From e3f4349374e532d0f9bb2bc163ff1783ca030fd6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 22 Aug 2006 13:13:23 +0000
Subject: [PATCH] documentation

---
 help/help.jhm                                |    3 +-
 help/helpTOC.xml                             |   10 +++--
 help/html/calculations/recoverInputdata.html |   13 +++++++
 help/html/features/dassettings.html          |   26 ++++++++-----
 help/html/features/hiddenRegions.html        |   52 +++++++++++++++-----------
 help/html/webServices/index.html             |   28 +++++++++++---
 help/html/webServices/jnet.html              |    6 +++
 help/html/webServices/mafft.html             |   17 ++++++---
 help/html/webServices/msaclient.html         |   38 +++++++++++++++++++
 help/html/webServices/multimafftjbs.gif      |  Bin 0 -> 7301 bytes
 10 files changed, 146 insertions(+), 47 deletions(-)
 create mode 100644 help/html/calculations/recoverInputdata.html
 create mode 100644 help/html/webServices/msaclient.html
 create mode 100644 help/html/webServices/multimafftjbs.gif

diff --git a/help/help.jhm b/help/help.jhm
index 8c314d3..41d245d 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -10,6 +10,7 @@
    <mapID target="cursor" url="html/features/cursorMode.html"/>
    <mapID target="search" url="html/features/search.html"/>   
    <mapID target="webservice" url="html/webServices/index.html"/>
+   <mapID target="msaservice" url="html/webServices/msaclient.html"/>
    <mapID target="clustal" url="html/webServices/clustalw.html"/>
    <mapID target="muscle" url="html/webServices/muscle.html"/>
    <mapID target="mafft" url="html/webServices/mafft.html"/>
@@ -35,7 +36,7 @@
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
    <mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>
-   
+   <mapID target="recoverInputdata" url="html/calculations/recoverInputdata.html"/>
    <mapID target="colours" url="html/colourSchemes/index.html" />
    <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
    <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index d08e3d2..5dec601 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,9 +3,11 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="false">
-        	<tocitem text="MAFFT Alignment" target="mafft"/>
         	<tocitem text="DAS Feature Fetching" target="das.settings"/>
-        	<tocitem text="Hide Regions" target="hiddenRegions"/> 	         
+        	<tocitem text="Hide Regions" target="hiddenRegions"/>
+              	<tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
+                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
+        	<tocitem text="MAFFT Alignment" target="mafft"/>
         </tocitem>
         <tocitem text="Release History" target="release"/>
         <tocitem text="Editing Alignments" target ="edit"/>	
@@ -22,10 +24,12 @@
           <tocitem text="DAS Features Settings" target="das.viewing"/>
         </tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
+          <tocitem text="Sequence Alignment" target="msaservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
                 <tocitem text="MAFFT Alignment" target="mafft"/>
-          	<tocitem text="JNet Prediction" target="jnet"/>
+            </tocitem>
+          <tocitem text="Secondary Structure Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>
diff --git a/help/html/calculations/recoverInputdata.html b/help/html/calculations/recoverInputdata.html
new file mode 100644
index 0000000..b582952
--- /dev/null
+++ b/help/html/calculations/recoverInputdata.html
@@ -0,0 +1,13 @@
+<html>
+<head><title>Viewing Input Data to PCA and Tree calculations</title></head>
+<body>
+
+<p><strong>Viewing Input Data to PCA and Tree calculations</strong></p>
+<p>It is always possible to retrieve the input data used to calculate
+  a tree or PCA plot by using the analysis window's 
+  <strong>&quot;File 
+  -&gt; Input Data...&quot;</strong> menu item. The Input Data will be
+  shown in a new alignment window, with any hidden columns
+  preserved.</p>
+</body>
+</html>
diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html
index 4e89532..f3e325d 100644
--- a/help/html/features/dassettings.html
+++ b/help/html/features/dassettings.html
@@ -4,19 +4,25 @@
 
 <body>
 <p><strong>DAS Settings</strong></p>
-<p>Jalview can retrieve features from multiple <a href="http://biodas.org/">DAS</a> 
-  sources. The DAS sources are selected in the DAS settings panel.</p>
+<p>Jalview can retrieve and visualize features from many <a href="http://biodas.org/">DAS</a> 
+  sources at once. The DAS sources are discovered and selected <em>via</em> the DAS settings panel.</p>
 <p><img src="das.jpg" width="497" height="365">
-<p>On start up of the DAS Settings panel, Jalview will use the registry URL (default 
-  is http://das.sanger.ac.uk/registry/das1/sources/) to retrieve a list of currently 
-  available DAS sources. These are all listed in the table using the sources' 
-  Nickname as an identifier. <br>
-  Click on a Nickname in the table to reveal more information about that service 
-  in the panel to the right of the table. 
