LibSBML::Event();
$e->setId("e");
- clear_OStringStream();
$e->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Event_trigger {
+ setUp();
my $expected = wrapXML("<event id=\"e\">\n" .
" <trigger>\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -1075,13 +1085,13 @@
my $t = new LibSBML::Trigger($node);
$e->setTrigger($t);
$e->setTimeUnits("second");
- clear_OStringStream();
$e->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Event_delay {
+ setUp();
my $expected = wrapXML("<event id=\"e\">\n" .
" <delay>\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -1093,13 +1103,13 @@
my $node = LibSBML::parseFormula("5");
my $d = new LibSBML::Delay($node);
$e->setDelay($d);
- clear_OStringStream();
$e->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Event_both {
+ setUp();
my $expected = wrapXML("<event id=\"e\">\n" .
" <trigger>\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -1124,13 +1134,13 @@
$e->setDelay($d);
$e->setTrigger($t);
$e->setTimeUnits("second");
- clear_OStringStream();
$e->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_Event_full {
+ setUp();
my $expected = wrapXML("<event id=\"e\">\n" .
" <trigger>\n" .
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" .
@@ -1156,43 +1166,42 @@
my $ea = new LibSBML::EventAssignment("k2", $math);
$e->setTrigger($t);
$e->addEventAssignment($ea);
- clear_OStringStream();
$e->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_NaN {
+ setUp();
my $expected = wrapXML("<parameter id=\"p\" value=\"NaN\"/>");
my $p = new LibSBML::Parameter("p", util_NaN());
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_INF {
+ setUp();
my $expected = wrapXML("<parameter id=\"p\" value=\"INF\"/>");
my $p = new LibSBML::Parameter("p", util_PosInf());
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_NegINF {
+ setUp();
my $expected = wrapXML("<parameter id=\"p\" value=\"-INF\"/>");
my $p = new LibSBML::Parameter("p", util_NegInf());
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
#---
sub test_WriteSBML_locale {
+ setUp();
my $expected = wrapXML("<parameter id=\"p\" value=\"3.31\"/>");
my $p = new LibSBML::Parameter("p", 3.31);
- clear_OStringStream();
$p->write($XOS);
ok( $expected eq $OSS->str() );
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ajo...@us...> - 2008-07-09 12:28:39
|
Revision: 7689
http://sbml.svn.sourceforge.net/sbml/?rev=7689&view=rev
Author: ajouraku
Date: 2008-07-09 05:28:32 -0700 (Wed, 09 Jul 2008)
Log Message:
-----------
* setLevelAndVersion function
Added a missing 'return' which needs to be called when a conversion error
(a conversion to L1V1) happens.
Modified Paths:
--------------
trunk/libsbml/src/sbml/SBMLDocument.cpp
Modified: trunk/libsbml/src/sbml/SBMLDocument.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBMLDocument.cpp 2008-07-09 08:45:46 UTC (rev 7688)
+++ trunk/libsbml/src/sbml/SBMLDocument.cpp 2008-07-09 12:28:32 UTC (rev 7689)
@@ -286,7 +286,9 @@
if (version == 1)
{
mErrorLog.add(CannotConvertToL1V1);
+ return conversionSuccess;
}
+
if (!conversion_errors(checkL1Compatibility()))
{
mModel->convertToL1();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ajo...@us...> - 2008-07-09 08:45:48
|
Revision: 7688
http://sbml.svn.sourceforge.net/sbml/?rev=7688&view=rev
Author: ajouraku
Date: 2008-07-09 01:45:46 -0700 (Wed, 09 Jul 2008)
Log Message:
-----------
Modified a constructor 'UnitFormulaFormatter::UnitFormulaFormatter(const Model *m)'.
Now, the given Model poitner is directly set to 'model' variable (a data member of
UnitFormulaFormatter). In other words, m->clone() is not called now.
I think we don't have to set a copy of the given Model object (m->clone()) to 'model'
variable because the 'model' variable is const and therefore never changed during
the lifetime of an UnitFormulaFormatter object.
This change may drastically reduce consumed memory and calculation time
required for Unit consistency check functions when the given model is large,
because the overhead of m->clone() could be large and the constructor of
UnitFormulaFormatter could be heavily called in the functions (especially in the
functions which depend on recursive calls).
Modified Paths:
--------------
trunk/libsbml/src/units/UnitFormulaFormatter.cpp
Modified: trunk/libsbml/src/units/UnitFormulaFormatter.cpp
===================================================================
--- trunk/libsbml/src/units/UnitFormulaFormatter.cpp 2008-07-09 07:51:53 UTC (rev 7687)
+++ trunk/libsbml/src/units/UnitFormulaFormatter.cpp 2008-07-09 08:45:46 UTC (rev 7688)
@@ -30,8 +30,8 @@
* constructs a UnitFormulaFormatter
*/
UnitFormulaFormatter::UnitFormulaFormatter(const Model *m)
+ : model(m)
{
- model = (Model *) (m->clone());
mContainsUndeclaredUnits = false;
mCanIgnoreUndeclaredUnits = 2;
depthRecursiveCall = 0;
@@ -42,7 +42,6 @@
*/
UnitFormulaFormatter::~UnitFormulaFormatter()
{
- delete model;
}
/*
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ajo...@us...> - 2008-07-09 07:51:56
|
Revision: 7687
http://sbml.svn.sourceforge.net/sbml/?rev=7687&view=rev
Author: ajouraku
Date: 2008-07-09 00:51:53 -0700 (Wed, 09 Jul 2008)
Log Message:
-----------
Fixed memory leaks.
1) validator/constraints/ArgumentsUnitsCheck.cpp
Added a missing delete call in checkUnitsFromPiecewise function.
