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+ <mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>
+
+ <mapID target="calcs.alquality" url="html/calculations/quality.html"/>
+ <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
+ <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
+
+ <mapID target="menus" url="html/menus/index.html"/>
+ <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
+ <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
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+
+ <mapID target="wsMenu" url="html/menus/wsmenu.html"/>
+ <mapID target="popMenu" url="html/menus/popupMenu.html"/>
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+
+ <mapID target="memory" url="html/memory.html" />
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-<?xml version="1.0" encoding="ISO-8859-1" ?>\r
-<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">\r
-<toc version="1.0">\r
-<tocitem text="Jalview Documentation" target="home" expand="true" >\r
- <tocitem text="What's new" target="new" expand="false">\r
- <tocitem text="DAS Feature Fetching" target="das.settings"/>\r
- <tocitem text="Hide Regions" target="hiddenRegions"/>\r
- <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>\r
- <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>\r
- <tocitem text="MAFFT Alignment" target="mafft"/>\r
- </tocitem>\r
- <tocitem text="Release History" target="release"/>\r
- <tocitem text="Editing Alignments" target ="edit"/> \r
- <tocitem text="Cursor Mode" target="cursor"/>\r
- <tocitem text="Key Strokes" target="keys"/>\r
- <tocitem text="Input / Output" target="io"/>\r
- <tocitem text="Making figures" target="export"/>\r
- <tocitem text="Hidden Regions" target="hiddenRegions"/>\r
- <tocitem text="Viewing PDB Files" target="viewingpdbs"/>\r
- <tocitem text="Sequence Features" target="seqfeatures" expand="false">\r
- <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
- <tocitem text="Sequence Features File" target="features.fileformat"/>\r
- <tocitem text="User Defined Sequence Features" target="search"/>\r
- <tocitem text="DAS Features Settings" target="das.viewing"/>\r
- </tocitem>\r
- <tocitem text="Web Services" target="webservice" expand="false">\r
- <tocitem text="Sequence Alignment" target="msaservice" expand="false">\r
- <tocitem text="Clustal Alignment" target="clustal"/>\r
- <tocitem text="Muscle Alignment" target="muscle"/>\r
- <tocitem text="MAFFT Alignment" target="mafft"/>\r
- </tocitem>\r
- <tocitem text="Secondary Structure Prediction" target="jnet"/>\r
- </tocitem>\r
- <tocitem text="Colour Schemes" target="colours" expand="false">\r
- <tocitem text="ClustalX" target="colours.clustal"/>\r
- <tocitem text="Zappo" target="colours.zappo"/>\r
- <tocitem text="Taylor" target="colours.taylor"/>\r
- <tocitem text="Hydrophobicity" target="colours.hydro"/>\r
- <tocitem text="Helix propensity" target="colours.helix"/>\r
- <tocitem text="Strand propensity" target="colours.strand"/>\r
- <tocitem text="Turn propensity" target="colours.turn"/>\r
- <tocitem text="Buried index" target="colours.buried"/>\r
- <tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
- <tocitem text="Blosum62" target="colours.blosum"/>\r
- <tocitem text="by Percentage Identity" target="colours.pid"/> \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
- <tocitem text="Calculating trees" target="trees"/>\r
- <tocitem text="Principal Component Analysis" target="pca"/>\r
- <tocitem text="Pairwise Alignments" target="pairwise"/>\r
- <tocitem text="Remove Redundancy" target="redundancy"/>\r
- </tocitem>\r
- <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
- <tocitem text="Conservation" target="calcs.alconserv"/>\r
- <tocitem text="Quality" target="calcs.alquality"/>\r
- <tocitem text="Consensus" target="calcs.consensus"/>\r
- <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
- </tocitem>\r
- <tocitem text="Window Menus" target="menus" expand="false">\r
- <tocitem text="Desktop Window" target="desktopMenu"/>\r
- <tocitem text="Alignment Window" target="alMenu">\r
- <tocitem text="File Menu" target="alwFile"/>\r
- <tocitem text="Edit Menu" target="alwEdit"/> \r
- <tocitem text="View Menu" target="alwView"/> \r
- <tocitem text="Colour Menu" target="alwColour"/>\r
- <tocitem text="Calculation Menu" target="alwCalc"/>\r
- <tocitem text="Web Service Menu" target="wsMenu"/>\r
- <tocitem text="Annotation Menus" target="annotMenus"/>\r
- <tocitem text="Popup Menu" target="popMenu"/>\r
- </tocitem>\r
- </tocitem>\r
- <tocitem text="Memory Settings" target="memory" expand="false">\r
- <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
- </tocitem>\r
-</tocitem>\r
-<tocitem text="Useful information" expand="true">\r
- <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
- <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
- <tocitem text="The Genetic Code" target="geneticCode"/>\r
-</tocitem>\r
-</toc>\r
+<?xml version="1.0" encoding="ISO-8859-1" ?>
+<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
+<toc version="1.0">
+<tocitem text="Jalview Documentation" target="home" expand="true" >
+ <tocitem text="What's new" target="new" expand="true">
+ <tocitem text="Multiple Views" target="multipleviews"/>
+ <tocitem text="Reload and Save" target="reloadsave"/>
+ <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
+ </tocitem>
+ <tocitem text="Release History" target="release"/>
+ <tocitem text="Editing Alignments" target ="edit"/>
+ <tocitem text="Cursor Mode" target="cursor"/>
+ <tocitem text="Key Strokes" target="keys"/>
+ <tocitem text="Input / Output" target="io"/>
+ <tocitem text="Making figures" target="export"/>
+ <tocitem text="Hidden Regions" target="hiddenRegions"/>
+ <tocitem text="Viewing PDB Files" target="viewingpdbs"/>
+ <tocitem text="Sequence Features" target="seqfeatures" expand="false">
+ <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
+ <tocitem text="Sequence Features File" target="features.fileformat"/>
+ <tocitem text="User Defined Sequence Features" target="search"/>
+ <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
+ <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
+ <tocitem text="DAS Feature Settings" target="das.settings"/>
+ </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="Multiple Alignment Subjobs" target="msaservice"/>
+ </tocitem>
+ <tocitem text="Secondary Structure Prediction" target="jnet"/>
+ </tocitem>
+ <tocitem text="Colour Schemes" target="colours" expand="false">
+ <tocitem text="ClustalX" target="colours.clustal"/>
+ <tocitem text="Zappo" target="colours.zappo"/>
+ <tocitem text="Taylor" target="colours.taylor"/>
+ <tocitem text="Hydrophobicity" target="colours.hydro"/>
+ <tocitem text="Helix propensity" target="colours.helix"/>
+ <tocitem text="Strand propensity" target="colours.strand"/>
+ <tocitem text="Turn propensity" target="colours.turn"/>
+ <tocitem text="Buried index" target="colours.buried"/>
+ <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
+ <tocitem text="Blosum62" target="colours.blosum"/>
+ <tocitem text="by Percentage Identity" target="colours.pid"/>
+ <tocitem text="User Defined" target="colours.user"/>
+ <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
+ <tocitem text="By conservation" target="colours.conservation"/>
+ <tocitem text="By Annotation" target="colours.annotation"/>
+ </tocitem>
+ <tocitem text="Calculations" target="calculations" expand="false">
+ <tocitem text="Sorting alignments" target="sorting"/>
+ <tocitem text="Calculating trees" target="trees"/>
