From 111dd186e61e22f4145272494d14b038df528c17 Mon Sep 17 00:00:00 2001 From: jprocter Date: Sun, 2 Sep 2012 16:05:07 +0100 Subject: [PATCH] JAL-1015 documentation for basic HTML sequence annotation report. --- help/help.jhm | 1 + help/helpTOC.xml | 4 +++- help/html/io/exportseqreport.html | 38 +++++++++++++++++++++++++++++++++++++ help/html/io/seqreport.gif | Bin 0 -> 25151 bytes help/html/menus/popupMenu.html | 10 +++++++++- 5 files changed, 51 insertions(+), 2 deletions(-) create mode 100644 help/html/io/exportseqreport.html create mode 100644 help/html/io/seqreport.gif diff --git a/help/help.jhm b/help/help.jhm index 91ef827..4288edc 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -35,6 +35,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 9406292..f594bd9 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -23,6 +23,7 @@ + @@ -46,6 +47,7 @@ + @@ -129,7 +131,7 @@ - + diff --git a/help/html/io/exportseqreport.html b/help/html/io/exportseqreport.html new file mode 100644 index 0000000..8a75b67 --- /dev/null +++ b/help/html/io/exportseqreport.html @@ -0,0 +1,38 @@ + + + +Viewing and exporting sequence annotation reports + + +

Viewing and exporting sequence annotation reports +
+Much of the information retrieved by Jalview about a sequence is visualized on the alignment. +Often, however, there are a huge number of ontology terms, cross-references, links to publications and other kinds of data shown + in the sequence ID tooltip that cannot be examined. In this case, you can view and export the information shown in a sequence's ID tooltip by right-clicking and +selecting the "(sequence's name)→Sequence Details ..." entry from the pop-up menu. +

+

Annotation Reports for a range of sequences
+If you would like to view the tooltips for a number of sequences, simply select them all and then use the Selection→Sequence Details ... entry in the pop-up menu. +

+Sequence Annotation is displayed as HTML in a report window +

Copying and pasting annotation to other programs
+The File→Save option in the sequence annotation report window allows the report to be saved as HTML, which will preserve links and any other metadata. It is also possible to copy and paste the text to other programs, but in some cases, the HTML will not be preserved. In that case, you can toggle the display of HTML source code with the Edit→Show HTML Source drop down menu entry. +

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b/help/html/menus/popupMenu.html @@ -28,6 +28,10 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).