Annotation Colouring

From: amwaterhouse Date: Tue, 4 Apr 2006 17:06:01 +0000 (+0000) Subject: New files X-Git-Tag: Release_2_08~67 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b66118c2f1447ade32ba9791150fc055a9137bfc;p=jalview.git New files --- diff --git a/help/html/colourSchemes/annotationColourSetting.jpg b/help/html/colourSchemes/annotationColourSetting.jpg new file mode 100755 index 0000000..7ca9acb Binary files /dev/null and b/help/html/colourSchemes/annotationColourSetting.jpg differ diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html new file mode 100755 index 0000000..ec01fa9 --- /dev/null +++ b/help/html/colourSchemes/annotationColouring.html @@ -0,0 +1,30 @@ + + +Annotation Colouring + + +

Annotation Colouring

Jalview 2.08 allows an alignment to be coloured on a per-column basis based + on any numerical annotation 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.
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.

+ + diff --git a/help/html/colourSchemes/annotationColours.jpg b/help/html/colourSchemes/annotationColours.jpg new file mode 100755 index 0000000..36d100e Binary files /dev/null and b/help/html/colourSchemes/annotationColours.jpg differ diff --git a/help/html/editing/editing.jpg b/help/html/editing/editing.jpg new file mode 100755 index 0000000..d67f17b Binary files /dev/null and b/help/html/editing/editing.jpg differ diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html new file mode 100755 index 0000000..c2a784c --- /dev/null +++ b/help/html/features/annotationsFormat.html @@ -0,0 +1,47 @@ + + +Annotations File Format + + +

Alignment Annotations File Format
+
+ A precalculated annotations fiile can read onto an alignment from the command + line ("-annotations"), by drag and dropping the the annotations file + onto an alignment or by selecting from the File menu "Load Features / Annotations".

The File is in tab delimited format. The file must have the line JALVIEW_ANNOTATION + as an identifier. Then a block of annotations are added in the form GRAPH_TYPE + Label Values

GRAPH_TYPE can be either BAR_GRAPH, LINE_GRAPH or NO_GRAPH. The values are + per alignment column, separated by "|". Multiple content per column + can be separated with commas, Jalview will display the content if it interprates + the content as a text label, or secondary structure character (H or E)

You can optionally associate an annotation with a sequence by adding a line + SEQUENCE_REFseq_namestartIndex All Annotations after a SEQUENCE_REF will be + associated with that sequence. Use SEQUENCE_REF ALIGNMENT to cancel the associtations.

The visual graphs can be coloured or combined with other graphs, or have an + arbitrary line drawn at a certain value using the following lines.

COLOUR<tab>graph name<tab>colour
+ COMBINE<tab>graph 1 name<tab>graph 2 name
+ GRAPHLINE<tab>graph name<tab>value<tab>label<tab>colour

An example Annotation file may look like this:

#Comment lines follow the hash symbol
+ JALVIEW_ANNOTATION
+ SEQUENCE_REF FER1_MESCR 5
+ BAR_GRAPH<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+ LINE_GRAPH<tab>Green Values<tab>1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+ LINE_GRAPH<tab>Red Values<tab>2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+ BAR_GRAPH<tab>Bar Graph<tab>2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+ NO_GRAPH<tab>Icons <tab>||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+ NO_GRAPH<tab>Purple Letters<tab>m|y|p|r|o|t|e|i|n

COLOUR<tab>Bar Graph 2<tab>blue
+ COLOUR<tab>Red Values<tab>255,0,0
+ COLOUR<tab>Green Values<tab>green
+ COLOUR<tab>Purple Letters<tab>151,52,228
+ COMBINE<tab>Green Values<tab>Red Values

GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black +
+

+ + diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html new file mode 100755 index 0000000..8e6ee13 --- /dev/null +++ b/help/html/features/featuresFormat.html @@ -0,0 +1,35 @@ + + +Features File Format + + +

Sequence Features File Format

(Prior to version 2.08 known as the "Groups file")
+ A precalculated Features file can read onto an alignment from the command line + ("-features"), by drag and dropping the features file onto an alignment + or by selecting from the File menu "Load Features / Annotations".

Specify the feature types first, then refer to the feature type for each sequence.

featureType<tab>colour
+ description<tab>sequenceId<tab>sequenceIndex<tab>start<tab>end<tab>featureType

eg
+ domain red
+ metal ion-binding site 00ff00
+ transit peptide 0,105,215
+ chain 225,105,0
+ modified residue 105,225,35
+ signal peptide 0,155,165
+ Your Own description here FER_CAPAA -1 3 93 domain
+ Your Own description here FER_CAPAN -1 48 144 chain
+ Your Own description here FER_CAPAN -1 50 140 domain
+ Your Own description here FER_CAPAN -1 136 136 modified residue
+ Your Own description here FER1_LYCES -1 1 47 transit peptide
+ Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide
+ Your Own description here Q93XJ9_SOLTU -1 49 144 chain

An additional option in Jalview 2.08 is to group features in the following + way:

STARTGROUP<tab>My feature groupA
+ ....Many Feature descriptions here
+ ENDGROUP<tab>My feature groupA
+

+ +