<html>\r
+<head><title>Input/Output</title></head>\r
<body>\r
<p><strong>Input</strong></p>\r
-<p>Jalview can read alignment files in any of the following formats:</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
-<p>Use the menu at the top of the main application window to read in files from\r
-</p>\r
+<p>Jalview can read alignment files in any of the following standard formats:</p>\r
+<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
+<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of\r
+ these file formats.</p>\r
+<p>Additionally, annotated whole sets of alignments and trees can be\r
+read from a <a href="../features/jalarchive.html">Jalview (jar)\r
+format</a> file using <strong>Desktop→Load\r
+Project</strong>. </p>\r
+<p>Use the <strong>Desktop→Input Alignment</strong> menu to read in files from:</p>\r
<ul>\r
- <li> the local file system</li>\r
- <li>a remote website</li>\r
- <li>or by copying and pasting into the "Cut & Paste" text window</li>\r
+ <li><strong>From File</strong>: the local file system</li>\r
+ <li><strong>From URL</strong>: the web (please use the full url)</li>\r
+ <li><strong>from Textbox</strong>: a copy and paste into the\r
+ "Cut & Paste" text window</li>\r
</ul>\r
-<p>If a file is of an unknown format or there is any other error reading the alignment\r
- file you will be given an error message, the alignment will not be read in.\r
+<p>Jalview will try to recognise the file type automatically (using\r
+some special <a href="fileformats.html">features</a>). If a\r
+file is of an unknown format or there is any other error reading the\r
+alignment file then you will be given an error message. If you think\r
+Jalview really should be able to read your file, then send an email\r
+containing the problem file to jalview@jalview.org.\r
</p>\r
+<p>Jalview can also read jalview specific files for <a href="../features/featuresFormat.html">sequence features</a>\r
+and <a href="../features/annotationsFormat.html">alignment annotation</a>.</p>\r
<p><strong>Output</strong> </p>\r
<p>Each alignment, whether it is the original or an edited version may be saved\r
- in the formats</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
-<p>The alignment may also be saved as a HTML web page. </p>\r
-<p>You may save a jpg image of your alignment. </p>\r
-<p>The alignment can be printed from a local printer.</p>\r
+ in the standard formats using <strong>File→Save As</strong></p>\r
+<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
+Jalview will by default append the sequence start and end to each sequence name, \r
+in the format /start-end. If you do not want this behaviour for a particular file \r
+output, open the "Output" tab on the <a href="../features/preferences.html">Preferences</a> window where you can \r
+select which file formats you want to append the start and end sequence positions \r
+for.\r
+<p>Quantitative and symbolic <a href="../features/annotation.html">alignment annotation</a> can be exported as a\r
+comma separated value file by right clicking on an annotation row\r
+under the alignment.</p>\r
+<p>You can also save the current set of alignments and their colours, annotations and\r
+trees in a Jalview archive file using <strong>Desktop→Save project</strong>. </p>\r
+<p> </p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff