<mapID target="colours.pid" url="html/colourSchemes/pid.html" />\r
<mapID target="colours.user" url="html/colourSchemes/user.html"/>\r
<mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>\r
- <mapID target="colours.conservation"\r
- url="html/colourSchemes/conservation.html"/>\r
+ <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>\r
+ <mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>\r
\r
<mapID target="calcs.alquality"\r
url="html/calculations/quality.html"/> \r
<tocitem text="Key Strokes" target="keys"/>\r
<tocitem text="Making figures" target="export"/>\r
<tocitem text="Editing Alignments" target ="edit"/>\r
+ <tocitem text="Sequence Features" target="seqfeatures"/>\r
<tocitem text="Web Services" target="webservice" expand="false">\r
<tocitem text="Clustal Alignment" target="clustal"/>\r
<tocitem text="Muscle Alignment" target="muscle"/>\r
<tocitem text="User Defined" target="colours.user"/>\r
<tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
<tocitem text="By conservation" target="colours.conservation"/>\r
+ <tocitem text="By Annotation" target="colours.annotation"/>\r
</tocitem>\r
<tocitem text="Calculations" target="calculations" expand="false">\r
<tocitem text="Sorting alignments" target="sorting"/>\r
<head><title>Annotations File Format</title></head>\r
\r
<body>\r
-<p><strong>Alignment Annotations File Format<br>\r
+<p><strong>Alignment Annotations File Format</strong><strong><br>\r
</strong><br>\r
- A precalculated annotations fiile can read onto an alignment from the command \r
+ Note: This format is primarily intended to be used for the applet, which does \r
+ not have an XML parser and where file size must be kept to a minimum to reduce \r
+ download time.</p>\r
+<p>A precalculated annotations fiile can read onto an alignment from the command \r
line ("-annotations"), by drag and dropping the the annotations file \r
onto an alignment or by selecting from the File menu "Load Features / Annotations".</p>\r
<p>The File is in tab delimited format. The file must have the line JALVIEW_ANNOTATION \r
associated with that sequence. Use SEQUENCE_REF ALIGNMENT to cancel the associtations.</p>\r
<p>The visual graphs can be coloured or combined with other graphs, or have an \r
arbitrary line drawn at a certain value using the following lines.</p>\r
-<p><font size="2" face="Courier New, Courier, mono">COLOUR<tab>graph name<tab>colour<br>\r
+<p><font size="3" face="Courier New, Courier, mono">COLOUR<tab>graph name<tab>colour<br>\r
COMBINE<tab>graph 1 name<tab>graph 2 name<br>\r
GRAPHLINE<tab>graph name<tab>value<tab>label<tab>colour</font></p>\r
<p>An example Annotation file may look like this:</p>\r
-<p><font size="2" face="Courier New, Courier, mono">#Comment lines follow the hash symbol<br>\r
+<p><font size="3" face="Courier New, Courier, mono">#Comment lines follow the hash symbol<br>\r
JALVIEW_ANNOTATION<br>\r
SEQUENCE_REF FER1_MESCR 5<br>\r
BAR_GRAPH<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\r
BAR_GRAPH<tab>Bar Graph<tab>2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>\r
NO_GRAPH<tab>Icons <tab>||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>\r
NO_GRAPH<tab>Purple Letters<tab>m|y|p|r|o|t|e|i|n</font></p>\r
-<p><font size="2" face="Courier New, Courier, mono">COLOUR<tab>Bar Graph 2<tab>blue<br>\r
+<p><font size="3" face="Courier New, Courier, mono">COLOUR<tab>Bar Graph 2<tab>blue<br>\r
COLOUR<tab>Red Values<tab>255,0,0<br>\r
COLOUR<tab>Green Values<tab>green<br>\r
COLOUR<tab>Purple Letters<tab>151,52,228<br>\r
COMBINE<tab>Green Values<tab>Red Values</font></p>\r
-<p><font size="2" face="Courier New, Courier, mono">GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black \r
+<p><font size="3" face="Courier New, Courier, mono">GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black \r
</font><br>\r
</p>\r
<p><br>\r
\r
<body>\r
<p><strong>Sequence Features File Format</strong></p>\r
+<p>Note: This format is primarily intended to be used for the applet, which does \r
+ not have an XML parser and where file size must be kept to a minimum to reduce \r
+ download time.</p>\r
<p>(Prior to version 2.08 known as the "Groups file")<br>\r
A precalculated Features file can read onto an alignment from the command line \r
("-features"), by drag and dropping the features file onto an alignment \r
<p>featureType<tab>colour<br>\r
description<tab>sequenceId<tab>sequenceIndex<tab>start<tab>end<tab>featureType</p>\r
<p>eg<br>\r
- <font size="2" face="Courier New, Courier, mono">domain red<br>\r
+ <font size="3" face="Courier New, Courier, mono">domain red<br>\r
metal ion-binding site 00ff00<br>\r
transit peptide 0,105,215<br>\r
chain 225,105,0<br>\r
Your Own description here Q93XJ9_SOLTU -1 49 144 chain</font></p>\r
<p>An additional option in Jalview 2.08 is to group features in the following \r
way: </p>\r
-<p><font size="2" face="Georgia, Times New Roman, Times, serif">STARTGROUP<tab>My feature groupA<br>\r
+<p><font size="3" face="Georgia, Times New Roman, Times, serif">STARTGROUP<tab>My feature groupA<br>\r
....Many Feature descriptions here<br>\r
ENDGROUP<tab>My feature groupA</font><br>\r
</p>\r
<li>Q - Define the top left corner of the selection area</li>\r
</ul>\r
<ul>\r
- <li>M - Define the bottom right corner of the selection area</li>\r
+ <li>M - Define the bottom right corner of the selection area<br>\r
+ </li>\r
+ <li>65,82<return> - Quick jump to column 65, sequence 82</li>\r
</ul>\r
<p> </p>\r
<p> </p>\r
<p><strong>Release History</strong> </p>\r
<table border="1">\r
<tr> \r
- <td ><div align="center"><em><strong>Release</strong></em></div></td>\r
+ <td nowrap><div align="center"><em><strong>Release</strong></em></div></td>\r
<td ><div align="center"><em><strong>New Features</strong></em></div></td>\r
<td "><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
</tr>\r
git://source.jalview.org / jalview.git / commitdiff