From 9fb8dbc0e26d57a235a48b6f6054905e149dd169 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 14 Jun 2005 16:29:21 +0000
Subject: [PATCH] help file bits.

---
 help/help.jhm                       |    1 +
 help/html/features/seqfeatures.html |   51 +++++++++++++++++----------
 help/html/io/file.png               |  Bin 0 -> 590 bytes
 help/html/io/fileformats.html       |   55 +++++++++++++++++++++++++++++
 help/html/io/index.html             |   65 +++++++++++++++++++++++------------
 5 files changed, 131 insertions(+), 41 deletions(-)
 create mode 100755 help/html/io/file.png
 create mode 100755 help/html/io/fileformats.html

diff --git a/help/help.jhm b/help/help.jhm
index 36a54e4..3a4aac4 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -13,6 +13,7 @@
    <mapID target="clustal" url="html/webServices/clustal.html"/>
    
    <mapID target="io" url="html/io/index.html"/>
+   <mapID target="alformats" url="html/io/fileformats.html"/>
    <mapID target="edit" url="html/editing/index.html"/>
 
    <mapID target="calculations" url="html/calculations/index.html"/>
diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index 88a4d5d..6264724 100755
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -13,33 +13,46 @@
 <em>e.g. a region of sequence with known structure</em>
 </li>
 </ul></p>
-<p>More information about the feature is given in a tooltip, which are
+<p>More information about the feature is given in a tooltip, which is
   viewed by moving the mouse pointer over a sequence feature. The
-  associated text for the feature will then be displayed in a small
-  label will appear near the pointer.</p>
+  description associated with the feature will then be displayed in a small
+  label near the pointer.</p>
 <p>After the Sequence Features option is selected, there may be some delay before
-  the features are actually rendered, as jalview must first determine if a
-  sequence is contained in uniprot and then retrieve its sequence
-  record. This delay should only happen once for a particular
-  alignment, as jalview caches uniprot records in a file in your home
+  the features are actually rendered, as jalview first determines if
+  the sequences are contained in Uniprot and then retrieves any sequence
+  records. This delay will normally only happen once for a particular
+  set of sequences, as jalview caches uniprot records in a file in your home
   directory called '.jalview.uniprot.xml'.
 
