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[Gmod-apollo-cmts] CVS: apollo/doc/html userguide.html,1.1.2.30,1.1.2.31
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From: Nomi H. <no...@us...> - 2002-08-29 21:59:31
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Update of /cvsroot/gmod/apollo/doc/html
In directory usw-pr-cvs1:/tmp/cvs-serv21859
Modified Files:
Tag: sanger_branch
userguide.html
Log Message:
Index: userguide.html
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/html/Attic/userguide.html,v
retrieving revision 1.1.2.30
retrieving revision 1.1.2.31
diff -C2 -d -r1.1.2.30 -r1.1.2.31
*** userguide.html 29 Aug 2002 05:30:21 -0000 1.1.2.30
--- userguide.html 29 Aug 2002 21:59:27 -0000 1.1.2.31
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*** 50,53 ****
--- 50,54 ----
<LI><a href="#ReadingGFF">Reading GFF files</a><BR>
<LI><a href="#ReadingEnsembl">Using the Ensembl CGI server</a><BR>
+ <LI><a href="#ReadingEnsembl">Layering</a><BR>
<LI><a href="#Styles">Styles</a><BR>
</UL>
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*** 285,293 ****
<P>If any of the features in the gff file have types which are not recognized
by Apollo they will be given a default pale gray color.
! This can be changed by right clicking over the appropriate feature box
in the types panel (see the <a href="#TypesPanel">types panel </a>section
! for details). We are working on providing configuration files for viewing
! other types of data; right now, the configuration is optimized for displaying the
! Drosophila annotations.
<P>
Please note that there is more than one flavor of GFF, and Apollo only supports
--- 286,292 ----
<P>If any of the features in the gff file have types which are not recognized
by Apollo they will be given a default pale gray color.
! This can be changed by right-clicking over the appropriate feature box
in the types panel (see the <a href="#TypesPanel">types panel </a>section
! for details).
<P>
Please note that there is more than one flavor of GFF, and Apollo only supports
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*** 302,305 ****
--- 301,310 ----
<center><img SRC="images/loadens_sm.gif" width=468 height=347></center>
+ <h3><a NAME="Layering"></a>Layering data</h3>
+
+ The "Open additional" menu item lets you layer more data from the same region
+ of the genome, showing both the current dataset and the new one. Please note that
+ this isn't completely working yet!
+
<h3><a NAME="Styles"></a>Styles</h3>
Apollo has a configuration file for each known data source. This file is
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*** 328,332 ****
color. For instance, with the default setup transposons are red and Genie gene predictions
are dark purple.
! <P><center><img SRC="images/mainwindow.gif" width=800 height=702></center>
<P>
<h3><a NAME="AnnotationsVsResults"></a>Annotations vs. results</h3>
--- 333,337 ----
color. For instance, with the default setup transposons are red and Genie gene predictions
are dark purple.
! <P><center><img SRC="images/mainwindow.gif" width=800 height=698></center>
<P>
<h3><a NAME="AnnotationsVsResults"></a>Annotations vs. results</h3>
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*** 861,865 ****
<a NAME="EdgeMatches"></a>Edge matches</h3>
To help you to compare different features in detail, all features that
! have the same 5' or 3' boundary the currently selected feature are highlighted
with white lines at the edges of the feature boxes. You can turn off edge
match highlighting by unclicking "Show edge matches" in the View menu.
--- 866,870 ----
<a NAME="EdgeMatches"></a>Edge matches</h3>
To help you to compare different features in detail, all features that
! have the same 5' or 3' boundary as the currently selected feature are highlighted
with white lines at the edges of the feature boxes. You can turn off edge
match highlighting by unclicking "Show edge matches" in the View menu.
***************
*** 1175,1185 ****
<P><center><img SRC="images/exon-detail-editor.gif" width=824 height=502></center><P>
! Clicking on the nucleotide sequence within an annotation
! brings up a graphic at the bottom of the window that show the exon
structure of the selected annotation and the translation start and
stop. The numbers on the exons indicate the translation reading frame
for that exon. One can click on specific regions of the graphic to
shift the sequence view so that it will center around the selected
! region of the transcript. Many manipulations are possible in the
Annotation Exon editor many of which are available from a menu that
pops up upon right clicking within the sequence region. These will be
--- 1180,1189 ----
<P><center><img SRC="images/exon-detail-editor.gif" width=824 height=502></center><P>
! The graphic at the bottom of the exon editor window shows the exon
structure of the selected annotation and the translation start and
stop. The numbers on the exons indicate the translation reading frame
for that exon. One can click on specific regions of the graphic to
shift the sequence view so that it will center around the selected
! region of the transcript [Note: that doesn't seem to be working.]. Many manipulations are possible in the
Annotation Exon editor many of which are available from a menu that
pops up upon right clicking within the sequence region. These will be
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*** 1731,1738 ****
<P>
<td>The class to use for the feature type.
! <P>Use DrawableResultSeqFeature for most things (blast hits, gene predictions)
! <P>Use DrawableAnnotatedSeqFeature for genes (has nice tented introns).
! <P>Another feature type is
! <P>DrawableSiteCodon (which is used for the start and stop codon).
display
<P> </td>
--- 1735,1742 ----
<P>
<td>The class to use for the feature type.
! <br>Use DrawableResultSeqFeature for most things (blast hits, gene predictions)
! Use DrawableAnnotatedSeqFeature for genes (has nice tented introns).
! Another feature type is
! DrawableSiteCodon (which is used for the start and stop codon).
display
<P> </td>
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*** 1805,1809 ****
<HR><P>
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! Last modified: Wed Aug 28 22:29:17 PDT 2002
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<HR><P>
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! Last modified: Thu Aug 29 14:44:15 PDT 2002
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