Input/Ouput

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=d57de42e7adf719280f2be9a9fd8b98bb128cf33;hb=ad4c2e9e85533f3a375d92deb45c59318bebdfef;hp=baacf405053f6c8bdfc65c10821db59475adb1f0;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index baacf40..d57de42 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,25 +1,48 @@ -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 (including MODELLER variant), 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.

Jalview can also read jalview specific files for sequence features +and alignment annotation.

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 jpg image of your alignment.

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

+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. In the case of PIR format, the output tab also contains a switch +for turning on the output of Modeller style structured description +lines. +

Quantitative and symbolic alignment annotation can be exported as a +comma separated value file by right clicking on an annotation row +under the alignment.

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