Directory BioTools/src/biotools/calc/

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vloux 2008-02-22 18:21

Fixed parsing bug in Interpro results

27 lines of code changed in:

• BioTools/src/biotools/calc: INTERPROText.java (+27 -12)

vloux 2007-02-07 14:49

Added classes to manage goterms, keywords and origin of a match.

5 lines of code changed in:

• BioTools/src/biotools/calc: HomologyResult.java (+5 -1)

vloux 2007-01-24 18:09

Added classes to manage goterms, keywords and origin of a match.
Display of origin in table and graphics

100 lines of code changed in:

• BioTools/src/biotools/calc: HomologyMatch.java (+93 -1), HomologyMatchPair.java (+6 -1), HomologyResult.java (+1 -1)

vloux 2006-10-31 16:43

Various test backbones
Added a test (BioToolsTest) that check the avalaibility of the executables described in ./biotool.props
Changed build.xml to run the proper test.
ATTN problem with Ant classloading -> ant must be launched with -lib and path to ant-junit.jar and junit.jar OR , in case of eclipse, those two modules have to be added on the ant classpath

9 lines of code changed in:

• BioTools/src/biotools/calc: INTERPROText.java (+9 -7)

vloux 2006-02-03 17:43

[#189]

Tests Biotools (encore du chemin ...)
Ajout fichiers input
Extension tests

Logging avec log4j

115 lines of code changed in:

• BioTools/src/biotools/calc: BioCalc.java (+2 -2), PSORTCalc.java (new 55), PSORTParams.java (new 58), SingleInOutTest.java (del)

vloux 2006-02-01 16:39

Ajout Psort (Feature Request #188).
Modifs BioTools
Test basique sur sortie "long" Gram+ et Gram-

357 lines of code changed in:

• BioTools/src/biotools/calc: PSORTText.java (+357 -37)

vloux 2005-10-20 17:01

BugFixes :
#130 Bug Parsing CDD
#132 Passage ? Interpro V4

Ajouts de tests (en cours):
CDD
Interpro
memsat
psort

321 lines of code changed in:

• BioTools/src/biotools/calc: BioCalc.java (+22 -3), CDDText.java (+19 -14), COILCalc.java (+1 -1), COILParams.java (+1 -2), CalcParams.java (-1), FROSTText.java (+11 -5), HomologyMatchPair.java (+16 -16), INTERPROCalc.java (+81 -40), INTERPROParams.java (+16 -2), INTERPROText.java (+7 -7), MEMSATText.java (+31 -31), PSORTText.java (new 116)

vloux 2005-09-14 15:41

Package Reorganisation :
Tests in a separate folder but still belong to the same package.

0 lines of code changed in:

• BioTools/src/biotools/calc: BLASTTest.java (del)

vloux 2005-09-01 17:00

PAM Summer cleaning

DBPooling with apache dbpc and jni.

PAM refactoring :
moving all select/update/insert statement into proteindb package :

reader/HomologyAlignPanel.java OK(1)(2)
reader/HomologyImagePanel.java OK(1)(2)
reader/HomologyPanel.java OK(1)(2)

reader/ProteinPanel.java OK (1),(2)

reader/QueryDataSets.java OK(1)
reader/QueryProteins.java OK(1)
reader/QueryProteinSources.java OK(1)

reader/SearchDataSets.java OK
reader/SearchProteinSources.javaOK
reader/SearchResults.java TODO (Need to reorganize the search ->
will be done at that moment)


admin/MonitorProteinRefTasks.java OK(1),(3)
admin/MonitorProteinTasks.java OK(1)
admin/MonitorTasks.java OK(1)
admin/RetireProteins.java OK(1)
admin/ShowAddProteins.java OK
admin/ShowRetireProteins.java OK

control/AfterActionMotivation.java OK
control/DetermineFunctionAction.java OK(1)
control/HomologyResultsMotivation.java OK(1)
control/NotifyFunctionMotivation.java OK
control/ParalogResultsMotivation.java DELETED
control/ProteinActionMotivation.java OK
control/ProteinActionQueue.java OK
control/ProteinRefActionQueue.java OK
control/SwissAnnotAction.java OK

(1)new methods in ProteinDB
(2) new DTO classes
(3) new classes in proteinDB

203 lines of code changed in:

• BioTools/src/biotools/calc: BLASTTest.java (new), CalcException.java (+18 -13), HomologyMatch.java (+84 -30), HomologyMatchPair.java (+72 -65), HomologyResult.java (+29 -25)

vloux 2005-08-09 11:22

Formatage code

2685 lines of code changed in:

