Annotation Colouring

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=ed0ab3feaf095959753e40e983a0c02b2df56755;hb=f3ee64e736d9c83256679e1cfed989d8dd560088;hp=e8c87e1326e7eb47c246e39ca3539350692cfcd6;hpb=0e6634756268f473daa6dc76ddd21890baa88820;p=jalview.git diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html index e8c87e1..ed0ab3f 100755 --- a/help/html/colourSchemes/annotationColouring.html +++ b/help/html/colourSchemes/annotationColouring.html @@ -1,61 +1,100 @@ -Annotation Colouring + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +Annotation Colouring + -

Annotation Colouring

Jalview allows the columns of an alignment to be coloured using any - numerical annotation rows added to that alignment.

-Select "Colour" → ".. - by Annotation" to bring up the Colour by Annotation settings window.
-

Select which annotation to base the colouring scheme on using the top left - selection box.
If the "Use Original Colours" box is selected, the colouring - scheme will use the colouring scheme present on the alignment before the Annotation - Colour Settings window was displayed.
The colour scheme can display a colour gradient from a colour - representing the minimum value in the selected annotation to a colour - representing the maximum value in the selected annotation. Use the - "Min Colour" and "Max Colour" to set the colour - gradient range. -
- New in Jalview 2.7: Press the "Defaults" - button to reset the minimum and maximum colours to their default - settings (these are configured in the applet's parameters or the application's user - preferences.) -
-

+ Annotation Colouring +

Jalview allows the columns of an alignment to be coloured using + any numerical annotation rows added to that alignment.

→

Select which annotation to base the colouring scheme on + using the top left selection box. Sequence associated alignment + annotation are shown with the seuqence's name appended.
If + the Per-sequence only tick box is not greyed out, + then ticking it will limit the list of available annotation rows + to just the labels for those that are sequence associated. + Annotation rows on each sequence with the same label (e.g. + T-COFFEE scores and protein + disorder predictions) will then be used to colour its + corresponding positions in the alignment.
Per-sequence + associated annotation colouring is currently only available in + the Desktop. +
If the "Use Original Colours" box is selected, + the colouring scheme will use the colouring scheme present on the + alignment before the Annotation Colour Settings window was + displayed.
Please Note: If no + colour scheme was applied previously, then the colours for lines + and labels at each position in the annotation row will be used, + for secondary structure symbols and graphs, this may be black by + default, so your alignment will be coloured black. +
Secondary structure annotation colouring
By + default, Jalview will employ the helix or sheet colours to shade + sequences and columns by available secondary structure annotation + tracks. In the case of RNA, each structure is processed to + identify distinct RNA helices and rendered in the same way as the + RNA Helices shading scheme. + Structure based sequence shading was added in Jalview + 2.8.2
The colour scheme can display a colour gradient from a + colour representing the minimum value in the selected annotation + to a colour representing the maximum value in the selected + annotation. Use the "Min Colour" and "Max + Colour" to set the colour gradient range. +
- Press the "Defaults" button to reset the + minimum and maximum colours to their default settings (these + are configured in the applet's parameters or the application's user preferences.).
  Default min + and max colours were introduced in Jalview 2.7 +
+
Select whether to colour the alignment above or below an adjustable threshold - with the selection box center left of the window.
Change the threshold value with the slider, or enter the - exact value in the text box. -
Select the "Threshold is Min/Max" checkbox to - assign colours using the thresholded range's minimum and maximum - values, otherwise the scale will be defined by the range of values in - the annotation row.

Select whether to colour the alignment above or below an + adjustable threshold with the selection box center left of the + window.
Change the threshold value with the slider, or enter the + exact value in the text box.
Select the "Threshold is Min/Max" checkbox to + assign colours using the thresholded range's minimum and maximum + values, otherwise the scale will be defined by the range of values + in the annotation row.

+ +