+ <tocitem text="Principal Component Analysis" target="pca"/>
+ <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
+ <tocitem text="Pairwise Alignments" target="pairwise"/>
+ <tocitem text="Remove Redundancy" target="redundancy"/>
+ </tocitem>
+ <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+ <tocitem text="Conservation" target="calcs.alconserv"/>
+ <tocitem text="Quality" target="calcs.alquality"/>
+ <tocitem text="Consensus" target="calcs.consensus"/>
+ <tocitem text="Annotations File Format" target="annotations.fileformat"/>
+ </tocitem>
+ <tocitem text="Window Menus" target="menus" expand="false">
+ <tocitem text="Desktop Window" target="desktopMenu"/>
+ <tocitem text="Alignment Window" target="alMenu">
+ <tocitem text="File Menu" target="alwFile"/>
+ <tocitem text="Edit Menu" target="alwEdit"/>
+ <tocitem text="View Menu" target="alwView"/>
+ <tocitem text="Colour Menu" target="alwColour"/>
+ <tocitem text="Calculation Menu" target="alwCalc"/>
+ <tocitem text="Web Service Menu" target="wsMenu"/>
+ <tocitem text="Annotation Menus" target="annotMenus"/>
+ <tocitem text="Popup Menu" target="popMenu"/>
+ </tocitem>
+ </tocitem>
+ <tocitem text="Memory Settings" target="memory" expand="false">
+ <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
+ </tocitem>
+</tocitem>
+<tocitem text="Useful information" expand="true">
+ <tocitem text="Amino Acid Table" target="aminoAcids"/>
+ <tocitem text="Amino Acid Properties" target="aaProperties"/>
+ <tocitem text="The Genetic Code" target="geneticCode"/>
+</tocitem>
+</toc>
-<html>\r
-<head><title>Alignment Consensus Annotation</title></head>\r
-<body>\r
-<p><strong>Alignment Consensus Annotation</strong></p>\r
-<p>The consensus displayed below the alignment is the percentage of the modal \r
- residue per column. By default this calculation takes includes gaps in column. \r
- You can choose to ignore gaps in the calculation by right clicking on the label \r
- "Consensus" to the left of the consensus bar chart. \r
-<p>If the modal value is shared by more than 1 residue, a "+" symbol \r
- is used in the display for the simple reason that it is not possible to display \r
- multiple characters in a single character space.\r
-</body>\r
-</html>\r
+<html>
+<head><title>Alignment Consensus Annotation</title></head>
+<body>
+<p><strong>Alignment Consensus Annotation</strong></p>
+<p>The consensus displayed below the alignment is the percentage of the modal
+ residue per column. By default this calculation takes includes gaps in column.
+ You can choose to ignore gaps in the calculation by right clicking on the label
+ "Consensus" to the left of the consensus bar chart.
+<p>If the modal value is shared by more than 1 residue, a "+" symbol
+ is used in the display for the simple reason that it is not possible to display
+ multiple characters in a single character space.
+<p><strong>Copying the consensus sequence</strong></p>
+<p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
+the consensus annotation label to copy the alignment's consensus sequence to the
+clipboard.
+</p>
+</body>
+</html>
-<html>\r
-<head><title>Principal Component Analysis</title></head>\r
-<body>\r
-<p><strong>Principal Component Analysis</strong></p>\r
-<p>This calculation creates a spatial representation of the\r
-similarities within a selected group, or all of the sequences in\r
-an alignment. After the calculation finishes, a 3D viewer displays the\r
-set of sequences as points in 'similarity space', and similar\r
-sequences tend to lie near each other in the space.</p>\r
-<p>Note: The calculation is computationally expensive, and may fail for very large sets of sequences -\r
- usually because the JVM has run out of memory. The next release of\r
- Jalview release will execute this calculation through a web service.</p>\r
-<p>Principal components analysis is a technique for examining the\r
-structure of complex data sets. The components are a set of dimensions\r
-formed from the measured values in the data set, and the principle\r
-component is the one with the greatest magnitude, or length. The\r
-sets of measurements that differ the most should lie at either end of\r
-this principle axis, and the other axes correspond to less extreme\r
-patterns of variation in the data set.\r
-</p>\r
-\r
-<p>In this case, the components are generated by an eigenvector\r
-decomposition of the matrix formed from the sum of BLOSUM scores at\r
-each aligned position between each pair of sequences. The basic method\r
-is described in the paper by G. Casari, C. Sander and\r
-A. Valencia. Structural Biology volume 2, no. 2, February 1995 (<a\r
-href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)\r
- and implemented at the SeqSpace server at the EBI.\r
-</p>\r
-\r
-<p><strong>The PCA Viewer</strong></p>\r
-<p>This is an interactive display of the sequences positioned within\r
- the similarity space. The colour of each sequence point is the same\r
- as the sequence group colours, white if no colour has been\r
- defined for the sequence, and green if the sequence is part of a\r
- the currently selected group.\r
-</p>\r
- <p>The 3d view can be rotated by dragging the mouse with the\r
- <strong>left mouse button</strong> pressed. The view can also be\r
- zoomed in and out with the up and down <strong>arrow\r
- keys</strong>. Labels will be shown for each sequence\r
- if the entry in the View menu is checked, and the plot background\r
- colour changed from the View→Background Colour.. dialog\r
- box. The File menu allows the view to be saved (File→Save\r
- submenu) as an EPS or PNG image or printed, and the original\r
- alignment data and matrix resulting from its PCA analysis to be\r
- retrieved.\r
-</p>\r
- </p>\r
-<p>A tool tip gives the sequence ID corresponding to a point in the\r
- space, and clicking a point toggles the selection of the\r
- corresponding sequence in the alignment window. Rectangular region\r
- based selection is also possible, by holding the 'S' key whilst\r
- left-clicking and dragging the mouse over the display.\r
-</p>\r
-<p>Initially, the display shows the first three components of the\r
- similarity space, but any eigenvector can be used by changing the selected\r
- dimension for the x, y, or z axis through each ones menu located\r
- below the 3d display.\r
-</p>\r
-<p>\r
-\r
-</body>\r
-</html>\r
+<html>
+<head><title>Principal Component Analysis</title></head>
+<body>
+<p><strong>Principal Component Analysis</strong></p>
+<p>This calculation creates a spatial representation of the
+similarities within a selected group, or all of the sequences in
+an alignment. After the calculation finishes, a 3D viewer displays the
+set of sequences as points in 'similarity space', and similar
+sequences tend to lie near each other in the space.</p>
+<p>Note: The calculation is computationally expensive, and may fail for very large sets of sequences -
+ usually because the JVM has run out of memory. A future release of
+ Jalview will be able to avoid this by executing the calculation via a web service.</p>
+<p>Principal components analysis is a technique for examining the
+structure of complex data sets. The components are a set of dimensions
+formed from the measured values in the data set, and the principle
+component is the one with the greatest magnitude, or length. The
+sets of measurements that differ the most should lie at either end of
+this principle axis, and the other axes correspond to less extreme
+patterns of variation in the data set.