2) math/ASTNode.cpp
Added a missing delete call in destructor
3) annotation/CVTerm.cpp
Removed a duplicated new call for mResources
4) sbml/Constraint.cpp
Added missing delete calls in destructor
5) sbml/InitialAssignment.cpp
Added a missing delete call in destructor
6) sbml/UnitDefinition.cp
Added missing delete calls for returned values of ListOf::remove
Modified Paths:
--------------
trunk/libsbml/src/annotation/CVTerm.cpp
trunk/libsbml/src/math/ASTNode.cpp
trunk/libsbml/src/sbml/Constraint.cpp
trunk/libsbml/src/sbml/InitialAssignment.cpp
trunk/libsbml/src/sbml/UnitDefinition.cpp
trunk/libsbml/src/validator/constraints/ArgumentsUnitsCheck.cpp
Modified: trunk/libsbml/src/annotation/CVTerm.cpp
===================================================================
--- trunk/libsbml/src/annotation/CVTerm.cpp 2008-07-09 01:22:28 UTC (rev 7686)
+++ trunk/libsbml/src/annotation/CVTerm.cpp 2008-07-09 07:51:53 UTC (rev 7687)
@@ -173,7 +173,6 @@
CVTerm* CVTerm::clone() const
{
CVTerm* term=new CVTerm(*this);
- term->mResources=new XMLAttributes(*this->mResources);
return term;
}
Modified: trunk/libsbml/src/math/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/math/ASTNode.cpp 2008-07-09 01:22:28 UTC (rev 7686)
+++ trunk/libsbml/src/math/ASTNode.cpp 2008-07-09 07:51:53 UTC (rev 7687)
@@ -276,7 +276,7 @@
delete mChildren;
size = mSemanticsAnnotations->getSize();
- while (size--) mSemanticsAnnotations->remove(0) ;
+ while (size--) delete static_cast<XMLNode*>(mSemanticsAnnotations->remove(0) );
delete mSemanticsAnnotations;
delete mDefinitionURL;
Modified: trunk/libsbml/src/sbml/Constraint.cpp
===================================================================
--- trunk/libsbml/src/sbml/Constraint.cpp 2008-07-09 01:22:28 UTC (rev 7686)
+++ trunk/libsbml/src/sbml/Constraint.cpp 2008-07-09 07:51:53 UTC (rev 7687)
@@ -61,6 +61,8 @@
*/
Constraint::~Constraint ()
{
+ if(mMath) delete mMath;
+ if(mMessage) delete mMessage;
}
Modified: trunk/libsbml/src/sbml/InitialAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.cpp 2008-07-09 01:22:28 UTC (rev 7686)
+++ trunk/libsbml/src/sbml/InitialAssignment.cpp 2008-07-09 07:51:53 UTC (rev 7687)
@@ -59,6 +59,7 @@
*/
InitialAssignment::~InitialAssignment ()
{
+ if(mMath) delete mMath;
}
Modified: trunk/libsbml/src/sbml/UnitDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/UnitDefinition.cpp 2008-07-09 01:22:28 UTC (rev 7686)
+++ trunk/libsbml/src/sbml/UnitDefinition.cpp 2008-07-09 07:51:53 UTC (rev 7687)
@@ -453,7 +453,7 @@
unit = (Unit *) units->get(n);
if (!strcmp(UnitKind_toString(unit->getKind()), "dimensionless"))
{
- units->remove(n);
+ delete units->remove(n);
kindsList.removeUnitKind("dimensionless");
}
}
@@ -476,7 +476,7 @@
unitKind))
{
Unit::merge(unit, (Unit *) units->get(i));
- units->remove(i);
+ delete units->remove(i);
kindsList.removeUnitKind(unitKind);
}
}
@@ -491,7 +491,7 @@
unit = (Unit *) units->get(n-1);
if (unit->getExponent() == 0)
{
- units->remove(n-1);
+ delete units->remove(n-1);
}
}
}
@@ -549,7 +549,7 @@
/* remove originals */
for (n = 0; n < numUnits; n++)
{
- units->remove(0);
+ delete units->remove(0);
}
delete [] indexArray;
Modified: trunk/libsbml/src/validator/constraints/ArgumentsUnitsCheck.cpp
===================================================================
--- trunk/libsbml/src/validator/constraints/ArgumentsUnitsCheck.cpp 2008-07-09 01:22:28 UTC (rev 7686)
+++ trunk/libsbml/src/validator/constraints/ArgumentsUnitsCheck.cpp 2008-07-09 07:51:53 UTC (rev 7687)
@@ -203,10 +203,10 @@
{
logInconsistentPiecewise(node, sb);
}
+ delete tempUD1;
}
delete tempUD;
- delete tempUD1;
for(n = 1; n < node.getNumChildren(); n+=2)
{
@@ -216,18 +216,18 @@
{
logInconsistentPiecewiseCondition(node, sb);
}
+ delete tempUD;
}
+ delete dim;
+ delete unit;
+ delete unitFormat;
+
for(n = 0; n < node.getNumChildren(); n++)
{
checkUnits(m, *node.getChild(n), sb, inKL, reactNo);
}
- delete tempUD;
- delete dim;
- delete unit;
- delete unitFormat;
-
}
/**
* Checks that the units of the function are consistent
@@ -278,13 +278,13 @@
delete tempUD;
}
+ delete unitFormat;
+ delete ud;
+
for (n = 0; n < node.getNumChildren(); n++)
{
checkUnits(m, *node.getChild(n), sb, inKL, reactNo);
}
-
- delete unitFormat;
- delete ud;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2008-07-09 01:22:31
|
Revision: 7686
http://sbml.svn.sourceforge.net/sbml/?rev=7686&view=rev
Author: mhucka
Date: 2008-07-08 18:22:28 -0700 (Tue, 08 Jul 2008)
Log Message:
-----------
Updated date stamp & cases archive.
Added Paths:
-----------
trunk/test-suite/.cases-archive-date
Added: trunk/test-suite/.cases-archive-date
===================================================================
--- trunk/test-suite/.cases-archive-date (rev 0)
+++ trunk/test-suite/.cases-archive-date 2008-07-09 01:22:28 UTC (rev 7686)
@@ -0,0 +1 @@
+2008-07-08
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <kb...@us...> - 2008-07-09 00:54:11
|
Revision: 7685
http://sbml.svn.sourceforge.net/sbml/?rev=7685&view=rev
Author: kbegley
Date: 2008-07-08 17:54:06 -0700 (Tue, 08 Jul 2008)
Log Message:
-----------
added javadocs for standalone app
Added Paths:
-----------
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/overview-tree.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/package-list
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/resources/
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/resources/inherit.gif
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/FailedTestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/HelpDialog.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/ListViewPane.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/MapViewPane.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/PassedTestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/PreferencesDialog.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SBMLTestCase.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SBMLTestRunnerApp.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SBMLTestSelection.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SkippedTestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/SwingWorker.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestCaseListModel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestCaseUpdater.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestConfiguration.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestResultDetails.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestResultMap.FieldListener.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestResultMap.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.aboutActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.checkUpdatesActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.helpActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.newActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.preferencesActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerView.quitActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestRunnerWorker.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.openBrowserActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.resetActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.settingsActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.startActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/TestTabPane.stopActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/ComponentTagsSelectorPanel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/CreateTestWizard.cancelActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/CreateTestWizard.finishActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/CreateTestWizard.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/CreateTestWizard.nextActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/CreateTestWizard.previousActionClass.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/LevelSelectorPanel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/TestTagSelectionPanel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/TestTypeSelectorPanel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/WizardPanel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/WizardPanelInterface.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/WrapperConfigurationPanel.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/package-frame.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/package-summary.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/Wizard/package-tree.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/package-frame.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/package-summary.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/sbml/test/package-tree.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/serialized-form.html
trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/stylesheet.css
Added: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html (rev 0)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-frame.html 2008-07-09 00:54:06 UTC (rev 7685)
@@ -0,0 +1,44 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<TITLE>
+All Classes
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameHeadingFont">
+<B>All Classes</B></FONT>
+<BR>
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard" target="classFrame">ComponentTagsSelectorPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard" target="classFrame">CreateTestWizard</A>
+<BR>
+<A HREF="sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard" target="classFrame">LevelSelectorPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard" target="classFrame">TestTagSelectionPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard" target="classFrame">TestTypeSelectorPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/WizardPanel.html" title="class in sbml.test.Wizard" target="classFrame">WizardPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard" target="classFrame"><I>WizardPanelInterface</I></A>
+<BR>
+<A HREF="sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard" target="classFrame">WrapperConfigurationPanel</A>
+<BR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+</BODY>
+</HTML>
Added: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html (rev 0)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/allclasses-noframe.html 2008-07-09 00:54:06 UTC (rev 7685)
@@ -0,0 +1,44 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<TITLE>
+All Classes
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+
+
+</HEAD>
+
+<BODY BGCOLOR="white">
+<FONT size="+1" CLASS="FrameHeadingFont">
+<B>All Classes</B></FONT>
+<BR>
+
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<BR>
+<A HREF="sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/WizardPanel.html" title="class in sbml.test.Wizard">WizardPanel</A>
+<BR>
+<A HREF="sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard"><I>WizardPanelInterface</I></A>
+<BR>
+<A HREF="sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<BR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+</BODY>
+</HTML>
Added: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html (rev 0)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/constant-values.html 2008-07-09 00:54:06 UTC (rev 7685)
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<TITLE>
+Constant Field Values
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Constant Field Values";
+}
+</SCRIPT>
+<NOSCRIPT>
+</NOSCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html?constant-values.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="constant-values.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H1>
+Constant Field Values</H1>
+</CENTER>
+<HR SIZE="4" NOSHADE>
+<B>Contents</B><UL>
+</UL>
+
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html?constant-values.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="constant-values.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+
+</BODY>
+</HTML>
Added: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html (rev 0)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/deprecated-list.html 2008-07-09 00:54:06 UTC (rev 7685)
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<TITLE>
+Deprecated List
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Deprecated List";
+}
+</SCRIPT>
+<NOSCRIPT>
+</NOSCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html?deprecated-list.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="deprecated-list.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Deprecated API</B></H2>
+</CENTER>
+<HR SIZE="4" NOSHADE>
+<B>Contents</B><UL>
+</UL>
+
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html?deprecated-list.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="deprecated-list.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+
+</BODY>
+</HTML>
Added: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html (rev 0)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/help-doc.html 2008-07-09 00:54:06 UTC (rev 7685)
@@ -0,0 +1,205 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<TITLE>
+API Help
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="API Help";
+}
+</SCRIPT>
+<NOSCRIPT>
+</NOSCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html?help-doc.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="help-doc.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<HR>
+<CENTER>
+<H1>
+How This API Document Is Organized</H1>
+</CENTER>
+This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.<H3>
+Package</H3>
+<BLOCKQUOTE>
+
+<P>
+Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain four categories:<UL>
+<LI>Interfaces (italic)<LI>Classes<LI>Enums<LI>Exceptions<LI>Errors<LI>Annotation Types</UL>
+</BLOCKQUOTE>
+<H3>
+Class/Interface</H3>
+<BLOCKQUOTE>
+
+<P>
+Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:<UL>
+<LI>Class inheritance diagram<LI>Direct Subclasses<LI>All Known Subinterfaces<LI>All Known Implementing Classes<LI>Class/interface declaration<LI>Class/interface description
+<P>
+<LI>Nested Class Summary<LI>Field Summary<LI>Constructor Summary<LI>Method Summary
+<P>
+<LI>Field Detail<LI>Constructor Detail<LI>Method Detail</UL>
+Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.</BLOCKQUOTE>
+</BLOCKQUOTE>
+<H3>
+Annotation Type</H3>
+<BLOCKQUOTE>
+
+<P>
+Each annotation type has its own separate page with the following sections:<UL>
+<LI>Annotation Type declaration<LI>Annotation Type description<LI>Required Element Summary<LI>Optional Element Summary<LI>Element Detail</UL>
+</BLOCKQUOTE>
+</BLOCKQUOTE>
+<H3>
+Enum</H3>
+<BLOCKQUOTE>
+
+<P>
+Each enum has its own separate page with the following sections:<UL>
+<LI>Enum declaration<LI>Enum description<LI>Enum Constant Summary<LI>Enum Constant Detail</UL>
+</BLOCKQUOTE>
+<H3>
+Tree (Class Hierarchy)</H3>
+<BLOCKQUOTE>
+There is a <A HREF="overview-tree.html">Class Hierarchy</A> page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with <code>java.lang.Object</code>. The interfaces do not inherit from <code>java.lang.Object</code>.<UL>
+<LI>When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.<LI>When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.</UL>
+</BLOCKQUOTE>
+<H3>
+Deprecated API</H3>
+<BLOCKQUOTE>
+The <A HREF="deprecated-list.html">Deprecated API</A> page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.</BLOCKQUOTE>
+<H3>
+Index</H3>
+<BLOCKQUOTE>
+The <A HREF="index-all.html">Index</A> contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.</BLOCKQUOTE>
+<H3>
+Prev/Next</H3>
+These links take you to the next or previous class, interface, package, or related page.<H3>
+Frames/No Frames</H3>
+These links show and hide the HTML frames. All pages are available with or without frames.