• BioTools/src/biotools/calc: Aln2FreqCalc.java (+7 -11), Aln2FreqParams.java (+16 -20), BLASTCalc.java (+19 -24), BLASTParams.java (+10 -12), BLASTText.java (+233 -227), BioCalc.java (+234 -248), CDDCalc.java (+20 -24), CDDParams.java (+8 -10), CDDText.java (+206 -203), CLUSTALWCalc.java (+14 -15), CLUSTALWParams.java (+15 -12), COILCalc.java (+19 -21), COILParams.java (+16 -18), COILText.java (+62 -62), CalcException.java (+15 -15), CalcParams.java (+73 -84), CalcResult.java (+2 -4), CalcResults.java (+17 -20), DoubleInSingleOut.java (+11 -11), FROSTCalc.java (+21 -25), FROSTParams.java (+9 -11), FROSTText.java (+89 -87), FileParameter.java (+6 -10), FileResult.java (+5 -8), FloatResult.java (+2 -6), HomologyMatch.java (+30 -32), HomologyMatchPair.java (+63 -64), HomologyResult.java (+25 -29), INTERPROCalc.java (+101 -104), INTERPROParams.java (+32 -29), INTERPROText.java (+117 -107), MEMSATCalc.java (+52 -58), MEMSATParams.java (+12 -16), MEMSATText.java (+101 -97), MULSATCalc.java (+20 -21), MULSATParams.java (+12 -16), MotifSpan.java (+21 -23), NucleicFeaturesResult.java (+6 -6), PICalc.java (+19 -20), PIParams.java (+9 -11), PIText.java (+31 -31), PetrinCalc.java (+26 -27), PetrinEntry.java (+4 -8), PetrinParams.java (+13 -17), PetrinText.java (+76 -75), ProfileFastAText.java (+77 -76), ProteinFeaturesResult.java (+15 -15), RRNAScanCalc.java (+27 -28), RRNAScanEntry.java (+23 -27), RRNAScanParams.java (+13 -17), RRNAScanText.java (+77 -74), ResultEntry.java (+16 -16), ResultEntryPosn.java (+11 -12), ResultText.java (+30 -32), SEGCalc.java (+22 -26), SEGParams.java (+14 -18), SEGText.java (+45 -45), SHOWCalc.java (+22 -24), SHOWEntry.java (+4 -9), SHOWParams.java (+13 -17), SHOWText.java (+76 -74), SIGSEQCalc.java (+19 -19), SIGSEQParams.java (+13 -17), SIGSEQText.java (+55 -54), SingleInOut.java (+10 -11), SingleInOutTest.java (+30 -21), SingleProfileResult.java (+33 -39), TMSpan.java (+13 -15), TRNAScanCalc.java (+26 -27), TRNAScanEntry.java (+4 -8), TRNAScanParams.java (+13 -17), TRNAScanText.java (+77 -75), ValuedSpan.java (+8 -10)

vloux 2005-08-09 11:09

BioTools :
+ ClustalWCalc
Modifications Location

Tests :
SingleInOutTest
NucleicPackageTest
NucleicTest

129 lines of code changed in:

• BioTools/src/biotools/calc: BioCalc.java (+2 -2), CLUSTALWCalc.java (new 51), CLUSTALWParams.java (new 55), SingleInOutTest.java (new 21)

vloux 2005-04-20 13:43

boolean NucleicFeature.existQualifier
Nettoyage du code.

409 lines of code changed in:

• BioTools/src/biotools/calc: BioCalc.java (+35 -12), CalcParams.java (+16 -2), CalcResults.java (+4 -1), FileParameter.java (+25 -3), FileResult.java (+25 -3), FloatResult.java (+40 -5), HomologyMatch.java (+23 -4), HomologyMatchPair.java (+34 -7), HomologyResult.java (+7), MotifSpan.java (+15 -3), NucleicFeaturesResult.java (+35 -6), ProteinFeaturesResult.java (+6), ResultEntry.java (+6 -1), ResultEntryPosn.java (+42 -14), ResultText.java (+19 -4), SingleProfileResult.java (+47 -7), ValuedSpan.java (+30 -4)

agmial 2005-04-13 15:30

J'ai enlev? des System.err/out.println qui polluaient les logs...

1 lines of code changed in:

• BioTools/src/biotools/calc: BioCalc.java (+1 -1), FROSTText.java (-2)

vloux 2005-04-11 14:43

Nettoyage du code : imports, methodes deprecated ...

117 lines of code changed in:

• BioTools/src/biotools/calc: Aln2FreqCalc.java (-6), Aln2FreqParams.java (-1), BLASTCalc.java (+2 -6), BLASTParams.java (-1), BLASTText.java (+5 -5), CDDCalc.java (+2 -6), CDDParams.java (-1), CDDText.java (+5 -5), COILCalc.java (+2 -6), COILParams.java (-1), COILText.java (+8 -4), CalcResult.java (-2), DoubleInSingleOut.java (-1), FROSTCalc.java (+2 -6), FROSTParams.java (-1), FROSTText.java (+5 -5), FileParameter.java (-1), FloatResult.java (-1), HomologyMatch.java (+1 -5), HomologyMatchPair.java (-3), HomologyResult.java (+2 -5), INTERPROCalc.java (+10 -7), INTERPROParams.java (-1), INTERPROText.java (+6 -4), MEMSATCalc.java (+6 -5), MEMSATParams.java (-1), MULSATCalc.java (+2 -6), MULSATParams.java (-1), MotifSpan.java (+1 -3), NucleicFeaturesResult.java (+1 -2), PICalc.java (+2 -6), PIParams.java (-1), PIText.java (+3 -4), PetrinCalc.java (+3 -6), PetrinParams.java (-1), PetrinText.java (+4 -4), ProfileFastAText.java (+7 -3), ProteinFeaturesResult.java (+1 -2), RRNAScanCalc.java (+3 -6), RRNAScanParams.java (-1), RRNAScanText.java (+4 -4), ResultEntry.java (+1 -3), ResultEntryPosn.java (-4), SEGCalc.java (+2 -6), SEGParams.java (-1), SEGText.java (+4 -4), SHOWCalc.java (+3 -6), SHOWParams.java (-1), SHOWText.java (+4 -4), SIGSEQCalc.java (+2 -6), SIGSEQParams.java (-1), SIGSEQText.java (+6 -5), SingleInOut.java (-1), TMSpan.java (-3), TRNAScanCalc.java (+3 -6), TRNAScanParams.java (-1), TRNAScanText.java (+4 -4), ValuedSpan.java (+1 -3)

agmial 2005-04-08 17:58

Parametres de FROST ... + petite boulette dans SIGSEQCalc

6 lines of code changed in:

• BioTools/src/biotools/calc: FROSTCalc.java (+4 -2), FROSTParams.java (+1 -1), SIGSEQCalc.java (+1 -1)

agmial 2005-04-08 13:44

Ajout de FROST dans biotools.calc
J'ai du ajouter quelques membres dans la classe HomologyMatchPair pour mettre les informations sur la structure

RB

265 lines of code changed in:

• BioTools/src/biotools/calc: FROSTCalc.java (new 49), FROSTParams.java (new 38), FROSTText.java (new 125), HomologyMatchPair.java (+53 -14)

vloux 2005-04-05 09:02

effac?s par erreur

5160 lines of code changed in:

• BioTools/src/biotools/calc: Aln2FreqCalc.java (new 32), Aln2FreqParams.java (new 50), BLASTCalc.java (new 50), BLASTParams.java (new 37), BLASTText.java (new 301), BioCalc.java (new 386), CDDCalc.java (new 50), CDDParams.java (new 37), CDDText.java (new 286), COILCalc.java (new 46), COILParams.java (new 46), COILText.java (new 89), CalcException.java (new 26), CalcParams.java (new 172), CalcResult.java (new 14), CalcResults.java (new 59), DoubleInSingleOut.java (new 26), FileParameter.java (new 39), FileResult.java (new 37), FloatResult.java (new 42), HomologyMatch.java (new 102), HomologyMatchPair.java (new 163), HomologyResult.java (new 70), INTERPROCalc.java (new 144), INTERPROParams.java (new 57), INTERPROText.java (new 177), MEMSATCalc.java (new 107), MEMSATParams.java (new 41), MEMSATText.java (new 123), MULSATCalc.java (new 46), MULSATParams.java (new 41), MotifSpan.java (new 97), NucleicFeaturesResult.java (new 64), PICalc.java (new 46), PIParams.java (new 37), PIText.java (new 46), PetrinCalc.java (new 56), PetrinEntry.java (new 54), PetrinParams.java (new 45), PetrinText.java (new 109), ProfileFastAText.java (new 123), ProteinFeaturesResult.java (new 42), RRNAScanCalc.java (new 57), RRNAScanEntry.java (new 54), RRNAScanParams.java (new 45), RRNAScanText.java (new 108), ResultEntry.java (new 52), ResultEntryPosn.java (new 42), ResultText.java (new 70), SEGCalc.java (new 51), SEGParams.java (new 46), SEGText.java (new 81), SHOWCalc.java (new 53), SHOWEntry.java (new 56), SHOWParams.java (new 42), SHOWText.java (new 108), SIGSEQCalc.java (new 45), SIGSEQParams.java (new 41), SIGSEQText.java (new 98), SingleInOut.java (new 27), SingleProfileResult.java (new 109), TMSpan.java (new 44), TRNAScanCalc.java (new 56), TRNAScanEntry.java (new 54), TRNAScanParams.java (new 45), TRNAScanText.java (new 109), ValuedSpan.java (new 52)

vloux 2005-04-04 15:26

Bugfixes

0 lines of code changed in:

• BioTools/src/biotools/calc: Aln2FreqCalc.java (del), Aln2FreqParams.java (del), BLASTCalc.java (del), BLASTParams.java (del), BLASTText.java (del), BioCalc.java (del), CDDCalc.java (del), CDDParams.java (del), CDDText.java (del), COILCalc.java (del), COILParams.java (del), COILText.java (del), CalcException.java (del), CalcParams.java (del), CalcResult.java (del), CalcResults.java (del), DoubleInSingleOut.java (del), FileParameter.java (del), FileResult.java (del), FloatResult.java (del), HomologyMatch.java (del), HomologyMatchPair.java (del), HomologyResult.java (del), INTERPROCalc.java (del), INTERPROParams.java (del), INTERPROText.java (del), MEMSATCalc.java (del), MEMSATParams.java (del), MEMSATText.java (del), MULSATCalc.java (del), MULSATParams.java (del), MotifSpan.java (del), NucleicFeaturesResult.java (del), PICalc.java (del), PIParams.java (del), PIText.java (del), PetrinCalc.java (del), PetrinEntry.java (del), PetrinParams.java (del), PetrinText.java (del), ProfileFastAText.java (del), ProteinFeaturesResult.java (del), README (del), RRNAScanCalc.java (del), RRNAScanEntry.java (del), RRNAScanParams.java (del), RRNAScanText.java (del), ResultEntry.java (del), ResultEntryPosn.java (del), ResultText.java (del), SEGCalc.java (del), SEGParams.java (del), SEGText.java (del), SHOWCalc.java (del), SHOWEntry.java (del), SHOWParams.java (del), SHOWText.java (del), SIGSEQCalc.java (del), SIGSEQParams.java (del), SIGSEQText.java (del), SingleInOut.java (del), SingleProfileResult.java (del), TMSpan.java (del), TRNAScanCalc.java (del), TRNAScanEntry.java (del), TRNAScanParams.java (del), TRNAScanText.java (del), ValuedSpan.java (del)

rbossy 2004-09-29 16:40

Initial revision

5160 lines of code changed in:

• BioTools/src/biotools/calc: Aln2FreqCalc.java (new 32), Aln2FreqParams.java (new 50), BLASTCalc.java (new 50), BLASTParams.java (new 37), BLASTText.java (new 301), BioCalc.java (new 386), CDDCalc.java (new 50), CDDParams.java (new 37), CDDText.java (new 286), COILCalc.java (new 46), COILParams.java (new 46), COILText.java (new 89), CalcException.java (new 26), CalcParams.java (new 172), CalcResult.java (new 14), CalcResults.java (new 59), DoubleInSingleOut.java (new 26), FileParameter.java (new 39), FileResult.java (new 37), FloatResult.java (new 42), HomologyMatch.java (new 102), HomologyMatchPair.java (new 163), HomologyResult.java (new 70), INTERPROCalc.java (new 144), INTERPROParams.java (new 57), INTERPROText.java (new 177), MEMSATCalc.java (new 107), MEMSATParams.java (new 41), MEMSATText.java (new 123), MULSATCalc.java (new 46), MULSATParams.java (new 41), MotifSpan.java (new 97), NucleicFeaturesResult.java (new 64), PICalc.java (new 46), PIParams.java (new 37), PIText.java (new 46), PetrinCalc.java (new 56), PetrinEntry.java (new 54), PetrinParams.java (new 45), PetrinText.java (new 109), ProfileFastAText.java (new 123), ProteinFeaturesResult.java (new 42), README (new), RRNAScanCalc.java (new 57), RRNAScanEntry.java (new 54), RRNAScanParams.java (new 45), RRNAScanText.java (new 108), ResultEntry.java (new 52), ResultEntryPosn.java (new 42), ResultText.java (new 70), SEGCalc.java (new 51), SEGParams.java (new 46), SEGText.java (new 81), SHOWCalc.java (new 53), SHOWEntry.java (new 56), SHOWParams.java (new 42), SHOWText.java (new 108), SIGSEQCalc.java (new 45), SIGSEQParams.java (new 41), SIGSEQText.java (new 98), SingleInOut.java (new 27), SingleProfileResult.java (new 109), TMSpan.java (new 44), TRNAScanCalc.java (new 56), TRNAScanEntry.java (new 54), TRNAScanParams.java (new 45), TRNAScanText.java (new 109), ValuedSpan.java (new 52)