Support the Vector NTI / AlignX alignment format

Data that should be parsed from the files

The files have .apr extension. A couple of example files are attached. Parse only sequences and their names from the IxAlignment objects.

Modifications in UGENE

In general, the format support should include the following:

• Opening of the alignments in read-only mode in the UGENE GUI.
• Conversion of the alignments into other writeable alignment formats, supported by UGENE:
  • In the UGENE GUI
  • In the Workflow Designer
  • In the Project View

In terms of this issue only the first item should be implemented. The other items should be done in terms of UGENE-5798.

Dialog on the file opening in UGENE

In the UGENE GUI the following dialog should appear when such files are opened:

• Dialog title: "Select Document Format"
• Inside the dialog: There is a group named "Options for filename" with two radio buttons inside:
  • "Open in read-only mode"
  • "Convert to another format:" with the following fields below:
    • "Save to file" edit box with the default file name and the browse button. The default file should have the same path and name as the input file, but different extension. The extension depends on the selected output format.
    • "File format" combo-box with the writable alignment formats. The "FASTA" value should be set by default.

Also, the dialog input settings should be saved between different dialog launches, i.e. if a user selects "ClustalW", the value stays selected by default for the next .apr file.