From: Brandon King Date: Tue, 17 Oct 2006 17:29:52 +0000 (+0000) Subject: Mussa Manual: create/load analysis section updated X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=16a7a04557c8ea2e5ac9a75e4b3fa6624d572893 Mussa Manual: create/load analysis section updated * Updated text/screenshots in the "Create new analysis" section (ticket #169) * Updated text/screenshots in "Load a mussa parameter file" section. (ticket #181) * Updated text/screenshots in "Load an analysis" section. 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King --------------- -Last updated: Oct 16th, 2006 +Last updated: Oct 17th, 2006 -Updated to Mussagl build: 287? (In process to 424) +Updated to Mussagl build: (In process to 424) .. Things to add @@ -507,11 +507,12 @@ Instructions: 'demo_w30_t20'. Mussa will create a folder with this name to store the analysis files in once it has been run. - 2. Choose a `window size`_. For this demo **choose 30**. - - 3. Choose a threshold_... for this demo **choose 20**. See the + 2. Choose a threshold_... for this demo **choose 20**. See the Threshold_ section for more detailed information. + 3. Choose a `window size`_. For this demo **choose 30**. + + 4. Choose the number of sequences_ you would like. For this demo **choose 3**. @@ -519,12 +520,13 @@ Instructions: :alt: Steps 1-4 :align: center -Now click on the 'Browse' button next to the sequence input box and -then select /examples/seq/human_mck_pro.fa file. Do the same in the -next two sequence input boxes selecting mouse_mck_pro.fa and -rabbit_mck_pro.fa as shown below. Note that you can create annotation -files using the mussa `Annotation File Format`_ to add annotations to -your sequence. +First enter the species name of "Human" in the first "Species" text +box. Now click on the 'Browse' button next to the sequence input box +and then select /examples/seq/human_mck_pro.fa file. Do the same in +the next two sequence input boxes selecting mouse_mck_pro.fa and +rabbit_mck_pro.fa as shown below. Make sure to give them a species +name as well. Note that you can create annotation files using the +mussa `Annotation File Format`_ to add annotations to your sequence. .. image:: images/define_analysis_step2.png :alt: Choose sequences @@ -537,10 +539,13 @@ something similar to the following screen shot. :alt: Mussagl Demo :align: center -This analysis is now saved in a directory called **demo_w30_t20** in -the current working directory. If you close and reopen Mussagl, you -can reload the saved analysis. See `Load an analysis`_ section below -for details. +By default your analysis is NOT saved. If you try to close an analysis +without saving, you will be prompted with a dialog box asking you if +you would like to save your analysis. The `Saving`_ section for +details on saving your analysis. When saving, choose directory and +give the analysis the name **demo_w30_t20**. If you close and reopen +Mussagl, you will then be able to load the saved analysis. See `Load +an analysis`_ section below for details. Load a mussa parameter file @@ -551,7 +556,7 @@ parameter file. See the `Parameter File Format`_ section for details on creating a .mupa file. Once you have a .mupa file created, load Mussagl and select the **File > -Load Mussa Parameters** menu option. Select the .mupa file and click +Create Analysis from File** menu option. Select the .mupa file and click open. .. image:: images/load_mupa_menu.png @@ -571,7 +576,7 @@ Load an analysis ~~~~~~~~~~~~~~~~ To load a previously run analysis open Mussagl and select the **File > -Load Analysis** menu option. Select an analysis **directory** and +Open Existing Analysis** menu option. Select an analysis **directory** and click open. .. image:: images/load_analysis_menu.png