Changeset 6961
- Timestamp:
- Oct 1, 2015, 1:23:03 PM (7 years ago)
- Location:
- trunk/doc/src/docbook
- Files:
-
- 4 added
- 5 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/src/docbook/user/annotations.xml
r6805 r6961 644 644 645 645 <para> 646 Click on an entry in the list of annotation types to show a 647 form for entering a value for it to the right. Depending 646 All possible annotation types are listed under the 647 <guilabel>Primary annotations</guilabel> section. Click 648 on an entry in the list to display a form for entering 649 a value for the annotation. Depending 648 650 on the options set on the annotation type the form may be a simple 649 651 free text field, a list of checkboxes or radiobuttons, or … … 652 654 653 655 <para> 654 Annotation types with an <guilabel> X</guilabel> in front656 Annotation types with an <guilabel>x</guilabel> in front 655 657 of their names already have a value. 656 658 </para> … … 659 661 Annotation types marked with angle brackets 660 662 <nohelp> 661 (<guiicon> 662 <inlinemediaobject> 663 <imageobject><imagedata fileref="figures/parameter.png" format="PNG" 664 /></imageobject> 665 </inlinemediaobject> 666 </guiicon>) 663 (<guiicon><inlinemediaobject><imageobject><imagedata fileref="figures/parameter.png" format="PNG" 664 /></imageobject></inlinemediaobject></guiicon>) 667 665 </nohelp> 668 666 are protocol parameters. … … 696 694 </para> 697 695 696 698 697 <seeother> 699 <other external_id="annotations. edit.inherited">Inherit annotations</other>698 <other external_id="annotations.inherit">Inherit annotations</other> 700 699 </seeother> 701 700 … … 705 704 <title>Inheriting annotations from other items</title> 706 705 707 <helptext external_id="annotations. edit.inherited"706 <helptext external_id="annotations.inherit" 708 707 title="Inherit annotations"> 709 708 <para> … … 712 711 it was created from. This is an important feature to make the 713 712 experimental factors work. Annotations that should be used as 714 experimental factors must be inherited to the r aw bioassay level.713 experimental factors must be inherited to the root raw bioassay level. 715 714 <nohelp>See <xref linkend="experiments_analysis.experiment.factors" /> for more 716 information about experimental factors.</nohelp> 717 </para> 715 information about experimental factors.</nohelp> Click on the 716 <guibutton>Inherit…</guibutton> button to open a dialog for inheriting 717 annotations. 718 </para> 719 720 <para> 721 Annotations can either be inherited by reference (the default) or as a cloned value. Inheriting 722 by reference means that if you change the value of the source annotation the new value is automatically 723 picked up by all items inheriting it. A cloned annotation is a copy 724 of the original annotation and it is not automatically updated if the original 725 annotation is modified. 726 </para> 727 728 <para> 729 Inherited and cloned annotations are listed under the <guilabel>Inherited & cloned</guilabel> 730 section. Inherited annotations are marked with <guiicon><inlinemediaobject><imageobject><imagedata 731 fileref="figures/inherited.png" format="PNG" 732 /></imageobject></inlinemediaobject></guiicon> and are always a references back to the original 733 value. Cloned annotations are marked with a double <guilabel>xx</guilabel>. Cloned annotations 734 that are out-of-sync with their source annotations are marked with <guiicon><inlinemediaobject><imageobject><imagedata 735 fileref="figures/cloned-outofsync.png" format="PNG" 736 /></imageobject></inlinemediaobject></guiicon>. 737 </para> 738 739 <variablelist> 740 <varlistentry> 741 <term> 742 <guilabel>Inherit...</guilabel> 743 </term> 744 <listitem> 745 <para>Opens the <guilabel>Inherit annotations</guilabel> dialog (see below).</para> 746 </listitem> 747 </varlistentry> 748 <varlistentry> 749 <term> 750 <guilabel>Delete</guilabel> 751 </term> 752 <listitem> 753 <para> 754 Will remove values from the checked primary annotations and delete 755 links to inherited and cloned annotations. 756 </para> 757 </listitem> 758 </varlistentry> 759 <varlistentry> 760 <term> 761 <guilabel>Sync, Clone, Unclone</guilabel> 762 </term> 763 <listitem> 764 <para> 765 Convert between INHERITED and CLONED annotation and synchronizes 766 cloned annotations with their source annotation in case the values 767 have changed. 