From: jprocter Date: Mon, 11 Jul 2005 13:49:21 +0000 (+0000) Subject: added help and documentation for annotation editing. X-Git-Tag: Release_2_01~10 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=effd8d76f34bc7fd4e069603d80565b7ea9d3ff0;p=jalview.git added help and documentation for annotation editing. --- diff --git a/help/help.jhm b/help/help.jhm index 7f70ca4..5324b0b 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -8,6 +8,7 @@ + @@ -51,6 +52,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index c2221ac..2b8f8b9 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -7,10 +7,11 @@ + - + @@ -46,8 +47,10 @@ - + + + diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html new file mode 100755 index 0000000..3ad7f3e --- /dev/null +++ b/help/html/features/annotation.html @@ -0,0 +1,83 @@ + +Alignment Annotation + +

Alignment Annotation

+ +

In addition to the definition of groups, Jalview also allows you to +mark particular columns of an alignment and add symbols and text in +the annotation area shown below the alignment (which may be hidden if +View→Show Annotation is not ticked). +

+ +

+Annotation rows are added using the Annotation Label +menu, which is obtained by clicking anywhere on the annotation row labels +area (below the sequence ID area). +

    +
  • Add New Row
    +Adds a new, named annotation row (a dialog box will pop up for you +to enter the label for the new row). +
  • Hide Row
    +Hides the annotation row whose label was clicked in order to bring +up the menu. +
  • Delete Row
    +Deletes the annotation row whose label was clicked in order to bring +up the menu. +
  • Show All Hidden Rows
    +Shows all hidden annotation rows. +
  • Show Values in Text Box
    +Opens a text box with a list of comma-separated values +corresponding to the annotation (numerical or otherwise) at each +position in the row. This is useful to export alignment quality +measurements for further analysis. +
    • +
+

+Editing Label and secondary structure Annotation

+

+Use the left mouse button to select a position along the row that are to +be annotated - these regions will be coloured red. Control and shift in combination +with the left-click will select more than one position, or a range of +positions on the alignment. +

+

Once the desired position has been selected, use the right mouse +button to open the annotation menu:

+
    +
  • Helix
    Mark selected positions with a helix glyph (a red +oval), and optional text label (see below). A +dialog box will open for you to enter the text. Consecutive ovals +will be rendered as an unbroken red line. +
    • +
  • Sheet
    Mark selected positions with a sheet glyph (a green +arrow oriented from left to right), and optional text label (see +below). A dialog box will open for you to enter the text. Consecutive +arrows will be joined together to form a single green arrow. +
    • +
  • Label
    Set the text label at the selected positions. A +dialog box will open for you to enter the text. If +more that one consecutive position is marked with the same label, only +the first position's label will be rendered. +
    • +
  • Colour
    Changes the colour of the annotation text label. +
    • +
  • Remove Annotation
    Blanks any annotation at the selected positions on +the row. Note: This cannot be undone +
    • +
+

+Annotation is stored and retrieved using Jalview Archives. Quantitative +annnotation is also possible, but currently only possible with the +JNet web service, or by creating your own Jalview Archive (which +contains XML conforming to the Jalview-Vamsas XML schema). +

+

Current Limitations

+ +

In the current version of Jalview, reordering of the annotation +rows is not possible. If you save +your annotation as a Jalview file, however, it will be reloaded with user +annotations at the top (nearest the alignment), above any of the +automatically generated Conservation, Quality or consensus +annotations.

+ + diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html new file mode 100755 index 0000000..f7b62ca --- /dev/null +++ b/help/html/menus/alwannotations.html @@ -0,0 +1,58 @@ + + +Annotation Panel Menus + + +

Annotation Panel Menus

+
    +
  • +Annotation Label Popup Menu
    +This menu is opened by clicking anywhere on the annotation row labels +area (below the sequence ID area). +
      +
    • +Add New Row
      +Adds a new, named annotation row (a dialog box will pop up for you +to enter the label for the new row). +
    • Hide Row
      +Hides the annotation row whose label was clicked in order to bring +up the menu. +
    • Delete Row
      +Deletes the annotation row whose label was clicked in order to bring +up the menu. +
    • Show All Hidden Rows
      +Shows all hidden annotation rows. +
    • Show Values in Text Box
      +Opens a text box with a list of comma-separated values +corresponding to the annotation (numerical or otherwise) at each +position in the row. This is useful to export alignment quality +measurements for further analysis. +
      • +
    +
    • +
  • Annotation Popup Menu
    This menu is opened when +right-clicking on the selected positions of an annotation. +
      +
    • Helix
      Mark selected positions with a helix glyph (a red +oval), and optional text label (see below). Consecutive ovals +will be rendered as an unbroken red line. +
      • +
    • Sheet
      Mark selected positions with a sheet glyph (a green +arrow oriented from left to right), and optional text label (see +below). Consecutive arrows will be joined together to form a single +green arrow. +
      • +
    • Label
      Sets the text label at the selected positions. If +more that one consecutive position is marked with the same label, only +the first position's label will be rendered. +
      • +
    • Colour
      Changes the colour of the annotation text label. +
      • +
    • Remove Annotation
      Blanks any annotation at the selected positions on +the row. Note: This cannot be undone +
      • +
    +
    • +
+ +