+</p>
+
+<p>In this case, the components are generated by an eigenvector
+decomposition of the matrix formed from the sum of BLOSUM scores at
+each aligned position between each pair of sequences. The basic method
+is described in the paper by G. Casari, C. Sander and
+A. Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
+href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
+ and implemented at the SeqSpace server at the EBI.
+</p>
+
+<p><strong>The PCA Viewer</strong></p>
+<p>This is an interactive display of the sequences positioned within
+ the similarity space. The colour of each sequence point is the same
+ as the sequence group colours, white if no colour has been
+ defined for the sequence, and green if the sequence is part of a
+ the currently selected group.
+</p>
+ <p>The 3d view can be rotated by dragging the mouse with the
+ <strong>left mouse button</strong> pressed. The view can also be
+ zoomed in and out with the up and down <strong>arrow
+ keys</strong> (and the roll bar of the mouse if present). Labels
+ will be shown for each sequence if the entry in the View menu is
+ checked, and the plot background colour changed from the
+ View→Background Colour.. dialog box. The File menu allows the
+ view to be saved (File→Save submenu) as an EPS or PNG image or
+ printed, and the original alignment data and matrix resulting from
+ its PCA analysis to be retrieved.
+</p>
+ </p>
+<p>A tool tip gives the sequence ID corresponding to a point in the
+ space, and clicking a point toggles the selection of the
+ corresponding sequence in the alignment window. Rectangular region
+ based selection is also possible, by holding the 'S' key whilst
+ left-clicking and dragging the mouse over the display.
+</p>
+<p>Initially, the display shows the first three components of the
+ similarity space, but any eigenvector can be used by changing the selected
+ dimension for the x, y, or z axis through each ones menu located
+ below the 3d display.
+</p>
+<p>
+
+</body>
+</html>
are also reflected in any other analysis windows associated with the
alignment, such as another tree viewer.</p>
-<p>
- Clicking on an internal node of the tree will rearrange the tree
- diagram, inverting the ordering of the branches at that node.
+<p>Moving the mouse over an internal node of the tree will highlight
+ it. You can then : <ul>
+ <li>Click the highlighted node to select all the sequences in that branch.
+ <li>Double-click the highlighted node to rearrange the tree
+ diagram by inverting the branch ordering at that
+ node.
+ <li>Right-click to open the 'Select Sub-Tree Colour' dialog box, to
+ pick a new colour for the sub-tree and associated sequences.
+ </ul>
</p>
<p>
Clicking anywhere along the extent of the tree (but not on a leaf or
associated with a tree. Trees calculated by Jalview have branch
lengths, which correspond to the distance measure used to construct
the tree. Tree imported from outside may also contain bootstrap information,
-or additional leaves from sequences not present in the associated
+and additional leaves from sequences not present in the associated
alignment.
</p>
<p>The view menu contains options controlling the way a tree is
-rendered and labelled:</p>
-<p><ul>
+rendered and labelled:
+<ul>
<li><strong>Fit to Window</strong><p>
The tree layout will be scaled to fit in the display
window. You may need to reduce the font size to minimise the leaf
</p></li>
<li><strong>Mark unlinked leaves</strong><p>
Toggles the display of a '*' at the beginning of a leaf label to
-indicate that there is no sequence corresponding to that leaf in the associated alignment.
+indicate that there is no sequence corresponding to that leaf in the
+associated alignment.
</p></li>
+<li><strong>Leaf Association</strong><p>
+Only visible when there are <a href="../features/multipleviews.html">multiple views</a> of the same
+alignment to show and edit which alignment views are associated with
+the leaves of the displayed tree.
