Changeset 3940

Nov 8, 2007, 1:05:47 PM (14 years ago)
Martin Svensson

Fixes #807 Documentation has been read and some minor changes have been done.

4 edited


  • trunk/doc/src/docbook/developerdoc/api_overview.xml

    r3926 r3940  
    4040      since we will always try to maintain backwards compatibility
    4141      for classes that are part of the public API. For other
    42       classes, changes may be instroduced at any time without
     42      classes, changes may be introduced at any time without
    4343      notice or specific documentation. In other words:
    4444    </para>
    5959      Methods, classes and other elements that have been tagged as
    6060      <code>@deprecated</code> should be considered as part of the internal API
    61       and may be removed in a subsequent relase without warning.
     61      and may be removed in a subsequent release without warning.
    6262    </para>
    12001200          interface to be able to store data in files instead of in the database.
    12011201          The interface creates a link to a <classname>FileSetData</classname> object,
    1202           which is can hold several <classname>FileSetMemberData</classname> items.
     1202          which can hold several <classname>FileSetMemberData</classname> items.
    12031203          Each member points to specific <classname>FileData</classname> item.
    12041204          A file set can only store one file of each <classname>DataFileTypeData</classname>.
    22252225          <para>
    22262226          The <methodname>FileSet.validate()</methodname> only validates
    2227           the files where the file types have specified plug-ins tha can
     2227          the files where the file types have specified plug-ins that can
    22282228          do the validation and metadata extraction. The method doesn't
    22292229          throw any exceptions. Instead, all validation errors
    22432243          <para>
    22442244          The core checks the <classname>DataFileType</classname> of all
    2245           members in the file set and create <classname>DataFileValidator</classname>
     2245          members in the file set and creates <classname>DataFileValidator</classname>
    22462246          and <classname>DataFileMetadataReader</classname> objects. Only one instance
    22472247          of each class is created. If the file set contains members which has the
  • trunk/doc/src/docbook/userdoc/array_lims.xml

    r3872 r3940  
    203203      <note>
    204         <title>Verify that probsets in a CDF file exists as reporters</title>
     204        <title>Verify that probsets in a CDF file exist as reporters</title>
    205205        <para>
    206206          File-only platforms, such as Affymetrix, require that all probesets
    207           must exists as reporters before data can be analysed. For other
     207          must exist as reporters before data can be analysed. For other
    208208          platforms this is usually checked when importing the features to
    209209          the database. Since no import takes place for file-only platforms,
    210210          another manual step takes it place. Use the &gbImport; button
    211           on the array design item view and select the
     211          in the array design item view and select the
    212212          <guilabel>Affymetrix CDF probeset importer</guilabel> plug-in.
    213213          If you have enough permissions this function will also let you create
  • trunk/doc/src/docbook/userdoc/platforms.xml

    r3872 r3940  
    278278        for client applications or plug-ins to find the raw data for an
    279279        experiment without actually knowing which file types that are
    280         used on various platforms
     280        used on various platforms.
    281281        </para>
    282282      </listitem>
  • trunk/doc/src/docbook/userdoc/rawbioassays.xml

    r3872 r3940  
    6969    in a tab-separated (or similar) form. Data from one hybridization
    7070    must be in a single file. Support for other file formats
    71     mat be added through plug-ins.
     71    may be added through plug-ins.
    7272  </note>
    134134            the same reporter on the same position. This
    135135            prevents mistakes but also speed up analysis
    136             since some optimzations can be used when assigning
     136            since some optimizations can be used when assigning
    137137            positions in bioassay sets.
    138138            The array design can be changed after raw data has been
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