X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=063f32962db55fcc2b8172c43fb807a4e74db040;hb=713db61b4724485414159cfc145f9ffa4a24bb6d;hp=b067512939d057b233a1c32aab535e8840836dee;hpb=c14dcae815b55dbe7feda2ddb97f06930529954d;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index b067512..063f329 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,40 +1,40 @@ -
Input
Jalview can read alignment files in any of the following standard formats:
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
-The EBI has examples of +
The EBI has examples of these file formats.
-Additionally annotated alignments can be read in from the Jalview format.
-Use the "Input Alignment" menu at the top of the main application - window to read in files from
+Additionally, annotated whole sets of alignments and trees can be +read from a Jalview (jar) +format file using Desktop→Load +Project.
+Use the Desktop→Input Alignment menu to read in files from:
If a file is of an unknown format or there is any other error reading the alignment - file you will be given an error message, the alignment will not be read in. +
Jalview will try to recognise the file type automatically (using +some special features). If a +file is of an unknown format or there is any other error reading the +alignment file then you will be given an error message. If you think +Jalview really should be able to read your file, then send an email +containing the problem file to jalview@jalview.org.
Output
-Each alignment, whether it is the original or an edited version may be saved - in the standard formats
+Each alignment, whether it is the original or an edited version may be saved + in the standard formats using File→Save As
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
-You may save annotated alignments in the Jalview file format.
+Jalview will by default append the sequence start and end to each sequence name, +in the format /start-end. If you do not want this behaviour for a particular file +output, open the "Output" tab on the Preferences window where you can +select which file formats you want to append the start and end sequence positions +for. +You can also save the current set of alignments and their colours, annotations and +trees in a Jalview archive file using Desktop→Save project.
- -
The alignment may also be saved as a HTML web page.
-You may save a Portable Networks Graphics (PNG) image of your alignment.
-You may save the alignment as an Encapsulated Postscript file. This is a vector
- graphics file which may be modified in various graphics applications, such as
- Adobe Illustrator.
-
- Tip: When importing to a Microsoft document, a snapshot image is taken of your
- file - this will be blurred. Right-click the image and choose "Edit image."
- This will restore the high quality EPS file format output.
- NB. Mac OSX users will find that eps files are automatically converted into
- PDF files.
The alignment can be printed from a local printer.