X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=7abe66ab9547823dc9a19d83d656e0c97a977fbd;hb=f98565987df73493376993566bad1784d9c75e84;hp=b029e9687e4dabb949e425599dcdca08aab954ef;hpb=86e85aa5eaf27310d84ad693fe38adcdf8a87ca9;p=jalview.git
diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index b029e96..7abe66a 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -1,5 +1,21 @@
-
+
The Alignment Annotations File
@@ -33,18 +49,19 @@ separated value fields. Each value field is itself a comma separated list of fie
GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "|" symbol) are shown below:
- BAR_GRAPH
Plots a histogram with labels below each bar.
- number,text character
+ number,text character,Tooltip text
- LINE_GRAPH
Draws a line between values on the annotation row.
number
- NO_GRAPH
For a row consisting of text labels and/or secondary structure symbols.
- {Secondary Structure Symbol},text label
+ {Secondary Structure Symbol},text label,Tooltip text
Currently supported secondary structure structure symbols are H (for helix) and E (for strand)
Any or all value fields may be left empty, as well as the BAR_GRAPH's
text character field, and either or both of the text-label and secondary
-structure symbol fields of the NO_GRAPH type annotation rows.
+structure symbol fields of the NO_GRAPH type annotation rows.
+Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.
You can associate an annotation with a sequence by preceding its
definition with the line:
@@ -52,10 +69,19 @@ definition with the line:
All Annotations defined after a SEQUENCE_REF command will then be
associated with that sequence, and the first field in the Value field
list will (optionally) be placed at the startIndex'th column.
+New in Jalview 2.4: the tooltip displayed when the mouse is moved over the row
+label for sequence associated annotation gives the associated
+sequence's name followed by the annotation row's description.
+New in Jalview 2.5 Desktop: Clicking on a sequence or group associated annotation row's label will highlight the sequence or sequence group in the alignment, and double clicking the annotation row label will select the associated sequence or group.
Sequence associations are turned off for subsequent annotation
definitions by:
SEQUENCE_REF ALIGNMENT
+Since version 2.5, Jalview allows annotation rows to be associated with a group defined on the alignment, by preceding the annotation row with the line:
+
GROUP_REF group_name
+Group association is turned off for subsequent annotation rows by
+GROUP_REF ALIGNMENT
+Annotations may be associated with both a sequence and a group, however - group annotations are still experimental and unexpected behaviour may be observed when editing alignments containing both group and sequence associated annotation rows.
LINE_GRAPH type annotations can be given a colour
(specified as 24 bit RGB triplet in hexadecimal or comma separated
values), combined onto the same vertical axis, and have ordinate lines
@@ -65,6 +91,14 @@ following commands (respectively):
COMBINE graph_1_name graph_2_name
GRAPHLINE graph_name value label colour
+
(Since Jalview 2.5) ROWPROPERTIES
+The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:
+ROWPROPERTIES Row label centrelabs=true( or false) showalllabs=true(default is false) scaletofit=true (default is false)
+This sets the visual display properties according to the given values for all the annotation rows with labels matching Row label. The properties mostly affect the display of multi-character column labels, and are as follows:
+
- centrelabs Centre each label on its column.
+- showalllabs Show every column label rather than only the first of a run of identical labels (setting this to true can have a drastic effect on secondary structure rows).
+- scaletofit Shrink each label's font size so that the label fits within the column. Useful when annotating an alignment with a specific column numbering system. (Not available in Jalview applet due to AWT 1.1 limitations)
+
(Since Jalview 2.2.1) SEQUENCE_GROUP
Groups of sequences can be defined using the tab delimited line
SEQUENCE_GROUP Group_Name Group_Start Group_End Sequences
@@ -95,14 +129,24 @@ GRAPHLINE graph_name value label colo
textCol1=black
textCol2=black
textColThreshold=0
- idColour=ff3322
-New Features in 2.4: