element proxl_input

diagram
properties	content  complex
children	search_program_info linkers reported_peptides matched_proteins static_modifications decoy_labels configuration_files
attributes	Name   Type   Use   Default   Fixed   Annotation fasta_filename   xs:string   required         documentation The filename (not including the path) of the FASTA file used to search the data. name   xs:string            documentation An optional name to be used for this search in ProXL. If not present, a default will be used. This name may be changed within ProXL. comment   xs:string            documentation An optional comment to be associated with this search when it is imported into ProXL.
identity constraints	Name   Refer   Selector   Field(s)   Annotation unique   reported_peptide_string_key      reported_peptides/reported_peptide   @reported_peptide_string   documentation Ensures the reported peptide strings are unique.
annotation	documentation Root element for all data
source	<xs:element name="proxl_input">   <xs:annotation>     <xs:documentation>Root element for all data</xs:documentation>   </xs:annotation>   <!-- Element name must match string in Java class XSD_ElementAttributeNamesConstants  -->   <xs:complexType>     <xs:sequence>       <xs:element ref="search_program_info"/>       <xs:element ref="linkers">         <xs:annotation>           <xs:documentation>The chemical linkers used in this experiment. There must be at least one.</xs:documentation>         </xs:annotation>       </xs:element>       <xs:element ref="reported_peptides">         <xs:annotation>           <xs:documentation>All the reported peptides from a PSM search. A reported peptide is a string that uniquely identifies an identified peptide (or linked pair of peptides) IN THIS SEARCH. (This string is not used by ProXL for this purpose.) A unique peptide i this context is one or two peptide sequences linked together at specific positions in those sequences, and with modifications at specific sites. E.g. PEP[16.01]TIDE would uniquely ID a peptide with this sequence with the given mass shift on the given position. or KEKTIDE(3)--PEPT[16.1]IDE(2) would uniquely identify the crosslink between two peptides with these ssequences at positions 3 and 2 (respectively) and where the second peptide has the shown modification. There is no syntax expected for reported peptide, but the reported peptide string must be unique, and no two reported peptides must describe the same peptide or pair of peptides linked at the same positions with the same modifications.</xs:documentation>         </xs:annotation>       </xs:element>       <xs:element ref="matched_proteins" minOccurs="0">         <xs:annotation>           <xs:documentation>Contains the protein sequences matched by peptides found in the experiment, and associated names, descriptions, and taxonomy IDs for those proteins. This will typically come from the FASTA file used to search the data. Only the proteins matched by the data should be included, not all the proteins in the FASTA file.</xs:documentation>         </xs:annotation>       </xs:element>       <xs:element ref="static_modifications" minOccurs="0"/>       <xs:element ref="decoy_labels" minOccurs="0">         <xs:annotation>           <xs:documentation>An optional list of decoy labels (strings that are prefixes on protein names that indicate the given protein is a decoy (e.g., "DECOY_") </xs:documentation>         </xs:annotation>       </xs:element>       <xs:element ref="configuration_files" minOccurs="0">         <xs:annotation>           <xs:documentation>(Optional) The configuration files associated with the search.</xs:documentation>         </xs:annotation>       </xs:element>     </xs:sequence>     <xs:attribute name="fasta_filename" type="xs:string" use="required">       <xs:annotation>         <xs:documentation>The filename (not including the path) of the FASTA file used to search the data.</xs:documentation>       </xs:annotation>     </xs:attribute>     <xs:attribute name="name" type="xs:string">       <xs:annotation>         <xs:documentation>An optional name to be used for this search in ProXL. If not present, a default will be used. This name may be changed within ProXL.</xs:documentation>       </xs:annotation>       <!-- Attribute name must match string in Java class XSD_ElementAttributeNamesConstants  -->     </xs:attribute>     <xs:attribute name="comment" type="xs:string">       <xs:annotation>         <xs:documentation>An optional comment to be associated with this search when it is imported into ProXL.</xs:documentation>       </xs:annotation>     </xs:attribute>   </xs:complexType>   <xs:unique name="reported_peptide_string_key">     <xs:annotation>       <xs:documentation>Ensures the reported peptide strings are unique.</xs:documentation>     </xs:annotation>     <xs:selector xpath="reported_peptides/reported_peptide"/>     <xs:field xpath="@reported_peptide_string"/>   </xs:unique> </xs:element>

attribute proxl_input/@fasta_filename

type	xs:string
properties	use  required
annotation	documentation The filename (not including the path) of the FASTA file used to search the data.
source	<xs:attribute name="fasta_filename" type="xs:string" use="required">   <xs:annotation>     <xs:documentation>The filename (not including the path) of the FASTA file used to search the data.</xs:documentation>   </xs:annotation> </xs:attribute>

attribute proxl_input/@name

type	xs:string
annotation	documentation An optional name to be used for this search in ProXL. If not present, a default will be used. This name may be changed within ProXL.
source	<xs:attribute name="name" type="xs:string">   <xs:annotation>     <xs:documentation>An optional name to be used for this search in ProXL. If not present, a default will be used. This name may be changed within ProXL.</xs:documentation>   </xs:annotation>   <!-- Attribute name must match string in Java class XSD_ElementAttributeNamesConstants  --> </xs:attribute>

attribute proxl_input/@comment

type	xs:string
annotation	documentation An optional comment to be associated with this search when it is imported into ProXL.
source	<xs:attribute name="comment" type="xs:string">   <xs:annotation>     <xs:documentation>An optional comment to be associated with this search when it is imported into ProXL.</xs:documentation>   </xs:annotation> </xs:attribute>

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