<mapID target="home" url="html/index.html" />\r
\r
<mapID target="new" url="html/whatsNew.html"/>\r
- <mapID target="search" url="html/features/search.html"/>\r
- <mapID target="wrap" url="html/features/wrap.html"/>\r
- <mapID target="overview" url="html/features/overview.html"/>\r
- <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
+ <mapID target="release" url="html/releases.html"/>\r
<mapID target="alannotation" url="html/features/annotation.html"/>\r
+ <mapID target="keys" url="html/keys.html"/>\r
\r
<mapID target="webservice" url="html/webServices/index.html"/>\r
<mapID target="clustal" url="html/webServices/clustalw.html"/>\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="Release History" target="release"/>\r
<tocitem text="Alignment Annotations" target ="alannotation"/>\r
\r
<tocitem text="Input / Output" target="io"/>\r
+ <tocitem text="Key Strokes" target="keys"/>\r
<tocitem text="Making figures" target="export"/>\r
<tocitem text="Editing Alignments" target ="edit"/>\r
<tocitem text="Web Services" target="webservice" 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="Search Menu" target="search"/> \r
- <tocitem text="View Menu" target="alwView"/> \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>\r
<tocitem text="Memory Settings" target="memory"/>\r
</tocitem>\r
-<tocitem text="Useful information" expand="false">\r
+<tocitem text="Useful information" expand="true">\r
<tocitem text="Amino Acid Table" target="aminoAcids"/>\r
<tocitem text="The Genetic Code" target="geneticCode"/>\r
</tocitem>\r
<p><em>Inserting / removing gaps</em> - hold down the "Shift" key. Click\r
a residue with the mouse and drag the residue to the right to insert gaps or\r
to the left to remove gaps.<br>\r
- If the residue selected is within a defined group, hold down either "Alt"\r
- or "Control" key and drag the residue left or right to edit all sequences\r
- in the defined group at once. </p>\r
+ If the residue selected is within a defined group, hold down either "Control" \r
+ key and drag the residue left or right to edit all sequences in the defined \r
+ group at once. </p>\r
<p><em>Copy/paste/cut/delete</em> - any sequences which are in the current selection\r
box (indicated in red) may be cut and / or copied to a new alignment or deleted.\r
</p>\r
-> View Mapping" from the structure viewer window. </p>\r
<p>Moving the mouse over the structure will highlight the residue in the alignment \r
window, and vice versa.</p>\r
+<p>"Colour by Charge/Cysteine" will colour all Aspartate and Glutamate \r
+ residues red, Lysine and Arginine will be blue and Cysteine residues will be \r
+ coloured yellow.</p>\r
<p><em>Tips for Viewing Structures</em></p>\r
<ul>\r
<li>Colour By Sequence follows the exact colours of the alignment window, including \r
<li>Use Wireframe, without depthcue, and without Z Buffering in order to accelerate \r
the rendering of the structure. </li>\r
<li>You can save an image of your structure as a PNG or EPS file.</li>\r
+ <li>Use the cursor keys Up and Down arrow to zoom in and zoom out</li>\r
</ul>\r
</body>\r
</html>\r
<ul>\r
<li><strong>File</strong> \r
<ul>\r
+ <li><strong>Fetch Sequence</strong><br>\r
+ <em>Shows a dialog window in which you can select known ids from Uniprot, \r
+ EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
+ Bioinformatics Institute. See <a href="features/seqfetch.html">Sequence \r
+ Fetcher</a></em>.</li>\r
<li><strong>Save As<br>\r
</strong><em>Save the alignment to local file. A file selection window \r
will open, use the "Files of type:" selection box to determine \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><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
<li><strong>Principal Component Analysis</strong><br>\r
<em>Shows a spatial clustering of the sequences based on the BLOSUM62 \r
scores in the alignment. See <a href="../calculations/pca.html">Principal \r
- Component Analysis</a>.</em> <br>\r
+ Component Analysis</a>.</em> </li>\r
+ <li><strong>Translate cDNA</strong><br>\r
+ <em>If you are viewing a cDNA alignment a very simple translation service \r
+ is available. The translation ignores all gaps in the cDNA sequences. \r
+ </em> <br>\r
</li>\r
</ul>\r
</li>\r
sequences.</em></li>\r
</ul>\r
</li>\r
- <li><strong>Secondary Structure Prediction</strong>\r
+ <li><strong>Secondary Structure Prediction</strong> \r
<ul>\r
<li><strong>JPred Secondary Structure Prediction</strong><br>\r
<em>Secondary structure prediction by network consensus. The behaviour \r
<body>\r
<p><strong>Alignment Window File Menu</strong></p>\r
<ul>\r
- <li><strong>File</strong></li>\r
+ <li><strong>File</strong><br>\r
+ </li>\r
+ <li><strong>Fetch Sequence</strong><br>\r
