[Gmod-gbrowse-cmts] Generic-Genome-Browser/docs CONFIGURE_HOWTO.txt,1.15,1.16

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Update of /cvsroot/gmod/Generic-Genome-Browser/docs
In directory sc8-pr-cvs1:/tmp/cvs-serv32539/docs

Modified Files:
	CONFIGURE_HOWTO.txt 
Log Message:
got a lot of work on the tutorial done, but another few pages at least needed

Index: CONFIGURE_HOWTO.txt
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/docs/CONFIGURE_HOWTO.txt,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** CONFIGURE_HOWTO.txt	6 Jun 2003 17:09:21 -0000	1.15
--- CONFIGURE_HOWTO.txt	22 Jun 2003 02:52:42 -0000	1.16
***************
*** 13,23 ****
    B. ADDING A NEW DATABASE TO THE BROWSER
       B1. The [GENERAL] Section
!      B2. Track Sections
!      B3. Glyphs and Glyph options
!      B4. Adding features to the overview
!      B5. Semantic Zooming
!      B6. Computed Options
!      B7. Declaring New Aggregators
!      B8. Grouping related features
    C. ADDING HISTOGRAMS
    D. INTERNATIONALIZATION
--- 13,24 ----
    B. ADDING A NEW DATABASE TO THE BROWSER
       B1. The [GENERAL] Section
!      B2. The [TRACK DEFAULTS] Section
!      B3. Track Sections
!      B4. Glyphs and Glyph options
!      B5. Adding features to the overview
!      B6. Semantic Zooming
!      B7. Computed Options
!      B8. Declaring New Aggregators
!      B9. Grouping related features
    C. ADDING HISTOGRAMS
    D. INTERNATIONALIZATION
***************
*** 488,588 ****
    images.    (You will probably not need to change this.)

-   * glyph
-      height
-      bgcolor
-      fgcolor
-      strand_arrow
- 
-    These options control the default graphical settings for any
-    annotation types that are not explicitly specified.  See the
-    section below on controlling the settings.  Likewise, any other
-    graphical options found in the [GENERAL] sections are treated as
-    defaults.
- 
-    * label density
- 
-    When there are too many annotations on the screen GBrowse automatically
-    disables the printing of identifying labels next to the feature.
-    "label density" controls where the cutoff occurs.  The value in the
-    example files is 25, meaning that labels will be turned off when
-    there are more than 25 annotations of a particular type on display
-    at once.
- 
-    * bump density
- 
-    When there are too many annotations on the screen GBrowse automatically
-    disables collision control.  The "bump density" option controls
-    where the cutoff occurs.  The value in the example files is 100,
-    meaning that when there more than 100 annotations of the same type
-    on the display, the browser will stop shifting them verticially to
-    prevent them from colliding, but will instead allow them to
-    overlap.
- 
-    * link
- 
-    The link option creates a default rule for creating outgoing links 
-    from the GBrowse display.  When the user clicks on a feature of
-    interest, he will be taken to the corresponding URL.
- 
-    The link option's value should be a URL containing one or more
-    variables.  Variables begin with a dollar sign ($), and are
-    replaced at run time with the information relating to the selected
-    annotation.  Recognized variables include:
- 
-      $name     The feature's name (group name)
-      $class    The feature's class (group class)
-      $method   The feature's method
-      $source   The feature's source
-      $ref      The name of the sequence segment (chromosome, contig) 
- 		  on which this feature is located
-      $start    The start position of this feature, relative to $ref
-      $end      The end position of this feature, relative to $ref
-      $segstart The left end of $ref displayed in the detailed view
-      $segend   The right end of $ref displayed in the detailed view
- 
-    For example, the wormbase.conf file uses this link rule:
- 
-      link = http://www.wormbase.org/db/get?name=$name;class=$class
- 
-    At run time, if the user clicks on an EST named yk1234.5, this
-    will generate the URL
- 
-    http://www.wormbase.org/db/get?name=yk1234.5;class=EST
- 
-    It is possible to override the global link rule on a
-    feature-by-feature basis.  See the next section for details on
-    this.  It is also possible to declare a subroutine to compute the
-    proper URL dynamically.  See COMPUTED OPTIONS for details.
- 
-    * link_target
- 
-    By default links will replace the contents of the current window.
-    If you wish, you can specify a new window to pop up when the user
-    clicks on a feature, or designate a named window or frame to
-    receive the contents of the link.  To do this, add the "link_target"
-    option to the general section or to a track stanza.  The format
-    is this:
- 
-       link_target = _blank
- 
-    The value uses the HTML targetting rules to name/create the window
-    to receive the value of the link.  The first time the link is
-    accessed, a window with the specified name is created.  The next
-    time the user clicks on a link with the same target, that window
-    will receive the content of the link if it is still present, or it
-    will be created again if it has been closed.  A target named
-    "_blank" is special and will always create a new window.
- 
-    The "link_target" option can also be computed dynamically.  See
-    COMPUTED OPTIONS for details.
- 
-    * title
- 
-    The title option controls the "tooltips" text that pops up when
-    the mouse hovers over a glyph in certain browsers.  The rules
-    for generating titles are the same as the "link" option discussed
-    above.  The "title" option can also be computed dynamically.
-    See COMPUTED OPTIONS for details.
- 
     * image widths

