<mapID target="clustal" url="html/webServices/clustal.html"/>\r
\r
<mapID target="io" url="html/io/index.html"/>\r
+ <mapID target="alformats" url="html/io/fileformats.html"/>\r
<mapID target="edit" url="html/editing/index.html"/>\r
\r
<mapID target="calculations" url="html/calculations/index.html"/>\r
<em>e.g. a region of sequence with known structure</em>\r
</li>\r
</ul></p>\r
-<p>More information about the feature is given in a tooltip, which are\r
+<p>More information about the feature is given in a tooltip, which is\r
viewed by moving the mouse pointer over a sequence feature. The\r
- associated text for the feature will then be displayed in a small\r
- label will appear near the pointer.</p>\r
+ description associated with the feature will then be displayed in a small\r
+ label near the pointer.</p>\r
<p>After the Sequence Features option is selected, there may be some delay before\r
- the features are actually rendered, as jalview must first determine if a\r
- sequence is contained in uniprot and then retrieve its sequence\r
- record. This delay should only happen once for a particular\r
- alignment, as jalview caches uniprot records in a file in your home\r
+ the features are actually rendered, as jalview first determines if\r
+ the sequences are contained in Uniprot and then retrieves any sequence\r
+ records. This delay will normally only happen once for a particular\r
+ set of sequences, as jalview caches uniprot records in a file in your home\r
directory called '.jalview.uniprot.xml'.\r
\r
-<p>The first step in this process is to try to use the ID (name) of\r
- each sequence as an ID search in Uniprot. If there is no match, The\r
- EBI Blast search is used in an attempt to obtain the Uniprot Id for\r
- each sequence. You will be notified of any 100% matches with\r
- Uniprot, but you must then manually change the name of the sequence,\r
- by right clicking on the sequence ID and selecting\r
- Sequence→Edit Name, before Jalview will show its sequence\r
+ <p><strong>The Sequence Identification Process</strong>\r
+\r
+ </p>\r
+<p>The first step in the procedure for matching uniprot IDs to\r
+ sequences is to use the ID (name) of\r
+ each sequence to retrieve Uniprot records directly.</p>\r
+<p>\r
+ If a uniprot record (or set of records) is found for a sequence,\r
+ then the sequence is aligned to the one in the Uniprot record\r
+ to determine the correct start and end residue positions (which are\r
+ displayed when the 'Show Full Sequence ID' option is set).\r
+</p>\r
+\r
+<p>If the alignment reveals differences between the sequence in the\r
+ alignment and the one in the record, then Jalview will assume that\r
+ the aligned sequence is not the one in the uniprot record.\r
+\r
+ </p>\r
+\r
+ <p> \r
+ In some cases, the ID used to retrieve Uniprot records may be out of\r
+ date and you will be notified of that a 100% match between the\r
+ sequence and a Uniprot record was identified, but the sequence name\r
+ must be manually changed (by right clicking on the sequence ID and selecting\r
+ <strong>Sequence→Edit Name</strong>), before Jalview will show its sequence\r
features.<ul>\r
<li>remember to save your alignment if you have updated any of the\r
sequence IDs!\r
</li>\r
</ul></p>\r
-<p>\r
- If a uniprot record (or set of records) is found for a sequence,\r
- then the sequence in aligned to the one in the Uniprot record\r
- to determine the correct start and end residue positions that will be\r
- displayed when the 'Show Full Sequence ID' option is set.</p>\r
</body>\r
</html>\r
--- /dev/null
+<html>
+<head>
+<title>Alignment Fileformats</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+<body>
+
+<p><strong>Alignment Fileformats</strong>
+<p>Jalview understands a wide range of sequence alignment formats. In
+order to determine which format has been used for an alignment,
