* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Alignment Consensus Annotation</title></head>
+<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 includes gaps in columns.
- 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>
+ <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
+ includes gaps in columns. 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>
+ <strong>Sequence logo</strong>
+ </p>
+ By clicking on the label you can also activate the sequence logo. It
+ indicates the relative amount of residues per column which can be
+ estimated by its size in the logo. The tooltip of a column gives the
+ exact numbers for all occurring residues.
+ <br />If columns of the alignment are very diverse, then it can
+ sometimes be difficult to see the sequence logo - in this case, right
+ click on the annotation row label and select
+ <strong>Normalise Consensus Logo</strong> to scale all columns of the
+ logo to the same height.
-<p><strong>Sequence logo</strong></p>
- By clicking on the label you can also activate the sequence logo. It
- indicates the relative amount of residues per column which can be
- estimated by its size in the logo. The tooltip of a column gives the
- exact numbers for all occurring residues.
- <br />If columns of the alignment are very diverse, then it can
- sometimes be difficult to see the sequence logo - in this case, right
- click on the annotation row label and select
- <strong>Normalise Consensus Logo</strong> to scale all columns of the
- logo to the same height.
-
-<p><strong>cDNA Consensus</strong></p>
-A <a href="../features/splitView.html">Split Frame View</a> of cDNA and Protein alignments will show the consensus for cDNA below the protein alignment.<br/>
-This may provide additional information on mutations in DNA that is not visible in the peptide alignment.
+ <p>
+ <strong>cDNA Consensus</strong>
+ </p>
+ A
+ <a href="../features/splitView.html">Split Frame View</a> of cDNA and
+ Protein alignments will show the consensus for cDNA below the protein
+ alignment.
+ <br /> This may provide additional information on mutations in DNA
+ that is not visible in the peptide alignment.
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Alignment Conservation Annotation</title></head>
-<body><p><strong>Alignment Conservation Annotation</strong></p>
-<p>This is an automatically calculated quantitative alignment
-annotation which measures the number of conserved physico-chemical
-properties conserved for each column of the alignment. Its calculation
-is based on the one used in
- the AMAS method of multiple sequence alignment analysis :<br>
-<ul>Livingstone
- C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
- for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
- No. 6 (745-756)).
-</ul>
-<em><a href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html">View an HTML version of the paper</a></em>
-</p>
-<p>Conservation is measured as a numerical index reflecting the conservation of
- <a href="../misc/aaproperties.html">physico-chemical
- properties</a> in the alignment: Identities score highest, and the next most
- conserved group contain substitutions to amino acids lying in the same physico-chemical
- class.</p>
- <p>Conservation is visualised on the alignment or a sequence group
- as a histogram giving the score for each column. Conserved columns are
- indicated by '*' (score of 11 with default amino acid property
- grouping), and columns with mutations where all properties are
- conserved are marked with a '+' (score of 10, indicating all
- properties are conserved).</p>
+<head>
+<title>Alignment Conservation Annotation</title>
+</head>
+<body>
+ <p>
+ <strong>Alignment Conservation Annotation</strong>
+ </p>
+ <p>
+ This is an automatically calculated quantitative alignment
+ annotation which measures the number of conserved physico-chemical
+ properties conserved for each column of the alignment. Its
+ calculation is based on the one used in the AMAS method of multiple
+ sequence alignment analysis :<br>
+ <ul>
+ Livingstone C.D. and Barton G.J. (1993), Protein Sequence
+ Alignments: A Strategy for the Hierarchical Analysis of Residue
+ Conservation.
+ <em>CABIOS</em> Vol.
+ <b>9</b> No. 6 (745-756)).
+ </ul>
+ <em><a
+ href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html"
+ >View an HTML version of the paper</a></em>
+ </p>
+ <p>
+ Conservation is measured as a numerical index reflecting the
+ conservation of <a href="../misc/aaproperties.html">physico-chemical
+ properties</a> in the alignment: Identities score highest, and the
+ next most conserved group contain substitutions to amino acids lying
+ in the same physico-chemical class.
+ </p>
+ <p>Conservation is visualised on the alignment or a sequence group
+ as a histogram giving the score for each column. Conserved columns
+ are indicated by '*' (score of 11 with default amino acid property
+ grouping), and columns with mutations where all properties are
+ conserved are marked with a '+' (score of 10, indicating all
+ properties are conserved).</p>
<p>
Mousing over a conservation histogram reveals a tooltip which
contains a series of symbols corresponding to the physicochemical
that the lack of a particular physicochemical property is conserved
(e.g. !proline).
</p>
- <p><em>Colouring an alignment by conservation</em><br>
-Conservation scores can be used to colour an alignment. This is
-explained further in the help page for <a
-href="../colourSchemes/conservation.html">conservation colouring</a>.
-</p>
+ <p>
+ <em>Colouring an alignment by conservation</em><br>
+ Conservation scores can be used to colour an alignment. This is
+ explained further in the help page for <a
+ href="../colourSchemes/conservation.html"
+ >conservation colouring</a>.
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Pairwise Alignment</title></head>
+<head>
+<title>Pairwise Alignment</title>
+</head>
<body>
-<p><strong>Pairwise alignment (Proteins only)</strong></p>
-<p>This calculation is performed on the selected sequences only. Java is not the
- fastest language in the world and aligning more than a handful of sequences
- will take a fair amount of time. <br>
- For each pair of sequences the best global alignment is found using BLOSUM62
- as the scoring matrix. The scores reported are the raw scores. The sequences
- are aligned using a dynamic programming technique and using the following gap
- penalties : </p>
-<p>Gap open : 12 <br>
- Gap extend : 2 </p>
-<p>When you select the pairwise alignment option a new window will come up which
- will display the alignments in a text format as they are calculated. Also displayed
- is information about the alignment such as alignment score, length and percentage
- identity between the sequences.</p>
-<p> </p>
+ <p>
+ <strong>Pairwise alignment (Proteins only)</strong>
+ </p>
+ <p>
+ This calculation is performed on the selected sequences only. Java
+ is not the fastest language in the world and aligning more than a
+ handful of sequences will take a fair amount of time. <br> For
+ each pair of sequences the best global alignment is found using
+ BLOSUM62 as the scoring matrix. The scores reported are the raw
+ scores. The sequences are aligned using a dynamic programming
+ technique and using the following gap penalties :
+ </p>
+ <p>
+ Gap open : 12 <br> Gap extend : 2
+ </p>
+ <p>When you select the pairwise alignment option a new window will
+ come up which will display the alignments in a text format as they
+ are calculated. Also displayed is information about the alignment
+ such as alignment score, length and percentage identity between the
+ sequences.</p>
+ <p> </p>
</body>
</html>
<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><em>Caveats</em><br/>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>
+ <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>
+ <em>Caveats</em><br />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><strong>About PCA</strong></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 principal
-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
-principal axis, and the other axes correspond to less extreme patterns
-of variation in the data set.</p>
+ <p>
+ <strong>About PCA</strong>
+ </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
+ principal 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 principal axis, and the other axes correspond to
+ less extreme patterns of variation in the data set.</p>
- <p>
- <em>Calculating PCAs for aligned sequences</em><br />Jalview can
- perform PCA analysis on both proteins and nucleotide sequence
- alignments. In both cases, components are generated by an eigenvector
- decomposition of the matrix formed from the sum of substitution matrix
- scores at each aligned position between each pair of sequences -
- computed with one of the available score matrices, such as
- <a href="scorematrices.html#blosum62">BLOSUM62</a>, <a
- href="scorematrices.html#pam250">PAM250</a>, or the <a
- href="scorematrices.html#simplenucleotide">simple single
- nucleotide substitution matrix</a>. The options available for
- calculation are given in the
- <strong><em>Change Parameters</em></strong> menu.</p>
- <p>
- <em>PCA Calculation modes</em><br/>
- The default Jalview calculation mode
- (indicated when <em><strong>Jalview PCA Calculation</strong></em> is
- ticked in the <strong><em>Change Parameters</em></strong> menu) is to
- perform a PCA on a matrix where elements in the upper diagonal give
- the sum of scores for mutating in one direction, and the lower
- diagonal is the sum of scores for mutating in the other. For protein
- substitution models like BLOSUM62, this gives an asymmetric matrix,
- and a different PCA to a matrix produced with the method 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. This method
- preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
- PCA Calculation</em></strong> option in the <strong><em>Change
- Parameters</em></strong> menu.
- </p>
- <img src="pcaviewer.gif">
- <p><strong>The PCA Viewer</strong></p>
-<p>This is an interactive display of the sequences positioned within
-the similarity space, as points in a rotateable 3D scatterplot. 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 (<strong>File→Save</strong> submenu) as an EPS or PNG
-image or printed, and the original alignment data and matrix resulting
-from its PCA analysis to be retrieved. The coordinates for the whole PCA
-space, or just the current view may also be exported as CSV files for
-visualization in another program or further analysis.<p>
-<p>Options for coordinates export are:</p>
-<ul>
-<li>Output Values - complete dump of analysis (TxT* matrix computed from sum of scores for all pairs of aligned residues from from i->j and j->i, conditioned matrix to be diagonalised, tridiagonal form, major eigenvalues found)</li>
-<li>Output Points - The eigenvector matrix - rows correspond to sequences, columns correspond to each dimension in the PCA</li>
-<li>Transformed Points - The 3D coordinates for each sequence as shown in the PCA plot</li></ul>
+ <p>
+ <em>Calculating PCAs for aligned sequences</em><br />Jalview can
+ perform PCA analysis on both proteins and nucleotide sequence
+ alignments. In both cases, components are generated by an
+ eigenvector decomposition of the matrix formed from the sum of
+ substitution matrix scores at each aligned position between each
+ pair of sequences - computed with one of the available score
+ matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+ <a href="scorematrices.html#pam250">PAM250</a>, or the <a
+ href="scorematrices.html#simplenucleotide"
+ >simple single nucleotide substitution matrix</a>. The options
+ available for calculation are given in the <strong><em>Change
+ Parameters</em></strong> menu.
+ </p>
+ <p>
+ <em>PCA Calculation modes</em><br /> The default Jalview calculation
+ mode (indicated when <em><strong>Jalview PCA
+ Calculation</strong></em> is ticked in the <strong><em>Change
+ Parameters</em></strong> menu) is to perform a PCA on a matrix where elements
+ in the upper diagonal give the sum of scores for mutating in one
+ direction, and the lower diagonal is the sum of scores for mutating
+ in the other. For protein substitution models like BLOSUM62, this
+ gives an asymmetric matrix, and a different PCA to a matrix produced
+ with the method 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. This
+ method preconditions the matrix by multiplying it with its
+ transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
+ PCA Calculation</em></strong> option in the <strong><em>Change
+ Parameters</em></strong> menu.
+ </p>
+ <img src="pcaviewer.gif">
+ <p>
+ <strong>The PCA Viewer</strong>
+ </p>
+ <p>This is an interactive display of the sequences positioned
+ within the similarity space, as points in a rotateable 3D
+ scatterplot. 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 (<strong>File→Save</strong>
+ submenu) as an EPS or PNG image or printed, and the original
+ alignment data and matrix resulting from its PCA analysis to be
+ retrieved. The coordinates for the whole PCA space, or just the
+ current view may also be exported as CSV files for visualization in
+ another program or further analysis.
+ <p>
+ <p>Options for coordinates export are:</p>
+ <ul>
+ <li>Output Values - complete dump of analysis (TxT* matrix
+ computed from sum of scores for all pairs of aligned residues from
+ from i->j and j->i, conditioned matrix to be diagonalised,
+ tridiagonal form, major eigenvalues found)</li>
+ <li>Output Points - The eigenvector matrix - rows correspond to
+ sequences, columns correspond to each dimension in the PCA</li>
+ <li>Transformed Points - The 3D coordinates for each sequence
+ as shown in the PCA plot</li>
+ </ul>
-<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 associated alignment window views.<!-- Rectangular region
+ <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 associated alignment window views.
+ <!-- Rectangular region
based selection is also possible, by holding the 'S' key whilst
-left-clicking and dragging the mouse over the display. --> By default,
-points are only associated with the alignment view from which the PCA
-was calculated, but this may be changed via the <strong>View→Associate
-Nodes</strong> sub-menu.</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. The <strong><em>Reset</em></strong> button will reset axis and rotation settings to their defaults.</p>
-<p>
-<p>
-<em>The output of points and transformed point coordinates was added to the Jalview desktop in v2.7.</em>
-<em>The Reset button and Change Parameters menu were added in Jalview 2.8.</em>
-<em>Support for PAM250 based PCA was added in Jalview 2.8.1.</em>
+left-clicking and dragging the mouse over the display. -->
+ By default, points are only associated with the alignment view from
+ which the PCA was calculated, but this may be changed via the <strong>View→Associate
+ Nodes</strong> sub-menu.
+ </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. The <strong><em>Reset</em></strong>
+ button will reset axis and rotation settings to their defaults.
+ </p>
+ <p>
+ <p>
+ <em>The output of points and transformed point coordinates was
+ added to the Jalview desktop in v2.7.</em> <em>The Reset button
+ and Change Parameters menu were added in Jalview 2.8.</em> <em>Support
+ for PAM250 based PCA was added in Jalview 2.8.1.</em>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Alignment Quality Annotation</title></head>
+<head>
+<title>Alignment Quality Annotation</title>
+</head>
<body>
-<p><strong>Alignment Quality Annotation</strong></p>
-<p>Alignment Quality is one of the automatically calculated
-quantitative alignment
-annotations displayed below the columns of a multiple sequence
-alignment (and can be used to shade the alignment). It is an ad-hoc
-measure of the likelihood of observing the mutations (if any) in a
-particular column of the alignment.</p>
-<p>
-More precisely, the quality score is inversely proportional to the
-average cost of all pairs of mutations observed in a particular column
-of the alignment - a high alignment quality score for a column would
-suggest that there are no mutations, or most mutations observed are
-favourable.