+<P>
+<H3>
+Serialized Form</H3>
+Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.
+<P>
+<H3>
+Constant Field Values</H3>
+The <a href="constant-values.html">Constant Field Values</a> page lists the static final fields and their values.
+<P>
+<FONT SIZE="-1">
+<EM>
+This help file applies to API documentation generated using the standard doclet.</EM>
+</FONT>
+<BR>
+<HR>
+
+
+<!-- ======= START OF BOTTOM NAVBAR ====== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html?help-doc.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="help-doc.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_bottom"></A>
+<!-- ======== END OF BOTTOM NAVBAR ======= -->
+
+<HR>
+
+</BODY>
+</HTML>
Added: trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html
===================================================================
--- trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html (rev 0)
+++ trunk/test-suite/src/StandAloneTestSuite/sbml-test-suite-javadocs/index-all.html 2008-07-09 00:54:06 UTC (rev 7685)
@@ -0,0 +1,452 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc (build 1.5.0_13) on Tue Jul 08 11:59:46 EST 2008 -->
+<TITLE>
+Index
+</TITLE>
+
+
+<LINK REL ="stylesheet" TYPE="text/css" HREF="./stylesheet.css" TITLE="Style">
+
+<SCRIPT type="text/javascript">
+function windowTitle()
+{
+ parent.document.title="Index";
+}
+</SCRIPT>
+<NOSCRIPT>
+</NOSCRIPT>
+
+</HEAD>
+
+<BODY BGCOLOR="white" onload="windowTitle();">
+
+
+<!-- ========= START OF TOP NAVBAR ======= -->
+<A NAME="navbar_top"><!-- --></A>
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
+<TR>
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./sbml/test/Wizard/package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./sbml/test/Wizard/package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="./help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="./index.html?index-all.html" target="_top"><B>FRAMES</B></A>
+ <A HREF="index-all.html" target="_top"><B>NO FRAMES</B></A>
+ <SCRIPT type="text/javascript">
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="./allclasses-noframe.html"><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+ <A HREF="./allclasses-noframe.html"><B>All Classes</B></A>
+</NOSCRIPT>
+
+
+</FONT></TD>
+</TR>
+</TABLE>
+<A NAME="skip-navbar_top"></A>
+<!-- ========= END OF TOP NAVBAR ========= -->
+
+<A HREF="#_A_">A</A> <A HREF="#_C_">C</A> <A HREF="#_G_">G</A> <A HREF="#_I_">I</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> <HR>
+<A NAME="_A_"><!-- --></A><H2>
+<B>A</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.cancelActionClass</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.finishActionClass</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.nextActionClass</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.previousActionClass</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#addPropertyChangeListener(java.beans.PropertyChangeListener)"><B>addPropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>addPropertyChangeListener - adds a new propertychangelistener
+</DL>
+<HR>
+<A NAME="_C_"><!-- --></A><H2>
+<B>C</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#changeCard(java.lang.String)"><B>changeCard(String)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>changeCard changes the viewable pages on the wizard
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard"><B>ComponentTagsSelectorPanel</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>ComponentTagsSelectorPanel is the class responsible for the component tag selection for the test wizard.<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#ComponentTagsSelectorPanel(sbml.test.Wizard.CreateTestWizard)"><B>ComponentTagsSelectorPanel(CreateTestWizard)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>ComponentTagSelectorPanel has one constructor that initializes the components for the wizard interface
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard"><B>CreateTestWizard</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>CreateTestWizard is the main class for creating a new test wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#CreateTestWizard(sbml.test.TestRunnerView)"><B>CreateTestWizard(TestRunnerView)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>CreateTestWizard constructor initializes componenet for the wizard and adds a listener for the selections
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.cancelActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>cancelActionClass - closes the wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html#CreateTestWizard.cancelActionClass(java.lang.String)"><B>CreateTestWizard.cancelActionClass(String)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.cancelActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.cancelActionClass</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.finishActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>finishActionClass completes the wizard and closes it and passes variables onto the test.<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html#CreateTestWizard.finishActionClass(java.lang.String)"><B>CreateTestWizard.finishActionClass(String)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.finishActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.finishActionClass</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.nextActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>nextActionClass sets the next page on the wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html#CreateTestWizard.nextActionClass(java.lang.String)"><B>CreateTestWizard.nextActionClass(String)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.nextActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.nextActionClass</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html" title="class in sbml.test.Wizard"><B>CreateTestWizard.previousActionClass</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>previousActionClass sets the previous page on the wizard<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html#CreateTestWizard.previousActionClass(java.lang.String)"><B>CreateTestWizard.previousActionClass(String)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.previousActionClass.html" title="class in sbml.test.Wizard">CreateTestWizard.previousActionClass</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_G_"><!-- --></A><H2>
+<B>G</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>getIdentifier
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getInputPath()"><B>getInputPath()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getNext()"><B>getNext()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>getNext
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getNext()"><B>getNext()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getNext()"><B>getNext()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getNext()"><B>getNext()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getNext()"><B>getNext()</B></A> -
+Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getNext()"><B>getNext()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getOutputPath()"><B>getOutputPath()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getPrevious()"><B>getPrevious()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>getPrevious
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getPrevious()"><B>getPrevious()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getPrevious()"><B>getPrevious()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getPrevious()"><B>getPrevious()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getPrevious()"><B>getPrevious()</B></A> -
+Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getPrevious()"><B>getPrevious()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>getQualifiedName
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
+Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getQualifiedName()"><B>getQualifiedName()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#getSelections()"><B>getSelections()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>getSelections gets the selection hashmap
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#getWrapperPath()"><B>getWrapperPath()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_I_"><!-- --></A><H2>
+<B>I</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#initializeSelections(java.util.HashMap)"><B>initializeSelections(HashMap<String, Object>)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>initializeSelections initializes the selection hashmap for the wizard
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#isFirst()"><B>isFirst()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#isFirst()"><B>isFirst()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#isFirst()"><B>isFirst()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#isFirst()"><B>isFirst()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#isFirst()"><B>isFirst()</B></A> -
+Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#isFirst()"><B>isFirst()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#isLast()"><B>isLast()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#isLast()"><B>isLast()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#isLast()"><B>isLast()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#isLast()"><B>isLast()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#isLast()"><B>isLast()</B></A> -
+Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#isLast()"><B>isLast()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#itemStateChanged(java.awt.event.ItemEvent)"><B>itemStateChanged(ItemEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>itemStateChanged is called when the user selects or deselects the checkboxes in the component tag selector panel of the wizard.
