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[Gmod-apollo-cmts] CVS: apollo/doc/html userguide.html,1.4,1.5
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From: Nomi H. <no...@us...> - 2002-09-24 23:39:44
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Update of /cvsroot/gmod/apollo/doc/html In directory usw-pr-cvs1:/tmp/cvs-serv25240 Modified Files: userguide.html Log Message: Index: userguide.html =================================================================== RCS file: /cvsroot/gmod/apollo/doc/html/userguide.html,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** userguide.html 23 Sep 2002 23:28:33 -0000 1.4 --- userguide.html 24 Sep 2002 23:39:41 -0000 1.5 *************** *** 97,100 **** --- 97,101 ---- <LI><a href="#ResizeFeature">Resizing features</a><BR> <LI><a href="#RectangleStyle">Changing feature style</a><BR> + <LI><a href="#DashSets">Showing sequencing gaps in ESTs<BR> <LI><a href="#FeatureLabels">Showing feature labels</a><BR> <LI><a href="#TypesPanelControl">Using the Types panel to control display of features</a><BR> *************** *** 710,713 **** --- 711,720 ---- <h3> + <a NAME="DashSets"></a>Showing sequencing gaps in ESTs</h3> + By default, sequencing gaps in EST results are shown as dashed lines. This is + controlled by the DashSets option in apollo.cfg. The color of the dashed lines + is set by the SequenceGapColor setting in apollo.cfg + + <h3> <a NAME="FeatureLabels"></a>Showing feature labels</h3> <P> *************** *** 846,850 **** associated with them.) You can also use "Open new sequence window" from the View menu. <P> ! <center><img SRC="images/sequence-window.gif" width=367 height=366></center> <P> You can also translate the sequence to amino acids or view the virtual cDNA sequence --- 853,857 ---- associated with them.) You can also use "Open new sequence window" from the View menu. <P> ! <center><img SRC="images/sequence-window.gif" width=470 height=314></center> <P> You can also translate the sequence to amino acids or view the virtual cDNA sequence *************** *** 965,972 **** After you create or edit annotations, you will probably want to save your work. Apollo supports several output formats, including <a href="http://www.sanger.ac.uk/Software/formats/GFF/">GFF</a> format and GAME XML. The GFF format is simpler (though less rich) ! and more compact. To save your annotations, select ! 'Save as...' from the File menu. <H3>Autosaving</H3> --- 972,981 ---- After you create or edit annotations, you will probably want to save your work. + To save your annotations, select + 'Save as...' from the File menu. Apollo supports several output formats, including <a href="http://www.sanger.ac.uk/Software/formats/GFF/">GFF</a> format and GAME XML. The GFF format is simpler (though less rich) ! and more compact. It is a good format for representing simple computational ! results, but is not the best choice for saving annotations. <H3>Autosaving</H3> *************** *** 1002,1005 **** --- 1011,1015 ---- into the blue annotation zone. For example, in this screenshot, the user has chosen a purple Genie prediction from the reverse strand and dragged it into the annotation area. + You can see the magenta "ghost" of the dragged Genie model in the blue annotation area. <P><center><img SRC="images/drag-to-create-gene-model.gif" width=146 height=196></center><P> As you drag the selected result(s), you will see a ghost image. When you drop them, *************** *** 1009,1016 **** Another way to create a gene model is by selecting features and using the right mouse popup menu option "Create gene model". A new annotation of that structure will appear in the evidence zone. ! (If you select exons from more than one gene a merge will occur.) [<b>Please note</b>: ! there is a bug in creating gene models from reverse-strand features--the new gene model ! will not appear until you click on another feature.] ! <h3>Modifying gene models</h3> --- 1019,1023 ---- Another way to create a gene model is by selecting features and using the right mouse popup menu option "Create gene model". A new annotation of that structure will appear in the evidence zone. ! (If you select exons from more than one gene a merge will occur.) <h3>Modifying gene models</h3> *************** *** 1543,1547 **** <tr> <td>DashSets</td> ! <td>This is a mysterious option that is poorly understood.</td> </tr> <tr> --- 1550,1555 ---- <tr> <td>DashSets</td> ! <td>Whether to use a dashed line to show sequence gaps in ESTs. (Color of dashed line ! is controlled by SequenceGapColor.)</td> </tr> <tr> *************** *** 1600,1604 **** <tr> <td>SequenceGapColor</td> ! <td>Color to use for showing gaps in the sequence.</td> </tr> <tr> --- 1608,1612 ---- <tr> <td>SequenceGapColor</td> ! <td>Color to use for showing gaps in ESTs.</td> </tr> <tr> *************** *** 1812,1816 **** <HR><P> <!-- hhmts start --> ! Last modified: Mon Sep 23 16:26:49 PDT 2002 <!-- hhmts end --> --- 1820,1824 ---- <HR><P> <!-- hhmts start --> ! Last modified: Tue Sep 24 16:39:11 PDT 2002 <!-- hhmts end --> |