-</p>
+ <p>
+ <strong>Alignment Quality Annotation</strong>
+ </p>
+ <p>Alignment Quality is one of the automatically calculated
+ quantitative alignment annotations displayed below the columns of a
+ multiple sequence alignment (and can be used to shade the
+ alignment). It is an ad-hoc measure of the likelihood of observing
+ the mutations (if any) in a particular column of the alignment.</p>
+ <p>More precisely, the quality score is inversely proportional to
+ the average cost of all pairs of mutations observed in a particular
+ column of the alignment - a high alignment quality score for a
+ column would suggest that there are no mutations, or most mutations
+ observed are favourable.</p>
-<p><em>The Algorithm</em><br>
-The quality score is calculated for each column in an alignment by
-summing, for all mutations, the ratio of the two BLOSUM 62 scores for
-a mutation pair and each residue's conserved BLOSUM62 score (which
-is higher). This value is normalised for each column, and then plotted
-on a scale from 0 to 1.
-</p>
-<p>
-Multiple alignment algorithms using the BLOSUM 62 substition matrices
-should, in theory, maximise alignment quality for an un-gapped
-alignment, and locally maximise quality for gapped alignments.
-</p>
+ <p>
+ <em>The Algorithm</em><br> The quality score is calculated for
+ each column in an alignment by summing, for all mutations, the ratio
+ of the two BLOSUM 62 scores for a mutation pair and each residue's
+ conserved BLOSUM62 score (which is higher). This value is normalised
+ for each column, and then plotted on a scale from 0 to 1.
+ </p>
+ <p>Multiple alignment algorithms using the BLOSUM 62 substition
+ matrices should, in theory, maximise alignment quality for an
+ un-gapped alignment, and locally maximise quality for gapped
+ alignments.</p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Viewing Input Data to PCA and Tree calculations</title></head>
+<head>
+<title>Viewing Input Data to PCA and Tree calculations</title>
+</head>
<body>
-<p><strong>Viewing Input Data to PCA and Tree calculations</strong></p>
-<p>It is always possible to retrieve the input data used to calculate
- a tree or PCA plot by using the analysis window's
- <strong>"File
- -> Input Data..."</strong> menu item. The Input Data will be
- shown in a new alignment window, with any hidden columns
- preserved.</p>
+ <p>
+ <strong>Viewing Input Data to PCA and Tree calculations</strong>
+ </p>
+ <p>
+ It is always possible to retrieve the input data used to calculate a
+ tree or PCA plot by using the analysis window's <strong>"File
+ -> Input Data..."</strong> menu item. The Input Data will be shown
+ in a new alignment window, with any hidden columns preserved.
+ </p>
</body>
</html>
<title>Removing Redundancy</title>
</head>
<body>
-<p><strong>Removing redundancy</strong></p>
-<p>Selecting the option in the Alignment window's <strong>Edit</strong>
-menu or pressing <strong>'CONTROL+D'</strong> brings up a dialog box
-asking you to select a threshold. If the percentage identity between the
-aligned positions of any two sequences in the visible alignment exceeds
-this value, the shorter sequence is discarded.<br><em>Note:</em> The redundancy
-calculation is done when the dialog box is opened. For large numbers
-of sequences this can take a long time as all pairs have to be compared.
-</p>
+ <p>
+ <strong>Removing redundancy</strong>
+ </p>
+ <p>
+ Selecting the option in the Alignment window's <strong>Edit</strong>
+ menu or pressing <strong>'CONTROL+D'</strong> brings up a dialog box
+ asking you to select a threshold. If the percentage identity between
+ the aligned positions of any two sequences in the visible alignment
+ exceeds this value, the shorter sequence is discarded.<br>
+ <em>Note:</em> The redundancy calculation is done when the dialog
+ box is opened. For large numbers of sequences this can take a long
+ time as all pairs have to be compared.
+ </p>
</body>
</html>
<p>
<ul>
<li>Jalview automatically assigns a reference sequence when <a
- href="../webServices/jnet.html">JPred4</a> predictions are
- imported.
+ href="../webServices/jnet.html"
+ >JPred4</a> predictions are imported.
</li>
<li><strong>Assigning a reference sequence</strong><br /> A
sequence can be marked as the reference sequence by right-clicking
<title>Substitution matrices in Jalview</title>
</head>
<body>
-<strong>Substitution Matrices available in Jalview</strong>
-<p>Jalview includes a small number of built in substitution matrices, used for different types of analysis.</p>
-<ul>
-<li><a href="#blosum62">BLOSUM62</a> is the standard protein sequence alignment and analysis matrix.</li>
-<li><a href="#pam250">PAM250</a> is another standard protein matrix, and (since 2.8.1) is available for Tree and PCA calculations.</li>
-<li><a href="#simplenucleotide">Simple Nucleotide Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.</li>
-<!-- <li><a href="#conservation">Conservation Matrices</a> A range of matrices for distinguishing amino-acids by physicochemical property conservation.
+ <strong>Substitution Matrices available in Jalview</strong>
+ <p>Jalview includes a small number of built in substitution
+ matrices, used for different types of analysis.</p>
+ <ul>
+ <li><a href="#blosum62">BLOSUM62</a> is the standard protein
+ sequence alignment and analysis matrix.</li>
+ <li><a href="#pam250">PAM250</a> is another standard protein
+ matrix, and (since 2.8.1) is available for Tree and PCA
+ calculations.</li>
+ <li><a href="#simplenucleotide">Simple Nucleotide
+ Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.</li>
+ <!-- <li><a href="#conservation">Conservation Matrices</a> A range of matrices for distinguishing amino-acids by physicochemical property conservation.
</li> -->
-</ul>
+ </ul>
-<p><strong><a name="blosum62"></a>BLOSUM62</strong><br/>
-<table border="1">
-<tr><td></td><td> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </td></tr>
-<tr><td>A</td><td>4</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>-3</td><td>0</td><td>-2</td><td>-1</td></tr>
-<tr><td>B</td><td>-2</td><td>4</td><td>-3</td><td>4</td><td>1</td><td>-3</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>3</td><td>-2</td><td>0</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-3</td><td>1</td></tr>
-<tr><td>C</td><td>0</td><td>-3</td><td>9</td><td>-3</td><td>-4</td><td>-2</td><td>-3</td><td>-3</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td><td>-3</td><td>-3</td><td>3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-3</td></tr>
-<tr><td>D</td><td>-2</td><td>4</td><td>-3</td><td>6</td><td>2</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td><td>-1</td><td>-4</td><td>-3</td><td>1</td><td>-1</td><td>0</td><td>-2</td><td>0</td><td>-1</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-3</td><td>1</td></tr>
-<tr><td>E</td><td>-1</td><td>1</td><td>-4</td><td>2</td><td>5</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-3</td><td>-2</td><td>0</td><td>-1</td><td>2</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>4</td></tr>
-<tr><td>F</td><td>-2</td><td>-3</td><td>-2</td><td>-3</td><td>-3</td><td>6</td><td>-3</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>0</td><td>-3</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>1</td><td>-1</td><td>3</td><td>-3</td></tr>
-<tr><td>G</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-2</td><td>-3</td><td>6</td><td>-2</td><td>-4</td><td>-2</td><td>-4</td><td>-3</td><td>0</td><td>-2</td><td>-2</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td></tr>
-<tr><td>H</td><td>-2</td><td>0</td><td>-3</td><td>-1</td><td>0</td><td>-1</td><td>-2</td><td>8</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>1</td><td>-2</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>2</td><td>0</td></tr>
-<tr><td>I</td><td>-1</td><td>-3</td><td>-1</td><td>-3</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>4</td><td>-3</td><td>2</td><td>1</td><td>-3</td><td>-3</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>-1</td><td>3</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td></tr>
-<tr><td>K</td><td>-1</td><td>0</td><td>-3</td><td>-1</td><td>1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>5</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>1</td><td>2</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>1</td></tr>
-<tr><td>L</td><td>-1</td><td>-4</td><td>-1</td><td>-4</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>2</td><td>-2</td><td>4</td><td>2</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>1</td><td>-2</td><td>-1</td><td>-1</td><td>-3</td></tr>
-<tr><td>M</td><td>-1</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>-1</td><td>2</td><td>5</td><td>-2</td><td>-2</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td></tr>
-<tr><td>N</td><td>-2</td><td>3</td><td>-3</td><td>1</td><td>0</td><td>-3</td><td>0</td><td>1</td><td>-3</td><td>0</td><td>-3</td><td>-2</td><td>6</td><td>-2</td><td>0</td><td>0</td><td>1</td><td>0</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-2</td><td>0</td></tr>
-<tr><td>P</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-1</td><td>-4</td><td>-2</td><td>-2</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>-2</td><td>7</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-4</td><td>-2</td><td>-3</td><td>-1</td></tr>
-<tr><td>Q</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>2</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-2</td><td>0</td><td>0</td><td>-1</td><td>5</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>3</td></tr>
-<tr><td>R</td><td>-1</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>2</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>1</td><td>5</td><td>-1</td><td>-1</td><td>-1</td><td>-3</td><td>-3</td><td>-1</td><td>-2</td><td>0</td></tr>
-<tr><td>S</td><td>1</td><td>0</td><td>-1</td><td>0</td><td>0</td><td>-2</td><td>0</td><td>-1</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>1</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>1</td><td>0</td><td>-2</td><td>-3</td><td>0</td><td>-2</td><td>0</td></tr>
-<tr><td>T</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>5</td><td>0</td><td>0</td><td>-2</td><td>0</td><td>-2</td><td>-1</td></tr>
-<tr><td>U</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td></tr>
-<tr><td>V</td><td>0</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>-3</td><td>3</td><td>-2</td><td>1</td><td>1</td><td>-3</td><td>-2</td><td>-2</td><td>-3</td><td>-2</td><td>0</td><td>-1</td><td>4</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td></tr>
-<tr><td>W</td><td>-3</td><td>-4</td><td>-2</td><td>-4</td><td>-3</td><td>1</td><td>-2</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>-4</td><td>-4</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-3</td><td>11</td><td>-2</td><td>2</td><td>-3</td></tr>
-<tr><td>X</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td></tr>
-<tr><td>Y</td><td>-2</td><td>-3</td><td>-2</td><td>-3</td><td>-2</td><td>3</td><td>-3</td><td>2</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>2</td><td>-1</td><td>7</td><td>-2</td></tr>
-<tr><td>Z</td><td>-1</td><td>1</td><td>-3</td><td>1</td><td>4</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-3</td><td>-1</td><td>0</td><td>-1</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>4</td></tr>
-</table>
-<p><strong><a name="pam250">PAM250</a></strong><br/>
-<em><strong>P</strong>ercentage <strong>A</strong>ccepted <strong>M</strong>utation matrix. PAM250 estimates substitutions after 250% of sites have changed (each site can be mutated multple times).<br/>
-Jalview 2.8.1 introduced support for PAM250 based <a href="../calculations/pca.html">PCA</a> and <a href="../calculations/tree.html">tree</a> calculations.</em>
-<table border="1">
-<tr><td></td><td> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </td></tr>
-<tr><td>A</td><td>2</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>0</td><td>1</td><td>0</td><td>-2</td><td>1</td><td>1</td><td>0</td><td>0</td><td>-6</td><td>0</td><td>-3</td><td>0</td></tr>
-<tr><td>B</td><td>0</td><td>3</td><td>-4</td><td>3</td><td>3</td><td>-4</td><td>0</td><td>1</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>2</td><td>-1</td><td>1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-5</td><td>-1</td><td>-3</td><td>2</td></tr>
-<tr><td>C</td><td>-2</td><td>-4</td><td>12</td><td>-5</td><td>-5</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-5</td><td>-6</td><td>-5</td><td>-4</td><td>-3</td><td>-5</td><td>-4</td><td>0</td><td>-2</td><td>-3</td><td>-2</td><td>-8</td><td>-3</td><td>0</td><td>-5</td></tr>
-<tr><td>D</td><td>0</td><td>3</td><td>-5</td><td>4</td><td>3</td><td>-6</td><td>1</td><td>1</td><td>-2</td><td>0</td><td>-4</td><td>-3</td><td>2</td><td>-1</td><td>2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-7</td><td>-1</td><td>-4</td><td>3</td></tr>
-<tr><td>E</td><td>0</td><td>3</td><td>-5</td><td>3</td><td>4</td><td>-5</td><td>0</td><td>1</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>-1</td><td>2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-7</td><td>-1</td><td>-4</td><td>3</td></tr>
-<tr><td>F</td><td>-3</td><td>-4</td><td>-4</td><td>-6</td><td>-5</td><td>9</td><td>-5</td><td>-2</td><td>1</td><td>-5</td><td>2</td><td>0</td><td>-3</td><td>-5</td><td>-5</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>7</td><td>-5</td></tr>
-<tr><td>G</td><td>1</td><td>0</td><td>-3</td><td>1</td><td>0</td><td>-5</td><td>5</td><td>-2</td><td>-3</td><td>-2</td><td>-4</td><td>-3</td><td>0</td><td>0</td><td>-1</td><td>-3</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-7</td><td>-1</td><td>-5</td><td>0</td></tr>
-<tr><td>H</td><td>-1</td><td>1</td><td>-3</td><td>1</td><td>1</td><td>-2</td><td>-2</td><td>6</td><td>-2</td><td>0</td><td>-2</td><td>-2</td><td>2</td><td>0</td><td>3</td><td>2</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>0</td><td>2</td></tr>
-<tr><td>I</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>5</td><td>-2</td><td>2</td><td>2</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>-5</td><td>-1</td><td>-1</td><td>-2</td></tr>
-<tr><td>K</td><td>-1</td><td>1</td><td>-5</td><td>0</td><td>0</td><td>-5</td><td>-2</td><td>0</td><td>-2</td><td>5</td><td>-3</td><td>0</td><td>1</td><td>-1</td><td>1</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-4</td><td>0</td></tr>
-<tr><td>L</td><td>-2</td><td>-3</td><td>-6</td><td>-4</td><td>-3</td><td>2</td><td>-4</td><td>-2</td><td>2</td><td>-3</td><td>6</td><td>4</td><td>-3</td><td>-3</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>2</td><td>-2</td><td>-1</td><td>-1</td><td>-3</td></tr>
-<tr><td>M</td><td>-1</td><td>-2</td><td>-5</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>2</td><td>0</td><td>4</td><td>6</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>-1</td><td>-1</td><td>2</td><td>-4</td><td>-1</td><td>-2</td><td>-2</td></tr>
-<tr><td>N</td><td>0</td><td>2</td><td>-4</td><td>2</td><td>1</td><td>-3</td><td>0</td><td>2</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>2</td><td>0</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>-2</td><td>-4</td><td>0</td><td>-2</td><td>1</td></tr>
-<tr><td>P</td><td>1</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-5</td><td>0</td><td>0</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>6</td><td>0</td><td>0</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-6</td><td>-1</td><td>-5</td><td>0</td></tr>
-<tr><td>Q</td><td>0</td><td>1</td><td>-5</td><td>2</td><td>2</td><td>-5</td><td>-1</td><td>3</td><td>-2</td><td>1</td><td>-2</td><td>-1</td><td>1</td><td>0</td><td>4</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-5</td><td>-1</td><td>-4</td><td>3</td></tr>
-<tr><td>R</td><td>-2</td><td>-1</td><td>-4</td><td>-1</td><td>-1</td><td>-4</td><td>-3</td><td>2</td><td>-2</td><td>3</td><td>-3</td><td>0</td><td>0</td><td>0</td><td>1</td><td>6</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>2</td><td>-1</td><td>-4</td><td>0</td></tr>
-<tr><td>S</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>1</td><td>-1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>-1</td><td>-2</td><td>0</td><td>-3</td><td>0</td></tr>
-<tr><td>T</td><td>1</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>0</td><td>-1</td><td>0</td><td>0</td><td>-2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>1</td><td>3</td><td>0</td><td>0</td><td>-5</td><td>0</td><td>-3</td><td>-1</td></tr>