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#itemStateChanged(java.awt.event.ItemEvent)"><B>itemStateChanged(ItemEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#itemStateChanged(java.awt.event.ItemEvent)"><B>itemStateChanged(ItemEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#itemStateChanged(java.awt.event.ItemEvent)"><B>itemStateChanged(ItemEvent)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_L_"><!-- --></A><H2>
+<B>L</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard"><B>LevelSelectorPanel</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD>LevelSelectorPanel<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#LevelSelectorPanel(sbml.test.Wizard.CreateTestWizard)"><B>LevelSelectorPanel(CreateTestWizard)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_M_"><!-- --></A><H2>
+<B>M</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#mayFinish()"><B>mayFinish()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#mayFinish()"><B>mayFinish()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#mayFinish()"><B>mayFinish()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#mayFinish()"><B>mayFinish()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WizardPanelInterface.html#mayFinish()"><B>mayFinish()</B></A> -
+Method in interface sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanelInterface.html" title="interface in sbml.test.Wizard">WizardPanelInterface</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html#mayFinish()"><B>mayFinish()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WrapperConfigurationPanel.html" title="class in sbml.test.Wizard">WrapperConfigurationPanel</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_P_"><!-- --></A><H2>
+<B>P</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/WizardPanel.html#propertyChangeSupport"><B>propertyChangeSupport</B></A> -
+Variable in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/WizardPanel.html" title="class in sbml.test.Wizard">WizardPanel</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_R_"><!-- --></A><H2>
+<B>R</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#removePropertyChangeListener(java.beans.PropertyChangeListener)"><B>removePropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>removePropertyChangeListener - removes a propertychangelistener
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#runWizard()"><B>runWizard()</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>runWizard sets the wizard to run
+</DL>
+<HR>
+<A NAME="_S_"><!-- --></A><H2>
+<B>S</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/package-summary.html"><B>sbml.test.Wizard</B></A> - package sbml.test.Wizard<DD> <DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#selections"><B>selections</B></A> -
+Variable in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#selections"><B>selections</B></A> -
+Variable in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#selections"><B>selections</B></A> -
+Variable in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#selections"><B>selections</B></A> -
+Variable in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#setSelections(java.util.HashMap)"><B>setSelections(HashMap<String, Object>)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>setSelections sets the selections hashmap to a new hashmap and fires a property change so that the new map can be validated
+<DT><A HREF="./sbml/test/Wizard/CreateTestWizard.html#shortcutKeyMask"><B>shortcutKeyMask</B></A> -
+Static variable in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/CreateTestWizard.html" title="class in sbml.test.Wizard">CreateTestWizard</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_T_"><!-- --></A><H2>
+<B>T</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard"><B>TestTagSelectionPanel</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD> <DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#TestTagSelectionPanel(sbml.test.Wizard.CreateTestWizard)"><B>TestTagSelectionPanel(CreateTestWizard)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard"><B>TestTypeSelectorPanel</B></A> - Class in <A HREF="./sbml/test/Wizard/package-summary.html">sbml.test.Wizard</A><DD> <DT><A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html#TestTypeSelectorPanel(sbml.test.Wizard.CreateTestWizard)"><B>TestTypeSelectorPanel(CreateTestWizard)</B></A> -
+Constructor for class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTypeSelectorPanel.html" title="class in sbml.test.Wizard">TestTypeSelectorPanel</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_U_"><!-- --></A><H2>
+<B>U</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#updateSelections(java.lang.String, java.lang.Integer)"><B>updateSelections(String, Integer)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html" title="class in sbml.test.Wizard">ComponentTagsSelectorPanel</A>
+<DD>updateSelections updates the selections hashmap that contains all of the tags and test details.
+<DT><A HREF="./sbml/test/Wizard/LevelSelectorPanel.html#updateSelections(java.lang.String, java.lang.Integer)"><B>updateSelections(String, Integer)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/LevelSelectorPanel.html" title="class in sbml.test.Wizard">LevelSelectorPanel</A>
+<DD>
+<DT><A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html#updateSelections(java.lang.String, java.lang.Integer)"><B>updateSelections(String, Integer)</B></A> -
+Method in class sbml.test.Wizard.<A HREF="./sbml/test/Wizard/TestTagSelectionPanel.html" title="class in sbml.test.Wizard">TestTagSelectionPanel</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_V_"><!-- --></A><H2>
+<B>V</B></H2>
+<DL>
+<DT><A HREF="./sbml/test/Wizard/ComponentTagsSelectorPanel.html#validateSelections(java.util.HashMap)"><B>validateSelections(HashMap<String, Object...
[truncated message content] |
|
From: <mh...@us...> - 2008-07-08 21:13:47
|
Revision: 7684
http://sbml.svn.sourceforge.net/sbml/?rev=7684&view=rev
Author: mhucka
Date: 2008-07-08 14:13:45 -0700 (Tue, 08 Jul 2008)
Log Message:
-----------
Changed to use SVN HeadURL instead of CVS Source keyword.
