Alignment Annotation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=8d78c59996c8f97e6877ea06f2626629addfe202;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=3ad7f3e6cd599e463eaa1a8d470f529cff1c13b7;hpb=effd8d76f34bc7fd4e069603d80565b7ea9d3ff0;p=jalview.git diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 3ad7f3e..8d78c59 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -1,83 +1,123 @@ - -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.

- - + + +Alignment Annotation + +

Alignment Annotation

+ +

In addition to the definition of groups and sequence features, + Jalview can display symbols and graphs under the columns of an + alignment, and allow 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). Any displayed annotation row can be hidden (using the pop-up + menu obtained by right-clicking the label), or re-ordered by dragging the label to a new + position with the left mouse button.

+Web services can also add annotation to an alignment (see the JNet and Disorder protein +structure prediction services), and as of Jalview 2.08 quantitative +and symbolic annotations can be added to an alignment via an Annotations File dragged into the +alignment window or loaded from the alignment's file menu. +

Interactive Alignment Annotation

+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.
Export Annotation (Application only)
+ Annotations can be saved to file or output to a text window in either the + Jalview annotations format or as a spreadsheet style set of comma separated values (CSV).
Show Values in Text Box (applet only)
+ 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. +
Scale Label To Column(introduced in 2.5)
+ Selecting this toggles whether column labels will be shrunk to fit within each column, or displayed using the view's standard font size.

+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. +
RNA Helix (only shown when working with nucleotide sequences)
+Mark selected positions as participating in a base pair +either upstream or downstream. When the dialog box opens, enter a +'(' to indicate these bases pair with columns upstream (to right), +and ')' to indicate this region pairs with bases to the left of the +highlighted columns.
If any brackets do not match up, then an +orange square will highlight the first position where a bracket was +found not to match. + +
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 +

+User defined annotation is stored and retrieved using Jalview Archives. +

Current Limitations

As of version 2.5, the Jalview user interface does not support the +creation and editing quantitative annotation (histograms and line graphs), or +to create annotation associated with a specific sequence. It is also incapable of +annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an +Annotation file.
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