DAS Features

Execute groovy script in FILE (where diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html index 9cffc51..92d9323 100644 --- a/help/html/features/commandline.html +++ b/help/html/features/commandline.html @@ -49,11 +49,11 @@ provided by InstallAnywhere any output from the application will be sent to output.txt, not standard out.
The Jalview application also requires a number of additional libraries on the - class path. The command line below adds the Jalview installation's - 'lib' directory to the list of directories that are searched for - jars to be added to the classpath: + class path. The command line below adds all the jar files in the + Jalview installation's 'lib' directory to the classpath, as well as + the Jalview application jar file:
-
java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE]
+
java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE]

Use '-help' to get more information on the command line arguments that diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html deleted file mode 100644 index 1965e70..0000000 --- a/help/html/features/dasfeatures.html +++ /dev/null @@ -1,77 +0,0 @@ - - - -DAS Features - - - -
- DAS Sequence Feature Retrieval -
-
Jalview includes a client for retrieving sequences and their - features via the Distributed Annotation System.
-
-
Open the Feature Settings panel by selecting "View - -> Feature Settings..."
-
Click on the "DAS - Settings" tabbed pane. -
-
Select the sources to use for DAS feature retrieval, then - click the "Fetch DAS Features" button. -
-
Cancelling Feature Retrieval
Press the Cancel - Fetch button to immediately stop feature retrieval. This - will not remove any features already added to the alignment, - but will halt any outstanding DAS requests.The cancel - fetch button is of particular use when one or more DAS - annotation servers are not responding! -
-
-
-
- If your DAS source selection contains sources which use UniProt - accession ids, you will be asked whether Jalview should find UniProt - Accession ids for the given sequence names. It is important to - realise that many DAS sources only use UniProt accession ids, rather - than Swissprot/UniProt sequence names.
The database - reference fetcher documentation describes how Jalview discovers - what database references are appropriate for the sequences in the - alignment. -
-
Note
Please remember to save your - alignment if either the start/end numbering, or the sequence IDs - were updated during the ID retrieval process.
-
-
-
- DAS support was introduced in Jalview Version 2.1. -
-
-
- The DAS registry at http://www.dasregistry.org was - decommissioned early in 2015. An unmaintained mirror is currently - hosted at http://www.ebi.ac.uk/das-srv/registry/. -
-
- - diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html deleted file mode 100644 index 9600070..0000000 --- a/help/html/features/dassettings.html +++ /dev/null @@ -1,74 +0,0 @@ - - - -DAS Settings - - - -
- DAS Settings -
-
- Jalview can retrieve sequences and features from many DAS sources. The DAS sources - that it uses are discovered and selected via the DAS - settings panel, opened either from the View→Feature Settings dialog - box from the alignment window's menu bar, or the Tools→Preferences - dialog box opened from the Desktop menu bar. -
-
- -
The available sources are listed in the table using each - source's Nickname as its identifier. Clicking on a source's entry in - the table reveals more information about that service in the panel - to the right. Select the tickbox in the "Use Source" - column for a source to add it to the set Jalview queries for - alignment and sequence features.
-
You can filter the visible DAS sources by authority, type and - "label". You should read the DAS documentation to - understand more about these values. -
- Updating the list of sources -
-
- When the DAS Settings panel is first opened, and when the 'Refresh - source' buton is pressed, a list of DAS sources is retrieved from - the DAS registry URL. Note that the registry hosted at - http://www.dasregistry.org/das/ was retired at the start of 2015. An - alternative service is currently hosted at - http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this - service, ensure your .jalview_properties file includes the following - line:
DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/ -
-
- Adding your own DAS Sources -
-
You can add your own DAS source to the list by clicking the - "Add Local Source" button. Enter the URL and nickname of - your additional service. It should be noted that Jalview 2.1 will - not query additional sources for more information, but this will be - implemented in future editions. -
- - diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index fd6b99f..4d13dcd 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -60,7 +60,10 @@ contains tab separated text fields. No comments are allowed.
-
The first set of lines contain type definitions: +
+ Feature Colours +
+
The first set of lines contain feature type definitions and their colours:
Feature label Feature Colour @@ -72,21 +75,37 @@