--- 489,492 ----
***************
*** 810,814 ****
      The default value is "key."

! B2. Track Sections

  Any other [Section] in the configuration file is treated as a
--- 714,829 ----
      The default value is "key."

! B2. The [TRACK DEFAULTS] section
! 
! The track defaults section specifies default values for each track.
! The following common options are recognized:
! 
!   * glyph
!     height
!     bgcolor
!     fgcolor
!     fontcolor
!     font2color
!     strand_arrow
! 
!    These options control the default graphical settings for any
!    annotation types that are not explicitly specified.  See the
!    section below on controlling the settings.  Any of the options
!    allowed in the [track] sections described below are allowed here.
! 
!    * label density
! 
!    When there are too many annotations on the screen GBrowse automatically
!    disables the printing of identifying labels next to the feature.
!    "label density" controls where the cutoff occurs.  The value in the
!    example files is 25, meaning that labels will be turned off when
!    there are more than 25 annotations of a particular type on display
!    at once.
! 
!    * bump density
! 
!    When there are too many annotations on the screen GBrowse automatically
!    disables collision control.  The "bump density" option controls
!    where the cutoff occurs.  The value in the example files is 100,
!    meaning that when there more than 100 annotations of the same type
!    on the display, the browser will stop shifting them verticially to
!    prevent them from colliding, but will instead allow them to
!    overlap.
! 
!    * link
! 
!    The link option creates a default rule for creating outgoing links 
!    from the GBrowse display.  When the user clicks on a feature of
!    interest, he will be taken to the corresponding URL.
! 
!    The link option's value should be a URL containing one or more
!    variables.  Variables begin with a dollar sign ($), and are
!    replaced at run time with the information relating to the selected
!    annotation.  Recognized variables include:
! 
!      $name     The feature's name (group name)
!      $class    The feature's class (group class)
!      $method   The feature's method
!      $source   The feature's source
!      $ref      The name of the sequence segment (chromosome, contig) 
! 		  on which this feature is located
!      $start    The start position of this feature, relative to $ref
!      $end      The end position of this feature, relative to $ref
!      $segstart The left end of $ref displayed in the detailed view
!      $segend   The right end of $ref displayed in the detailed view
! 
!    For example, the wormbase.conf file uses this link rule:
! 
!      link = http://www.wormbase.org/db/get?name=$name;class=$class
! 
!    At run time, if the user clicks on an EST named yk1234.5, this
!    will generate the URL
! 
!    http://www.wormbase.org/db/get?name=yk1234.5;class=EST
! 
!    It is possible to override the global link rule on a
!    feature-by-feature basis.  See the next section for details on
!    this.  It is also possible to declare a subroutine to compute the
!    proper URL dynamically.  See COMPUTED OPTIONS for details.
! 
!    A special link type of AUTO will cause the feature to link to
!    the gbrowse_details script, which summarizes information about
!    the feature.  The default is not to link at all.
! 
!    * link_target
! 
!    By default links will replace the contents of the current window.
!    If you wish, you can specify a new window to pop up when the user
!    clicks on a feature, or designate a named window or frame to
!    receive the contents of the link.  To do this, add the "link_target"
!    option to the [TRACK DEFAULTS] section or to a track stanza.  The format
!    is this:
! 
!       link_target = _blank
! 
!    The value uses the HTML targetting rules to name/create the window
!    to receive the value of the link.  The first time the link is
!    accessed, a window with the specified name is created.  The next
!    time the user clicks on a link with the same target, that window
!    will receive the content of the link if it is still present, or it
!    will be created again if it has been closed.  A target named
!    "_blank" is special and will always create a new window.
! 
!    The "link_target" option can also be computed dynamically.  See
!    COMPUTED OPTIONS for details.
! 
!    * title
! 
!    The title option controls the "tooltips" text that pops up when
!    the mouse hovers over a glyph in certain browsers.  The rules
!    for generating titles are the same as the "link" option discussed
!    above.  The "title" option can also be computed dynamically.
!    See COMPUTED OPTIONS for details.
! 
!    The special value "AUTO" causes a default description to appear
!    describing the name, type and position of the feature.  This is
!    also assumed if the title option is missing or blank.
! 
! B3. Track Sections

