Changeset 3400
- Timestamp:
- May 29, 2007, 8:47:04 AM (16 years ago)
- Location:
- trunk
- Files:
-
- 7 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/src/docbook/userdoc/annotations.xml
r3396 r3400 34 34 <title>Annotation Types</title> 35 35 36 <helptext id="annotationtype.view.properties"36 <helptext external_id="annotationtype.view.properties" 37 37 title="Annotation types"> 38 38 <para> … … 565 565 566 566 <para> 567 Annotation types marked with angle brackets are protocol 568 parameters. 567 Annotation types marked with angle brackets 568 <nohelp> 569 (<inlinemediaobject> 570 <imageobject><imagedata fileref="figures/parameter.gif" format="GIF" 571 /></imageobject> 572 </inlinemediaobject>)</nohelp> 573 are protocol parameters. 569 574 </para> 570 575 … … 589 594 <listitem> 590 595 <para> 591 <guilabel>uncategorized</guilabel>: Display only anno atation types596 <guilabel>uncategorized</guilabel>: Display only annotation types 592 597 that hasn't been put into a category. 593 598 </para> … … 596 601 </para> 597 602 603 <seeother> 604 <other external_id="annotations.edit.inherited">Inherit annotations</other> 605 </seeother> 598 606 599 607 </helptext> … … 601 609 <sect2 id="annotations.inheriting"> 602 610 <title>Inheriting annotations from other items</title> 611 612 <helptext external_id="annotations.edit.inherited" 613 title="Inherit annotations"> 614 <para> 615 An item may inherit annotations from any of it's parent items. 616 E.g. an extract can inherit annotations from the sample or biosource 617 it was created from. This is an important feature to make the 618 experimental factors work. Annotations that should be used as 619 experimental factors must be inherited to the raw bioassay level. 620 <nohelp>See <xref linkend="experiments_analysis.experiment.factors" /> for more 621 information about experimental factors.</nohelp> 622 </para> 623 624 <nohelp> 625 <figure 626 id="annotations.figures.inherit"> 627 <title>Inheriting annotations from a parent item</title> 628 <screenshot> 629 <mediaobject> 630 <imageobject> 631 <imagedata 632 fileref="figures/inherit_annotations.png" format="PNG" /> 633 </imageobject> 634 </mediaobject> 635 </screenshot> 636 </figure> 637 </nohelp> 638 639 <para> 640 On this screen is a tree-like structure in two levels. The first level 641 lists all parent items which has at least one annotations. The second 642 level lists the annotations and protocol parameters for the item. 643 Selecting an item in the first level will inherit all annotations 644 from that item, including those that you maybe add later. 645 Selecting an annotation or protocol parameter at the second level 646 will inherit only the selected one. 647 </para> 648 649 <note> 650 <itemizedlist> 651 <listitem> 652 <para> 653 The inheritance is implemented by reference. This means that if 654 you change the value of an annotation the new value is automatically 655 picked up by those inheriting it. 656 </para> 657 </listitem> 658 <listitem> 659 <para> 660 You can't inherit annotations from an item which doesn't have 661 annotations. 662 </para> 663 </listitem> 664 <listitem> 665 <para> 666 If you delete an annotation from a parent item, the inheritance will 667 be lost, even if you later add a value again. 668 </para> 669 </listitem> 670 </itemizedlist> 671 </note> 672 673 <warning> 674 <para> 675 If you rearrange links to parent items after you have 676 specified inheritance, it may happen that you are inheriting 677 annotation from non-parent items. This will be flagged with a warning 678 icon in the list, and must be fixed manually. The experiment validation 679 tool is an excellent help for locating this kind of problems. 680 <nohelp>See <xref linkend="experiments_analysis.experiment.overview" />.</nohelp> 681 </para> 682 </warning> 683 684 <seeother> 685 <other external_id="annotations.edit">Annotations and parameters</other> 686 <other external_id="experiment.edit.factors">Experimental factors</other> 687 <other external_id="experiment.overview">Experiment validation tool</other> 688 </seeother> 689 690 </helptext> 691 603 692 </sect2> 604 693 -
trunk/doc/src/docbook/userdoc/experiments.xml
r3394 r3400 272 272 in the analysis of your data the values must be accessible 273 273 from the raw bioassays. Since most of your annotations are 274 probably made at the sample level the raw bioassays must275 inherit those annotations.276 <nohelp>Read <xref linkend="annotations " />274 probably made at the sample or biosource level the raw bioassays 275 must inherit those annotations. 276 <nohelp>Read <xref linkend="annotations.inheriting" /> 277 277 for more information about this.</nohelp> 278 278 </para> … … 300 300 <sect2 id="experiments_analysis.experiment.overview"> 301 301 <title>Experiment overview</title> 302 303 <helptext external_id="experiment.overview" 304 title="Experiment overview"> 302 305 303 306 <para> … … 310 313 </para> 311 314 315 <nohelp> 312 316 <para> 313 317 You can access the overview of an experiment by navigating … … 327 331 </screenshot> 328 332 </figure> 329 330 <helptext external_id="experiment.overview" 331 title="Experiment overview"> 333 </nohelp> 334 332 335 <para> 333 336 The page is divided into three sections: … … 416 419 <varlistentry> 417 420 <term> 418 <indexterm><primary>Presets</primary><secondary>experiment validation</secondary></indexterm>419 421 <guilabel>Presets</guilabel></term> 420 422 <listitem> -
trunk/www/lims/plates/edit_plate.jsp
r2978 r3400 296 296 </t:tab> 297 297 298 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.in erited">298 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited"> 299 299 300 300 <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp" -
trunk/www/views/experiments/bioassays/edit_bioassay.jsp
r2978 r3400 181 181 </t:tab> 182 182 183 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.in erited">183 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited"> 184 184 <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../../common/annotations/wait.jsp" 185 185 width="100%" height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0 -
trunk/www/views/experiments/bioassaysets/edit_bioassayset.jsp
r2978 r3400 193 193 </t:tab> 194 194 195 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.in erited">195 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited"> 196 196 <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../../common/annotations/wait.jsp" 197 197 width="100%" height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0 -
trunk/www/views/rawbioassays/edit_rawbioassay.jsp
r2978 r3400 695 695 </t:tab> 696 696 697 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.in erited">697 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited"> 698 698 <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp" 699 699 width="100%" height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0 -
trunk/www/views/scans/edit_scan.jsp
r2978 r3400 440 440 </t:tab> 441 441 442 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.in erited">442 <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited"> 443 443 444 444 <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp"
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