Input/Output

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=5794a7a225e439dc95a440cd9eb19bf99a970154;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=3db67ee361be76a93ef798051315234d33ecd4fd;hpb=9fb8dbc0e26d57a235a48b6f6054905e149dd169;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index 3db67ee..5794a7a 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,61 +1,75 @@ - -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 - 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:

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

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 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.

Export

The alignment view can be printed using -File→Print, or exported in a number of ways via the -File→Export menu: -

HTML
for viewing in a web browser -
PNG - a Portable Networks Graphics image
For low quality -diagrams and powerpoint presentations -
EPS - an Encapsulated Postscript Document
For high quality -diagrams and publications. -

- -

Tips for working with EPS Files

The EPS file generated by jalview contains vector - graphics which are directly editable in graphics applications such as - Adobe Illustrator.
When importing an EPS into to a Microsoft office document, a snapshot image of the - file will be displayed which often looks blurred. Right-click the - image and choose "Edit image." to convert it to word - drawing objects which give a truer WYSIWIG representation. -
- Mac OSX users will find that eps files are automatically converted into - PDF files. -

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 (including MODELLER variant), Pfam/Stockholm

The EBI has examples +of these file formats.

Additionally, whole sets of coloured and annotated alignments and +trees can be read from a Jalview +(jar) format file using Desktop→Load Project.

Press "Control O" to open a file browser, or use +the Desktop→Input Alignment menu to read in +alignments from:

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

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 help@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 standard formats using File→Save +As

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

Preferences

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.