  Any other [Section] in the configuration file is treated as a
***************
*** 954,958 ****
    option.

!   f) group pattern

    This option lets you connect related features by dotted lines based
--- 969,973 ----
    option.

!   f) group_pattern

    This option lets you connect related features by dotted lines based
***************
*** 966,970 ****
  ---

! B3. Glyphs and Glyph Options

  A large variety of glyphs are available, and more are being added as
--- 981,985 ----
  ---

! B4. Glyphs and Glyph Options

  A large variety of glyphs are available, and more are being added as
***************
*** 980,996 ****
--- 995,1033 ----

    generic		a rectangle
+ 
    arrow			an arrow
+ 
+   anchored_arrow	a span with vertical bases |---------|.  If one 
+ 			or the other end of the feature is off-screen, the
+ 			base will be replaced by an arrow.
+ 
    cds                   shows the reading frame of spliced transcripts; used
                          in conjunction with the "coding" aggregator.
+ 
    diamond		a point-like feature represented as a triangle
+ 
    dna                   DNA and GC content
+ 
    heterogeneous_segments a multi-segmented feature in which each segment can
                          have a distinctive color.  For Jim Kent's WABA features,
                          this works with the waba_alignment aggregator.
+ 
+   processed_transcript  multi-purpose representation of a spliced mRNA, including
+ 			positions of UTRs
+ 
    segments		a multi-segmented feature such as an alignment
+ 
+   span			like anchored_arrow, except that the ends are
+ 			truncated at the edge of the panel, not turned
+ 			into an arrow
+ 
    triangle		a point-like feature represented as a diamond
+ 
    transcript		a gene model
+ 
    transcript2		a slightly different representation of a gene model
+ 
    translation		1-, 3- and 6-frame translations
+ 
    wormbase_transcript	yet another gene model that can show UTR segments
  			(for features that conform to the WormBase gene
***************
*** 1006,1009 ****
--- 1043,1047 ----

    arrow				Bio::Graphics::Glyph::arrow
+   anchored_arrow		Bio::Graphics::Glyph::anchored_arrow
    cds				Bio::Graphics::Glyph::cds
    crossbox			Bio::Graphics::Glyph::crossbox
***************
*** 1063,1067 ****
  ---

! B4. Adding features to the overview

  You can make any set of tracks appear in the overview by creating a
--- 1101,1105 ----
  ---

! B5. Adding features to the overview

  You can make any set of tracks appear in the overview by creating a
***************
*** 1083,1087 ****
  ---

! B5. Semantic Zooming

  Sometimes you will want to change the appearance of a track when the
--- 1121,1125 ----
  ---

! B6. Semantic Zooming

  Sometimes you will want to change the appearance of a track when the
***************
*** 1138,1142 ****
  ---

! B6. Computed Options

  Some options can be computed at run time by using Perl subroutines as
--- 1176,1180 ----
  ---

! B7. Computed Options

  Some options can be computed at run time by using Perl subroutines as
***************
*** 1248,1252 ****
  ---

! B7. Declaring New Aggregators

  The Bio::DB::GFF data model recognizes a single-level of "grouping" of
--- 1286,1290 ----
  ---

! B8. Declaring New Aggregators

  The Bio::DB::GFF data model recognizes a single-level of "grouping" of
***************
*** 1335,1339 ****
  "aggregator_name" is the name of the aggregator.

! B8. GROUPING FEATURES

  gbrowse recognizes the concept of a "group" of related features that
--- 1373,1377 ----
  "aggregator_name" is the name of the aggregator.

! B9. GROUPING FEATURES

  gbrowse recognizes the concept of a "group" of related features that