+<p>The available sources are listed in the table using each source's
+Nickname as its identifier. Clicking on a source's entry in the table
+reveals more information about that service in the panel to the
+right. Select the tickbox in the &quot;Use Source&quot; column for a
+source to add it to the set Jalview queries for alignment and sequence
+features.
+</p>
 <p>You can filter the visible DAS sources by authority, type and &quot;label&quot;. 
   You should read the DAS documentation to understand more about these values.
-<p>Tick the box &quot;Use Source&quot; so that Jalview will use a particular source 
-  when fetching features. 
+<p><strong>Updating the list of sources</strong></p>
+<p>When the DAS Settings panel is first opened, and when the <strong>'Refresh
+  source'</strong> buton is pressed, a list of DAS sources
+  is retrieved from the DAS registry URL (set by default to the DAS
+  registration server at
+  http://das.sanger.ac.uk/registry/das1/sources/).</p>
+<p><strong>Adding your own DAS Sources</strong></p>
 <p>You can add your own DAS source to the list by clicking the &quot;Add Local 
   Source&quot; button. Enter the URL and nickname of your additional service. 
   It should be noted that Jalview 2.1 will not query additional sources for more 
diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html
index 929481b..172ce80 100644
--- a/help/html/features/hiddenRegions.html
+++ b/help/html/features/hiddenRegions.html
@@ -5,34 +5,44 @@
 <p>Use the keyboard key &quot;H&quot; to hide / reveal selected columns and sequences. 
   To hide / reveal only selected sequences, use &quot;Shift H&quot;, to hide / 
   reveal only selected columns, use &quot;Control H&quot;.</p>
-<p>&nbsp;</p>
-<p>To <strong>hide selected sequences </strong>from an alignment, use the &quot;View 
-  -&gt; Hide -&gt; Selected Sequences&quot; menu item or simply select &quot;Hide 
-  Sequences&quot; from the Popup menu after a right click on the sequence Ids. 
+<p><strong><em>Hiding Sequences</em></strong><br>
+To hide selected sequences in an alignment, use the <strong>&quot;View 
+  -&gt; Hide -&gt; Selected Sequences&quot;</strong> menu item or simply select <strong>&quot;Hide 
+  Sequences&quot;</strong> from the Popup menu after a right click on the sequence Ids. 
 </p>
 <p>Hidden sequences will not be used in any calculations, editing or web service 
   alignments performed on visible sequences. </p>
-<p>A more advanced hide involves a right-mouse click on a sequence, then selecting 
-  &quot;SequenceID -&gt; Represent Group with SequenceId&quot;. Using this method 
+<p><strong><em>Hidden Sequences Representatives</em></strong><br>
+A more advanced hide involves a right-mouse click on a sequence, then selecting 
+  <strong>&quot;SequenceID -&gt; Represent Group with SequenceId&quot;</strong>. Using this method 
   of hiding sequences, any edits performed on the visible group representative 
   will be propogated to all the sequences in that group. <br>
-  The hidden sequences will not be used in any calculations or web service alignments. 