+</p>
</ul>
</p>
</body>
--- /dev/null
+<html>\r
+<head>\r
+<title>Creating and Editing Sequence Features</title>\r
+</head>\r
+<body>\r
+<strong>Creating and Editing Sequence Features</strong>\r
+<p>Double clicking on a sequence feature opens the <strong>"Amend/Delete Features"</strong> dialog box.\r
+<img src="">\r
+</p>\r
+<!-- update the features.html - link this bit in -->\r
+<p><em>Sequence feature editing was implemented in Jalview 2.2</em></p>\r
+</body>\r
+</html>
\ No newline at end of file
--- /dev/null
+<html>\r
+<head>\r
+<title>Multiple Alignment Views</title>\r
+</head>\r
+<body>\r
+<p><strong>Multiple Alignment Views<strong></p>\r
+<p>Multiple alignment views allow's the same alignment to be viewed in\r
+many different ways, either as multiple alignment tabs, or simultaneously in\r
+linked alignment windows. A view is an independent visualization of\r
+the same alignment, so each may have a different ordering, colouring,\r
+row and column hiding and seuqence feature and annotation display\r
+setting, but alignment, feature and annotation edits are common to\r
+all, since this affects the underlying data.\r
+</p>\r
+<p>\r
+A new view is created using the <strong>"View→New View"</strong> menu item, or by pressing\r
+<strong>Control+T</strong>. A newly created view will be identical to\r
+the view it was created from, but any changes to the way the alignment\r
+is coloured or displayed will only affect the new view.\r
+</p>\r
+<p>A particular view may focus on some specific aspect of an alignment -\r
+for example, hiding all but the region of an alignment containing a\r
+particular domain. <strong>Right-clicking</strong> a view's tab opens\r
+the View Name dialog box, allowing it to be renamed to something more\r
+meaningful.\r
+</p>\r
+<p><strong>Viewing Multiple Views Simultaneously</strong></p>\r
+<p>Multiple views of an alignment are, by default, gathered together as tabs\r
+within a single alignment window. They can be viewed simultanously by\r
+pressing <strong>X</strong> (or via\r
+<strong>"View→Expand"</strong>) to expand each view\r
+into its own linked alignment window. Expanded views are gathered\r
+back into into a single tabbed alignment window by pressing\r
+<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).\r
+</p>\r
+<p><strong>Tree Viewers and Multiple Views</strong></p>\r
+<p>A tree calculated on a particular view, or loaded onto it, is by\r
+default associated with just that view. However, the <a\r
+href="../calculations/treeviewer.html">Tree Viewer's</a> \r
+<strong>"View→Associate leaves"</strong> submenu\r
+allows a tree's view association to be changed to to any or all other\r
+views.</p>\r
+<p><em>Multiple Views were introduced in Jalview 2.2</em></p></body>\r
+</html>
\ No newline at end of file
--- /dev/null
+<html>\r
+<head>\r
+<title>Reload and Save Alignment</title>\r
+</head>\r
+<body>\r
+<p><strong>Reload and Save Alignment</strong></p>\r
+<p>Jalview remembers the original source of an alignment if it has\r
+been loaded from a file or\r
+URL.<ul>\r
+<li><strong>"File→Reload"</strong> will reload the\r
+alignment from its original source, discarding any edits or applied\r
+colouring and features since the last save.</li>\r
+<li><strong>"File→Save"</strong> will save the\r
+alignment back to the same filename, with the same format, easing the\r
+the process of editing and updating an alignment file <em>in\r
+place</em>.\r
+</li>\r
+</ul>\r
+</body>\r
+</html>
\ No newline at end of file
-<html>\r
-<head><title>Home Page</title></head>\r
-\r
-<body>\r
-<IMG src="align.gif"><font size="4">\r
-<br><br>\r
-<strong>Jalview Documentation</strong></font>\r
-<br><br>\r
-JalView (1999) is a fast Java multiple alignment editor and analysis tool. It\r
-features many of the functions of <a href="http://www.compbio.dundee.ac.uk/Software/Amas/amas.html">AMAS</a>,\r
-for the analysis of sub-families and the prediction of functional sites, but is\r
-fully interactive.\r
-<p></p>\r
-<p> If you use JalView in your work, please cite the bioinformatics paper: </p>\r
-<p>Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview\r
- Java Alignment Editor", Bioinformatics, 20, 426-7.</p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Home Page</title></head>
+
+<body>
+<IMG src="align.gif"><font size="4">
+<br><br>
+<strong>Jalview Documentation</strong></font>
+<br><br>
+Jalview (2004) is a fast Java multiple alignment editor and analysis tool. It
+features many of the functions of <a href="http://www.compbio.dundee.ac.uk/Software/Amas/amas.html">AMAS</a>,
+for the analysis of sub-families and the prediction of functional sites, but is
+fully interactive. (View the <a href="http://www.jalview.org">Jalview homepage</a>).
+<p></p>
+<p> If you use Jalview in your work, please cite the bioinformatics paper: </p>
+<p>Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview
+ Java Alignment Editor", Bioinformatics, 20, 426-7.</p>
+</body>
+</html>
-<html>\r
-<head><title>Key Strokes</title></head>\r
-<body>\r
-<p><strong>Key Strokes</strong></p>\r
-<p>\r
-Jalview responds a number of key strokes, and has two distinct modes of\r
-keyboard operation. The <em>F2</em> key switches between 'Normal' and\r
-<a href="features/cursorMode.html">'Cursor'</a> mode operation.\r
-</p>\r
-<table border="1">\r
- <tr> \r
- <td><strong>Key</strong></td>\r
- <td><strong>Which Mode</strong></td>\r
- <td><strong>Action</strong></td>\r
- </tr>\r
- <!--<tr>\r
-<td><strong>Escape</strong></td><td>Both</td>\r
-<td>The Panic button.</td></tr>\r
-<tr> -->\r
- <td><strong> Escape</strong></td>\r
- <td>Normal</td>\r
- <td>Clears the current selection region, highlighted columns and highlghted \r
- residues. </td>\r
- </tr>\r
- <tr> \r
- <td><strong>Escape</strong></td>\r
- <td>Cursor</td>\r
- As in normal mode, but also cancels any partially entered commands</td></tr>\r
- <tr> \r
- <td><strong><em>F1</em></strong></td>\r
- <td>Both</td>\r
- Show Help Documentation</td></tr>\r
- <tr> \r
- <td><strong><em>F2</em></strong></td>\r
- <td></td>\r
- <td>Toggle Cursor mode on / off</td>\r
- </tr>\r
- <tr> \r
- <td><strong>Control 'Z'</strong></td>\r
- <td>Both</td>\r
- <td>Undoes the last sequence edit</td>\r
- </tr>\r
- <tr> \r
- <td><strong>Up Arrow</strong></td>\r
- <td>Normal</td>\r
- Moves selected sequence(s) up the alignment</td></tr>\r
- <tr> \r
- <td><strong>Down Arrow</strong></td>\r
- <td>Normal</td>\r
- Moves selected sequence(s) down the alignment.</td></tr>\r
- <tr><strong>Cursor Keys<br>\r
- (Arrow Keys)</strong></td>\r
- <td>Cursor</td>\r
- <td>Move cursor around alignment</td>\r
- </tr>\r
- <tr> \r
