<mapID target="pdbviewer" url="html/features/pdbviewer.html"/>\r
<mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>\r
<mapID target="preferences" url="html/features/preferences.html"/> \r
- <mapID target="io" url="html/io/index.html"/>\r
+ <mapID target="io" url="html/io/index.html"/>\r
+ <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>\r
<mapID target="export" url="html/io/export.html"/>\r
<mapID target="alformats" url="html/io/fileformats.html"/>\r
<mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>\r
<mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>\r
<mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>\r
<mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>\r
-\r
+ \r
<mapID target="calcs.alquality" url="html/calculations/quality.html"/> \r
<mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>\r
\r
<tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>\r
<tocitem text="Annotations File" target="annotations.fileformat"/>\r
<tocitem text="Colour by Annotation Value" target="colours.annotation"/>\r
+ <tocitem text="Modeller PIR File IO" target="io.modellerpir"/>\r
</tocitem>\r
<tocitem text="Release History" target="release"/>\r
<tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
the current alignment) exceeds this value then one of the sequences (the \r
shorter) is discarded. Press the "Apply" button to remove redundant \r
sequences. The "Undo" button will undo the last redundancy deletion.</em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>Adds gaps to the end of all the sequences so they are all \r
- the same length. This is useful for making a tree using unaligned sequences.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ <li><strong>Pad Gaps<br>\r
+ </strong><em>When selected, the alignment will be kept at minimal\r
+ width (no empty columns before or after the first or last aligned\r
+ residue). This is useful when making a tree using unaligned\r
+ sequences and when working with alignment analysis programs which\r
+ require 'properly aligned sequences' to be all the same length.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ </em></li>\r
</em><br>\r
</li>\r
</ul>\r
<ul>\r
<li><strong>Find<br>\r
</strong><em>Select this to <a href="../features/search.html">search</a> \r
- for residues, sequence name or residue position within the alignment. \r
+ for residues, sequence name or residue position within the\r
+ alignment and create new sequence features from the queries. \r
<br>\r
</em></li>\r
</ul>\r
<li><strong>Font<br>\r
</strong><em>Change the font of the display from the "Choose Font" \r
dialog box, which is shown when this item is selected. </em></li>\r
+ <li><strong>Smooth Fonts</strong><em><br>\r
+ If selected, the alignment will be drawn with anti-aliasing on which looks \r
+ better, but performace is reduced.\r
+ </em></li>\r
<li><strong>Wrap<br>\r
</strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>" \r
to the width of the alignment window. This is useful if your alignment \r
be displayed below the alignment. The default setting is to display the \r
conservation calculation, quality calculation and consensus values as \r
bar charts. </em></li>\r
- <li><strong>Sequence Features<br>\r
+ <li><strong>Fetch Sequence Features<br>\r
</strong><em>If the sequence names are Swissprot entries Jalview will \r
use the names to retrieve <a href="../features/seqfeatures.html">sequence \r
features</a> from the EBI. Features which are 1 residue in length are \r
<br>\r
Note: The retrieved information will update the sequence start and end \r
labels if they are incorrect. </em></li>\r
- <li><strong>Seqence Settings </strong><br>\r
- <em>If features have been added to the alignment then the priority of \r
- rendering the features can be altered so that overlapping features can \r
- be displayed or hidden. See <a href="features/seqfeatures.html">Sequence \r
- Features</a>.</em></li>\r
+ <li><strong>Show Sequence Features</strong><br><em>Show or\r
+ hide sequence features on this alignment.</em></li>\r
+ <li><strong>Seqence Feature Settings...</strong><em><br>\r
+ <em>Control the colour and display of sequence features on the\r
+ alignment. See <a\r
+ href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><br>\r
+ </em></li>\r
<li><strong><a href="../features/overview.html">Overview Window</a><br>\r
</strong><em>A scaled version of the alignment will be displayed in a \r
small window. A red box will indicate the currently visible area of the \r
</strong><em>Use this to set the threshold value for colouring above Identity. \r
Useful if the window has been closed. <br>\r
</em></li>\r
+ <li><strong>By Annotation</strong><br>\r
+ <em>Colours the alignment on a per-column value from a specified annotation. \r
+ See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
+ </li>\r
</ul>\r
</li>\r
<li><strong>Calculate</strong> \r
is discarded. Press the "Apply" button to remove redundant sequences. \r
The "Undo" button will undo the last redundancy deletion.</em></li>\r
<li><strong>Pad Gaps<br>\r
- </strong><em>Adds gaps to the end of all the sequences so they are all the \r
- same length. This is useful for making a tree using unaligned sequences.<br>\r
+ </strong><em>When selected, the alignment will be kept at minimal\r
+ width (no empty columns before or after the first or last aligned\r
+ residue). This is useful when making a tree using unaligned\r
+ sequences and when working with alignment analysis programs which\r
+ require 'properly aligned sequences' to be all the same length.<br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
</em></li>\r
</ul>\r
alignment. Note: the ids of the tree file and your alignment\r
MUST be the same.<br>\r
</em></li>\r
+ <li><strong>Load Features / Annotations<br>\r
+ </strong><em>Jalview load precalculated <a href="../features/featuresFormat.html">sequence \r
+ features</a> or <a href="../features/annotationsFormat.html">alignment \r
+ annotations</a>.</em></li>\r
<li><strong>Close<br>\r
</strong><em>Close the alignment window. Make sure you have\r
saved your alignment before you close - either as a Jalview\r
displayed below the alignment. The default setting is to display the conservation \r
calculation, quality calculation and consensus values as bar charts. </em><br>\r
</li>\r
- <li><strong>Sequence Features<br>\r
+ <li><strong>Fetch Sequence Features<br>\r
</strong><em>If the sequence names are Swissprot entries Jalview will use \r
the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> \r
from the EBI. Features which are 1 residue in length are coloured red, sequences \r
Note: The retrieved information will update the sequence start and end labels \r
if they are incorrect. </em><br>\r
</li>\r
- <li><strong>Seqence Settings </strong><em><br>\r
- <em>If features have been added to the alignment then the priority of rendering \r
- the features can be altered so that overlapping features can be displayed \r
- or hidden. See <a href="../features/seqfeatures.html">Sequence Features</a>.</em><br>\r
+ <li><strong>Show Sequence Features</strong><br><em>Show or\r
+ hide sequence features on this alignment.</em></li>\r
+ <li><strong>Seqence Feature Settings...</strong><em><br>\r
+ <em>Control the colour and display of sequence features on the\r
+ alignment. See <a\r
+ href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><br>\r
</em></li>\r
<li><strong><a href="../features/overview.html">Overview Window</a><br>\r
</strong><em>A scaled version of the alignment will be displayed in a small \r
internal Jalview schema), and sequence description strings are now\r
preserved in the archive.</li>\r
<li>Jalview can now correctly read and write <a\r
-href="http://salilab.org/modeller/modeller.html">MODELLER</a> style\r
-PIR description lines for proteins with a PDB reference.\r
+href="io/modellerpir.html">MODELLER style\r
+PIR</a> files.\r
</li>\r
</ul>\r
<p>See the <a href="releases.html">Release History</a> page for details of all\r
git://source.jalview.org / jalview.git / commitdiff