Modified Paths:
--------------
trunk/specifications/sbml-mathml/sbml-mathml.xsd
Modified: trunk/specifications/sbml-mathml/sbml-mathml.xsd
===================================================================
--- trunk/specifications/sbml-mathml/sbml-mathml.xsd 2008-07-08 16:03:06 UTC (rev 7683)
+++ trunk/specifications/sbml-mathml/sbml-mathml.xsd 2008-07-08 21:13:45 UTC (rev 7684)
@@ -5,7 +5,7 @@
* Author(s) : Andrew Finney, Michael Hucka
* Organization: SBML Team <sbm...@ca...>
* Revision : $Id$
- * Source : $Source$
+ * Source : $HeadURL$
*
* Copyright 2003-2006 California Institute of Technology, the Japan Science
* and Technology Corporation, and the University of Hertfordshire.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2008-07-08 16:03:11
|
Revision: 7683
http://sbml.svn.sourceforge.net/sbml/?rev=7683&view=rev
Author: sarahkeating
Date: 2008-07-08 09:03:06 -0700 (Tue, 08 Jul 2008)
Log Message:
-----------
Added check for an id entered as an empty string.
The checkIdSyntax function cannot just check for an empty string as ids are not required on all elements. This check needs to happen directly after the id has been read where you can check if the parser thinks it has assigned a value to the id and whether that value has zero size i.e. it has been entered as id="".
Modified Paths:
--------------
trunk/libsbml/src/sbml/Compartment.cpp
trunk/libsbml/src/sbml/CompartmentType.cpp
trunk/libsbml/src/sbml/Event.cpp
trunk/libsbml/src/sbml/EventAssignment.cpp
trunk/libsbml/src/sbml/FunctionDefinition.cpp
trunk/libsbml/src/sbml/InitialAssignment.cpp
trunk/libsbml/src/sbml/Model.cpp
trunk/libsbml/src/sbml/Parameter.cpp
trunk/libsbml/src/sbml/Reaction.cpp
trunk/libsbml/src/sbml/Rule.cpp
trunk/libsbml/src/sbml/SBase.cpp
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/Species.cpp
trunk/libsbml/src/sbml/SpeciesReference.cpp
trunk/libsbml/src/sbml/SpeciesType.cpp
trunk/libsbml/src/sbml/UnitDefinition.cpp
Added Paths:
-----------
trunk/libsbml/src/validator/test/test-data/10103-fail-01-80.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-81.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-82.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-83.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-84.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-85.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-86.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-87.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-88.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-89.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-90.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-91.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-92.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-93.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-94.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-95.xml
trunk/libsbml/src/validator/test/test-data/10103-fail-01-96.xml
Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/Compartment.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -514,7 +514,11 @@
// id: SId { use="required" } (L2v1, L2v2)
//
const string id = (level == 1) ? "name" : "id";
- attributes.readInto(id, mId, getErrorLog(), true);
+ bool assigned = attributes.readInto(id, mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString(id, level, version, "<compartment>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/CompartmentType.cpp
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/CompartmentType.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -168,7 +168,11 @@
//
// id: SId { use="required" } (L2v2)
//
- attributes.readInto("id", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("id", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("id", level, version, "<compartmentType>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/Event.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -567,7 +567,11 @@
//
// id: SId { use="optional" } (L2v1, L2v2)
//
- attributes.readInto("id", mId, getErrorLog(), false);
+ bool assigned = attributes.readInto("id", mId, getErrorLog(), false);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("id", level, version, "<event>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/EventAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/EventAssignment.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -393,7 +393,11 @@
//
// variable: SId { use="required" } (L2v1, L2v2)
//
- attributes.readInto("variable", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("variable", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("variable", level, version, "<eventAssignment>");
+ }
SBase::checkIdSyntax();
Modified: trunk/libsbml/src/sbml/FunctionDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/FunctionDefinition.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/FunctionDefinition.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -384,7 +384,11 @@
//
// id: SId { use="required" } (L2v1, L2v2)
//
- attributes.readInto("id", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("id", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("id", level, version, "<functionDefinition>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/InitialAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/InitialAssignment.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -385,7 +385,11 @@
//
// symbol: SId { use="required" } (L2v2)
//
- attributes.readInto("symbol", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("symbol", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("symbol", level, version, "<initialAssignment>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/Model.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -2315,7 +2315,11 @@
// id: SId { use="optional" } (L2v1, L2v2)
//
const string id = (level == 1) ? "name" : "id";
- attributes.readInto(id, mId, getErrorLog(), false);
+ bool assigned = attributes.readInto(id, mId, getErrorLog(), false);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString(id, level, version, "<model>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/Parameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/Parameter.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/Parameter.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -358,7 +358,11 @@
// id: SId { use="required" } (L2v1, L2v2)
//
const string id = (level == 1) ? "name" : "id";
- attributes.readInto(id, mId, getErrorLog(), true);
+ bool assigned = attributes.readInto(id, mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString(id, level, version, "<parameter>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/Reaction.cpp
===================================================================
--- trunk/libsbml/src/sbml/Reaction.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/Reaction.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -851,7 +851,11 @@
// id: SId { use="required" } (L2v1, L2v2)
//
const string id = (level == 1) ? "name" : "id";
- attributes.readInto(id, mId, getErrorLog(), true);
+ bool assigned = attributes.readInto(id, mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString(id, level, version, "<rule>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/Rule.cpp
===================================================================
--- trunk/libsbml/src/sbml/Rule.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/Rule.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -719,7 +719,11 @@
// species: SName { use="required" } (L1v2)
//
const string s = (level == 1 && version == 1) ? "specie" : "species";
- attributes.readInto(s, mId, getErrorLog(), true);
+ bool assigned = attributes.readInto(s, mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString(s, level, version, "<rule>");
+ }
SBase::checkIdSyntax();
}
else if ( isCompartmentVolume() )
@@ -727,7 +731,11 @@
//
// compartment: SName { use="required" } (L1v1, L1v2)
//
- attributes.readInto("compartment", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("compartment", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("compartment", level, version, "<rule>");
+ }
SBase::checkIdSyntax();
}
else if ( isParameter() )
@@ -735,7 +743,11 @@
//
// name: SName { use="required" } (L1v1, L1v2)
//
- attributes.readInto("name", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("name", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("name", level, version, "<rule>");
+ }
SBase::checkIdSyntax();
//
@@ -752,7 +764,11 @@
//
// variable: SId { use="required" } (L2v1, L2v2)
//
- attributes.readInto("variable", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("variable", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("variable", level, version, "<rule>");
+ }
SBase::checkIdSyntax();
}
Modified: trunk/libsbml/src/sbml/SBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/SBase.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/SBase.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -1760,6 +1760,28 @@
/** @cond doxygen-libsbml-internal */
/*
+ * Helper to log a common type of error.