- <td><strong>Control 'A'</strong></td>\r
- <td>Both</td>\r
- <td>Selects all sequences in the alignment</td>\r
- </tr>\r
- <tr> \r
- <td><strong>Control 'C'</strong></td>\r
- <td>Both</td>\r
- <td>Copies the selected region into the clipboard as a Fasta format file<br> \r
- <em>nb. not available in applet, as no clipboard is available</em></td>\r
- </tr>\r
- <tr> \r
- <td><strong>Control 'V'</strong></td>\r
- <td>Both</td>\r
- Pastes the contents of the clipboard to a new alignment window. (same as the \r
- Alignment Window menu Edit->Paste command)<br>\r
- <em>nb. if the paste is from a Jalview alignment, any sequence and alignment \r
- annotations will also be copied over.</em></td></tr>\r
- <tr> \r
- <td><strong>Control 'X'</strong></td>\r
- <td>Both</td>\r
- <td>Cuts the (fully) selected sequences from the alignment. \r
- <!-- not yet in this version \r
-This will not happen if only some\r
-columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->\r
- </td>\r
- </tr>\r
- <tr> \r
- <td><strong>Control 'F'</strong></td>\r
- <td>Both</td>\r
- <td>Launches the search window</td>\r
- </tr>\r
- <tr> \r
- <td><strong>H</strong></td>\r
- <td>Both</td>\r
- <td>Hides / Reveals selected columns and sequences</td>\r
- </tr>\r
- <tr> \r
- <td><strong>Control 'H'</strong></td>\r
- <td>Both</td>\r
- <td>Hides / Reveals selected columns</td>\r
- </tr>\r
- <tr> \r
- <td><strong>Shift 'H'</strong></td>\r
- <td>Both</td>\r
- <td>Hides / Reveals selected sequences</td>\r
- </tr>\r
-</table>\r
-<p>The compound commands available in the Cursor mode are summarised\r
-below. Single letter commands can be prefixed by digits to specify a repetition\r
-number, and some more complex commands take one or more numeric\r
-parameters (prefixing the command key and separated by commas).</p>\r
-<table border=1><tr><td><strong>Compound\r
-Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>\r
-<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a\r
-numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit\r
-command.</td></tr>\r
-<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or\r
-more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>\r
-<tr><td><strong><strong><em>p1</em></strong>,<strong><em>p2</em></strong><br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (<strong><em>p1</em></strong>) and row (<strong><em>p2</em></strong>) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>\r
-<tr><td><strong><em>p</em>S</strong></td><td>Cursor</td><td>Jump to the <strong><em>p</em></strong>'th sequence in the alignment.</td></tr>\r
-<tr><td><strong><em>p</em>P</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th amino acid in current sequence.</td></tr>\r
-<tr><td><strong><em>p</em>C</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th column in the alignment.</td></tr>\r
-<tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>\r
-<tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>\r
-<tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts\r
-one (or optionally <strong><em>p</em></strong>) gaps at the current position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
-<tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes\r
-one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
-<tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes\r
-one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr></table>\r
-<p> </p>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Key Strokes</title></head>
+<body>
+<p><strong>Key Strokes</strong></p>
+<p>
+Jalview has two distinct modes of keyboard operation - in 'Normal'
+ mode, single keystrokes (including those shown next to menu items)
+ provide short cuts to common commands. In <a
+ href="features/cursorMode.html">'Cursor'</a> mode (enabled by
+ <em>F2</em>), some of these are disabled and more complex 'Compound
+ Keystrokes' can be entered to perform precise navigation, selection
+ and editing operations.
+</p>
+<table border="1">
+ <tr>
+ <td><strong>Key</strong></td>
+ <td><strong>Which Mode</strong></td>
+ <td><strong>Action</strong></td>
+ </tr>
+ <!--<tr>
+<td><strong>Escape</strong></td><td>Both</td>
+<td>The Panic button.</td></tr>
+<tr> -->
+ <tr><td><strong> Escape</strong></td>
+ <td>Normal</td>
+ <td>Clears the current selection region, highlighted columns and highlghted
+ residues. </td>
+ </tr>
+ <tr>
+ <td><strong>Escape</strong></td>
+ <td>Cursor</td>
+ <td>As in normal mode, but also cancels any partially entered commands</td></tr>
+ <tr>
+ <td><strong><em>F1</em></strong></td>
+ <td>Both</td>
+ <td>Show Help Documentation</td></tr>
+ <tr>
+ <td><strong><em>F2</em></strong></td>
+ <td></td>
+ <td>Toggle Cursor mode on / off</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'Z'</strong></td>
+ <td>Both</td>
+ <td>Undoes the last sequence edit</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'Y'</strong></td>
+ <td>Both</td>
+ <td>Redo the last sequence edit undone.</td>
+ </tr>
+ <tr>
+ <td><strong>Up Arrow</strong></td>
+ <td>Normal</td>
+ <td>Moves selected sequence(s) up the alignment</td></tr>
+ <tr>
+ <td><strong>Down Arrow</strong></td>
+ <td>Normal</td>
+ <td>Moves selected sequence(s) down the alignment.</td></tr>
+ <tr><td><strong>Cursor Keys<br>
+ (Arrow Keys)</strong></td>
+ <td>Cursor</td>
+ <td>Move cursor around alignment</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'A'</strong></td>
+ <td>Both</td>
+ <td>Selects all sequences in the alignment</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'I'</strong></td>
+ <td>Both
+ </td>
+ <td>Invert sequence selection.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Control Alt 'I'</strong></td>
+ <td>Both
+ </td>
+ <td>Invert column selection.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Control 'C'</strong></td>
+ <td>Both</td>
+ <td>Copies the selected region into the clipboard as a Fasta format file<br>
+ <em>nb. not available in applet, as no clipboard is available</em></td>
+ </tr>
+ <tr>
+ <td><strong>Control 'V'</strong></td>
+ <td>Both</td>
+ <td>
+ Paste the contents of the clipboard to the current alignment
+ window. (Alignment Window->Edit->Paste->Add to this Alignment)<br>
+ <em>nb. if the paste is from a Jalview alignment, any sequence and alignment
+ annotations will also be copied over.</em></td></tr>
+ <tr>
+ <td><strong>Control Shift 'V'</strong></td>
+ <td>Both</td>
+ <td>Paste the contents of the clipboard to a new alignment
+ window. (Alignment Window->Edit->Paste->To New Alignment)</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'X'</strong></td>
+ <td>Both</td>
+ <td>Cuts the (fully) selected sequences from the alignment.