+ <em>Shows a dialog window in which you can select known ids from Uniprot, \r
+ EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
+ Bioinformatics Institute. See <a href="features/seqfetch.html">Sequence Fetcher</a>.</em></li>\r
</ul>\r
<ul>\r
<li><strong>Save As<br>\r
<ul>\r
<li><strong>View</strong></li>\r
</ul>\r
-<blockquote>\r
+<blockquote> \r
<ul>\r
<li><strong>Font<br>\r
- </strong><em>Change the font of the display from the\r
- "Choose Font" dialog box, which is shown when this\r
- item is selected. <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. <br>\r
</em></li>\r
<li><strong>Wrap<br>\r
- </strong><em>When ticked, the alignment display is\r
- "<a href="../features/wrap.html">wrapped</a>" to the\r
- width of the alignment window. This is useful if your alignment\r
- has only a few sequences to view its full width at once.<br>\r
- Options are available to show the residue numbering at the start and/or\r
- end of an alignment as well as showing the alignment position above each\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 has \r
+ only a few sequences to view its full width at once.<br>\r
+ Options are available to show the residue numbering at the start and/or \r
+ end of an alignment as well as showing the alignment position above each \r
sequence row. <br>\r
- <strong>NOTE</strong>: When in wrapped alignment view, the\r
- alignment cannot be edited or have regions selected on it. <br>\r
+ <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot \r
+ be edited or have regions selected on it. <br>\r
</em><strong> </strong></li>\r
<li><strong>Show Full Sequence ID<br>\r
- </strong><em>If this box is selected the sequence name will have the start\r
+ </strong><em>If this box is selected the sequence name will have the start \r
and end position of the sequence appended to the name, in the format NAME/START-END<br>\r
</em></li>\r
<li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using the\r
- selected background colour. Useful if used in conjunction with "Colour\r
+ If this is selected the background of a residue will be coloured using the \r
+ selected background colour. Useful if used in conjunction with "Colour \r
Text." <br>\r
</em></li>\r
<li><strong>Text<br>\r
- </strong><em>If this is selected the residues will be displayed using the\r
+ </strong><em>If this is selected the residues will be displayed using the \r
standard 1 character amino acid alphabet.<br>\r
</em></li>\r
<li><strong>Colour Text<br>\r
- </strong><em>If this is selected the residues will be coloured according\r
- to the background colour associated with that residue. The colour is slightly\r
+ </strong><em>If this is selected the residues will be coloured according \r
+ to the background colour associated with that residue. The colour is slightly \r
darker than background so the amino acid symbol remains visible. <br>\r
</em></li>\r
<li><strong>Show Gaps<br>\r
- </strong><em>When this is selected, gap characters will be displayed as "."\r
- or "-". If unselected, then gap characters will appear as blank spaces.\r
- <br>\r
+ </strong><em>When this is selected, gap characters will be displayed as \r
+ "." or "-". If unselected, then gap characters will \r
+ appear as blank spaces. <br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>\r
</em></li>\r
<li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will be\r
- displayed below the alignment. The default setting is to display the conservation\r
+ </strong><em>If this is selected the "Annotation Panel" will be \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
- </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> from the EBI. Features which are\r
- 1 residue in length are coloured red, sequences longer than 1 residue are\r
- coloured blue. Move the mouse over a coloured feature to display the details\r
- of the feature. <br>\r
- Note: The retrieved information will update the sequence start and end labels\r
- if they are incorrect. <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
+ longer than 1 residue are coloured blue. Move the mouse over a coloured \r
+ feature to display the details of the feature. <br>\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
</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
- window. A red box will indicate the currently visible area of the alignment.\r
+ </strong><em>A scaled version of the alignment will be displayed in a small \r
+ window. A red box will indicate the currently visible area of the alignment. \r
Move the visible region using the mouse. </em><strong> </strong></li>\r
</ul>\r
</blockquote>\r
<em>copy and paste an alignment into a text window</em></li>\r
