Alignment Annotation

From effd8d76f34bc7fd4e069603d80565b7ea9d3ff0 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 11 Jul 2005 13:49:21 +0000 Subject: [PATCH] added help and documentation for annotation editing. --- help/help.jhm | 2 + help/helpTOC.xml | 7 ++- help/html/features/annotation.html | 83 +++++++++++++++++++++++++++++++++++ help/html/menus/alwannotations.html | 58 ++++++++++++++++++++++++ 4 files changed, 148 insertions(+), 2 deletions(-) create mode 100755 help/html/features/annotation.html create mode 100755 help/html/menus/alwannotations.html 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 +
+

+ + -- 1.7.10.2