+ <!-- not yet in this version
+This will not happen if only some
+columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Control 'F'</strong></td>
+ <td>Both</td>
+ <td>Launches the search window</td>
+ </tr>
+ <tr>
+ <td><strong>H</strong></td>
+ <td>Both</td>
+ <td>Hides / Reveals selected columns and sequences</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'H'</strong></td>
+ <td>Both</td>
+ <td>Hides / Reveals selected columns</td>
+ </tr>
+ <tr>
+ <td><strong>Shift 'H'</strong></td>
+ <td>Both</td>
+ <td>Hides / Reveals selected sequences</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'O'</strong></td>
+ <td>Both</td>
+ <td>Input new alignment from file</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'S'</strong></td>
+ <td>Both</td>
+ <td>Save alignment with current filename and format</td>
+ </tr>
+ <tr>
+ <td><strong>Control Shift 'S'</strong></td>
+ <td>Both</td>
+ <td>Save alignment as a new file or with a different format</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'P'</strong></td>
+ <td>Both</td>
+ <td>Opens the print dialog box to print the current view</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'W'</strong></td>
+ <td>Both</td>
+ <td>Closes the current view or the current alignment</td>
+ </tr>
+ <tr>
+ <td><strong>Backspace</strong></td>
+ <td>Normal</td>
+ <td>Delete the currently selected rows or columns from the alignment.</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'L'</strong></td>
+ <td>Left</td>
+ <td>Remove columns to left of left-most column marker.</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'R'</strong></td>
+ <td>Both</td>
+ <td>Remove columns to right of right-most column marker.</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'E'</strong></td>
+ <td>Both</td>
+ <td>Remove gapped columns</td>
+ </tr>
+ <tr>
+ <td><strong>Control Shift 'E'</strong></td>
+ <td>Both</td>
+ <td>Remove all gaps</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'D'</strong></td>
+ <td>Both</td>
+ <td>Open the 'Remove redundancy' Dialog box.</td>
+ </tr>
+
+ <tr>
+ <td><strong></strong></td>
+ <td>Normal</td>
+ <td></td>
+ </tr>
+
+
+</table>
+<p>The compound commands available in the Cursor mode are summarised
+below. Single letter commands can be prefixed by digits to specify a repetition
+number, and some more complex commands take one or more numeric
+parameters (prefixing the command key and separated by commas).</p>
+<table border=1><tr><td><strong>Compound
+Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>
+<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a
+numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit
+command.</td></tr>
+<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or
+more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>
+<tr><td><strong><strong><em>p1</em></strong>,<strong><em>p2</em></strong><br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (<strong><em>p1</em></strong>) and row (<strong><em>p2</em></strong>) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>
+<tr><td><strong><em>p</em>S</strong></td><td>Cursor</td><td>Jump to the <strong><em>p</em></strong>'th sequence in the alignment.</td></tr>
+<tr><td><strong><em>p</em>P</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th amino acid in current sequence.</td></tr>
+<tr><td><strong><em>p</em>C</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th column in the alignment.</td></tr>
+<tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>
+<tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>
+<tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts
+one (or optionally <strong><em>p</em></strong>) gaps at the current position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>
+<tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes
+one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>
+<tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes
+one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr></table>
+<p> </p>
+<p> </p>
+</body>
+</html>
-<html>\r
-<head><title>Release History</title></head>\r
-<body>\r
-<p><strong>Release History</strong> </p>\r
-<table border="1">\r
- <tr> \r
- <td width="60" 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
- <tr> \r
- <td>\r
-<div align="center"><strong>2.1.1</strong><br>\r
- 12/9/06</div></td>\r
- <td><ul>\r
- <li>Copy consensus sequence to clipboard</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Image output - rightmost residues are rendered if sequence id panel \r
- has been resized</li>\r
- <li>Image output - all offscreen group boundaries are rendered </li>\r
- <li>Annotation files with sequence references - all elements in file are \r
- relative to sequence position</li>\r
- <li>Mac Applet users can use Alt key for group editing</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.1</strong><br>\r
- 22/8/06</div></td>\r
- <td><ul>\r
- <li>MAFFT Multiple Alignment in default Web Service list</li>\r
- <li>DAS Feature fetching</li>\r
- <li>Hide sequences and columns</li>\r
- <li>Export Annotations and Features</li>\r
- <li>GFF file reading / writing</li>\r
- <li>Associate structures with sequences from local PDB files</li>\r
- <li>Add sequences to exisiting alignment</li>\r
- <li>Recently opened files / URL lists</li>\r
- <li>Applet can launch the full application</li>\r
- <li>Applet has transparency for features (Java 1.2 required)</li>\r
- <li>Applet has user defined colours parameter</li>\r
- <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Redundancy Panel reinstalled in the Applet</li>\r
- <li>Monospaced font - EPS / rescaling bug fixed</li>\r
- <li>Annotation files with sequence references bug fixed</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.08.1</strong><br>\r
- 2/5/06</div></td>\r
- <td><ul>\r
- <li>Change case of selected region from Popup menu</li>\r
- <li>Choose to match case when searching</li>\r
- <li>Middle mouse button and mouse movement can compress / expand the visible \r
- width and height of the alignment</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Annotation Panel displays complete JNet results</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.08b</strong><br>\r
- 18/4/06</div></td>\r
- <td> </td>\r
- <td><ul>\r
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>\r
- <li>Righthand label on wrapped alignments shows correct value</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.08</strong><br>\r
- 10/4/06</div></td>\r
- <td><ul>\r
- <li>Editing can be locked to the selection area</li>\r
- <li>Keyboard editing</li>\r
- <li>Create sequence features from searches</li>\r
- <li>Precalculated annotations can be loaded onto alignments</li>\r
- <li>Features file allows grouping of features</li>\r
- <li>Annotation Colouring scheme added</li>\r
- <li>Smooth fonts off by default - Faster rendering</li>\r
- <li>Choose to toggle Autocalculate Consensus On/Off</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Drag & Drop fixed on Linux</li>\r
- <li>Jalview Archive file faster to load/save, sequence descriptions saved. \r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.07</strong><br>\r
- 12/12/05</div></td>\r
- <td><ul>\r
- <li>PDB Structure Viewer enhanced</li>\r
- <li>Sequence Feature retrieval and display enhanced</li>\r
- <li>Choose to output sequence start-end after sequence name for file output</li>\r
- <li>Sequence Fetcher WSDBFetch@EBI</li>\r
- <li>Applet can read feature files, PDB files and can be used for HTML \r