</ul>\r
</li>\r
+ <li><strong>Fetch Sequence<br>\r
+ </strong><em>Shows a dialog window in which you can select known ids from \r
+ Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by \r
+ the European Bioinformatics Institute.</em></li>\r
<li><strong>Save Project</strong><br>\r
<em>Saves all currently open alignment windows with their current view \r
- settings and any associated trees, as a <a href="../features/jalarchive.html">Jalview Archive</a> (which has a .jar extension).</em></li>\r
+ settings and any associated trees, as a <a href="../features/jalarchive.html">Jalview \r
+ Archive</a> (which has a .jar extension).</em></li>\r
<li><strong>Load Project</strong><br>\r
<em>Loads Jalview archives <strong>only</strong>.</em></li>\r
<li><strong>Quit</strong><br>\r
<head><title>What's new ?</title></head>\r
<body>\r
<p><strong>What's new ?</strong> </p>\r
-<p>If you are reading this then you will already have seen some of the recent changes\r
- made to Jalview.<br>\r
- Jalview takes advantage of some of the more recent user interface developments\r
- in the Java programming language. For instance Jalview is now a multi windowed\r
- application, this keeps all your Jalview windows neatly together in one main\r
- application window. </p>\r
-<p>If you were familiar with the original Jalview, here is a list of important\r
- features you should know about the current development:</p>\r
-<ul>\r
- <li>Editing sequences is no longer the default when mouse clicking the alignment.\r
- Instead, mouse clicking on the alignment creates a "selection region"\r
- which may be full sequences or groups of residues.</li>\r
- <li>To insert or edit the gaps in one sequence in alignment, the "Shift"\r
- key must be held down when dragging the mouse.</li>\r
- <li>To insert or edit gaps for a group of sequences, the "Alt" key\r
- (or in X windows the "Control" key) must be held down.</li>\r
- <li>Selecting colour schemes in the colour menu either sets just the "background"\r
- colourscheme for the alignment, or - when the tickbox "Apply colour to\r
- all groups" is ticked, applies the scheme to the background and all groups\r
- defined on the alignment.</li>\r
- <li>Use the right mouse button (apple and click on the Mac) whilst the pointer\r
- is within the selection area to access the "define" region menu\r
- to define a new region, give it a name, and change its colourscheme and display\r
- properties.</li>\r
- <li>Conservation is automatically updated whenever the alignment is edited</li>\r
- <li>There is no "quick draw" option</li>\r
- <li>Edits can be undone, and redone!</li>\r
-</ul>\r
-<table border="1">\r
- <tr> \r
- <td><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><div align="center"><strong>2.07</strong><br>\r
- 7 /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
- </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>Applet can read feature files, PDB files and can be used for HTML \r
- form input</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><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>Jalview Version 2.07 </p>\r
+<p><a href="features/seqfetch.html">Sequence Fetcher</a> has been added to quickly \r
+ retrieve sequences with known ids from several databases.</p>\r
+<p><a href="features/seqfeatures.html">Sequence Features enhanced</a> to allow \r
+ the user to display all features of a Uniprot file on the alignment and subsequently \r
+ colour, hide or show overlapping features. </p>\r
+<p><a href="io/fileformats.html">Choose to omit /start-end from sequences when \r
+ saving files.</a> This is important for saving files to be used by some programs \r
+ which cannot read the original Jalview sequence output with the appended /start-end.</p>\r
+<p><a href="features/pdbviewer.html">PDB structure viewer enhanced</a>. Mapping \r
+ between sequence and structure has been enhanced, colours on the alignment are \r
+ reflected in the structure viewer.</p>\r
+<p><a href="http://www.jalview.org/examples/applet.html">Jalview Applet can read \r
+ in feature files, PDB files be used as input to HTML form</a> See the website \r
+ to find out the new parameters available for the Applet Version of Jalview.</p>\r
<p> </p>\r
+<p><strong>Issues Resolved</strong></p>\r
+<p>Group Editing is possible with Control and mouse click. Alt key and mouse press \r
+ does not work as this translates as the middle mouse button, which since 2.04 \r
+ is now used to scroll the alignment and change the font size. </p>\r
+<p>HTML export now writes groups and features which were previously missing.</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
git://source.jalview.org / jalview.git / commitdiff