+jalview tries to detect some text or formatting unique to one of the formats:
+</p>
+<table width="100%" border="1">
+<tr><td width="17%">Format</td>
+<td width="60%">Unique File Feature</td>
+<td width="23%">File Extension</td>
+<tr>
+<td width="17%">FASTA</td>
+<td width="60%">>SequenceName<br>
+THISISASEQENCE<br></td>
+<td width="23%">.fa, .fasta</td>
+</tr><tr><td width="17%">MSF</td>
+<td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br>
+<em>..</em><br>
+//<br></td>
+<td width="23%">.msf</td>
+</tr><tr><td width="17%">CLUSTALW</td>
+<td width="60%">CLUSTAL</td>
+<td width="23%">.aln</td>
+</tr><tr><td width="17%">PILEUP</td>
+<td width="60%">PileUp</td>
+<td width="23%"></td>
+</tr><tr><td width="17%">PIR</td>
+<td width="60%">>P1;</td>
+<td width="23%">.pir</td>
+</tr><tr><td width="17%">BLC</td>
+<td width="60%">>Seq1<br>
+>Seq2</td>
+<td width="23%">.blc</td>
+</tr><tr><td width="17%">PFAM</td>
+<td width="60%">SequenceName THISISASEQENCE</td>
+<td width="23%">.pfam</td>
+</tr>
+</table>
+<p>The file extensions are used to associate jalview alignment icons
+with alignment files: <img src="file.png" width=12 height=12 >
+</p>
+</body>
+</html>
<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 alignments can be read in from the Jalview format. </p>\r
-<p>Use the "Input Alignment" menu at the top of the main application\r
- window to read in files from </p>\r
+<p>Additionally, annotated whole sets of alignments and trees can be\r
+read from a Jalview\r
+(jar) format file using <strong>Desktop→Load 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 website URL</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><strong>Output</strong> </p>\r
<p>Each alignment, whether it is the original or an edited version may be saved\r
- in the standard formats</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
-<p>You may save annotated alignments in the Jalview file format. </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
<p><strong>Export<a name="export"></a></strong></p>\r
-<p>The alignment may also be saved as a HTML web page. </p>\r
-<p>You may save a Portable Networks Graphics (PNG) image of your alignment. </p>\r
-<p>You may save the alignment as an Encapsulated Postscript file. This is a vector\r
- graphics file which may be modified in various graphics applications, such as\r
- Adobe Illustrator.<br>\r
- <br>\r
- Tip: When importing to a Microsoft document, a snapshot image is taken of your\r
- file - this will be blurred. Right-click the image and choose "Edit image."\r
- This will restore the high quality EPS file format output. <br>\r
- NB. Mac OSX users will find that eps files are automatically converted into\r
- PDF files. </p>\r
-<p>The alignment can be printed from a local printer.</p>\r
+<p>The alignment view can be printed using\r
+<strong>File→Print</strong>, or exported in a number of ways via the\r
+<strong>File→Export</strong> menu:\r
+<ul>\r
+<li>HTML<br><em>for viewing in a web browser</em>\r
+</li>\r
+<li>PNG - a Portable Networks Graphics image<br><em>For low quality\r
+diagrams and powerpoint presentations</em>\r
+</li>\r
+<li>EPS - an Encapsulated Postscript Document<br><em>For high quality\r
+diagrams and publications.</em>\r
+</li></ul>\r
+ \r
+<p><em>Tips for working with EPS Files</em></p><ul><li>The EPS file generated by jalview contains vector\r
+ graphics which are directly editable in graphics applications such as\r
+ Adobe Illustrator.</li>\r
+<li>When importing an EPS into to a Microsoft office document, a snapshot image of the\r
+ file will be displayed which often looks blurred. Right-click the\r
+ image and choose "Edit image." to convert it to word\r
+ drawing objects which give a truer WYSIWIG representation.\r
+ </li>\r
+ <li>\r
+ Mac OSX users will find that eps files are automatically converted into\r
+ PDF files. \r
+ </li>\r
+</p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / commitdiff