-<tr><td>U</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-1</td></tr>
-<tr><td>V</td><td>0</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>4</td><td>-2</td><td>2</td><td>2</td><td>-2</td><td>-1</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>-6</td><td>-1</td><td>-2</td><td>-2</td></tr>
-<tr><td>W</td><td>-6</td><td>-5</td><td>-8</td><td>-7</td><td>-7</td><td>0</td><td>-7</td><td>-3</td><td>-5</td><td>-3</td><td>-2</td><td>-4</td><td>-4</td><td>-6</td><td>-5</td><td>2</td><td>-2</td><td>-5</td><td>-4</td><td>-6</td><td>17</td><td>-4</td><td>0</td><td>-6</td></tr>
-<tr><td>X</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-1</td></tr>
-<tr><td>Y</td><td>-3</td><td>-3</td><td>0</td><td>-4</td><td>-4</td><td>7</td><td>-5</td><td>0</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-2</td><td>-5</td><td>-4</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>0</td><td>-2</td><td>10</td><td>-4</td></tr>
-<tr><td>Z</td><td>0</td><td>2</td><td>-5</td><td>3</td><td>3</td><td>-5</td><td>0</td><td>2</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-6</td><td>-1</td><td>-4</td><td>3</td></tr>
-</table>
+ <p>
+ <strong><a name="blosum62"></a>BLOSUM62</strong><br />
+ <table border="1">
+ <tr>
+ <td></td>
+ <td> A </td>
+ <td> B </td>
+ <td> C </td>
+ <td> D </td>
+ <td> E </td>
+ <td> F </td>
+ <td> G </td>
+ <td> H </td>
+ <td> I </td>
+ <td> K </td>
+ <td> L </td>
+ <td> M </td>
+ <td> N </td>
+ <td> P </td>
+ <td> Q </td>
+ <td> R </td>
+ <td> S </td>
+ <td> T </td>
+ <td> U </td>
+ <td> V </td>
+ <td> W </td>
+ <td> X </td>
+ <td> Y </td>
+ <td> Z </td>
+ </tr>
+ <tr>
+ <td>A</td>
+ <td>4</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>B</td>
+ <td>-2</td>
+ <td>4</td>
+ <td>-3</td>
+ <td>4</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>9</td>
+ <td>-3</td>
+ <td>-4</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-3</td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td>-2</td>
+ <td>4</td>
+ <td>-3</td>
+ <td>6</td>
+ <td>2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>E</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-4</td>
+ <td>2</td>
+ <td>5</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>4</td>
+ </tr>
+ <tr>
+ <td>F</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>6</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>3</td>
+ <td>-3</td>
+ </tr>
+ <tr>
+ <td>G</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>6</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ </tr>
+ <tr>
+ <td>H</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>8</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>I</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>4</td>
+ <td>-3</td>
+ <td>2</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>3</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ </tr>
+ <tr>
+ <td>K</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>5</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>2</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>L</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>4</td>
+ <td>2</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ </tr>
+ <tr>
+ <td>M</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>5</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>N</td>
+ <td>-2</td>
+ <td>3</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>6</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>0</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>P</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>7</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>Q</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>2</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>5</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>R</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>5</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>S</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>4</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>T</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>5</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>U</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>V</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>3</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>4</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ </tr>
+ <tr>
+ <td>W</td>
+ <td>-3</td>
+ <td>-4</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-4</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>11</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>-3</td>
+ </tr>
+ <tr>
+ <td>X</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>Y</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>3</td>
+ <td>-3</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>7</td>
+ <td>-2</td>
+ </tr>
+ <tr>
+ <td>Z</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>4</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>3</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>4</td>
+ </tr>
+ </table>
+ <p>
+ <strong><a name="pam250">PAM250</a></strong><br /> <em><strong>P</strong>ercentage
+ <strong>A</strong>ccepted <strong>M</strong>utation matrix. PAM250
+ estimates substitutions after 250% of sites have changed (each
+ site can be mutated multple times).<br /> Jalview 2.8.1 introduced
+ support for PAM250 based <a href="../calculations/pca.html">PCA</a>
+ and <a href="../calculations/tree.html">tree</a> calculations.</em>
+ <table border="1">
+ <tr>
+ <td></td>
+ <td> A </td>
+ <td> B </td>
+ <td> C </td>
+ <td> D </td>
+ <td> E </td>
+ <td> F </td>
+ <td> G </td>
+ <td> H </td>
+ <td> I </td>
+ <td> K </td>
+ <td> L </td>
+ <td> M </td>
+ <td> N </td>
+ <td> P </td>
+ <td> Q </td>
+ <td> R </td>
+ <td> S </td>
+ <td> T </td>
+ <td> U </td>
+ <td> V </td>
+ <td> W </td>
+ <td> X </td>
+ <td> Y </td>
+ <td> Z </td>
+ </tr>
+ <tr>
+ <td>A</td>
+ <td>2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-6</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>B</td>
+ <td>0</td>
+ <td>3</td>
+ <td>-4</td>
+ <td>3</td>
+ <td>3</td>
+ <td>-4</td>
+ <td>0</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-5</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>12</td>
+ <td>-5</td>
+ <td>-5</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-5</td>
+ <td>-6</td>
+ <td>-5</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>-5</td>
+ <td>-4</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-8</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-5</td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td>0</td>
+ <td>3</td>
+ <td>-5</td>
+ <td>4</td>
+ <td>3</td>
+ <td>-6</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-7</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>E</td>
+ <td>0</td>
+ <td>3</td>
+ <td>-5</td>
+ <td>3</td>
+ <td>4</td>
+ <td>-5</td>
+ <td>0</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-7</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>F</td>
+ <td>-3</td>
+ <td>-4</td>
+ <td>-4</td>
+ <td>-6</td>
+ <td>-5</td>
+ <td>9</td>
+ <td>-5</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-5</td>
+ <td>2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-5</td>
+ <td>-5</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>7</td>
+ <td>-5</td>
+ </tr>
+ <tr>
+ <td>G</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-5</td>
+ <td>5</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-7</td>
+ <td>-1</td>
+ <td>-5</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>H</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>6</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>0</td>
+ <td>3</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>I</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>5</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>4</td>
+ <td>-5</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ </tr>
+ <tr>
+ <td>K</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>-5</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-5</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>5</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>3</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>L</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-6</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>2</td>
+ <td>-4</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>-3</td>
+ <td>6</td>
+ <td>4</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-3</td>
+ </tr>
+ <tr>
+ <td>M</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-5</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>0</td>
+ <td>4</td>
+ <td>6</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>2</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ </tr>
+ <tr>
+ <td>N</td>
+ <td>0</td>
+ <td>2</td>
+ <td>-4</td>
+ <td>2</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>0</td>
+ <td>1</td>
+ <td>0</td>
+ <td>1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>P</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-5</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>6</td>
+ <td>0</td>
+ <td>0</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-6</td>
+ <td>-1</td>
+ <td>-5</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>Q</td>
+ <td>0</td>
+ <td>1</td>
+ <td>-5</td>
+ <td>2</td>
+ <td>2</td>
+ <td>-5</td>
+ <td>-1</td>
+ <td>3</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>0</td>
+ <td>4</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-5</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>R</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>3</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0</td>
+ <td>1</td>
+ <td>6</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>S</td>
+ <td>1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>2</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>T</td>
+ <td>1</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>1</td>
+ <td>3</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-5</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>U</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>V</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>4</td>
+ <td>-2</td>
+ <td>2</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>4</td>
+ <td>-6</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ </tr>
+ <tr>
+ <td>W</td>
+ <td>-6</td>
+ <td>-5</td>
+ <td>-8</td>
+ <td>-7</td>
+ <td>-7</td>
+ <td>0</td>
+ <td>-7</td>
+ <td>-3</td>
+ <td>-5</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-4</td>
+ <td>-4</td>
+ <td>-6</td>
+ <td>-5</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>-5</td>
+ <td>-4</td>
+ <td>-6</td>
+ <td>17</td>
+ <td>-4</td>
+ <td>0</td>
+ <td>-6</td>
+ </tr>
+ <tr>
+ <td>X</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-3</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-1</td>
+ </tr>
+ <tr>
+ <td>Y</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>0</td>
+ <td>-4</td>
+ <td>-4</td>
+ <td>7</td>
+ <td>-5</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>-5</td>
+ <td>-4</td>
+ <td>-4</td>
+ <td>-3</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-2</td>
+ <td>10</td>
+ <td>-4</td>
+ </tr>
+ <tr>
+ <td>Z</td>
+ <td>0</td>
+ <td>2</td>
+ <td>-5</td>
+ <td>3</td>
+ <td>3</td>
+ <td>-5</td>
+ <td>0</td>
+ <td>2</td>
+ <td>-2</td>
+ <td>0</td>
+ <td>-3</td>
+ <td>-2</td>
+ <td>1</td>
+ <td>0</td>
+ <td>3</td>
+ <td>0</td>
+ <td>0</td>
+ <td>-1</td>
+ <td>-1</td>
+ <td>-2</td>
+ <td>-6</td>
+ <td>-1</td>
+ <td>-4</td>
+ <td>3</td>
+ </tr>
+ </table>
-<p><strong><a name="simplenucleotide">Simple Nucleotide Substitution</a></strong><br>
-This is an ad-hoc matrix which, in addition to penalising mutations between the common nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA.
-In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, and N is allowed to match any other base weakly. This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match any of (ACGTU), and unfavourably match each other.
-<table border="1">
-<tr><td></td><td> A </td><td> C </td><td> G </td><td> I </td><td> N </td><td> R </td><td> T </td><td> U </td><td> X </td><td> Y </td></tr>
-<tr><td>A</td><td>10</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>1</td><td>-8</td></tr>
-<tr><td>C</td><td>-8</td><td>10</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td></tr>
-<tr><td>G</td><td>-8</td><td>-8</td><td>10</td><td>1</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>1</td><td>-8</td></tr>
-<tr><td>I</td><td>1</td><td>1</td><td>1</td><td>10</td><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td><td>0</td></tr>
-<tr><td>N</td><td>1</td><td>1</td><td>1</td><td>1</td><td>10</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr>
-<tr><td>R</td><td>1</td><td>-8</td><td>1</td><td>0</td><td>1</td><td>10</td><td>-8</td><td>-8</td><td>0</td><td>-8</td></tr>
-<tr><td>T</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>10</td><td>10</td><td>1</td><td>1</td></tr>
-<tr><td>U</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>10</td><td>10</td><td>1</td><td>1</td></tr>
-<tr><td>X</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>1</td><td>10</td><td>0</td></tr>
-<tr><td>Y</td><td>-8</td><td>1</td><td>-8</td><td>0</td><td>1</td><td>-8</td><td>1</td><td>1</td><td>0</td><td>10</td></tr>
-</table>
-<strong><em>This nucleotide matrix was introduced in
- Jalview 2.8. If you'd like to improve it - please take a look at <a
- href="http://issues.jalview.org/browse/JAL-1027">Issue JAL-1027
- - introduce a nucleotide substitution matrix that supports RNA/DNA
- and ambiguity codes</a>
- </em></strong>
- </p>
-<!-- <p><strong><a name="conservation">Physicochemical property conservation</a></strong><br>
+ <p>
+ <strong><a name="simplenucleotide">Simple Nucleotide
+ Substitution</a></strong><br> This is an ad-hoc matrix which, in
+ addition to penalising mutations between the common nucleotides
+ (ACGT), includes T/U equivalence in order to allow both DNA and/or
+ RNA. In addition, it encodes weak equivalence between R and Y with
+ AG and CTU, respectively, and N is allowed to match any other base
+ weakly. This matrix also includes I (Inosine) and X (Xanthine), but
+ encodes them to weakly match any of (ACGTU), and unfavourably match
+ each other.
+ <table border="1">
+ <tr>
+ <td></td>
+ <td> A </td>
+ <td> C </td>
+ <td> G </td>
+ <td> I </td>
+ <td> N </td>
+ <td> R </td>
+ <td> T </td>
+ <td> U </td>
+ <td> X </td>
+ <td> Y </td>
+ </tr>
+ <tr>
+ <td>A</td>
+ <td>10</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>-8</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td>-8</td>
+ <td>10</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>G</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>10</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>-8</td>
+ </tr>
+ <tr>
+ <td>I</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>10</td>
+ <td>1</td>
+ <td>0</td>
+ <td>1</td>
+ <td>1</td>
+ <td>0</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>N</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>10</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>R</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>0</td>
+ <td>1</td>
+ <td>10</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>0</td>
+ <td>-8</td>
+ </tr>
+ <tr>
+ <td>T</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>10</td>
+ <td>10</td>
+ <td>1</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>U</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>10</td>
+ <td>10</td>
+ <td>1</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>X</td>
+ <td>1</td>
+ <td>1</td>
+ <td>1</td>
+ <td>0</td>
+ <td>1</td>
+ <td>0</td>
+ <td>1</td>
+ <td>1</td>
+ <td>10</td>
+ <td>0</td>
+ </tr>
+ <tr>
+ <td>Y</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>0</td>
+ <td>1</td>
+ <td>-8</td>
+ <td>1</td>
+ <td>1</td>
+ <td>0</td>
+ <td>10</td>
+ </tr>
+ </table>
+ <strong><em>This nucleotide matrix was introduced in
+ Jalview 2.8. If you'd like to improve it - please take a look at <a
+ href="http://issues.jalview.org/browse/JAL-1027"
+ >Issue JAL-1027 - introduce a nucleotide substitution matrix that
+ supports RNA/DNA and ambiguity codes</a>
+ </em></strong>
+ </p>
+ <!-- <p><strong><a name="conservation">Physicochemical property conservation</a></strong><br>
Three different matrices are provided which reflect differences in physicochemical properties for different amino-acids.
