CR-JAL-8 JAL-2344: Refactor file format options as interfaces instead of text strings

closed on 07 Feb 17

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JAL-2344: Refactor file format options as interfaces instead of text strings

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General Comments 2
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Resolved
Number of files included: 46

jalview 0
- Folder examples/groovy 0
  - File fileFormat.groovy 0 Remove
- Folder src 0
  - Folder MCview 0
    - File PDBViewer.java 0 Remove
  - Folder jalview 0
    - Folder appletgui 0
      - File APopupMenu.java 0 Remove
      - File AlignFrame.java 0 Remove
      - File CutAndPasteTransfer.java 0 Remove
    - Folder bin 0
      - File JalviewLite.java 0 Remove
      - File JalviewLiteURLRetrieve.java 0 Remove
    - Folder datamodel 0
      - File PDBEntry.java 1 Remove
    - Folder gui 0
      - File AlignFrame.java 0 Remove
      - File CutAndPasteTransfer.java 0 Remove
      - File Desktop.java 0 Remove
      - File FeatureSettings.java 0 Remove
      - File PopupMenu.java 0 Remove
      - File Preferences.java 0 Remove
      - File TreePanel.java 0 Remove
      - File UserDefinedColours.java 0 Remove
      - File WsParamSetManager.java 0 Remove
    - Folder io 0
      - File AlignFile.java 0 Remove
      - File AlignmentFileI.java 0 Remove
      - File AlignmentFileReaderI.java 0 Remove
      - File AlignmentFileWriterI.java 0 Remove
      - File AppletFormatAdapter.java 0 Remove
      - File FileFormat.java 0 Remove
      - File FileFormatI.java 0 Remove
      - File FileFormats.java 0 Remove
      - File FileLoader.java 0 Remove
      - File FormatAdapter.java 0 Remove
      - File HTMLOutput.java 0 Remove
      - File HtmlSvgOutput.java 0 Remove
      - File IdentifyFile.java 0 Remove
      - File JalviewFileChooser.java 4 Remove
      - File JalviewFileView.java 0 Remove
      - File StructureFile.java 0 Remove
    - Folder jbgui 0
      - File GAlignFrame.java 0 Remove
    - Folder util 0
      - File ImageMaker.java 0 Remove
    - Folder ws 0
      - Folder dbsources 0
        
        File EmblXmlSource.java 0 Remove
        
        File Pdb.java 2 Remove
        
        File Uniprot.java 0 Remove
      - Folder ebi 0
        
        File EBIFetchClient.java 0 Remove
      - Folder jws1 0
        
        File JPredThread.java 0 Remove
      - Folder rest/params 0
        
        File Alignment.java 2 Remove
- Folder test/jalview 0
  - Folder io 0
    - File FileFormatsTest.java 2 Remove
    - File FormatAdapterTest.java 0 Remove
  - Folder ws/jabaws 0
    - File DisorderAnnotExportImport.java 0 Remove
    - File JpredJabaStructExportImport.java 0 Remove
    - File RNAStructExportImport.java 0 Remove

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Participant	Role	Time Spent	Comments	Latest Comment
Mungo Carstairs	Author	48m	6	1) AlignFrame.outputFeatures() - format parameter here is...
Kira Mourão	Reviewer - Complete	2m	7	Needs to be resolved
Total		50m	13

Linked Issue:
JAL-2344

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Objectives

Currently, supported file formats are handled as text strings (constants in AppletFormatAdapter).
This is fragile (updates needed in several places for a new format), verbose (if-then-else statements), not type safe, does not support plug-in of additional formats.

Enhance the code to use interfaces that describe file formats, with file format types as implementors of these interfaces.

Branches in review

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Issues Raised From Comments

Key	Summary	State	Assignee
JAL-2391

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General Comments

Kira Mourão

There are a few places in the code where I think strings could have been repl...

There are a few places in the code where I think strings could have been replaced with IFileFormat. See:
jalview.appletgui.AlignFrame::outputFeatures
jalview.datamodel.PDBEntry::format
jalview.gui.AlignFrame::saveAs_actionPerformed
jalview.ws.ebi.EbiFetchClient::fetch*, buildUrl
jalview.ws.rest.params.AnnotationFile::formatForInput

Also jalview.bin.JalviewLite and jalview.javascript.JalviewLiteJsApi but not sure if these are used?

24 Jan 17

Mungo Carstairs

Resolved

07 Feb 17

Mungo Carstairs

1) AlignFrame.outputFeatures() - format parameter here is a choice of Jalview...

1) AlignFrame.outputFeatures() - format parameter here is a choice of Jalview or GFF, not a FileFormat in our sense - leave as is
2) PDBEntry$Type.format - part of raised issue JAL-2391
3) gui.AlignFrame.saveAs_actionPerformed: this uses FileFormatI where it can, or the string representation in user preferences, not sure what more can be done here
4) EBIFetchClient - format here is to specify format of returned data, and service dependent (and could change!)

e.g. something like "display=xml" or "pdb" or "mmcif" or "uniprotxml" or "xml"
sometimes relate to a Jalview FileFormatI but strictly should be decoupled from it - covered in JAL-2391 also
5) AnnotationFile.format is a choice of "JalviewAnnotation" or "CsvAnnotationRow" - I think out of scope of the current changes
6) JalviewLiteJsApi provides a Javascript-to-Java bridge - see jalviewLiteJs.html and the 'Jalview Lite embedded' launch configuration / embedded.html - has to work in strings

26 Jan 17

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CR-JAL-8

JAL-2344: Refactor file format options as interfaces instead of text strings

CR-JAL-8 13

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Issues Raised From Comments

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Kira Mourão

Mungo Carstairs

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JAL-2344: Refactor file format options as interfaces instead of text strings

CR-JAL-8 13

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Issues Raised From Comments

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Kira Mourão

Mungo Carstairs

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