--- /dev/null
+<html>\r
+\r
+<head><title>Annotation Colouring</title></head>\r
+\r
+<body>\r
+<p><strong> Annotation Colouring </strong></p>\r
+<p>Jalview 2.08 allows an alignment to be coloured on a per-column basis based \r
+ on any numerical annotation added to that alignment. </p>\r
+Select "Colour" <strong>→</strong> ".. \r
+ by Annotation" to bring up the Colour by Annotation settings window. <br>\r
+ <br><div align="center">\r
+ <img src="annotationColourSetting.jpg" width="426" height="140"> </div>\r
+<ul>\r
+ <li>Select which annotation to base the colouring scheme on using the top left \r
+ selection box.</li>\r
+ <li> If the "Use Original Colours" box is selected, the colouring \r
+ scheme will use the colouring scheme present on the alignment before the Annotation \r
+ Colour Settings window was displayed. </li>\r
+ <li>The colour scheme can display a colour gradient from a colour representing \r
+ the minimum value in the selected annotation to a colour representing the \r
+ maximum value in the selected annotation. Use the "Min Colour" and \r
+ "Max Colour" to set the colour gradient range.</li>\r
+ <li>Select whether to colour the alignment above or below an adjustable threshold \r
+ with the selection box center left of the window. </li>\r
+ <li>Change the threshold value with the slider, or enter the exact value in \r
+ the text box. </li>\r
+</ul>\r
+<p align="center"><img src="annotationColours.jpg" width="475" height="262"> </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<head><title>Annotations File Format</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Annotations File Format<br>\r
+ </strong><br>\r
+ 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
+ as an identifier. Then a block of annotations are added in the form GRAPH_TYPE \r
+ Label Values</p>\r
+<p>GRAPH_TYPE can be either BAR_GRAPH, LINE_GRAPH or NO_GRAPH. The values are \r
+ per alignment column, separated by "|". Multiple content per column \r
+ can be separated with commas, Jalview will display the content if it interprates \r
+ the content as a text label, or secondary structure character (H or E)</p>\r
+<p>You can optionally associate an annotation with a sequence by adding a line \r
+ SEQUENCE_REFseq_namestartIndex All Annotations after a SEQUENCE_REF will be \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
+ 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
+ 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
+ LINE_GRAPH<tab>Green Values<tab>1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2<br>\r
+ LINE_GRAPH<tab>Red Values<tab>2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2<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
+ 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
+ </font><br>\r
+</p>\r
+<p><br>\r
+</p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<head><title>Features File Format</title></head>\r
+\r
+<body>\r
+<p><strong>Sequence Features File Format</strong></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
+ or by selecting from the File menu "Load Features / Annotations".</p>\r
+<p>Specify the feature types first, then refer to the feature type for each sequence.</p>\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
+ metal ion-binding site 00ff00<br>\r
+ transit peptide 0,105,215<br>\r
+ chain 225,105,0<br>\r
+ modified residue 105,225,35<br>\r
+ signal peptide 0,155,165<br>\r
+ Your Own description here FER_CAPAA -1 3 93 domain<br>\r
+ Your Own description here FER_CAPAN -1 48 144 chain<br>\r
+ Your Own description here FER_CAPAN -1 50 140 domain<br>\r
+ Your Own description here FER_CAPAN -1 136 136 modified residue<br>\r
+ Your Own description here FER1_LYCES -1 1 47 transit peptide<br>\r
+ Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide<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
+ ....Many Feature descriptions here<br>\r
+ ENDGROUP<tab>My feature groupA</font><br>\r
+</p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff
