From 2c5694fd8e15641a6ac2c116f2fb0744254727c5 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 22 Apr 2010 14:15:54 +0000 Subject: [PATCH] non-positional feature export in gff and features file: bug #54325 --- help/html/features/seqfeatures.html | 91 ++++++++++++++++--------------- help/html/releases.html | 24 ++++---- src/jalview/gui/AnnotationExporter.java | 8 +-- src/jalview/io/FeaturesFile.java | 48 +++++++++++----- 4 files changed, 98 insertions(+), 73 deletions(-) diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 9efa19f..13fd306 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -1,43 +1,48 @@ - -Sequence Features - -

Sequence Features

-

Jalview can colour parts of a sequence based on the presence of -sequence features - which may be retrieved from database records (such -as Uniprot), the result of sequence motif -searches or simply read from a sequence features file.

-

Sequence Feature Groups

-

Since Jalview 2.08, sequence features assigned to a sequence can be -organised into groups, which may indicate that the features were all retrieved -from the same database (such as Uniprot features), or generated by the -same analysis process (as might be specified in a sequence features file).

-

Sequence Feature Inheritance

-

Since Jalview 2.08, sequence features are global to a set of -sequences appearing (independently or together) in many different -alignments. Practically, this means features loaded onto one alignment -can be viewed in any alignments involving the same sequences. The same -sequence appears in different alignments when a new alignment is -generated by submitting an existing set of sequences to one of the -alignment or prediction web services, and when sequences are copied -and pasted into other alignment windows.

-

View→Show Sequence Features

-

Toggle the display of sequence features in this alignment. If -feature retrieval has not already been carried out, then Jalview will -automatically try to fetch sequence features (as described below).

-

View→Sequence Feature Settings... -

Once sequence features have been loaded, their display can be fully controlled - using the alignment window's Sequence Feature Settings dialog box. Feature - colour schemes and display parameters are unique to a particular alignment, - so it is possible to colour the same sequence features differently in different - alignment views.
- Since Jalview 2.1, it is possible to add DAS features - to an alignment via the DAS tabbed pane of the feature settings window.

-

Precalculated Sequence Features may be added to an alignment from the command - line, drag and drop, or from the "File->Load Features / Annotations" - menu item. See the Features File Format for - more details.

- - + +Sequence Features + +

Sequence Features

+

Jalview can colour parts of a sequence based on the presence of +sequence features - which may be retrieved from database records (such +as Uniprot), the result of sequence motif +searches or simply read from a sequence features file.

+

Sequence Feature Groups

+

Since Jalview 2.08, sequence features assigned to a sequence can be +organised into groups, which may indicate that the features were all retrieved +from the same database (such as Uniprot features), or generated by the +same analysis process (as might be specified in a sequence features file).

+

Sequence Feature Inheritance

+

Since Jalview 2.08, sequence features are global to a set of +sequences appearing (independently or together) in many different +alignments. Practically, this means features loaded onto one alignment +can be viewed in any alignments involving the same sequences. The same +sequence appears in different alignments when a new alignment is +generated by submitting an existing set of sequences to one of the +alignment or prediction web services, and when sequences are copied +and pasted into other alignment windows.

+

View→Show Sequence Features

+

Toggle the display of sequence features in this alignment. If +feature retrieval has not already been carried out, then Jalview will +automatically try to fetch sequence features (as described below).

+

View→Sequence Feature Settings...

+

Once sequence features have been loaded, their display can be fully controlled + using the alignment window's Sequence Feature Settings dialog box. Feature + colour schemes and display parameters are unique to a particular alignment, + so it is possible to colour the same sequence features differently in different + alignment views.
+ Since Jalview 2.1, it is possible to add DAS features + to an alignment via the DAS tabbed pane of the feature settings window.

+

View→Sequence ID Tooltip→Show Non-Positional features
+ Only available in application

+

Toggles the display of non-positional features in the sequence ID tooltip, + and whether they will be included when sequence features are exported using + "File→Export Features".

+

Precalculated Sequence Features may be added to an alignment from the command + line, drag and drop, or from the "File→Load Features / Annotations" + menu item. See the Features File Format for + more details.

+ + diff --git a/help/html/releases.html b/help/html/releases.html index ea95696..fcb9534 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -24,26 +24,17 @@ Vamsas Capabilities Application