768 </para> 769 </listitem> 770 </varlistentry> 771 </variablelist> 718 772 719 773 <nohelp> … … 733 787 734 788 <para> 735 On this screen is a tree-like structure in two levels. The first level 736 lists all parent items which has at least one annotations. The second 789 In this dialog there is a tree-like structure in two levels to the left. 790 The first level 791 lists all parent items which has at least one annotation. The second 737 792 level lists the annotations and protocol parameters for the item. 738 793 Selecting an item in the first level will inherit all annotations 739 from that item, including those that you maybe add later. 740 Selecting an annotation or protocol parameter at the second level 741 will inherit only the selected one. 794 from that item. Selecting an annotation or protocol parameter at 795 the second level will inherit only the selected one. 742 796 </para> 743 797 … … 757 811 <listitem> 758 812 <para> 759 The inheritance is implemented by reference. This means that if 760 you change the value of an annotation the new value is automatically 761 picked up by those inheriting it. 762 </para> 763 </listitem> 764 <listitem> 765 <para> 766 You cannot inherit annotations from an item which does not have 767 annotations. 813 Already inherited annotations are not shown in the dialog. 814 </para> 815 </listitem> 816 <listitem> 817 <para> 818 By default, the inheritance is implemented by reference. To convert 819 it to a cloned annotation select it in the list and click on <guilabel>clone</guilabel>. 820 <nohelp> 821 <figure> 822 <title>Convert to a cloned annotation</title> 823 <screenshot> 824 <mediaobject> 825 <imageobject> 826 <imagedata 827 fileref="figures/clone_annotation.png" format="PNG" /> 828 </imageobject> 829 </mediaobject> 830 </screenshot> 831 </figure> 832 </nohelp> 833 768 834 </para> 769 835 </listitem> … … 845 911 <para> 846 912 For each annotation type you can select if you want to 847 <guilabel>inherit</guilabel> new annotations or <guilabel>remove</guilabel> 848 existing inherited annotations. It is possible to use different 913 <guilabel>inherit</guilabel> or <guilabel>clone</guilabel> new annotations, 914 <guilabel>remove</guilabel> existing inherited annotations or 915 <guilabel>resync</guilabel> existing cloned annotation. It is possible to use different 849 916 actions for different annotation types. 850 917 </para> -
trunk/doc/src/docbook/user/experiments.xml
r5800 r6961 291 291 To be able to use the values of the experimental factors 292 292 in the analysis of your data the values must be accessible 293 from the raw bioassays. Since most of your annotations are 294 probably made at the sample or biosource level the raw bioassays 295 must inherit those annotations. 296 <nohelp>Read <xref linkend="annotations.inheriting" /> 297 for more information about this.</nohelp> 298 </para> 299 293 from the <guilabel>root raw bioassays</guilabel>. A root raw bioassay 294 is a wrapper around a raw bioassay that is part of the experiment and 295 it has two purposes: 296 </para> 297 298 <itemizedlist> 299 <listitem> 300 <para> 301 Hold experimental factor values for the raw bioassay in the 302 context of the current experiment without affecting other 303 experiments were the same raw bioassay is used. 304 </para> 305 </listitem> 306 <listitem> 307 <para> 308 Give the owner of the experiment control over the experimental factor 309 values used. In a multi-project setting this is important since the 310 owner of the raw bioassay may not permit changes to the raw bioassay. 311 Use the <guilabel>clone</guilabel> feature when inheriting 312 annotations to the root raw bioassay to make sure that downstream 313 analysis is not affected by changes made to the original parent 314 annotations (unless you do a manual <guilabel>resync</guilabel>). 315 </para> 316 </listitem> 317 </itemizedlist> 318 319 <para> 320 Since most of your annotations are probably made at the sample or biosource 321 level the root raw bioassays must inherit or clone those annotations. 322 The experiment view page lists all experimental factors and their current 323 values for each root raw bioassay. 324 </para> 325 326 <para> 327 There is a quick access to the <link linkend="annotations.batch-inherit">batch inherit</link> 328 function that makes it easy to inherit any annotations that are missing. 329 <nohelp>See also <xref linkend="annotations.inheriting" /> for more information about inheriting annotations.</nohelp> 330 </para> 331 332 <nohelp> 333 <figure id="experiments_analysis.figures.experiment_factor_values"> 334 <title>Experimental factor values</title> 335 <screenshot> 336 <mediaobject> 337 <imageobject><imagedata 338 fileref="figures/experiment_factor_values.png" format="PNG" 339 /></imageobject> 340 </mediaobject> 341 </screenshot> 342 </figure> 343 </nohelp> 344 300 345 <tip> 301 346 <para>
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