- form input</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>HTML output writes groups and features</li>\r
- <li>Group editing is Control and mouse click</li>\r
- <li>File IO bugs</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.06</strong><br>\r
- 28/9/05</div></td>\r
- <td><ul>\r
- <li>View annotations in wrapped mode</li>\r
- <li>More options for PCA viewer</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>GUI bugs resolved</li>\r
- <li>Runs with -nodisplay from command line</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td height="63"> <div align="center"><strong>2.05b</strong><br>\r
- 15/9/05</div></td>\r
- <td><ul>\r
- <li>Choose EPS export as lineart or text</li>\r
- <li>Jar files are executable</li>\r
- <li>Can read in Uracil - maps to unknown residue</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Known OutOfMemory errors give warning message</li>\r
- <li>Overview window calculated more efficiently</li>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.05</strong><br>\r
- 30/8/05</div></td>\r
- <td><ul>\r
- <li>Edit and annotate in "Wrapped" view</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.04</strong><br>\r
- 24/8/05</div></td>\r
- <td><ul>\r
- <li>Hold down mouse wheel & scroll to change font size</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Improved JPred client reliability</li>\r
- <li>Improved loading of Jalview files</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.03</strong><br>\r
- 18/8/05</div></td>\r
- <td><ul>\r
- <li>Set Proxy server name and port in preferences</li>\r
- <li>Multiple URL links from sequence ids</li>\r
- <li>User Defined Colours can have a scheme name and added to Colour Menu</li>\r
- <li>Choose to ignore gaps in consensus calculation</li>\r
- <li>Unix users can set default web browser</li>\r
- <li>Runs without GUI for batch processing</li>\r
- <li>Dynamically generated Web Service Menus</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>InstallAnywhere download for Sparc Solaris</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.02</strong><br>\r
- 18/7/05</div></td>\r
- <td> </td>\r
- <td><ul>\r
- <li>Copy & Paste order of sequences maintains alignment order.</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.01</strong><br>\r
- 12/7/05</div></td>\r
- <td><ul>\r
- <li>Use delete key for deleting selection.</li>\r
- <li>Use Mouse wheel to scroll sequences.</li>\r
- <li>Help file updated to describe how to add alignment annotations.</li>\r
- <li>Version and build date written to build properties file.</li>\r
- <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Delete gaps bug fixed.</li>\r
- <li>FileChooser sorts columns.</li>\r
- <li>Can remove groups one by one.</li>\r
- <li>Filechooser icons installed.</li>\r
- <li>Finder ignores return character when searching. Return key will initiate \r
- a search.<br>\r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.0</strong><br>\r
- 20/6/05</div></td>\r
- <td ><ul>\r
- <li> New codebase</li>\r
- </ul></td>\r
- <td > </td>\r
- </tr>\r
-</table>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Release History</title></head>
+<body>
+<p><strong>Release History</strong> </p>
+<table border="1">
+ <tr>
+ <td width="60" nowrap><div align="center"><em><strong>Release</strong></em></div></td>
+ <td ><div align="center"><em><strong>New Features</strong></em></div></td>
+ <td ><div align="center"><em><strong>Issues Resolved</strong></em></div></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.2</strong><br>
+ 27/11/06</div></td><td><ul>
+ <li>Multiple views on alignment
+<li>Sequence feature editing
+<li>"Reload" alignment
+<li>"Save" to current filename
+<li>Background dependent text colour
+<li>Right align sequence ids
+<li>User-defined lower case residue colours
+<li>Format Menu
+<li>Select Menu
+<li>Menu item accelerator keys
+<li>Control-V pastes to current alignment
+<li>Cancel button for DAS Feature Fetching
+<li>PCA and PDB Viewers zoom via mouse roller
+<li>User-defined sub-tree colours and sub-tree selection
+<li>'New Window' button on the 'Output to Text box'
+</ul>
+ </td>
+ <td>
+<ul>
+<li>New memory efficient Undo/Redo System
+<li>Optimised symbol lookups and conservation/consensus calculations
+<li>Region Conservation/Consensus recalculated after edits
+<li>Fixed Remove Empty Columns Bug (empty columns at end of alignment)
+<li>Slowed DAS Feature Fetching for increased robustness.
+<li>Made angle brackets in ASCII feature descriptions display correctly
+<li>Re-instated Zoom function for PCA
+<li>Sequence descriptions conserved in web service analysis results
+<li>Uniprot ID discoverer uses any word separated by ∣
+<li>WsDbFetch query/result association resolved
+<li>Tree leaf to sequence mapping improved
+<li>Smooth fonts switch moved to FontChooser dialog box.
+</ul></td>
+ </tr>
+ <tr>
+ <td>
+<div align="center"><strong>2.1.1</strong><br>
+ 12/9/06</div></td>
+ <td><ul>
+ <li>Copy consensus sequence to clipboard</li>
+ </ul></td>
+ <td><ul>
+ <li>Image output - rightmost residues are rendered if sequence id panel
+ has been resized</li>
+ <li>Image output - all offscreen group boundaries are rendered </li>
+ <li>Annotation files with sequence references - all elements in file are
+ relative to sequence position</li>
+ <li>Mac Applet users can use Alt key for group editing</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.1</strong><br>
+ 22/8/06</div></td>
+ <td><ul>
+ <li>MAFFT Multiple Alignment in default Web Service list</li>
+ <li>DAS Feature fetching</li>
+ <li>Hide sequences and columns</li>
+ <li>Export Annotations and Features</li>
+ <li>GFF file reading / writing</li>
+ <li>Associate structures with sequences from local PDB files</li>
+ <li>Add sequences to exisiting alignment</li>
+ <li>Recently opened files / URL lists</li>
+ <li>Applet can launch the full application</li>
+ <li>Applet has transparency for features (Java 1.2 required)</li>
+ <li>Applet has user defined colours parameter</li>
+ <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
+ </ul></td>
+ <td><ul>
+ <li>Redundancy Panel reinstalled in the Applet</li>
+ <li>Monospaced font - EPS / rescaling bug fixed</li>
+ <li>Annotation files with sequence references bug fixed</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.08.1</strong><br>
+ 2/5/06</div></td>
+ <td><ul>
+ <li>Change case of selected region from Popup menu</li>
+ <li>Choose to match case when searching</li>
+ <li>Middle mouse button and mouse movement can compress / expand the visible
+ width and height of the alignment</li>
+ </ul></td>
+ <td><ul>
+ <li>Annotation Panel displays complete JNet results</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.08b</strong><br>
+ 18/4/06</div></td>
+ <td> </td>
+ <td><ul>
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>Righthand label on wrapped alignments shows correct value</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.08</strong><br>
+ 10/4/06</div></td>
+ <td><ul>
+ <li>Editing can be locked to the selection area</li>
+ <li>Keyboard editing</li>
+ <li>Create sequence features from searches</li>
+ <li>Precalculated annotations can be loaded onto alignments</li>
+ <li>Features file allows grouping of features</li>
+ <li>Annotation Colouring scheme added</li>
+ <li>Smooth fonts off by default - Faster rendering</li>
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ </ul></td>
+ <td><ul>
+ <li>Drag & Drop fixed on Linux</li>
+ <li>Jalview Archive file faster to load/save, sequence descriptions saved.