+ */
+void
+SBase::logEmptyString( string attribute,
+ const unsigned int level,
+ const unsigned int version,
+ string element )
+
+{
+ ostringstream msg;
+
+ msg << "Attribute '" << attribute << "' on an "
+ << element << " must not be an empty string.";
+
+ getErrorLog()->logError(NotSchemaConformant,
+ level, version, msg.str());
+}
+/** @endcond doxygen-libsbml-internal */
+
+
+/** @cond doxygen-libsbml-internal */
+/*
* Convenience method for easily logging problems from within method
* implementations.
*
@@ -2083,24 +2105,7 @@
if (size == 0)
{
- // Identifiers are not required on the following objects, so it's ok
- // // if they're zero-length.
-
- // if (getTypeCode() == SBML_MODEL
- //|| getTypeCode() == SBML_ALGEBRAIC_RULE
- //|| getTypeCode() == SBML_EVENT
- //|| getTypeCode() == SBML_MODIFIER_SPECIES_REFERENCE
- //|| getTypeCode() == SBML_SPECIES_REFERENCE)
- // {
- return;
- // }
- // else
- // {
- // // This is a schema validation error: no id on an object that needs it.
- // logError(NotSchemaConformant, getLevel(), getVersion(),
- // "Missing 'id' on an element that requires an identifier");
- // return;
- // }
+ return;
}
unsigned int n = 0;
Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/SBase.h 2008-07-08 16:03:06 UTC (rev 7683)
@@ -1180,6 +1180,15 @@
/**
+ * Helper to log a common type of error.
+ */
+ void logEmptyString( std::string attribute,
+ const unsigned int level,
+ const unsigned int version,
+ std::string element);
+
+
+ /**
* Subclasses should override this method to read values from the given
* XMLAttributes set into their specific fields. Be sure to call your
* parents implementation of this method as well.
Modified: trunk/libsbml/src/sbml/Species.cpp
===================================================================
--- trunk/libsbml/src/sbml/Species.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/Species.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -685,7 +685,11 @@
// id: SId { use="required" } (L2v1, L2v2)
//
const string id = (level == 1) ? "name" : "id";
- attributes.readInto(id, mId, getErrorLog(), true);
+ bool assigned = attributes.readInto(id, mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString(id, level, version, "<species>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/SpeciesReference.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesReference.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/SpeciesReference.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -200,7 +200,11 @@
//
// id: SId { use="optional" } (L2v2)
//
- attributes.readInto("id" , mId, getErrorLog());
+ bool assigned = attributes.readInto("id", mId, getErrorLog());
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("id", level, version, "<speciesReference>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/SpeciesType.cpp
===================================================================
--- trunk/libsbml/src/sbml/SpeciesType.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/SpeciesType.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -168,7 +168,11 @@
//
// id: SId { use="required" } (L2v2)
//
- attributes.readInto("id", mId, getErrorLog(), true);
+ bool assigned = attributes.readInto("id", mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString("id", level, version, "<speciesType>");
+ }
SBase::checkIdSyntax();
//
Modified: trunk/libsbml/src/sbml/UnitDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/UnitDefinition.cpp 2008-07-07 18:33:25 UTC (rev 7682)
+++ trunk/libsbml/src/sbml/UnitDefinition.cpp 2008-07-08 16:03:06 UTC (rev 7683)
@@ -906,7 +906,11 @@
// id: SId { use="required" } (L2v1, L2v2)
//
const string id = (level == 1) ? "name" : "id";
- attributes.readInto(id, mId, getErrorLog(), true);
+ bool assigned = attributes.readInto(id, mId, getErrorLog(), true);
+ if (assigned && mId.size() == 0)
+ {
+ logEmptyString(id, level, version, "<unitDefinition>");
+ }
SBase::checkIdSyntax();
//
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-80.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-80.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-80.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+ <model>
+ <listOfCompartments>
+ <compartment id="" size="1"/>
+ </listOfCompartments>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-81.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-81.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-81.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+ <model>
+ <listOfCompartmentTypes>
+ <compartmentType id=""/>
+ </listOfCompartmentTypes>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-82.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-82.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-82.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--
+Pass: (1803) A Compartment, Species, or Parameter referenced by an
+EventAssignment must have constant='false'.
+-->
+
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment id="c" constant="false"/>
+ </listOfCompartments>
+ <listOfEvents>
+ <event id="">
+ <trigger>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply> <neq/> <cn> 1 </cn> <cn> 2 </cn> </apply>
+ </math>
+ </trigger>
+ <listOfEventAssignments>
+ <eventAssignment variable="c"/>
+ </listOfEventAssignments>
+ </event>
+ </listOfEvents>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-83.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-83.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-83.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--
+Pass: (1803) A Compartment, Species, or Parameter referenced by an
+EventAssignment must have constant='false'.
+-->
+
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment id="c" constant="false"/>
+ </listOfCompartments>
+ <listOfEvents>
+ <event id="e">
+ <trigger>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply> <neq/> <cn> 1 </cn> <cn> 2 </cn> </apply>
+ </math>
+ </trigger>
+ <listOfEventAssignments>
+ <eventAssignment variable=""/>
+ </listOfEventAssignments>
+ </event>
+ </listOfEvents>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-84.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-84.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-84.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfFunctionDefinitions>
+ <functionDefinition id="">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar><ci> x </ci></bvar>
+ <apply>
+ <power/> <ci> x </ci> <cn> 3 </cn>
+ </apply>
+ </lambda>
+ </math>
+ </functionDefinition>
+ </listOfFunctionDefinitions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-85.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-85.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-85.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--
+Fail: (1900) An InitialAssignment's symbol must be the id of a Compartment,
+Species, or Parameter.