+  The hidden representative sequences will not be used in any
+  calculations or web service alignments (<em>nb. this may change in
+  the future</em>)
 </p>
-<p>&nbsp;</p>
-<p>To <strong>hide selected columns</strong> from an alignment, use the &quot;View 
-  -&gt; Hide -&gt; Selected Columns&quot; menu item, or right click within a region 
+<p><strong><em>Hiding Columns</em></strong><br>
+To hide selected columns in an alignment, use the <strong>&quot;View 
+  -&gt; Hide -&gt; Selected Columns&quot;</strong> menu item, or right click within a region 
   of selected columns in the scale above the alignment (only available in non 
-  wrapped mode) and select &quot;Hide Columns&quot;. </p>
-<p>Hidden columns will not be used in any calculations. This allows you to eg. 
-  create trees from the visible alignment and ignore any poorly aligned sections 
-  of the alignment, without cutting and deleting them permanently from your alignment.<br>
-  It is possible to retrieve the input data to any trees, PCA analysis windows 
-  which were created from alignments containing hidden columns by using the &quot;File 
-  -&gt; Input Data...&quot; menu item from the tree window. </p>
-<p> Editing the alignment is bound by the hidden columns, ie you cannot move residues 
-  across a hidden column boundary.</p>
-<p>Any web service alignments performed on sequences which contain hidden columns 
-  send the alignment as a series of chunks delimited by the hidden columns. </p>
+  wrapped mode) and select <strong>&quot;Hide Columns&quot;</strong>. </p>
+<p>When an alignment view contains hidden columns, certain constraints
+apply:<ul><li>Editing the alignment is bound by the hidden columns, <em>i.e.</em> you cannot move residues 
+  across a hidden column boundary.</li>
+<li><strong>Tree</strong>, <strong>pairwise alignment</strong> and <strong>PCA</strong> calculations will only be
+performed using the <em>visible</em> parts of the alignment.
+</li>
+<li><a
+  href="../webservices/msaclient.html">Multiple Sequence
+  Alignments</a> are performed locally on on each visible chunk of
+  the input, and concatenated with the hidden regions to form the
+  final result.</p>
+</li>
+</ul>
+<p>The analysis and web service calculations where hidden columns are
+  excluded are termed <em>column-separable</em>. Calculations which
+  are not column-separable will be performed on the whole alignmnent
+  or sequence set, not just the visible regions.</p>
 <p>&nbsp;</p>
 <p>&nbsp;</p>
 <p>&nbsp;</p>
diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 22cb247..6b5c5e1 100755
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -21,17 +21,33 @@
                   possible for some services.
                   </p>
                   <p>Current services:
-                  <ul>
-                  <li>ClustalW Multiple Alignment<br>
-                  The clustal W service remains one of the more popular Jalview features.
+                  <ul><a href="msaclient.html"><strong>Multiple
+                  Sequence Alignment Services</strong></a><ul>
+                  <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>
+                  The clustal W service remains one of the more
+                  popular Jalview features.
                   </li>
-                  <li>Muscle Multiple Alignment<br>
+                  <li><a href="muscle.html">Muscle Multiple Alignment</a><br>
                   High Quality and High Throughput multiple alignments of proteins. This
                   method can sometimes be more accurate than ClustalW when dealing with
                   diverse sets of sequences.
                   </li>
-                  <li>JNet Secondary Structure Prediction<br>
-                  This is a front end to the existing JNet www server.
+                  <li><a href="mafft.html">MAFFT</a><br>
+                  Multiple Alignment with Fast Fourier Transforms -
+                  a highly accurate and high throughput dna and amino
+                  acid alignment method, performing at least as well
+                  as ClustalW and Muscle.
+                  </li>
+                  </ul>                  
+                  </li>
+                  <li><strong>Secondary Structure Prediction</strong>
+                  <ul>
+                  <li><a href="jnet.html">JNet</a><br>This is a front end to the existing <a
+                  href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet
+                  www server</a> allowing single sequence or profile
+                  based prediction.
+                  </li>
+                  </ul>
                   </li>
                   </ul>
                   </p>
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index a94ec44..7a6015a 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -36,6 +36,12 @@ then the alignment will be used for a Jnet prediction on the
 nearest the top of the alignment window).
