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Commit ada215f

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author
Hernan Morales
committed
Add MultiQC wrapper + tests
Complete MAFFT wrapper. Add tests Fix requestDirectoryPath
1 parent 2dae8b5 commit ada215f

10 files changed

Lines changed: 1281 additions & 34 deletions

‎repository/BioNGS/BioMultiQCWrapper.class.st‎

Lines changed: 456 additions & 0 deletions
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‎repository/BioPharo7/BioObject.extension.st‎

Lines changed: 11 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,21 +1,20 @@
1-
Extension { #name : #BioObject }
1+
Extension { #name : 'BioObject' }
22

3-
{ #category : #'*BioPharo7' }
3+
{ #category : '*BioPharo7' }
44
BioObject class >> requestDirectoryPath [
55
" Answer a <FileReference> with selected directory "
66

7-
| tmpFileDialog |
8-
tmpFileDialog := FileDialogWindow basicNew
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initialize;
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title: 'Select a directory';
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answerDirectory;
7+
| reference |
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StOpenDirectoryPresenter new
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openFolder: FileLocator workingDirectory;
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title: 'Choose directory';
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okAction: [ :directoryReference | reference := directoryReference ];
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openModal.
13-
tmpFileDialog isNil ifTrue: [ self error: 'FileDialogWindow is broken' ].
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^ tmpFileDialog answer "pathString"
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^ reference
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]
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{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
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BioObject class >> requestOpenCSVFile [
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" Open request dialog to select a CSV file "
2120

@@ -24,7 +23,7 @@ BioObject class >> requestOpenCSVFile [
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label: 'Choose CSV file'
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]
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27-
{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
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BioObject class >> requestOpenFASTAFile [
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" Open request dialog to select a FASTA file "
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@@ -33,7 +32,7 @@ BioObject class >> requestOpenFASTAFile [
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label: 'Choose FASTA file'
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]
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36-
{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
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BioObject class >> requestOpenXMLFile [
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" Open request dialog to select a XML file "
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‎repository/BioPharo7/ZipArchiveMember.extension.st‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
1-
Extension { #name : #ZipArchiveMember }
1+
Extension { #name : 'ZipArchiveMember' }
22

3-
{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
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ZipArchiveMember >> extractInDirectory: aDirectory overwrite: overwriteAll [
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"Extract this entry into the given directory. Answer #okay, #failed, #abort, or #retryWithOverwrite."
66
| path fileDir file localName |

‎repository/BioPharo7/ZnBufferedReadStream.extension.st‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
1-
Extension { #name : #ZnBufferedReadStream }
1+
Extension { #name : 'ZnBufferedReadStream' }
22

3-
{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
44
ZnBufferedReadStream >> name [
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" Answer a <String> identifying the receiver "
66

77
^ self wrappedStream name.
88
]
99

10-
{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
1111
ZnBufferedReadStream >> reset [
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stream reset.

‎repository/BioPharo7/ZnCharacterReadStream.extension.st‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
1-
Extension { #name : #ZnCharacterReadStream }
1+
Extension { #name : 'ZnCharacterReadStream' }
22

3-
{ #category : #'*BioPharo7' }
3+
{ #category : '*BioPharo7' }
44
ZnCharacterReadStream >> blastXMLDtdLocations [
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" Answer a <Collection> of known NCBI Blast Output DTD locations "
66

@@ -9,7 +9,7 @@ ZnCharacterReadStream >> blastXMLDtdLocations [
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with: '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">'
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]
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{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
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ZnCharacterReadStream >> isBlastXMLFormat [
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" Only answer <true> when the receiver's contents *looks like* a NCBI Blast format, not performing any validity check "
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@@ -19,7 +19,7 @@ ZnCharacterReadStream >> isBlastXMLFormat [
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^ answer
2020
]
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22-
{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
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ZnCharacterReadStream >> isGenBankFlatFormat [
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" Only answer <true> when the receiver's contents *looks like* a GenBank flat format, not performing any validity check "
2525

@@ -35,7 +35,7 @@ ZnCharacterReadStream >> isGenBankFlatFormat [
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^ flatSignature beginsWith: 'LOCUS '
3636
]
3737

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{ #category : #'*BioPharo7' }
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{ #category : '*BioPharo7' }
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ZnCharacterReadStream >> isXML [
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" See superimplementor's comment "
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@@ -51,13 +51,13 @@ ZnCharacterReadStream >> isXML [
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^ xmlSignature isXML
5252
]
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54-
{ #category : #'*BioPharo7' }
54+
{ #category : '*BioPharo7' }
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ZnCharacterReadStream >> name [
5656

5757
^ self wrappedStream name
5858
]
5959

60-
{ #category : #'*BioPharo7' }
60+
{ #category : '*BioPharo7' }
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ZnCharacterReadStream >> nextMatchAll: aColl [
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"Answer true if next N objects are the ones in aColl,
6363
else false. Advance stream of true, leave as was if false."
@@ -71,14 +71,14 @@ ZnCharacterReadStream >> nextMatchAll: aColl [
7171
^ true
7272
]
7373

74-
{ #category : #'*BioPharo7' }
74+
{ #category : '*BioPharo7' }
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ZnCharacterReadStream >> nextMatchAllAnyOf: aCollection [
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^ aCollection anySatisfy: [ : subCol | self nextMatchAll: subCol ].
7878

7979
]
8080

81-
{ #category : #'*BioPharo7' }
81+
{ #category : '*BioPharo7' }
8282
ZnCharacterReadStream >> readStream [
8383
" Compatibility with SAXParser "
8484

‎repository/BioPharo7/ZnEncodedStream.extension.st‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
1-
Extension { #name : #ZnEncodedStream }
1+
Extension { #name : 'ZnEncodedStream' }
22

3-
{ #category : #'*BioPharo7' }
3+
{ #category : '*BioPharo7' }
44
ZnEncodedStream >> nextPutTerminator [
55
" Append a line ending terminator to the receiver "
66

77
self wrappedStream nextPutAll: (String perform: self platformTerminator)
88
]
99

10-
{ #category : #'*BioPharo7' }
10+
{ #category : '*BioPharo7' }
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ZnEncodedStream >> reset [
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self position: 0

‎repository/BioPharo7/package.st‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
Package { #name : #BioPharo7 }
1+
Package { #name : 'BioPharo7' }

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