Changes between Version 2 and Version 3 of Extensions/DigesterAndExQuestImporter

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Timestamp:
03/26/10 11:38:17 (5 months ago)
Author:
gregory
Comment:

Refs #665. Replacing bad info :-)

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  • Extensions/DigesterAndExQuestImporter

    v2 v3  
    11[[PageOutline]] 
    2 = Spectrum File Inspector = 
     2= Digester & !ExQuest Importer = 
    33 
    4 Extension to inspect spectra in a selected spectrum file. 
     4Importers for Digester and !ExQuest data. 
    55 
    6  Author: Olle Månsson, Department of Theoretical Physics, Lund University, Sweden 
     6 Author: Fredrik Levander, Lund University, Sweden 
    77  
    88 License: [http://www.gnu.org/licenses/gpl-2.0.html GNU General Public License version 2.] 
    99 
    10  
    1110== Documentation == 
    1211 
    13 The extension allows inspection of spectra in a selected spectrum file. 
    14 It shows a list of spectrum Id values in the file. Clicking on a spectrum Id value 
    15 will display the corresponding spectrum. 
     12''These extensions were part of the Proteios 2.1 release. If you are running proteios 2.2 or later you will need to download the extension binary (or build from source) and reinstall the plug-ins as a proteios administrator to use the plug-ins.'' 
    1613 
    17 General specification: 
     14 Binaries in the immun_lth_se bundle at: 
     15  ''http://dev.thep.lu.se/proteios_extensions/htdocs/downloads/ '' 
    1816 
    19  * If more than one file are selected, the first one is used. 
    20  * If the file is not a supported type of spectrum file (including non-spectrum files), a message reporting this is shown. 
    21  * A table of spectrum id values for the spectra in the file is shown. For a spectrum file without explicit spectrum id values, the order number of the spectra in the file is used. 
    22  * Clicking on a spectrum id value shows a plot of the corresponding spectrum next to the table. Initially the first spectrum in the table is plotted. 
    23  * The extension uses existing classes to get a reader for the spectrum file and plot the spectra, in order to take advantage of later enhancements of these classes, e.g. by supporting more types of spectrum files and showing more detailed spectrum plots. 
     17 Source code checkout:  
     18  ''svn co http://dev.thep.lu.se/proteios_extensions/svn/se/lth/immun/trunk'' 
    2419 
    25 Version 0.2: 
    2620 
    27  * For MGF (Mascot Generic Format) files, if an optional spectrum title exists, the spectrum order number is appended by " - " and the spectrum title (also available for version 0.1 if used with Proteios SE 2.5). 
    28  * Spectrum properties are displayed in a box below the spectrum plot. 
     21=== `ExQuest` import === 
    2922 
    30 Version 0.3: 
     23To import `ExQuest` mappings to the hits report, a specific extension needs to be used. First you need to make sure that the gel has been entered into your project so that it is visible under Gels. You also need to upload the `ExQuest` spot cutter picklist to your project directory. Then check the file check box for the `ExQuest` file in the `Files` view and select `Extensions->ExQuest cutter import for a gel`. Then select the appropriate gel in the select  box and press the `Create Job` button.  
    3124 
    32  * Spectrum file instrument and contact properties are displayed in a box below the spectrum properties. Spectrum file properties are currently only supported for mzData and mzML spectrum files. 
     25When the job has finished you will find the mapping from Gel to microtitre plate in the Hits report. Then you can import the final target plate mapping from the 'Digester file'. To do this, upload the digester file to your project directory, check the file check box and select `Extensions->Digester import to a plate`. You then need to enter the External ID of the target plate, and press `Create Job[s]`. Once the job is finished you are ready to import peak lists using step 2 of the [http://www.proteios.org/wiki/GelBasedReport Hits Report Wizard]. 
    3326 
    34 Version 0.4: 
    35  
    36  * Spectrum file inspector extension updated to forward action to class `InspectActiveSpectrumFile`, that is part of the standard Proteios SE code since version 2.7.0. Features of spectrum file inspector extension therefore now depends on the Proteios SE version number. For Proteios SE 2.7.0 and 2.8.0, the functionality of Spectrum file inspector extension version 0.4 should equal that of version 0.3. 
    3727 
    3828== Source Checkout == 
    … …  
    4030The extension source code can be checked out from the subversion repository using the following command: 
    4131 
    42  `svn co http://www.proteios.org/svn/trunk/contrib/SpectrumFileInspector` 
     32 `svn co http://www.proteios.org/svn/trunk/contrib/immun` 
    4333 
    44