+ </li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.07</strong><br>
+ 12/12/05</div></td>
+ <td><ul>
+ <li>PDB Structure Viewer enhanced</li>
+ <li>Sequence Feature retrieval and display enhanced</li>
+ <li>Choose to output sequence start-end after sequence name for file output</li>
+ <li>Sequence Fetcher WSDBFetch@EBI</li>
+ <li>Applet can read feature files, PDB files and can be used for HTML
+ form input</li>
+ </ul></td>
+ <td><ul>
+ <li>HTML output writes groups and features</li>
+ <li>Group editing is Control and mouse click</li>
+ <li>File IO bugs</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.06</strong><br>
+ 28/9/05</div></td>
+ <td><ul>
+ <li>View annotations in wrapped mode</li>
+ <li>More options for PCA viewer</li>
+ </ul></td>
+ <td><ul>
+ <li>GUI bugs resolved</li>
+ <li>Runs with -nodisplay from command line</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td height="63"> <div align="center"><strong>2.05b</strong><br>
+ 15/9/05</div></td>
+ <td><ul>
+ <li>Choose EPS export as lineart or text</li>
+ <li>Jar files are executable</li>
+ <li>Can read in Uracil - maps to unknown residue</li>
+ </ul></td>
+ <td><ul>
+ <li>Known OutOfMemory errors give warning message</li>
+ <li>Overview window calculated more efficiently</li>
+ <li>Several GUI bugs resolved</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.05</strong><br>
+ 30/8/05</div></td>
+ <td><ul>
+ <li>Edit and annotate in "Wrapped" view</li>
+ </ul></td>
+ <td><ul>
+ <li>Several GUI bugs resolved</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.04</strong><br>
+ 24/8/05</div></td>
+ <td><ul>
+ <li>Hold down mouse wheel & scroll to change font size</li>
+ </ul></td>
+ <td><ul>
+ <li>Improved JPred client reliability</li>
+ <li>Improved loading of Jalview files</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td> <div align="center"><strong>2.03</strong><br>
+ 18/8/05</div></td>
+ <td><ul>
+ <li>Set Proxy server name and port in preferences</li>
+ <li>Multiple URL links from sequence ids</li>
+ <li>User Defined Colours can have a scheme name and added to Colour Menu</li>
+ <li>Choose to ignore gaps in consensus calculation</li>
+ <li>Unix users can set default web browser</li>
+ <li>Runs without GUI for batch processing</li>
+ <li>Dynamically generated Web Service Menus</li>
+ </ul></td>
+ <td><ul>
+ <li>InstallAnywhere download for Sparc Solaris</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td> <div align="center"><strong>2.02</strong><br>
+ 18/7/05</div></td>
+ <td> </td>
+ <td><ul>
+ <li>Copy & Paste order of sequences maintains alignment order.</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td><div align="center"><strong>2.01</strong><br>
+ 12/7/05</div></td>
+ <td><ul>
+ <li>Use delete key for deleting selection.</li>
+ <li>Use Mouse wheel to scroll sequences.</li>
+ <li>Help file updated to describe how to add alignment annotations.</li>
+ <li>Version and build date written to build properties file.</li>
+ <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>
+ </ul></td>
+ <td><ul>
+ <li>Delete gaps bug fixed.</li>
+ <li>FileChooser sorts columns.</li>
+ <li>Can remove groups one by one.</li>
+ <li>Filechooser icons installed.</li>
+ <li>Finder ignores return character when searching. Return key will initiate
+ a search.<br>
+ </li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td> <div align="center"><strong>2.0</strong><br>
+ 20/6/05</div></td>
+ <td ><ul>
+ <li> New codebase</li>
+ </ul></td>
+ <td > </td>
+ </tr>
+</table>
+<p> </p>
+</body>
+</html>
-<html>\r
-<head><title>What's new ?</title></head>\r
-<body>\r
-<p><strong>What's new ?</strong> </p>\r
-<p>Jalview Version 2.1</p>\r
-<p>The multiple sequence alignment program <a href="webServices/mafft.html">MAFFT</a> \r
- is available from the default Web Service list.</p>\r
-<p>The sequence feature retrieval system using DBFetch from EBI has been replaced \r
- with <a href="features/dassettings.html">DAS Feature fetching</a> capabilities.</p>\r
-<p><a href="features/hiddenRegions.html">Hide sequences and columns</a></p>\r
-<p>Export Annotations and Features</p>\r
-<p>GFF file reading / writing</p>\r
-<p>Associate structures with sequences from local PDB files</p>\r
-<p>Add sequences to existing alignment</p>\r
-<p>Recently opened files / URL lists</p>\r
-<p>Applet can launch the full application</p>\r
-<p>Applet has transparency for features (Java 1.2 required)</p>\r
-<p>Applet has user defined colours parameter</p>\r
-<p> </p>\r
-<p><strong>Issues Resolved</strong></p>\r
-<p>Redundancy Panel reinstalled in the Applet</p>\r
-<p>Monospaced font - EPS / rescaling bug fixed</p>\r
-<p>Annotation files with sequence references bug fixed</p>\r
-<p> </p>\r
-<p>See the <a href="releases.html">Release History</a> page for details of all\r
- new features and resolved issues. </p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>What's new ?</title></head>
+<body>
+<p><strong>What's new ?</strong> </p>
+
+<p><strong>Jalview Version 2.2</strong></p>
+<p>Multiple views with different styles, colours, hidden regions for one alignment
+</p>
+<p>Easily add, amend and delete sequence features
+</p>
+<p>"Reload" alignment from File or URL to revert to original
+</p>
+<p>"Save" to current filename or "Save As" to new filename
+</p>
+<p>Set different text colour for dark or light background
+</p>
+<p>Right align sequence ids
+</p>
+<p>Set colour of lower case residues in a user defined colour scheme
+</p>
+<p>Menu Rearrangements: New <strong>Format</strong> for alignment layout and <strong>Select</strong> for region selection.
+</p>
+</p><p>Menu item accelerator keys added
+</p>
+<p>Control-V pastes sequences to active window, Control-Shift-V pastes to a new window.
+</p>
+<p>Raise/Minimise alignment and all associated windows from desktop window's <strong>window</strong> menu
+</p>
+<p>Select and colour whole branches of a tree</p>
+<p>'New Window' button on the 'Output to Text box' alignment output
+option to open a new alignment window after editing.</p>
+<p><strong>Issues Resolved</strong></p>
+</p>
+<p>
+Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system.
+</p>
+<p>Remove empty columns - if empty columns exist at the end of the
+alignment bug fixed.
+</p>
+<p>DAS feature fetching slowed down, doesn't overload DAS servers
+</p>
+<p>DAS feature fetching can be cancelled
+</p>
+<p>Correct display of > and < symbols for feature descriptions without explicit <html> tags.
+</p>
+<p>Zoom working in PCA viewer
+</p>
+<p>Sequence Descriptions retained after running a web service
+</p>
+<p> </p>
+<p>See the <a href="releases.html">Release History</a> page for details of all
+ new features and resolved issues. </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff