4a3f3df9cab079354e8a9f4cf6c56f616f1ea0ab kent Fri Apr 6 16:29:22 2012 -0700 Removing MySQL linking dependency. diff --git src/hg/autoXml/dasBed.dtdx src/hg/autoXml/dasBed.dtdx deleted file mode 100644 index 6a76eb7..0000000 --- src/hg/autoXml/dasBed.dtdx +++ /dev/null @@ -1,43 +0,0 @@ -<!ELEMENT DAS_BED (TEXT? SEGMENT*)> Top level data structure -<!ATTLIST DAS_BED id CDATA #REQUIRED> Some database ID. -<!ATTLIST DAS_BED version CDATA "1.0"> Version name. -<!ATTLIST DAS_BED label CDATA #IMPLIED> One or two word label. Defaults to id. -<!ATTLIST DAS_BED description CDATA #IMPLIED> One line description. Defaults to label. -<!ATTLIST DAS_BED author CDATA "anonymous"> Overall author list. -<!ATTLIST DAS_BED href CDATA #IMPLIED> Top level URL. See below for details - -<!ELEMENT TEXT (#PCDATA)> A tag around a possibly long description. - -<!ELEMENT SEGMENT (F*)> Encloses annotations around a segment of genome -<!ATTLIST SEGMENT id CDATA #REQUIRED> Sequence id (as in DASGFF's SEGMENT) -<!ATTLIST SEGMENT version CDATA #REQUIRED> Goes with sequence id. -<!ATTLIST SEGMENT start INT #REQUIRED> Start coordinate (1 based) -<!ATTLIST SEGMENT end INT #REQUIRED> End coordinate (inclusive) -<!ATTLIST SEGMENT strand CDATA #REQUIRED> +, or -. - -<!ELEMENT F (TEXT* F* B*)> A feature. May contain subfeatures. -<!ATTLIST F id CDATA #REQUIRED> Some database ID. -<!ATTLIST F start INT #REQUIRED> Start of first block relative to parent start. -<!ATTLIST F end INT #REQUIRED> End of last block relative to parent start. -<!ATTLIST F label CDATA #IMPLIED> One or two word label. Defaults to id. -<!ATTLIST F version CDATA #IMPLIED> Version number. -<!ATTLIST F description CDATA #IMPLIED> One line description. Defaults to label. -<!ATTLIST F author CDATA #IMPLIED> Track author. Defaults to DASBED URL. -<!ATTLIST F href CDATA #IMPLIED> Track level URL. Defaults to DASBED URL. -<!ATTLIST F strand CDATA #IMPLIED> +, -, or not even present (relative to parent). -<!ATTLIST F score INT -1> A number between 0 and 1000. -<!ATTLIST F thickStart INT -1> CDS start for genes. -<!ATTLIST F thickEnd INT -1> CDS end for genes. -<!ATTLIST F frame INT -1> Coding frame 1,2, or 3. -<!ATTLIST F qId CDATA #IMPLIED> ID of query sequence in an alignment. - -<!ELEMENT B> A block. Can hold alignment info. Deliberately small. -<!ATTLIST B start INT #REQUIRED> Start in sequence relative to item start. -<!ATTLIST B end INT #REQUIRED> End in sequence relative to item start. -<!ATTLIST B score INT -1> Score between 0 and 1000. -<!ATTLIST B qAli CDATA #IMPLIED> Query side of alignment including '-' chars. -<!ATTLIST B tAli CDATA #IMPLIED> Target (in segment) side of alignment. -<!ATTLIST B qStart INT -1> Query start coordinate. -<!ATTLIST B qEnd INT -1> Query end coordinate. - -