Input/Ouput

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=332cdca3d44614256770aca9f3c6f6bc5dd3b195;hb=004a903480d9f41447e4b6a597e3fa430083460c;hp=c7c4bf8a042527210e9b7c02b0ba0bc850d08458;hpb=ff761b8bfedf4dde4672eaed9e51bbf71bfe207e;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index c7c4bf8..332cdca 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,30 +1,35 @@ -Input/Ouput +Input/Output

Input

Jalview can read alignment files in any of the following formats:

Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM

Use the menu at the top of the main application window to read in files from -

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 + these file formats.

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 remote website
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 formats

Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM

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 file can - be easily imported into Microsoft Powerpoint, Microsoft Word or 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.

The alignment can be printed from a local printer.

+ in the standard formats using File→Save As

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

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