Input/Ouput

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=332cdca3d44614256770aca9f3c6f6bc5dd3b195;hb=a9abe07c6490582e506047fa6ad5edafbc25213f;hp=b067512939d057b233a1c32aab535e8840836dee;hpb=c14dcae815b55dbe7feda2ddb97f06930529954d;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index b067512..332cdca 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,40 +1,35 @@ -Input/Ouput +Input/Output

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:

the local file system
a website URL
or by copying and pasting into the "Cut & Paste" text window
From File: the local file system
From URL: the web (please use the full url)
from Textbox: a copy and paste into the + "Cut & Paste" text window

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.

You can also save the current set of alignments and their colours, annotations and +trees in a Jalview archive file using Desktop→Save project.

Export

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.