Class Software

    • Field Detail

      • TYPE

        private static final Item TYPE
        The type of item represented by this class.
        See Also:
        Item.SOFTWARE, getType()
        Last modified
        $Date: 2017-05-22 14:35:27 +0200 (må, 22 maj 2017) $
      • FEATURE_EXTRACTION

        public static final String FEATURE_EXTRACTION
        The id for the SoftwareType item representing the softwaretype "feature extraction software".
        Since:
        3.0
        See Also:
        Constant Field Values
      • ALIGNMENT

        public static final String ALIGNMENT
        The id for the SoftwareType item representing software used for aligning sequenced data against a known reference database.
        Since:
        3.0
        See Also:
        Constant Field Values
      • MAX_VERSIONSTRING_LENGTH

        public static final int MAX_VERSIONSTRING_LENGTH
        The maximum length of the version variable that can be stored in the database. Check the length against this value before calling the setVersionString(String) method to avoid exceptions.
        See Also:
        Constant Field Values
    • Constructor Detail

      • Software

        Software​(SoftwareData data)
        Creates a new software item.
        Parameters:
        data - the data
    • Method Detail

      • getDefaultSystemId

        public static String getDefaultSystemId​(Item itemType)
        Get the system id for the software subtype that should be used on an item that doesn't have a subtype. This includes Subtypable items with a null ItemSubtype and all other non-subtypable items which can be linked to a software.
        Parameters:
        itemType - The item type
        Returns:
        The system id of the default software type or null
        Since:
        3.0
      • getNew

        public static Software getNew​(DbControl dc)
                               throws BaseException
        Create a new Software item.
        Parameters:
        dc - The DbControl which will be used for permission checking and database access.
        Returns:
        The new Software item
        Throws:
        BaseException - This exception is thrown if there is another error
      • getType

        public Item getType()
        Description copied from interface: Identifiable
        Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.
        Specified by:
        getType in interface Identifiable
        Returns:
        A value indicating the type of item
      • getEntryDate

        public Date getEntryDate()
        Description copied from interface: Registered
        Get the date that the item was registered in the database.
        Specified by:
        getEntryDate in interface Registered
        Returns:
        A date or null if this is not known
      • setEntryDate

        public void setEntryDate​(Date entryDate)
        Description copied from interface: Registered
        Set the date the entry was registered in the database. Implementations should only allow this property to be set before the item is first stored in the database. The intention of this method is to facilitate export/import of data between server.
        Specified by:
        setEntryDate in interface Registered
        Parameters:
        entryDate - A date or null to use today's date
      • getAnnotatableParents

        public Set<Annotatable> getAnnotatableParents()
        Description copied from interface: Annotatable
        Get all parents objects which are annotatable and the logged in user has read permission to. If the item doesn't have any annotatable parents, it may return null or an empty set. The method should only return the immediate parent(s), not parents to parents, etc. As of BASE 3.1 this method may also return child items if the child item is a Subtypable item that has a subtype with the ItemSubtype.getPushAnnotations() flag set.
        Specified by:
        getAnnotatableParents in interface Annotatable
        Returns:
        Always null
        Since:
        3.3
      • isUsed

        public boolean isUsed()
                       throws BaseException
        Check if:
        • a RawBioAssay was created with this software
        • a DerivedBioassay was created with this software
        Overrides:
        isUsed in class BasicItem
        Returns:
        TRUE if this item is used, FALSE otherwise
        Throws:
        BaseException - If not able to tell if item is used or not.
        See Also:
        BasicItem.getUsingItems()
      • getVersionString

        public String getVersionString()
        Get the versionstring of this Software item.
        Returns:
        A string with the version of this item, or null if not known