A single colour specified as either a red,green,blue 24 bit triplet in hexadecimal (eg. 00ff00) or as comma separated numbers - (ranging from 0 to 255))
+ (ranging from 0 to 255))
+ (For help with colour values, see https://www.w3schools.com/colors/colors_converter.asp.)
A graduated colourscheme specified as a "|" separated list of fields:
-[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]] +[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
The fields are as follows:
-
label
Indicate that the feature +
label
Indicates that the feature description should be used to create a colour for features of this type.
Note: if no threshold value is - needed then the final '|' may be omitted.
This + needed then only 'label' is required.
This keyword was added in Jalview 2.6
+
score
Indicates that the feature + score should be used to create a graduated colour for features of + this type, in conjunction with mincolor, maxcolor.
This keyword was added in Jalview 2.11. + It may be omitted (score is the default) if mincolor and maxcolor are specified. +
+ +
attribute|attName
Indicates that the value of feature + attribute 'attName' should be used to create a colour for features of + this type. +
For example, attribute|clinical_significance to colour by clinical_significance. +
To colour by range of a numeric attribute, include mincolor and maxcolor, or omit to colour by text (category). +
(Note: the value of the attribute used for colouring will also be shown in the tooltip as you mouse over features.) +
A sub-attribute should be written as, for example, CSQ:IMPACT. +
This keyword was added in Jalview 2.11
+
mincolor and maxcolor
Colour triplets specified as hexadecimal or comma separated values (may be left blank for a label style colourscheme, @@ -99,10 +118,15 @@
minvalue and maxvalue
Minimum and maximum values defining the range of scores for - which the colour range will be defined over. If minvalue is + which the colour range will be defined over.
If minvalue is greater than maxvalue then the linear mapping will have negative gradient.
+
novalue
+ Specifies the colour to use if colouring by attribute, when the attribute is absent. + Valid options are novaluemin, novaluemax, novaluenone, to use mincolor, maxcolor, or no colour. +
If not specified this will default to novaluemin.
+
thresholdtype
Either "none", "below", or "above". below and above require an additional threshold @@ -113,12 +137,46 @@

+
+ Feature Filters +
+
This section is optional, and allows one or more filters to be defined for each feature type. +
Only features that satisfy the filter conditions will be displayed. +
Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS. +
Each line has the format: +
featureType <tab> (filtercondition1) [and|or] (filtercondition2) [and|or]...
+ The parentheses are not needed if there is only one condition. + Combine multiple conditions with either and or or (but not a mixture). +
Each condition is written as: +
Label or Score or AttributeName condition [value]
+ where either the label (description), (numeric) score, or (text or numeric) attribute is tested against the condition. +
condition is not case sensitive, and should be one of +
+
Contains - description (or attribute) should contain the given value (not case sensitive); example clinical_significance contains Pathogenic
+
NotContains - description (or attribute) should not contain the given value
+
Matches - description (or attribute) should match the given value (not case sensitive)
+
NotMatches - description (or attribute) should not match the given value (not case sensitive)
+
Present - attribute is present on the feature (no value required); example CSQ:SIFT present
+
NotPresent - attribute is not present on the feature (no value required)
+
EQ - feature score, or specified attribute, is equal to the (numeric) value
+
NE, LT, LE, GT, GE - tests for not equal to / less than / less than or equal to / greater than / greater than or equal to the value
+
+ A non-numeric value always fails a numeric test.
If either attribute name, or value to compare, contains spaces, then enclose in single quotes: + 'mutagenesis site' contains 'decreased affinity' +
Tip: some examples of filter syntax are given below; or to see more, first configure colours and filters in Jalview, then File | Export Features to Textbox in Jalview Format. +
Feature filters were added in Jalview 2.11 +
+ +
+ Feature Instances +
+
The remaining lines in the file are the sequence annotation definitions, where the now defined features are attached to regions on particular sequences. Each feature can optionally include some descriptive text which is displayed in a tooltip when the mouse is - near the feature on that sequence (and can also be used to generate - a colour the feature).
+ near the feature on that sequence (and may also be used to generate + a colour for the feature).

If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or @@ -204,6 +262,13 @@ signal peptide 0,155,165 helix ff0000 strand 00ff00 coil cccccc +kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0 + +STARTFILTERS +metal ion-binding site Label Contains sulfur +kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8) +ENDFILTERS + 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 @@ -211,10 +276,16 @@ 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 -startgroup secondarystucture + +STARTGROUP secondarystucture PDB secondary structure annotation FER1_SPIOL -1 52 59 strand PDB secondary structure annotation FER1_SPIOL -1 74 80 helix -endgroup secondarystructure +ENDGROUP secondarystructure + +STARTGROUP kd +Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8 +ENDGROUP kd + GFF FER_CAPAA GffGroup domain 3 93 . .
diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index 0cd6168..ac2489b 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -61,16 +61,10 @@
--> Superposing structures based on - their aligned sequences
If several structures are - available on the alignment, you may add additional structures to an - existing Jmol view by selecting their entry in the appropriate - pop-up menu. Jalview will ask you if you wish to add the structure - to the existing alignment, and if you do, it will import and - superimpose the new PDB file using the corresponding positions from - the alignment. If the alignment is subsequently edited, you can use - the Jmol→Align menu option from - the menu bar of the structure view window to superpose the - structures using the updated alignment.
Sequence + their aligned sequences
If several structures are shown + in a view, you can superimpose them using the corresponding + positions from the alignment via the Jmol→Align + menu option from the menu bar of the structure view window.
Sequence based structure superposition was added in Jalview 2.6

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index b29b66b..52e88db 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -65,10 +65,6 @@ Preferences tab contains settings affecting the export of sequence alignments and EPS files.

Type	variant
Start/end	22
Description	G,C

Type	Disulphide Bond
Start/end	28:31
Description	a description

Type	variant
Start/end	22-33
Description	G,C
Score	12.5
Group	group
Child		ENSP002
Parent		ENSG001

Type	Pfam
Start/end	8-83
Description	Fer2 Status: True Positive Pfam 8_8
Group	Uniprot