 </li>
 </ul>
+<p><strong>Note</strong>: JNet secondary structure prediction is a
+ 'non-column-separable' service - predictions are based on the
+ sequence profile of contiguous stretches of amino-acid sequence. This
+ means that all columns of the alignment, or selection will be submitted
+ for prediction, not just the visible ones (see <a
+ href="../features/hiddenRegions.html">hiding columns</a>).
 <p>The result of a JNet prediction for a sequence is a new annotated
  alignment window:</p>
 <img src="jnetprediction.gif">
diff --git a/help/html/webServices/mafft.html b/help/html/webServices/mafft.html
index 34ee58b..4ee0237 100644
--- a/help/html/webServices/mafft.html
+++ b/help/html/webServices/mafft.html
@@ -1,13 +1,18 @@
 <html>
-<head><title>MAFFT Alignment</title></head>
+<head><title>MAFFT Multiple Sequence Alignments</title></head>
 <body>
-<p><strong>MAFFT Alignments</strong></p>
-<p>MAFFT is a program for the alignment of many protein sequences.</p>
+<p><strong>MAFFT Multiple Sequence Alignments</strong></p>
 <p> Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) &quot;MAFFT version 
   5: improvement in accuracy of multiple sequence alignment.&quot; Nucleic Acids 
   Research, 33 511-518</p>
-<p> This alignment method is applied to the selected region, if any, or the whole 
-  sequence set when the <strong>Web Service&#8594;Alignment&#8594;MAFFT Multiple 
-  Sequence Alignment</strong> menu item is selected. </p>
+<p>MAFFT is a program for the multiple alignment of nucleic acid or protein
+sequences, and is available from the <strong>Web
+Service&#8594;Alignment&#8594;MAFFT Multiple Sequence
+Alignment</strong> entry in the web services menu.</p>
+<p>MAFFT utilizes algorithms for spectral correlation to identify
+homologous regions in a fast-fourier transform representation of each
+sequence. The Jalview web service runs MAFFT using the
+'--auto' option which picks optimal parameters
+for the set of sequences to be aligned.</p>
 </body>
 </html>
diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
new file mode 100644
index 0000000..6fea43e
--- /dev/null
+++ b/help/html/webServices/msaclient.html
@@ -0,0 +1,38 @@
+<html>
+<head>
+<title>Multiple Sequence Alignment Web Service</title>
+</head>
+<body>
+<strong>Multiple Sequence Alignment Web Services</strong>
+<p>
+Multiple sequence alignment services are accessed from the <strong>Web
+Service&#8594;Alignment</strong> menu. When an entry from this menu is
+selected, either the currently selected residues, or the whole
+sequence set (if there is no selection or only one sequence is
+selected) will be submitted for multiple sequence alignment.
+</p>
+<p>There are two kinds of multiple sequence alignment operations
+available:<ul>
+<li><em>alignment</em> - where a new alignment is constructed from the input
+</li>
+<li><em>realignment</em> -
+where any existing alignments in the input are passed to the service
+for profile based alignment.
+</li>
+</ul>
+</p>
+<p>
+<strong>Multiple Alignments of Sequences with hidden columns</strong><br>
+Multiple alignment services are 'column separable' analysis
+operations. If the input contains <a
+href="../features/hiddenRegions.html">hidden columns</a> then each
+visible segment of the input sequence set will be submitted for
+alignment separately, and the results concatenated (with the hidden
+regions preserved) once all alignment functions have completed. Each
+sub-job's state is reported in its own tab:
+<p><center><strong>Multiple Multiple Sequence Alignment sub jobs running at
+once</strong><center></p>
+<center><img src="multimafftjbs.gif" align="centre"></center>
+</p>
+</body>
+</html>
diff --git a/help/html/webServices/multimafftjbs.gif b/help/html/webServices/multimafftjbs.gif
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literal 0
HcmV?d00001

-- 
1.7.10.2