+-->
+
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" level="2" version="2">
+ <model>
+ <listOfCompartments>
+ <compartment id="c" constant="false"/>
+ </listOfCompartments>
+ <listOfInitialAssignments>
+ <initialAssignment symbol=""/>
+ </listOfInitialAssignments>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-86.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-86.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-86.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3"
+ xmlns:xhtml="http://www.w3.org/1999/xhtml">
+ <model id="">
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-87.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-87.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-87.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfParameters>
+ <parameter id="" units="ampere"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-88.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-88.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-88.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3"
+ xmlns:xhtml="http://www.w3.org/1999/xhtml">
+ <model>
+ <listOfUnitDefinitions>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit kind="mole" scale="-3"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="mmls">
+ <listOfUnits>
+ <unit kind="mole" scale="-3"/>
+ <unit kind="litre" exponent="-1"/>
+ <unit kind="second" exponent="-1"/>
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="mml">
+ <listOfUnits>
+ <unit kind="mole" scale="-3"/>
+ <unit kind="litre" exponent="-1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="cell" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="x0" compartment="cell" initialConcentration="1"/>
+ <species id="x1" compartment="cell" initialConcentration="1"/>
+ <species id="s1" compartment="cell" initialConcentration="1"/>
+ <species id="s2" compartment="cell" initialConcentration="1"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="vm" value="2" units="mmls"/>
+ <parameter id="km" value="2" units="mml"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="">
+ <listOfReactants>
+ <speciesReference species="x0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <notes>
+ <xhtml:p>((vm * s1)/(km + s1))*cell</xhtml:p>
+ </notes>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <ci> vm </ci>
+ <ci> s1 </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <ci> km </ci>
+ <ci> s1 </ci>
+ </apply>
+ </apply>
+ <ci> cell </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-89.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-89.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-89.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment id="c" constant="false"/>
+ </listOfCompartments>
+ <listOfRules>
+ <assignmentRule variable=""/>
+ </listOfRules>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-90.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-90.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-90.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+Pass: (1700) An AssignmentRule's variable must be the id of a Compartment,
+Species, or Parameter.
+-->
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <specie name="s" compartment="c" initialAmount="0"/>
+ </listOfSpecies>
+ <listOfRules>
+ <compartmentVolumeRule compartment="" formula="c"/>
+ </listOfRules>
+ <listOfReactions>
+ <reaction name="r">
+ <listOfReactants>
+ <specieReference specie="s"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-91.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-91.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-91.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+Pass: (1700) An AssignmentRule's variable must be the id of a Compartment,
+Species, or Parameter.
+-->
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <specie name="s" compartment="c" initialAmount="0"/>
+ <specie name="s1" compartment="c" initialAmount="0"/>
+ </listOfSpecies>
+ <listOfRules>
+ <specieConcentrationRule specie="" formula="s"/>
+ </listOfRules>
+ <listOfReactions>
+ <reaction name="r">
+ <listOfReactants>
+ <specieReference specie="s"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-92.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-92.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-92.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+Pass: (1700) An AssignmentRule's variable must be the id of a Compartment,
+Species, or Parameter.
+-->
+<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="1">
+ <model>
+ <listOfCompartments>
+ <compartment name="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <specie name="s" compartment="c" initialAmount="0"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter name="p" value="2"/>
+ </listOfParameters>
+ <listOfRules>
+ <parameterRule name="" formula="3"/>
+ </listOfRules>
+ <listOfReactions>
+ <reaction name="r">
+ <listOfReactants>
+ <specieReference specie="s"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-93.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-93.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-93.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3"
+ xmlns:xhtml="http://www.w3.org/1999/xhtml">
+ <model id="unitsexample">
+ <listOfCompartments>
+ <compartment id="cell" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="" compartment="cell" initialConcentration="1"/>
+ </listOfSpecies>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-94.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-94.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-94.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--
+Pass: (1600) A Reaction must contain at least one SpeciesReference in
+its list of reactants or products.
+-->
+
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
+ <model>
+ <listOfCompartments>
+ <compartment id="c"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="s" compartment="c"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="r">
+ <listOfReactants>
+ <speciesReference id="" species="s"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-95.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-95.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-95.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3"
+ xmlns:xhtml="http://www.w3.org/1999/xhtml">
+ <model id="unitsexample">
+ <listOfSpeciesTypes>
+ <speciesType id=""/>
+ </listOfSpeciesTypes>
+ </model>
+</sbml>
Added: trunk/libsbml/src/validator/test/test-data/10103-fail-01-96.xml
===================================================================
--- trunk/libsbml/src/validator/test/test-data/10103-fail-01-96.xml (rev 0)
+++ trunk/libsbml/src/validator/test/test-data/10103-fail-01-96.xml 2008-07-08 16:03:06 UTC (rev 7683)
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3"
+ xmlns:xhtml="http://www.w3.org/1999/xhtml">
+ <model>
+ <listOfUnitDefinitions>
+ <unitDefinition id="">
+ <listOfUnits>
+ <unit kind="mole" scale="-3"/>
+ <unit kind="litre" exponent="-1"/>
+ <unit kind="second" exponent="-1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ </model>
+</sbml>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: Sarah K. <ske...@ca...> - 2008-07-07 18:34:23
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From: <sar...@us...> - 2008-07-07 18:33:27
|
Revision: 7682
http://sbml.svn.sourceforge.net/sbml/?rev=7682&view=rev
Author: sarahkeating
Date: 2008-07-07 11:33:25 -0700 (Mon, 07 Jul 2008)
Log Message:
-----------
changed name as Tags was not a good name in SVN
Modified Paths:
--------------
trunk/test-suite/src/TestTags/Tags_on_semantic_cases.xls
Added Paths:
-----------
trunk/test-suite/src/TestTags/
Copied: trunk/test-suite/src/TestTags (from rev 7681, trunk/test-suite/src/Tags)
Modified: trunk/test-suite/src/TestTags/Tags_on_semantic_cases.xls
===================================================================
(Binary files differ)
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From: Sarah K. <ske...@ca...> - 2008-07-07 11:52:01
|
1 message has been excluded from this view by a project administrator.