-<p>The first step in this process is to try to use the ID (name) of
-  each sequence as an ID search in Uniprot. If there is no match, The
-  EBI Blast search is used in an attempt to obtain the Uniprot Id for
-  each sequence. You will be  notified of any 100% matches with
-  Uniprot, but you must then manually change the name of the sequence,
-  by right clicking on the sequence ID and selecting
-  Sequence&#8594;Edit Name, before Jalview will show its sequence
+  <p><strong>The Sequence Identification Process</strong>
+
+  </p>
+<p>The first step in the procedure for matching uniprot IDs to
+  sequences is to use the ID (name) of
+  each sequence to retrieve Uniprot records directly.</p>
+<p>
+  If a uniprot record (or set of records) is found for a sequence,
+  then the sequence is aligned to the one in the Uniprot record
+  to determine the correct start and end residue positions (which are
+  displayed when the 'Show Full Sequence ID' option is set).
+</p>
+
+<p>If the alignment reveals differences between the sequence in the
+  alignment and the one in the record, then Jalview will assume that
+  the aligned sequence is not the one in the uniprot record.
+
+  </p>
+
+  <p> 
+  In some cases, the ID used to retrieve Uniprot records may be out of
+  date and you will be notified of that a 100% match between the
+  sequence and a Uniprot record was identified, but the sequence name
+  must be manually changed (by right clicking on the sequence ID and selecting
+  <strong>Sequence&#8594;Edit Name</strong>), before Jalview will show its sequence
   features.<ul>
   <li>remember to save your alignment if you have updated any of the
   sequence IDs!
   </li>
   </ul></p>
-<p>
-  If a uniprot record (or set of records) is found for a sequence,
-  then the sequence in aligned to the one in the Uniprot record
-  to determine the correct start and end residue positions that will be
-  displayed when the 'Show Full Sequence ID' option is set.</p>
 </body>
 </html>
diff --git a/help/html/io/file.png b/help/html/io/file.png
new file mode 100755
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GIT binary patch
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diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html
new file mode 100755
index 0000000..5c888ff
--- /dev/null
+++ b/help/html/io/fileformats.html
@@ -0,0 +1,55 @@
+<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%">&gt;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%">&gt;P1;</td>
+<td width="23%">.pir</td>
+</tr><tr><td width="17%">BLC</td>
+<td width="60%">&gt;Seq1<br>
+&gt;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>
diff --git a/help/html/io/index.html b/help/html/io/index.html
index bd2a790..3db67ee 100755
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -6,35 +6,56 @@
 <p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>
 <p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of
   these file formats.</p>
-<p>Additionally annotated alignments can be read in from the Jalview format. </p>
-<p>Use the &quot;Input Alignment&quot; menu at the top of the main application
-  window to read in files from </p>
+<p>Additionally, annotated whole sets of alignments and trees can be
+read from a Jalview
+(jar) format file using <strong>Desktop&#8594;Load Project</strong>. </p>
+<p>Use the <strong>Desktop&#8594;Input Alignment</strong> menu to read in files from:</p>
 <ul>
-  <li> the local file system</li>
-  <li>a website URL</li>
-  <li>or by copying and pasting into the &quot;Cut &amp; Paste&quot; text window</li>
+  <li><strong>From File</strong>: the local file system</li>
+  <li><strong>From URL</strong>: the web (please use the full url)</li>
+  <li><strong>from Textbox</strong>: a copy and paste into the
+  &quot;Cut &amp; Paste&quot; text window</li>
 </ul>
-<p>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.
+<p>Jalview will try to recognise the file type automatically (using
+some special <a href="fileformats.html">features</a>). 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.
 </p>
 <p><strong>Output</strong> </p>
 <p>Each alignment, whether it is the original or an edited version may be saved
-  in the standard formats</p>
+  in the standard formats using <strong>File&#8594;Save As</strong></p>
 <p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>
-<p>You may save annotated alignments in the Jalview file format. </p>
+<p>You can also save the current set of alignments and their colours, annotations and
+trees in a Jalview archive file using <strong>Desktop&#8594;Save project</strong>. </p>
 <p>&nbsp;</p>
 <p><strong>Export<a name="export"></a></strong></p>
-<p>The alignment may also be saved as a HTML web page. </p>
-<p>You may save a Portable Networks Graphics (PNG) image of your alignment. </p>
-<p>You may save the alignment as an Encapsulated Postscript file. This is a vector
-  graphics file which may be modified in various graphics applications, such as
-  Adobe Illustrator.<br>
-  <br>
-  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 &quot;Edit image.&quot;
-  This will restore the high quality EPS file format output. <br>
-  NB. Mac OSX users will find that eps files are automatically converted into
-  PDF files. </p>
-<p>The alignment can be printed from a local printer.</p>
+<p>The alignment view can be printed using
+<strong>File&#8594;Print</strong>, or exported in a number of ways via the
+<strong>File&#8594;Export</strong> menu:
+<ul>
+<li>HTML<br><em>for viewing in a web browser</em>
+</li>
+<li>PNG - a Portable Networks Graphics image<br><em>For low quality
+diagrams and powerpoint presentations</em>
+</li>
+<li>EPS - an Encapsulated Postscript Document<br><em>For high quality
+diagrams and publications.</em>
+</li></ul>
+  
+<p><em>Tips for working with EPS Files</em></p><ul><li>The EPS file generated by jalview contains vector
+  graphics which are directly editable in graphics applications such as
+  Adobe Illustrator.</li>
+<li>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 &quot;Edit image.&quot; to convert it to word
+  drawing objects which give a truer WYSIWIG representation.
+  </li>
+  <li>
+  Mac OSX users will find that eps files are automatically converted into
+  PDF files. 
+  </li>
+</p>
 </body>
 </html>
-- 
1.7.10.2