<ul><li><em>Conservation Both</em><br>Matrix elements count number of properties shared, and number of properties that both amino-acids *do not* have (e.g. hydrophobic and not polar).
</li> -->
-</ul>
- </body>
+ </ul>
+</body>
</html>
<title>Sorting Sequences</title>
</head>
<body>
-<p><strong>Sorting Sequences</strong></p>
-<p>Any group of selected sequences may be reordered by pressing the
-up or down arrow keys. The whole alignment may also be reordered by
-the use of the functions in the Sort menu (<strong>Calculate→Sort</strong>):
-</p>
-<ul>
-<li><p><strong>Sort by ID</strong></p>
-<p>Orders the sequences by the alphanumeric (0-9A-Za-z)
-precedence of their names.</p><p>
-</li>
-<li><p><strong>Sort by Group</strong></p>
-<p>Places sequences in the same group adjacent to each other.</p><p>
-</li>
-<li><p><strong>Sort by Pairwise Identity</strong></p>
-<p>Places pairs of sequences together that align with the greatest
-fraction of conserved residues.
-</p><p>
-</li>
-<li><p><strong>Sort by Tree Order</strong></p>
-<p>The leaf ordering of a particular phylogenetic tree is used to
-order the sequences corresponding to those leaves in the
-alignment.<br>
-If a tree has been calculated from or associated with the current
-alignment, its name will appear in the submenu <strong>Sort→By Tree Order</strong>.</p><p>
-</li>
-<li><p><strong>Sort by alignment ordering</strong></p>
-<p>Multiple alignment methods often order the sequences in their
-alignments by some measure of sequence identity.<br>
-If the current alignment has been generated by one of Jalview's
-alignment web services, the alignment ordering can be recovered by
-its corresponding entry in the Sort menu.
-</p>
-</li>
-<li><p><strong>Sort by Score</strong></p>
-<p>This menu appears if the alignment contains any <a href="../features/annotationsFormat.html">sequence associated
-alignment annotation</a> with associated score values. Each entry is the
-label for a distinct group of sequence associated annotation
-scores which can be used for sorting.</p>
-</ul>
-<p><strong>Reversing the Order</strong></p>
-<p>Selecting any item from the Sort menu will sort sequences in an
-ascending order according to the property defining the sort. If the
-same sort is re-applied, the sequences will be sorted in the inverse
-order. In the case of trees and alignment orderings, Jalview will
-remember your last choice for sorting the alignment and only apply the
-inverse ordering if you select the same tree or alignment ordering
-item again.</p>
+ <p>
+ <strong>Sorting Sequences</strong>
+ </p>
+ <p>
+ Any group of selected sequences may be reordered by pressing the up
+ or down arrow keys. The whole alignment may also be reordered by the
+ use of the functions in the Sort menu (<strong>Calculate→Sort</strong>):
+ </p>
+ <ul>
+ <li><p>
+ <strong>Sort by ID</strong>
+ </p>
+ <p>Orders the sequences by the alphanumeric (0-9A-Za-z)
+ precedence of their names.</p>
+ <p></li>
+ <li><p>
+ <strong>Sort by Group</strong>
+ </p>
+ <p>Places sequences in the same group adjacent to each other.</p>
+ <p></li>
+ <li><p>
+ <strong>Sort by Pairwise Identity</strong>
+ </p>
+ <p>Places pairs of sequences together that align with the
+ greatest fraction of conserved residues.</p>
+ <p></li>
+ <li><p>
+ <strong>Sort by Tree Order</strong>
+ </p>
+ <p>
+ The leaf ordering of a particular phylogenetic tree is used to
+ order the sequences corresponding to those leaves in the
+ alignment.<br> If a tree has been calculated from or
+ associated with the current alignment, its name will appear in
+ the submenu <strong>Sort→By Tree Order</strong>.
+ </p>
+ <p></li>
+ <li><p>
+ <strong>Sort by alignment ordering</strong>
+ </p>
+ <p>
+ Multiple alignment methods often order the sequences in their
+ alignments by some measure of sequence identity.<br> If the
+ current alignment has been generated by one of Jalview's
+ alignment web services, the alignment ordering can be recovered
+ by its corresponding entry in the Sort menu.
+ </p></li>
+ <li><p>
+ <strong>Sort by Score</strong>
+ </p>
+ <p>
+ This menu appears if the alignment contains any <a
+ href="../features/annotationsFormat.html"
+ >sequence associated alignment annotation</a> with associated
+ score values. Each entry is the label for a distinct group of
+ sequence associated annotation scores which can be used for
+ sorting.
+ </p>
+ </ul>
+ <p>
+ <strong>Reversing the Order</strong>
+ </p>
+ <p>Selecting any item from the Sort menu will sort sequences in an
+ ascending order according to the property defining the sort. If the
+ same sort is re-applied, the sequences will be sorted in the inverse
+ order. In the case of trees and alignment orderings, Jalview will
+ remember your last choice for sorting the alignment and only apply
+ the inverse ordering if you select the same tree or alignment
+ ordering item again.</p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Alignment RNA Structure Consensus Annotation</title></head>
-<body><p><strong>Alignment RNA Structure Consensus Annotation</strong></p>
+<head>
+<title>Alignment RNA Structure Consensus Annotation</title>
+</head>
+<body>
+ <p>
+ <strong>Alignment RNA Structure Consensus Annotation</strong>
+ </p>
-<p>The RNA structure consensus displayed below the alignment is the
-percentage of valid base pairs per column. It is calculated in
-relation to a secondary structure and just paired columns are
-calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) and
-the wobble base pair (G-T/U) are regarded as valid pairings.<br>
-The amount of valid base pairs is indicated by the profile in the
-Alignment Annotation row.<br>
-By default this calculation includes gaps in columns. You can choose
-to ignore gaps in the calculation by right clicking on the label
-"StrConsensus" to the left of the structure consensus bar
-chart.<br>
-
-<p><strong>Structure logo</strong></p>
-By clicking on the label you can also activate the structure logo. It is very
-similar to a sequence logo but counts the numbers of base pairs. There
-are two residues per column, the actual column and the interacting
-base. The opening bracket is always the one on the left side.<br>
-Like sequence logos the relative amount of a specific base pair can be
-estimated by its size in the logo. The tool tip of a column gives the
-exact numbers for all occurring valid base pairs.
-</p>
+ <p>
+ The RNA structure consensus displayed below the alignment is the
+ percentage of valid base pairs per column. It is calculated in
+ relation to a secondary structure and just paired columns are
+ calculated. The canonical Watson-Crick base pairings (A-T/U, G-C)
+ and the wobble base pair (G-T/U) are regarded as valid pairings.<br>
+ The amount of valid base pairs is indicated by the profile in the
+ Alignment Annotation row.<br> By default this calculation
+ includes gaps in columns. You can choose to ignore gaps in the
+ calculation by right clicking on the label "StrConsensus"
+ to the left of the structure consensus bar chart.<br>
+ <p>
+ <strong>Structure logo</strong>
+ </p>
+ By clicking on the label you can also activate the structure logo. It
+ is very similar to a sequence logo but counts the numbers of base
+ pairs. There are two residues per column, the actual column and the
+ interacting base. The opening bracket is always the one on the left
+ side.
+ <br> Like sequence logos the relative amount of a specific base
+ pair can be estimated by its size in the logo. The tool tip of a
+ column gives the exact numbers for all occurring valid base pairs.
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Tree Calculation</title></head>
+<head>
+<title>Tree Calculation</title>
+</head>
<body>
-<p><strong>Calculation of trees from alignments</strong></p>
-<p>Trees are calculated on either the complete alignment, or just the
-currently selected group of sequences, using the functions in the
-<strong>Calculate→Calculate tree</strong> submenu.
-Once calculated, trees are displayed in a new <a
-href="../calculations/treeviewer.html">tree viewing window</a>. There are
-four different calculations, using one of two distance measures and
-constructing the tree from one of two algorithms :
-</p>
-<p><strong>Distance Measures</strong></p>
-<p>Trees are calculated on the basis of a measure of similarity
-between each pair of sequences in the alignment :
-
-
+ <p>
+ <strong>Calculation of trees from alignments</strong>
+ </p>
+ <p>
+ Trees are calculated on either the complete alignment, or just the
+ currently selected group of sequences, using the functions in the <strong>Calculate→Calculate
+ tree</strong> submenu. Once calculated, trees are displayed in a new <a
+ href="../calculations/treeviewer.html"
+ >tree viewing window</a>. There are four different calculations, using
+ one of two distance measures and constructing the tree from one of
+ two algorithms :
+ </p>
+ <p>
+ <strong>Distance Measures</strong>
+ </p>
+ <p>Trees are calculated on the basis of a measure of similarity
+ between each pair of sequences in the alignment :
<ul>
<li><strong>PID</strong><br>The percentage identity
between the two sequences at each aligned position.
residues)'.</em>
</li>
</ul>
- <li><strong>BLOSUM62, PAM250, DNA</strong><br/>These
- options use one of the available substitution matrices to compute
- a sum of scores for the residue pairs at each aligned position.
- <ul><li>For details about each model, see the
- <a href="scorematrices.html">list of built-in score matrices</a>.
+ <li><strong>BLOSUM62, PAM250, DNA</strong><br />These options
+ use one of the available substitution matrices to compute a sum of
+ scores for the residue pairs at each aligned position.
+ <ul>
+ <li>For details about each model, see the <a
+ href="scorematrices.html"
+ >list of built-in score matrices</a>.
</li>
- </ul></li>
+ </ul></li>
<li><strong>Sequence Feature Similarity</strong><br>Trees
are constructed from a distance matrix formed from Jaccard
distances between sequence features observed at each column of the
same type will be grouped together in trees computed with this
metric. <em>This measure was introduced in Jalview 2.9</em></li>
</ul>
- <p><strong>Tree Construction Methods</strong></p>
-<p>Jalview currently supports two kinds of agglomerative clustering
-methods. These are not intended to substitute for rigorous
-phylogenetic tree construction, and may fail on very large alignments.
-<ul>
-<li><strong>UPGMA tree</strong><br>
- UPGMA stands for Unweighted Pair-Group Method using Arithmetic
- averages. Clusters are iteratively formed and extended by finding a
- non-member sequence with the lowest average dissimilarity over the
- cluster members.
-<p></p>
-</li>
-<li><strong>Neighbour Joining tree</strong><br>
- First described in 1987 by Saitou and Nei, this method applies a
- greedy algorithm to find the tree with the shortest branch
- lengths.<br>
- This method, as implemented in Jalview, is considerably more
- expensive than UPGMA.
-</li>
-</ul>
-<p>A newly calculated tree will be displayed in a new <a
-href="../calculations/treeviewer.html">tree viewing window</a>. In
-addition, a new entry with the same tree viewer window name will be added in the Sort
-menu so that the alignment can be reordered to reflect the ordering of
-the leafs of the tree. If the tree was calculated on a selected region
-of the alignment, then the title of the tree view will reflect this.</p>
+ <p>
+ <strong>Tree Construction Methods</strong>
+ </p>
+ <p>Jalview currently supports two kinds of agglomerative
+ clustering methods. These are not intended to substitute for
+ rigorous phylogenetic tree construction, and may fail on very large
+ alignments.
+ <ul>
+ <li><strong>UPGMA tree</strong><br> UPGMA stands for
+ Unweighted Pair-Group Method using Arithmetic averages. Clusters
+ are iteratively formed and extended by finding a non-member
+ sequence with the lowest average dissimilarity over the cluster
+ members.
+ <p></p></li>
+ <li><strong>Neighbour Joining tree</strong><br> First
+ described in 1987 by Saitou and Nei, this method applies a greedy
+ algorithm to find the tree with the shortest branch lengths.<br>
+ This method, as implemented in Jalview, is considerably more
+ expensive than UPGMA.</li>
+ </ul>
+ <p>
+ A newly calculated tree will be displayed in a new <a
+ href="../calculations/treeviewer.html"
+ >tree viewing window</a>. In addition, a new entry with the same tree
+ viewer window name will be added in the Sort menu so that the
+ alignment can be reordered to reflect the ordering of the leafs of
+ the tree. If the tree was calculated on a selected region of the
+ alignment, then the title of the tree view will reflect this.
+ </p>
-<p><strong>External Sources for Phylogenetic Trees</strong></p>
- <p>A number of programs exist for the reliable construction of
- phylogenetic trees, which can cope with large numbers of sequences,
- use better distance methods and can perform bootstrapping. Jalview
- can read <a
- href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>
- format tree files using the 'Load Associated Tree' entry of the
- alignment's File menu. Sequences in the alignment will be
- automatically associated to nodes in the tree, by matching Sequence
- IDs to the tree's leaf names.
+ <p>
+ <strong>External Sources for Phylogenetic Trees</strong>
+ </p>
+ <p>
+ A number of programs exist for the reliable construction of
+ phylogenetic trees, which can cope with large numbers of sequences,
+ use better distance methods and can perform bootstrapping. Jalview
+ can read <a
+ href="http://evolution.genetics.washington.edu/phylip/newick_doc.html"
+ >Newick</a> format tree files using the 'Load Associated Tree' entry
+ of the alignment's File menu. Sequences in the alignment will be
+ automatically associated to nodes in the tree, by matching Sequence
+ IDs to the tree's leaf names.
</p>
<title>The Tree Viewing Window</title>
</head>
<body>
-<p><strong>The Tree Viewing Window</strong></p>
-<p>
- The tree viewing window is opened when a tree has been <a href="tree.html">calculated
- from an alignment</a>, or imported via a file or web service. It includes <a href="#menus">menus</a> for
- controlling layout and file and figure creation, and enables
- various selection and colouring operations on the
- associated sequences in the alignment.</p>
-<p>
-<strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
- Selecting sequence ids at the leaves of the tree selects the
- corresponding sequences in the original alignment. These selections
- are also reflected in any other analysis windows associated with the
- alignment, such as another tree viewer.</p>
-<p><strong><em>Grouping sequences by partitioning the tree at a particular distanec</em></strong><br>
- Clicking anywhere along the extent of the tree (but not on a leaf or
- internal node) defines a tree 'partition', by cutting every branch
- of the tree spanning the depth where the mouse-click occurred. Groups
- are created containing sequences at the leaves of each connected
- sub tree. These groups are each given a different colour, which are
- reflected in other windows in the same way as if the sequence ids
- were selected, and can be edited in the same way as user defined
- sequence groups.
-</p>
-<p>Tree partitions are useful for comparing clusters produced by
-different methods and measures. They are also an effective way of
-identifying specific patterns of conservation and mutation
-corresponding to the overall phylogenetic structure, when combined
-with the <a href="../colourSchemes/conservation.html">conservation
-based colour scheme</a>.</p>
-<p>
-<strong><em>Selecting Subtrees and changing the branch order and subtree group colour</em></strong><br>
-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.
+ <p>
+ <strong>The Tree Viewing Window</strong>
+ </p>
+ <p>
+ The tree viewing window is opened when a tree has been <a
+ href="tree.html"
+ >calculated from an alignment</a>, or imported via a file or web
+ service. It includes <a href="#menus">menus</a> for controlling
+ layout and file and figure creation, and enables various selection
+ and colouring operations on the associated sequences in the
+ alignment.
+ </p>
+ <p>
+ <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
+ Selecting sequence ids at the leaves of the tree selects the
+ corresponding sequences in the original alignment. These selections
+ are also reflected in any other analysis windows associated with the
+ alignment, such as another tree viewer.
+ </p>
+ <p>
+ <strong><em>Grouping sequences by partitioning the
+ tree at a particular distanec</em></strong><br> Clicking anywhere along
+ the extent of the tree (but not on a leaf or internal node) defines
+ a tree 'partition', by cutting every branch of the tree spanning the
+ depth where the mouse-click occurred. Groups are created containing
+ sequences at the leaves of each connected sub tree. These groups are
+ each given a different colour, which are reflected in other windows
+ in the same way as if the sequence ids were selected, and can be
+ edited in the same way as user defined sequence groups.
+ </p>
+ <p>
+ Tree partitions are useful for comparing clusters produced by
+ different methods and measures. They are also an effective way of
+ identifying specific patterns of conservation and mutation
+ corresponding to the overall phylogenetic structure, when combined
+ with the <a href="../colourSchemes/conservation.html">conservation
+ based colour scheme</a>.
+ </p>
+ <p>
+ <strong><em>Selecting Subtrees and changing the branch
+ order and subtree group colour</em></strong><br> 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><strong><a name="menus">
-File Menu</a></strong></p>
-<p>This menu allows the displayed tree to be saved as a Newick tree
-file (Save→Newick File), printed or exported as an image (PNG) or
-Postscript file. Finally, data used to calculate the tree can be
-retrieved with the 'Input Data...' entry.
-</p>
-<p><strong>View Menu</strong></p>
-<p>When the tree viewer is opened, it displays all the annotation
-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,
-and additional leaves from sequences not present in the associated
-alignment.
-</p>
-<p>The view menu mostly contains options controlling the way a tree is
-rendered and labeled:
-<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
-label overlap when this option is selected.
-</p></li>
-<li><strong>Font Size ...</strong><em>n</em><p>
-Brings up a dialog box to set the font size for the leaf
-names. <em>n</em> is the current font size.
-</p></li>
-<li><strong>Show Distances</strong><p>
-Labels each branch or leaf with its associated branch
-length.</p></li>
-<li><strong>Show Bootstrap values</strong><p>
-Labels each branch or leaf with its associated bootstrap value.
-</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.
-</p></li>
- <li><strong>Sort Alignment By Tree</strong>
- <p>
- Sorts any associated alignment views using the current tree. (<em>Only
- available in the Jalview Desktop</em>)
- </p>
- </li>
- <li><strong>Associate Leaves with ...</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>
+ </p>
+ <p>
+ <strong><a name="menus"> File Menu</a></strong>
+ </p>
+ <p>This menu allows the displayed tree to be saved as a Newick
+ tree file (Save→Newick File), printed or exported as an image
+ (PNG) or Postscript file. Finally, data used to calculate the tree
+ can be retrieved with the 'Input Data...' entry.</p>
+ <p>
+ <strong>View Menu</strong>
+ </p>
+ <p>When the tree viewer is opened, it displays all the annotation
+ 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, and additional leaves from sequences not present in the
+ associated alignment.</p>
+ <p>The view menu mostly contains options controlling the way a
+ tree is rendered and labeled:
+ <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 label
+ overlap when this option is selected.</p></li>
+ <li><strong>Font Size ...</strong><em>n</em>
+ <p>
+ Brings up a dialog box to set the font size for the leaf names.
+ <em>n</em> is the current font size.
+ </p></li>
+ <li><strong>Show Distances</strong>
+ <p>Labels each branch or leaf with its associated branch length.</p></li>
+ <li><strong>Show Bootstrap values</strong>
+ <p>Labels each branch or leaf with its associated bootstrap
+ value.</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.</p></li>
+ <li><strong>Sort Alignment By Tree</strong>
+ <p>
+ Sorts any associated alignment views using the current tree. (<em>Only
+ available in the Jalview Desktop</em>)
+ </p></li>
+ <li><strong>Associate Leaves with ...</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>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Above PID Colours</title>
+<head>
+<title>Above PID Colours</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p> <strong>Colouring above a percentage identity threshold</strong></p>
-<p> Selecting this option causes the colour scheme to be applied to only those
- residues that occur in that column more than a certain percentage of the time.
- For instance selecting the threshold to be 100 will only colour those columns
- with 100 % identity. This threshold option can be applied to the Zappo, Taylor,
- Hydrophobicity and User colour schemes. </p>
+ <p>
+ <strong>Colouring above a percentage identity threshold</strong>
+ </p>
+ <p>Selecting this option causes the colour scheme to be applied to
+ only those residues that occur in that column more than a certain
+ percentage of the time. For instance selecting the threshold to be
+ 100 will only colour those columns with 100 % identity. This
+ threshold option can be applied to the Zappo, Taylor, Hydrophobicity
+ and User colour schemes.</p>
</body>
</html>
</head>
<body>
- <p>
- <strong> Annotation Colouring </strong>
- </p>
- <p>Jalview allows the columns of an alignment to be coloured using
- any numerical annotation rows added to that alignment.</p>
- Select "Colour"
- <strong>→</strong> ".. by Annotation" to bring up the
- Colour by Annotation settings window.
- <br>
- <br>
- <div align="center">
- <img src="annotationColourSetting.gif" width="471" height="256">
- </div>
- <ul>
- <li>Select which annotation to base the colouring scheme on using
- the top left selection box.<br />If the <strong>Per-sequence
- only</strong> tick box is not greyed out, then ticking it will limit the
- available annotation rows to just those that are sequence associated
- (e.g. T-COFFEE scores and <a
- href="../webServices/proteinDisorder.html">protein disorder
- predictions</a>), which will colour each sequence according to its own
- per-residue scores.<br />
- <em>Per-sequence associated annotation colouring was introduced
- in Jalview 2.8</em>
- </li>
- <li>If the "Use Original Colours" box is selected, the
- colouring scheme will use the colouring scheme present on the
- alignment before the Annotation Colour Settings window was displayed.
- <br /> <em><strong>Please Note:</strong> If no colour scheme was
- applied previously, then the colours for lines and labels at each
- position in the annotation row will be used, for secondary structure
- symbols and graphs, this may be black by default, so your alignment
- will be coloured black.</em>
- </li>
- <li><em>Secondary structure annotation colouring</em><br />By
- default, Jalview will employ the helix or sheet colours to shade
- sequences and columns by available secondary structure annotation
- tracks. In the case of RNA, each structure is processed to identify
- distinct RNA helices and rendered in the same way as the <a
- href="rnahelicesColouring.html">RNA Helices shading scheme</a>. <em>Structure based sequence shading was added in Jalview 2.8.2</em></li>
- <li>The colour scheme can display a colour gradient from a colour
- representing the minimum value in the selected annotation to a colour
- representing the maximum value in the selected annotation. Use the
- "Min Colour" and "Max Colour" to set the colour
- gradient range.
- <ul>
- <li>Press the "Defaults" button to reset the minimum
- and maximum colours to their default settings (these are configured
- in the applet's parameters or the <a
- href="../features/preferences.html">application's user
- preferences</a>.).<br />
- <em>Default min and max colours were introduced in Jalview 2.7</em>
- </ul>
- </li>
+ <p>
+ <strong> Annotation Colouring </strong>
+ </p>
+ <p>Jalview allows the columns of an alignment to be coloured using
+ any numerical annotation rows added to that alignment.</p>
+ Select "Colour"
+ <strong>→</strong> ".. by Annotation" to bring up the
+ Colour by Annotation settings window.
+ <br>
+ <br>
+ <div align="center">
+ <img src="annotationColourSetting.gif" width="471" height="256">
+ </div>
+ <ul>
+ <li>Select which annotation to base the colouring scheme on
+ using the top left selection box.<br />If the <strong>Per-sequence
+ only</strong> tick box is not greyed out, then ticking it will limit the
+ available annotation rows to just those that are sequence
+ associated (e.g. T-COFFEE scores and <a
+ href="../webServices/proteinDisorder.html"
+ >protein disorder predictions</a>), which will colour each sequence
+ according to its own per-residue scores.<br /> <em>Per-sequence
+ associated annotation colouring was introduced in Jalview 2.8</em>
+ </li>
+ <li>If the "Use Original Colours" box is selected,
+ the colouring scheme will use the colouring scheme present on the
+ alignment before the Annotation Colour Settings window was
+ displayed. <br /> <em><strong>Please Note:</strong> If no
+ colour scheme was applied previously, then the colours for lines
+ and labels at each position in the annotation row will be used,
+ for secondary structure symbols and graphs, this may be black by
+ default, so your alignment will be coloured black.</em>
+ </li>
+ <li><em>Secondary structure annotation colouring</em><br />By
+ default, Jalview will employ the helix or sheet colours to shade
+ sequences and columns by available secondary structure annotation
+ tracks. In the case of RNA, each structure is processed to
+ identify distinct RNA helices and rendered in the same way as the
+ <a href="rnahelicesColouring.html">RNA Helices shading scheme</a>.
+ <em>Structure based sequence shading was added in Jalview
+ 2.8.2</em></li>
+ <li>The colour scheme can display a colour gradient from a
+ colour representing the minimum value in the selected annotation
+ to a colour representing the maximum value in the selected
+ annotation. Use the "Min Colour" and "Max
+ Colour" to set the colour gradient range.
+ <ul>
+ <li>Press the "Defaults" button to reset the
+ minimum and maximum colours to their default settings (these
+ are configured in the applet's parameters or the <a
+ href="../features/preferences.html"
+ >application's user preferences</a>.).<br /> <em>Default min
+ and max colours were introduced in Jalview 2.7</em>
+ </ul>
+ </li>
- <li>Select whether to colour the alignment above or below an
- adjustable threshold with the selection box center left of the
- window.</li>
- <li>Change the threshold value with the slider, or enter the
- exact value in the text box.</li>
- <li>Select the "Threshold is Min/Max" checkbox to
- assign colours using the thresholded range's minimum and maximum
- values, otherwise the scale will be defined by the range of values in
- the annotation row.</li>
- </ul>
- <p align="center">
- <img src="annotationColours.gif" width="582" height="464">
- </p>
+ <li>Select whether to colour the alignment above or below an
+ adjustable threshold with the selection box center left of the
+ window.</li>
+ <li>Change the threshold value with the slider, or enter the
+ exact value in the text box.</li>
+ <li>Select the "Threshold is Min/Max" checkbox to
+ assign colours using the thresholded range's minimum and maximum
+ values, otherwise the scale will be defined by the range of values
+ in the annotation row.</li>
+ </ul>
+ <p align="center">
+ <img src="annotationColours.gif" width="582" height="464">
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Blosum Colour Scheme</title>
+<head>
+<title>Blosum Colour Scheme</title>
<style type="text/css">
<!--
td {
<body>
-<p><strong>Blosum62</a></strong> </p>
-<p>Gaps are coloured white. If a residue matches the consensus sequence residue
- at that position it is coloured dark blue. If it does not match the consensus
- residue but the 2 residues have a positive Blosum62 score, it is coloured light
- blue.</p>
+ <p>
+ <strong>Blosum62</a></strong>
+ </p>
+ <p>Gaps are coloured white. If a residue matches the consensus
+ sequence residue at that position it is coloured dark blue. If it
+ does not match the consensus residue but the 2 residues have a
+ positive Blosum62 score, it is coloured light blue.</p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Buried Colour Scheme</title>
+<head>
+<title>Buried Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Buried index</strong></p>
-<div align="center">
- <table width="400" border="1">
- <tr>
- <td bgcolor="#0000ff">C</td>
- <td bgcolor="#0054ab">I</td>
- <td bgcolor="#005fa0">V</td>
- <td bgcolor="#007b84">L</td>
- <td bgcolor="#008778">F</td>
- </tr>
- <tr>
- <td bgcolor="#009768">M</td>
- <td bgcolor="#009d62">G</td>
- <td bgcolor="#00a35c">A</td>
- <td bgcolor="#00a857">W</td>
- <td bgcolor="#00b649">X</td>
- </tr>
- <tr>
- <td bgcolor="#00d52a">S</td>
- <td bgcolor="#00d52a">H</td>
- <td bgcolor="#00db24">T</td>
- <td bgcolor="#00e01f">P</td>
- <td bgcolor="#00e619">Y</td>
- </tr>
- <tr>
- <td bgcolor="#00eb14">N</td>
- <td bgcolor="#00eb14">B</td>
- <td bgcolor="#00eb14">D</td>
- <td bgcolor="#00f10e">Q</td>
- <td bgcolor="#00f10e">Z</td>
- </tr>
- <tr> </td>
- <td bgcolor="#00f10e">E</td>
- <td bgcolor="#00fc03">R</td>
- <td bgcolor="#00ff00">K</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Buried index</strong>
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+ <tr>
+ <td bgcolor="#0000ff">C</td>
+ <td bgcolor="#0054ab">I</td>
+ <td bgcolor="#005fa0">V</td>
+ <td bgcolor="#007b84">L</td>
+ <td bgcolor="#008778">F</td>
+ </tr>
+ <tr>
+ <td bgcolor="#009768">M</td>
+ <td bgcolor="#009d62">G</td>
+ <td bgcolor="#00a35c">A</td>
+ <td bgcolor="#00a857">W</td>
+ <td bgcolor="#00b649">X</td>
+ </tr>
+ <tr>
+ <td bgcolor="#00d52a">S</td>
+ <td bgcolor="#00d52a">H</td>
+ <td bgcolor="#00db24">T</td>
+ <td bgcolor="#00e01f">P</td>
+ <td bgcolor="#00e619">Y</td>
+ </tr>
+ <tr>
+ <td bgcolor="#00eb14">N</td>
+ <td bgcolor="#00eb14">B</td>
+ <td bgcolor="#00eb14">D</td>
+ <td bgcolor="#00f10e">Q</td>
+ <td bgcolor="#00f10e">Z</td>
+ </tr>
+ <tr>
+ </td>
+ <td bgcolor="#00f10e">E</td>
+ <td bgcolor="#00fc03">R</td>
+ <td bgcolor="#00ff00">K</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Clustal Colour Scheme</title>
+<head>
+<title>Clustal Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Clustal X Colour Scheme</strong></p>
- <p>This is an emulation of the default colourscheme used for alignments in
- Clustal X, a graphical interface for the ClustalW multiple sequence alignment
- program. Each residue in the alignment is assigned a colour if the
- amino acid profile of the alignment at that position
- meets some minimum criteria specific for the residue type.</p>
- <p>The table below gives these criteria as clauses: {+X%,xx,y},
- where X is the minimum percentage presence for any of the xx (or y) residue types.</p>
-<div align="center">
- <p> </p><table border="1">
-<tr><th>Clustal X Default Colouring</th></tr>
- <tr>
- <td><table border="1">
-<tr><th>Residue at position</th><th>Applied Colour</th><th>{ Threshhold, Residue group }</th></tr>
-<tr><td>A,I,L,M,F,W,V</td><td bgcolor="#80a0f0">BLUE</td><td>{+60%, WLVIMAFCHP}</td></tr>
-<tr><td>R,K</td><td bgcolor="#f01505">RED</td><td>{+60%,KR},{+80%, K,R,Q}</td></tr>
-<tr><td>N</td><td bgcolor="#15c015">GREEN</td><td>{+50%, N}, {+85%, N,Y}</td></tr>
-<tr><td>C</td><td bgcolor="#80a0f0">BLUE</td>
-<td>{+60%, WLVIMAFCHP}</td></tr>
-<tr><td>C</td><td bgcolor="#f08080">PINK</td>
-<td>{100%, C}</td></tr>
-<tr><td>Q</td><td bgcolor="#15c015">GREEN</td><td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td></tr>
-<tr><td>E</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td></tr>
-<tr><td>D</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td></tr>
-<tr><td>G</td><td bgcolor="#f09048">ORANGE</td><td>{+0%, G}</td></tr>
-<tr><td>H,Y</td><td bgcolor="#15a4a4">CYAN</td><td>{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}</td></tr>
-<tr><td>P</td><td bgcolor="#c0c000">YELLOW</td><td>{+0%, P}</td></tr>
-<tr><td>S,T</td><td bgcolor="#15c015">GREEN</td><td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td></tr>
-</table>
-</td></tr></table>
-</div>
+ <p>
+ <strong>Clustal X Colour Scheme</strong>
+ </p>
+ <p>This is an emulation of the default colourscheme used for
+ alignments in Clustal X, a graphical interface for the ClustalW
+ multiple sequence alignment program. Each residue in the alignment
+ is assigned a colour if the amino acid profile of the alignment at
+ that position meets some minimum criteria specific for the residue
+ type.</p>
+ <p>The table below gives these criteria as clauses: {+X%,xx,y},
+ where X is the minimum percentage presence for any of the xx (or y)
+ residue types.</p>
+ <div align="center">
+ <p> </p>
+ <table border="1">
+ <tr>
+ <th>Clustal X Default Colouring</th>
+ </tr>
+ <tr>
+ <td><table border="1">
+ <tr>
+ <th>Residue at position</th>
+ <th>Applied Colour</th>
+ <th>{ Threshhold, Residue group }</th>
+ </tr>
+ <tr>
+ <td>A,I,L,M,F,W,V</td>
+ <td bgcolor="#80a0f0">BLUE</td>
+ <td>{+60%, WLVIMAFCHP}</td>
+ </tr>
+ <tr>
+ <td>R,K</td>
+ <td bgcolor="#f01505">RED</td>
+ <td>{+60%,KR},{+80%, K,R,Q}</td>
+ </tr>
+ <tr>
+ <td>N</td>
+ <td bgcolor="#15c015">GREEN</td>
+ <td>{+50%, N}, {+85%, N,Y}</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td bgcolor="#80a0f0">BLUE</td>
+ <td>{+60%, WLVIMAFCHP}</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td bgcolor="#f08080">PINK</td>
+ <td>{100%, C}</td>
+ </tr>
+ <tr>
+ <td>Q</td>
+ <td bgcolor="#15c015">GREEN</td>
+ <td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td>
+ </tr>
+ <tr>
+ <td>E</td>
+ <td bgcolor="#c048c0">MAGENTA</td>
+ <td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td bgcolor="#c048c0">MAGENTA</td>
+ <td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td>
+ </tr>
+ <tr>
+ <td>G</td>
+ <td bgcolor="#f09048">ORANGE</td>
+ <td>{+0%, G}</td>
+ </tr>
+ <tr>
+ <td>H,Y</td>
+ <td bgcolor="#15a4a4">CYAN</td>
+ <td>{+60%, WLVIMAFCHP}, {+85%,
+ W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
+ </tr>
+ <tr>
+ <td>P</td>
+ <td bgcolor="#c0c000">YELLOW</td>
+ <td>{+0%, P}</td>
+ </tr>
+ <tr>
+ <td>S,T</td>
+ <td bgcolor="#15c015">GREEN</td>
+ <td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Colouring by Conservation</title></head>
+<head>
+<title>Colouring by Conservation</title>
+</head>
<body>
-<p><strong>Colouring by Conservation</strong></p>
-<p>This is an approach to alignment colouring which highlights
- regions of an alignment where physicochemical properties are
- conserved. It is based on the one used in
- the AMAS method of multiple sequence alignment analysis (Livingstone
- C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
- for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9
- No. 6 (745-756)). See the <a href="../calculations/conservation.html">conservation calculation</a> help page for
- a more thorough explanation of the calculation.
-</p>
-<p>For an already coloured alignment, the conservation index at each
- alignment position is used to modify the shading intensity of the
- colour at that position. This means that the most conserved columns
- in each group have the most intense colours, and the least conserved
- are the palest. The slider controls the contrast between these
- extremes.</p>
-<p>Conservation can be calculated over all sequences in an alignment, or just
- within specific groups (such as those defined by
- <a href="../calculations/tree.html">phylogenetic tree partitioning</a>).
- The option 'apply to all groups' controls whether the contrast
- slider value will be applied to the indices for the currently
- selected group, or all groups defined over the alignment.</p>
+ <p>
+ <strong>Colouring by Conservation</strong>
+ </p>
+ <p>
+ This is an approach to alignment colouring which highlights regions
+ of an alignment where physicochemical properties are conserved. It
+ is based on the one used in the AMAS method of multiple sequence
+ alignment analysis (Livingstone C.D. and Barton G.J. (1993), Protein
+ Sequence Alignments: A Strategy for the Hierarchical Analysis of
+ Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). See the <a
+ href="../calculations/conservation.html"
+ >conservation calculation</a> help page for a more thorough
+ explanation of the calculation.
+ </p>
+ <p>For an already coloured alignment, the conservation index at
+ each alignment position is used to modify the shading intensity of
+ the colour at that position. This means that the most conserved
+ columns in each group have the most intense colours, and the least
+ conserved are the palest. The slider controls the contrast between
+ these extremes.</p>
+ <p>
+ Conservation can be calculated over all sequences in an alignment,
+ or just within specific groups (such as those defined by <a
+ href="../calculations/tree.html"
+ >phylogenetic tree partitioning</a>). The option 'apply to all groups'
+ controls whether the contrast slider value will be applied to the
+ indices for the currently selected group, or all groups defined over
+ the alignment.
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Helix Colour Scheme</title>
+<head>
+<title>Helix Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Helix Propensity</strong> </p>
-<div align="center">
- <table width="400" border="1">
- <tr>
- <td bgcolor="#ff00ff">E</td>
- <td bgcolor="#ef10ef">M</td>
- <td bgcolor="#e718e7">A</td>
- <td bgcolor="#c936c9">Z</td>
- <td bgcolor="#ae51ae">L</td>
- </tr>
- <tr>
- <td bgcolor="#a05fa0">K</td>
- <td bgcolor="#986798">F</td>
- <td bgcolor="#926d92">Q</td>
- <td bgcolor="#8a758a">I</td>
- <td bgcolor="#8a758a">W</td>
- </tr>
- <tr>
- <td bgcolor="#857a85">V</td>
- <td bgcolor="#778877">D</td>
- <td bgcolor="#758a75">X</td>
- <td bgcolor="#758a75">H</td>
- <td bgcolor="#6f906f">R</td>
- </tr>
- <tr>
- <td bgcolor="#49b649">B</td>
- <td bgcolor="#47b847">T</td>
- <td bgcolor="#36c936">S</td>
- <td bgcolor="#23dc23">C</td>
- <td bgcolor="#21de21">Y</td>
- </tr>
- <tr> </td>
- <td bgcolor="#1be41b">N</td>
- <td bgcolor="#00ff00">G</td>
- <td bgcolor="#00ff00">P</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Helix Propensity</strong>
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+ <tr>
+ <td bgcolor="#ff00ff">E</td>
+ <td bgcolor="#ef10ef">M</td>
+ <td bgcolor="#e718e7">A</td>
+ <td bgcolor="#c936c9">Z</td>
+ <td bgcolor="#ae51ae">L</td>
+ </tr>
+ <tr>
+ <td bgcolor="#a05fa0">K</td>
+ <td bgcolor="#986798">F</td>
+ <td bgcolor="#926d92">Q</td>
+ <td bgcolor="#8a758a">I</td>
+ <td bgcolor="#8a758a">W</td>
+ </tr>
+ <tr>
+ <td bgcolor="#857a85">V</td>
+ <td bgcolor="#778877">D</td>
+ <td bgcolor="#758a75">X</td>
+ <td bgcolor="#758a75">H</td>
+ <td bgcolor="#6f906f">R</td>
+ </tr>
+ <tr>
+ <td bgcolor="#49b649">B</td>
+ <td bgcolor="#47b847">T</td>
+ <td bgcolor="#36c936">S</td>
+ <td bgcolor="#23dc23">C</td>
+ <td bgcolor="#21de21">Y</td>
+ </tr>
+ <tr>
+ </td>
+ <td bgcolor="#1be41b">N</td>
+ <td bgcolor="#00ff00">G</td>
+ <td bgcolor="#00ff00">P</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Hydrophobic Colour Scheme</title>
+<head>
+<title>Hydrophobic Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Hydrophobicity</strong></p>
-<p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J.
- Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this
- table are coloured red and the most hydrophilic ones are coloured blue.</p>
-<div align="center">
- <table width="400" border="1">
- <tr>
- <td bgcolor="#ff0000">I</td>
- <td bgcolor="#f60009">V</td>
- <td bgcolor="#ea0015">L</td>
- <td bgcolor="#cb0034">F</td>
- <td bgcolor="#c2003d">C</td>
- </tr>
- <tr>
- <td bgcolor="#b0004f">M</td>
- <td bgcolor="#ad0052">A</td>
- <td bgcolor="#6a0095">G</td>
- <td bgcolor="#680097">X</td>
- <td bgcolor="#61009e">T</td>
- </tr>
- <tr>
- <td bgcolor="#5e00a1">S</td>
- <td bgcolor="#5b00a4">W</td>
- <td bgcolor="#4f00b0">Y</td>
- <td bgcolor="#4600b9">P</td>
- <td bgcolor="#1500ea">H</td>
- </tr>
- <tr>
- <td bgcolor="#0c00f3">E</td>
- <td bgcolor="#0c00f3">Z</td>
- <td bgcolor="#0c00f3">Q</td>
- <td bgcolor="#0c00f3">D</td>
- <td bgcolor="#0c00f3">B</td>
- </tr>
- <tr> </td>
- <td bgcolor="#0c00f3">N</td>
- <td bgcolor="#0000ff">K</td>
- <td bgcolor="#0000ff">R</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Hydrophobicity</strong>
+ </p>
+ <p>According to the hydrophobicity table of Kyte, J., and
+ Doolittle, R.F., J. Mol. Biol. 1157, 105-132, 1982. The most
+ hydrophobic residues according to this table are coloured red and
+ the most hydrophilic ones are coloured blue.</p>
+ <div align="center">
+ <table width="400" border="1">
+ <tr>
+ <td bgcolor="#ff0000">I</td>
+ <td bgcolor="#f60009">V</td>
+ <td bgcolor="#ea0015">L</td>
+ <td bgcolor="#cb0034">F</td>
+ <td bgcolor="#c2003d">C</td>
+ </tr>
+ <tr>
+ <td bgcolor="#b0004f">M</td>
+ <td bgcolor="#ad0052">A</td>
+ <td bgcolor="#6a0095">G</td>
+ <td bgcolor="#680097">X</td>
+ <td bgcolor="#61009e">T</td>
+ </tr>
+ <tr>
+ <td bgcolor="#5e00a1">S</td>
+ <td bgcolor="#5b00a4">W</td>
+ <td bgcolor="#4f00b0">Y</td>
+ <td bgcolor="#4600b9">P</td>
+ <td bgcolor="#1500ea">H</td>
+ </tr>
+ <tr>
+ <td bgcolor="#0c00f3">E</td>
+ <td bgcolor="#0c00f3">Z</td>
+ <td bgcolor="#0c00f3">Q</td>
+ <td bgcolor="#0c00f3">D</td>
+ <td bgcolor="#0c00f3">B</td>
+ </tr>
+ <tr>
+ </td>
+ <td bgcolor="#0c00f3">N</td>
+ <td bgcolor="#0000ff">K</td>
+ <td bgcolor="#0000ff">R</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
</style>
</head>
<body>
-<p><strong>Colour schemes</strong></p>
-<p>Jalview allows the user to set a background colour for the whole
-alignment view or for each group defined on regions within it.</p>
-<p>To change the background colour, simply select the colour from
-the "Colour" menu.</p>
-<p>To change the colour of a group, right click on any residue
-within a group and use the popup menu to define the group colour.</p>
-<p>At the top of the "Colour" menu the tick box
-"Apply Background Colour to all groups". This is ticked by
-default so that a chosen colour scheme will be applied to all existing
-groups. If you wish to maintain the colour scheme for defined groups,
-make sure you deselect this option before changing the background
-colour.</p>
-<p>The <strong>"Colour→<a
- href="../colourSchemes/textcolour.html">Colour Text...</a>"</strong> entry
-opens a dialog box to set a different text colour for light and dark
-background, and the intensity threshold for transition between them.</p>
-<p>The default colour schemes are summarised in the table below:
-<div align="center">
-<p> </p>
-<p><strong>Protein Colour Schemes</strong></p>
-<table border="1">
- <tr>
- <td>
- <table border="1">
- <tr>
- <td nowrap></td>
- <td>A</td>
- <td>R</td>
- <td>N</td>
- <td>D</td>
- <td>C</td>
- <td>Q</td>
- <td>E</td>
- <td>G</td>
- <td>H</td>
- <td>I</td>
- <td>L</td>
- <td>K</td>
- <td>M</td>
- <td>F</td>
- <td>P</td>
- <td>S</td>
- <td>T</td>
- <td>W</td>
- <td>Y</td>
- <td>V</td>
- <td>B</td>
- <td>X</td>
- <td>Z</td>
- </tr>
- <tr>
- <td height="24">Clustal</td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#f01505"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#c048c0"></td>
- <td bgcolor="#f08080"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#c048c0"></td>
- <td bgcolor="#f09048"></td>
- <td bgcolor="#15a4a4"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#f01505"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#80a0f0"></td>
- <td bgcolor="#15a4a4"></td>
- <td bgcolor="#80a0f0"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td height="24">Zappo</td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#6464ff"></td>
- <td bgcolor="#ffafaf"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ffc800"></td>
- <td bgcolor="#ffafaf"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td>Taylor</td>
- <td bgcolor="#ccff00"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#cc00ff"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#ff00cc"></td>
- <td bgcolor="#ff0066"></td>
- <td bgcolor="#ff9900"></td>
- <td bgcolor="#0066ff"></td>
- <td bgcolor="#66ff00"></td>
- <td bgcolor="#33ff00"></td>
- <td bgcolor="#6600ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#00ff66"></td>
- <td bgcolor="#ffcc00"></td>
- <td bgcolor="#ff3300"></td>
- <td bgcolor="#ff6600"></td>
- <td bgcolor="#00ccff"></td>
- <td bgcolor="#00ffcc"></td>
- <td bgcolor="#99ff00"></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td>Hydrophobicity</td>
- <td bgcolor="#ad0052"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#c2003d"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#6a0095"></td>
- <td bgcolor="#1500ea"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#ea0015"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#b0004f"></td>
- <td bgcolor="#cb0034"></td>
- <td bgcolor="#4600b9"></td>
- <td bgcolor="#5e00a1"></td>
- <td bgcolor="#61009e"></td>
- <td bgcolor="#5b00a4"></td>
- <td bgcolor="#4f00b0"></td>
- <td bgcolor="#f60009"></td>
- <td bgcolor="#0c00f3"></td>
- <td bgcolor="#680097"></td>
- <td bgcolor="#0c00f3"></td>
- </tr>
- <tr>
- <td>Helix Propensity</td>
- <td bgcolor="#e718e7"></td>
- <td bgcolor="#6f906f"></td>
- <td bgcolor="#1be41b"></td>
- <td bgcolor="#778877"></td>
- <td bgcolor="#23dc23"></td>
- <td bgcolor="#926d92"></td>
- <td bgcolor="#ff00ff"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#758a75"></td>
- <td bgcolor="#8a758a"></td>
- <td bgcolor="#ae51ae"></td>
- <td bgcolor="#a05fa0"></td>
- <td bgcolor="#ef10ef"></td>
- <td bgcolor="#986798"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#36c936"></td>
- <td bgcolor="#47b847"></td>
- <td bgcolor="#8a758a"></td>
- <td bgcolor="#21de21"></td>
- <td bgcolor="#857a85"></td>
- <td bgcolor="#49b649"></td>
- <td bgcolor="#758a75"></td>
- <td bgcolor="#c936c9"></td>
- </tr>
- <tr>
- <td nowrap>Strand Propensity</td>
- <td bgcolor="#5858a7"></td>
- <td bgcolor="#6b6b94"></td>
- <td bgcolor="#64649b"></td>
- <td bgcolor="#2121de"></td>
- <td bgcolor="#9d9d62"></td>
- <td bgcolor="#8c8c73"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#4949b6"></td>
- <td bgcolor="#60609f"></td>
- <td bgcolor="#ecec13"></td>
- <td bgcolor="#b2b24d"></td>
- <td bgcolor="#4747b8"></td>
- <td bgcolor="#82827d"></td>
- <td bgcolor="#c2c23d"></td>
- <td bgcolor="#2323dc"></td>
- <td bgcolor="#4949b6"></td>
- <td bgcolor="#9d9d62"></td>
- <td bgcolor="#c0c03f"></td>
- <td bgcolor="#d3d32c"></td>
- <td bgcolor="#ffff00"></td>
- <td bgcolor="#4343bc"></td>
- <td bgcolor="#797986"></td>
- <td bgcolor="#4747b8"></td>
- </tr>
- <tr>
- <td>Turn Propensity</td>
- <td bgcolor="#2cd3d3"></td>
- <td bgcolor="#708f8f"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#e81717"></td>
- <td bgcolor="#a85757"></td>
- <td bgcolor="#3fc0c0"></td>
- <td bgcolor="#778888"></td>
- <td bgcolor="#ff0000"></td>
- <td bgcolor="#708f8f"></td>
- <td bgcolor="#00ffff"></td>
- <td bgcolor="#1ce3e3"></td>
- <td bgcolor="#7e8181"></td>
- <td bgcolor="#1ee1e1"></td>
- <td bgcolor="#1ee1e1"></td>
- <td bgcolor="#f60909"></td>
- <td bgcolor="#e11e1e"></td>
- <td bgcolor="#738c8c"></td>
- <td bgcolor="#738c8c"></td>
- <td bgcolor="#9d6262"></td>
- <td bgcolor="#07f8f8"></td>
- <td bgcolor="#f30c0c"></td>
- <td bgcolor="#7c8383"></td>
- <td bgcolor="#5ba4a4"></td>
- </tr>
- <tr>
- <td>Buried Index</td>
- <td bgcolor="#00a35c"></td>
- <td bgcolor="#00fc03"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#0000ff"></td>
- <td bgcolor="#00f10e"></td>
- <td bgcolor="#00f10e"></td>
- <td bgcolor="#009d62"></td>
- <td bgcolor="#00d52a"></td>
- <td bgcolor="#0054ab"></td>
- <td bgcolor="#007b84"></td>
- <td bgcolor="#00ff00"></td>
- <td bgcolor="#009768"></td>
- <td bgcolor="#008778"></td>
- <td bgcolor="#00e01f"></td>
- <td bgcolor="#00d52a"></td>
- <td bgcolor="#00db24"></td>
- <td bgcolor="#00a857"></td>
- <td bgcolor="#00e619"></td>
- <td bgcolor="#005fa0"></td>
- <td bgcolor="#00eb14"></td>
- <td bgcolor="#00b649"></td>
- <td bgcolor="#00f10e"></td>
- </tr>
- </table>
- </td>
- </tr>
-</table>
-<p> </p>
-<p><strong>Nucleotide Colour Schemes</strong></p>
-<table border="1">
- <tr>
- <td>
- <table border="1">
- <tr>
- <td nowrap></td>
- <td>A</td> <!--Adenine-->
- <td>C</td> <!--Cytosine-->
- <td>G</td> <!--Guanine-->
- <td>T</td> <!--Thymine-->
- <td>U</td> <!--Uracil-->
- <td>I</td> <!--Inosine-->
- <td>X</td> <!--Xanthine-->
- <td>R</td> <!--Unknown Purine-->
- <td>Y</td> <!--Unknown Pyrimidine-->
- <td>N</td> <!--Unknown-->
- <td>W</td> <!--Weak nucleotide (A or T)-->
- <td>S</td> <!--Strong nucleotide (G or C)-->
- <td>M</td> <!--Amino (A or C)-->
- <td>K</td> <!--Keto (G or T)-->
- <td>B</td> <!--Not A (G or C or T)-->
- <td>H</td> <!--Not G (A or C or T)-->
- <td>D</td> <!--Not C (A or G or T)-->
- <td>V</td> <!--Not T (A or G or C-->
- </tr>
- <tr>
- <td height="24">Nucleotide</td>
- <td bgcolor="#64F73F"></td>
- <td bgcolor="#FFB340"></td>
- <td bgcolor="#EB413C"></td>
- <td bgcolor="#3C88EE"></td>
- <td bgcolor="#3C88EE"></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- <tr>
- <td height="24">Purine/Pyrimidine</td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td bgcolor="#40E0D0"></td>
- <td></td>
- <td></td>
- <td bgcolor="#FF83FA"></td>
- <td bgcolor="#40E0D0"></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- <td></td>
- </tr>
- </table>
- </td>
- </tr>
-</table>
+ <p>
+ <strong>Colour schemes</strong>
+ </p>
+ <p>Jalview allows the user to set a background colour for the
+ whole alignment view or for each group defined on regions within it.</p>
+ <p>To change the background colour, simply select the colour from
+ the "Colour" menu.</p>
+ <p>To change the colour of a group, right click on any residue
+ within a group and use the popup menu to define the group colour.</p>
+ <p>At the top of the "Colour" menu the tick box
+ "Apply Background Colour to all groups". This is ticked by
+ default so that a chosen colour scheme will be applied to all
+ existing groups. If you wish to maintain the colour scheme for
+ defined groups, make sure you deselect this option before changing
+ the background colour.</p>
+ <p>
+ The <strong>"Colour→<a
+ href="../colourSchemes/textcolour.html"
+ >Colour Text...</a>"
+ </strong> entry opens a dialog box to set a different text colour for light
+ and dark background, and the intensity threshold for transition
+ between them.
+ </p>
+ <p>The default colour schemes are summarised in the table below:
+ <div align="center">
+ <p> </p>
+ <p>
+ <strong>Protein Colour Schemes</strong>
+ </p>
+ <table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td>
+ <td>R</td>
+ <td>N</td>
+ <td>D</td>
+ <td>C</td>
+ <td>Q</td>
+ <td>E</td>
+ <td>G</td>
+ <td>H</td>
+ <td>I</td>
+ <td>L</td>
+ <td>K</td>
+ <td>M</td>
+ <td>F</td>
+ <td>P</td>
+ <td>S</td>
+ <td>T</td>
+ <td>W</td>
+ <td>Y</td>
+ <td>V</td>
+ <td>B</td>
+ <td>X</td>
+ <td>Z</td>
+ </tr>
+ <tr>
+ <td height="24">Clustal</td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f08080"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#c048c0"></td>
+ <td bgcolor="#f09048"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#f01505"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td bgcolor="#15a4a4"></td>
+ <td bgcolor="#80a0f0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Zappo</td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#6464ff"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffc800"></td>
+ <td bgcolor="#ffafaf"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Taylor</td>
+ <td bgcolor="#ccff00"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#cc00ff"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#ff00cc"></td>
+ <td bgcolor="#ff0066"></td>
+ <td bgcolor="#ff9900"></td>
+ <td bgcolor="#0066ff"></td>
+ <td bgcolor="#66ff00"></td>
+ <td bgcolor="#33ff00"></td>
+ <td bgcolor="#6600ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#00ff66"></td>
+ <td bgcolor="#ffcc00"></td>
+ <td bgcolor="#ff3300"></td>
+ <td bgcolor="#ff6600"></td>
+ <td bgcolor="#00ccff"></td>
+ <td bgcolor="#00ffcc"></td>
+ <td bgcolor="#99ff00"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>Hydrophobicity</td>
+ <td bgcolor="#ad0052"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#c2003d"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#6a0095"></td>
+ <td bgcolor="#1500ea"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#ea0015"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#b0004f"></td>
+ <td bgcolor="#cb0034"></td>
+ <td bgcolor="#4600b9"></td>
+ <td bgcolor="#5e00a1"></td>
+ <td bgcolor="#61009e"></td>
+ <td bgcolor="#5b00a4"></td>
+ <td bgcolor="#4f00b0"></td>
+ <td bgcolor="#f60009"></td>
+ <td bgcolor="#0c00f3"></td>
+ <td bgcolor="#680097"></td>
+ <td bgcolor="#0c00f3"></td>
+ </tr>
+ <tr>
+ <td>Helix Propensity</td>
+ <td bgcolor="#e718e7"></td>
+ <td bgcolor="#6f906f"></td>
+ <td bgcolor="#1be41b"></td>
+ <td bgcolor="#778877"></td>
+ <td bgcolor="#23dc23"></td>
+ <td bgcolor="#926d92"></td>
+ <td bgcolor="#ff00ff"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#ae51ae"></td>
+ <td bgcolor="#a05fa0"></td>
+ <td bgcolor="#ef10ef"></td>
+ <td bgcolor="#986798"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#36c936"></td>
+ <td bgcolor="#47b847"></td>
+ <td bgcolor="#8a758a"></td>
+ <td bgcolor="#21de21"></td>
+ <td bgcolor="#857a85"></td>
+ <td bgcolor="#49b649"></td>
+ <td bgcolor="#758a75"></td>
+ <td bgcolor="#c936c9"></td>
+ </tr>
+ <tr>
+ <td nowrap>Strand Propensity</td>
+ <td bgcolor="#5858a7"></td>
+ <td bgcolor="#6b6b94"></td>
+ <td bgcolor="#64649b"></td>
+ <td bgcolor="#2121de"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#8c8c73"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#60609f"></td>
+ <td bgcolor="#ecec13"></td>
+ <td bgcolor="#b2b24d"></td>
+ <td bgcolor="#4747b8"></td>
+ <td bgcolor="#82827d"></td>
+ <td bgcolor="#c2c23d"></td>
+ <td bgcolor="#2323dc"></td>
+ <td bgcolor="#4949b6"></td>
+ <td bgcolor="#9d9d62"></td>
+ <td bgcolor="#c0c03f"></td>
+ <td bgcolor="#d3d32c"></td>
+ <td bgcolor="#ffff00"></td>
+ <td bgcolor="#4343bc"></td>
+ <td bgcolor="#797986"></td>
+ <td bgcolor="#4747b8"></td>
+ </tr>
+ <tr>
+ <td>Turn Propensity</td>
+ <td bgcolor="#2cd3d3"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#e81717"></td>
+ <td bgcolor="#a85757"></td>
+ <td bgcolor="#3fc0c0"></td>
+ <td bgcolor="#778888"></td>
+ <td bgcolor="#ff0000"></td>
+ <td bgcolor="#708f8f"></td>
+ <td bgcolor="#00ffff"></td>
+ <td bgcolor="#1ce3e3"></td>
+ <td bgcolor="#7e8181"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#1ee1e1"></td>
+ <td bgcolor="#f60909"></td>
+ <td bgcolor="#e11e1e"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#738c8c"></td>
+ <td bgcolor="#9d6262"></td>
+ <td bgcolor="#07f8f8"></td>
+ <td bgcolor="#f30c0c"></td>
+ <td bgcolor="#7c8383"></td>
+ <td bgcolor="#5ba4a4"></td>
+ </tr>
+ <tr>
+ <td>Buried Index</td>
+ <td bgcolor="#00a35c"></td>
+ <td bgcolor="#00fc03"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#0000ff"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#00f10e"></td>
+ <td bgcolor="#009d62"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#0054ab"></td>
+ <td bgcolor="#007b84"></td>
+ <td bgcolor="#00ff00"></td>
+ <td bgcolor="#009768"></td>
+ <td bgcolor="#008778"></td>
+ <td bgcolor="#00e01f"></td>
+ <td bgcolor="#00d52a"></td>
+ <td bgcolor="#00db24"></td>
+ <td bgcolor="#00a857"></td>
+ <td bgcolor="#00e619"></td>
+ <td bgcolor="#005fa0"></td>
+ <td bgcolor="#00eb14"></td>
+ <td bgcolor="#00b649"></td>
+ <td bgcolor="#00f10e"></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ <p> </p>
+ <p>
+ <strong>Nucleotide Colour Schemes</strong>
+ </p>
+ <table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td>
+ <!--Adenine-->
+ <td>C</td>
+ <!--Cytosine-->
+ <td>G</td>
+ <!--Guanine-->
+ <td>T</td>
+ <!--Thymine-->
+ <td>U</td>
+ <!--Uracil-->
+ <td>I</td>
+ <!--Inosine-->
+ <td>X</td>
+ <!--Xanthine-->
+ <td>R</td>
+ <!--Unknown Purine-->
+ <td>Y</td>
+ <!--Unknown Pyrimidine-->
+ <td>N</td>
+ <!--Unknown-->
+ <td>W</td>
+ <!--Weak nucleotide (A or T)-->
+ <td>S</td>
+ <!--Strong nucleotide (G or C)-->
+ <td>M</td>
+ <!--Amino (A or C)-->
+ <td>K</td>
+ <!--Keto (G or T)-->
+ <td>B</td>
+ <!--Not A (G or C or T)-->
+ <td>H</td>
+ <!--Not G (A or C or T)-->
+ <td>D</td>
+ <!--Not C (A or G or T)-->
+ <td>V</td>
+ <!--Not T (A or G or C-->
+ </tr>
+ <tr>
+ <td height="24">Nucleotide</td>
+ <td bgcolor="#64F73F"></td>
+ <td bgcolor="#FFB340"></td>
+ <td bgcolor="#EB413C"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Purine/Pyrimidine</td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
-</div>
-<p align="center"> </p>
+ </div>
+ <p align="center"> </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Nucleotide Colour Scheme</title>
+<head>
+<title>Nucleotide Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Nucleotide Colours</strong></p>
-<div align="center">
- <table width="200" border="1">
- <tr>
- <td bgcolor="#64F73F">A</td>
- <td bgcolor="#FFB340">C</td>
- <td bgcolor="#EB413C">G</td>
- <td bgcolor="#3C88EE">T</td>
- <td bgcolor="#3C88EE">U</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Nucleotide Colours</strong>
+ </p>
+ <div align="center">
+ <table width="200" border="1">
+ <tr>
+ <td bgcolor="#64F73F">A</td>
+ <td bgcolor="#FFB340">C</td>
+ <td bgcolor="#EB413C">G</td>
+ <td bgcolor="#3C88EE">T</td>
+ <td bgcolor="#3C88EE">U</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Percentage Identity Colour Scheme</title>
+<head>
+<title>Percentage Identity Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>PID Colours</strong><br>
- <br>
- The PID option colours the residues (boxes and/or text) according to the percentage
- of the residues in each column that agree with the consensus sequence. Only
- the residues that agree with the consensus residue for each column are coloured.</p>
-<div align="center">
-<table width="200" border="1">
- <tr>
- <td bgcolor="#6464FF">> 80 %</td>
- </tr>
- <tr>
- <td bgcolor="#9999FF">> 60 %</td>
- </tr>
- <tr>
- <td bgcolor="#CCCCFF">> 40%</td>
- </tr>
- <tr>
- <td>< 40%</td>
- </tr>
-</table>
-</div>
+ <p>
+ <strong>PID Colours</strong><br> <br> The PID option
+ colours the residues (boxes and/or text) according to the percentage
+ of the residues in each column that agree with the consensus
+ sequence. Only the residues that agree with the consensus residue
+ for each column are coloured.
+ </p>
+ <div align="center">
+ <table width="200" border="1">
+ <tr>
+ <td bgcolor="#6464FF">> 80 %</td>
+ </tr>
+ <tr>
+ <td bgcolor="#9999FF">> 60 %</td>
+ </tr>
+ <tr>
+ <td bgcolor="#CCCCFF">> 40%</td>
+ </tr>
+ <tr>
+ <td>< 40%</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Purine/Pyrimidine Colour Scheme</title>
+<head>
+<title>Purine/Pyrimidine Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Purine/Pyrimidine Colours</strong></p>
-<div align="center">
- <table width="200" border="1">
- <tr>
- <td bgcolor="#FF83FA">Purines <BR> A, G, R</td>
- <td bgcolor="#40E0D0">Pyrimidines <BR> C, U, T, Y</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Purine/Pyrimidine Colours</strong>
+ </p>
+ <div align="center">
+ <table width="200" border="1">
+ <tr>
+ <td bgcolor="#FF83FA">Purines <BR> A, G, R
+ </td>
+ <td bgcolor="#40E0D0">Pyrimidines <BR> C, U, T, Y
+ </td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>RNA Helices Colouring</title></head>
+<head>
+<title>RNA Helices Colouring</title>
+</head>
<body>
-<p><strong> RNA Helices Colouring </strong></p>
-<p>An RNA alignment loaded from a Stockholm file can be coloured
- based on its helices. The helices are determined from the
- secondary structure line in the Stockholm file (#GC SS_cons)
- written in WUSS notation
- that specifies base pairing. See <a href="http://en.wikipedia.org/wiki/Stockholm_format">
- Wikipedia</a> or <a href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html">
- Jalview RNA Support Blog</a> for more information about Stockholm files and WUSS notation.</p>
-Select "Colour" <strong>→</strong> "
- By RNA Helices" to colour the alignment by RNA helices. <br>
+ <p>
+ <strong> RNA Helices Colouring </strong>
+ </p>
+ <p>
+ An RNA alignment loaded from a Stockholm file can be coloured based
+ on its helices. The helices are determined from the secondary
+ structure line in the Stockholm file (#GC SS_cons) written in WUSS
+ notation that specifies base pairing. See <a
+ href="http://en.wikipedia.org/wiki/Stockholm_format"
+ > Wikipedia</a> or <a
+ href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html"
+ > Jalview RNA Support Blog</a> for more information about Stockholm
+ files and WUSS notation.
+ </p>
+ Select "Colour"
+ <strong>→</strong> " By RNA Helices" to colour the
+ alignment by RNA helices.
<br>
-<p><em>Features</em></p>
-<ul>
-<li>Colours are generated randomly for the number of helices present.
-Reselect the "By RNA Helices" option to generate another set of random colors. </li>
-<li>Sequence logo is in <a href="purinepyrimidine.html">
-Purine/Pyrimidine colour scheme</a>. </li>
-<li>Line above the "Secondary Structure" line in annotation panel is WUSS notation present
-in the input file.</li>
-</ul>
-
-
-
+ <br>
+ <p>
+ <em>Features</em>
+ </p>
+ <ul>
+ <li>Colours are generated randomly for the number of helices
+ present. Reselect the "By RNA Helices" option to generate another
+ set of random colors.</li>
+ <li>Sequence logo is in <a href="purinepyrimidine.html">
+ Purine/Pyrimidine colour scheme</a>.
+ </li>
+ <li>Line above the "Secondary Structure" line in annotation
+ panel is WUSS notation present in the input file.</li>
+ </ul>
+
+
+
<div align="center">
- <img src="rnahelicescoloring.png" width="600" height="140"> </div>
-
+ <img src="rnahelicescoloring.png" width="600" height="140">
+ </div>
+
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Strand Colour Scheme</title>
+<head>
+<title>Strand Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Strand propensity</strong></p>
-<div align="center">
- <table width="400" border="1">
- <tr>
- <td bgcolor="#ffff00">V</td>
- <td bgcolor="#ecec13">I</td>
- <td bgcolor="#d3d32c">Y</td>
- <td bgcolor="#c2c23d">F</td>
- <td bgcolor="#c0c03f">W</td>
- </tr>
- <tr>
- <td bgcolor="#b2b24d">L</td>
- <td bgcolor="#9d9d62">T</td>
- <td bgcolor="#9d9d62">C</td>
- <td bgcolor="#8c8c73">Q</td>
- <td bgcolor="#82827d">M</td>
- </tr>
- <tr>
- <td bgcolor="#797986">X</td>
- <td bgcolor="#6b6b94">R</td>
- <td bgcolor="#64649b">N</td>
- <td bgcolor="#60609f">H</td>
- <td bgcolor="#5858a7">A</td>
- </tr>
- <tr>
- <td bgcolor="#4949b6">S</td>
- <td bgcolor="#4949b6">G</td>
- <td bgcolor="#4747b8">Z</td>
- <td bgcolor="#4747b8">K</td>
- <td bgcolor="#4343bc">B</td>
- </tr>
- <tr> </td>
- <td bgcolor="#2323dc">P</td>
- <td bgcolor="#2121de">D</td>
- <td bgcolor="#0000ff">E</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Strand propensity</strong>
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+ <tr>
+ <td bgcolor="#ffff00">V</td>
+ <td bgcolor="#ecec13">I</td>
+ <td bgcolor="#d3d32c">Y</td>
+ <td bgcolor="#c2c23d">F</td>
+ <td bgcolor="#c0c03f">W</td>
+ </tr>
+ <tr>
+ <td bgcolor="#b2b24d">L</td>
+ <td bgcolor="#9d9d62">T</td>
+ <td bgcolor="#9d9d62">C</td>
+ <td bgcolor="#8c8c73">Q</td>
+ <td bgcolor="#82827d">M</td>
+ </tr>
+ <tr>
+ <td bgcolor="#797986">X</td>
+ <td bgcolor="#6b6b94">R</td>
+ <td bgcolor="#64649b">N</td>
+ <td bgcolor="#60609f">H</td>
+ <td bgcolor="#5858a7">A</td>
+ </tr>
+ <tr>
+ <td bgcolor="#4949b6">S</td>
+ <td bgcolor="#4949b6">G</td>
+ <td bgcolor="#4747b8">Z</td>
+ <td bgcolor="#4747b8">K</td>
+ <td bgcolor="#4343bc">B</td>
+ </tr>
+ <tr>
+ </td>
+ <td bgcolor="#2323dc">P</td>
+ <td bgcolor="#2121de">D</td>
+ <td bgcolor="#0000ff">E</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Taylor Colour Scheme</title>
+<head>
+<title>Taylor Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong><a name="taylor">Taylor</a></strong></p>
-<p>These colours were invented by Willie Taylor and an entertaining description
- of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>
-<div align="center">
- <table width="400" border="1">
- <tr>
- <td bgcolor="#ccff00">A</td>
- <td bgcolor="#99ff00">V</td>
- <td bgcolor="#66ff00">I</td>
- <td bgcolor="#33ff00">L</td>
- </tr>
- <tr>
- <td bgcolor="#00ff00">M</td>
- <td bgcolor="#00ff66">F</td>
- <td bgcolor="#00ffcc">Y</td>
- <td bgcolor="#00ccff">W</td>
- </tr>
- <tr>
- <td bgcolor="#0066ff">H</td>
- <td bgcolor="#0000ff">R</td>
- <td bgcolor="#6600ff">K</td>
- <td bgcolor="#cc00ff">N</td>
- </tr>
- <tr>
- <td bgcolor="#ff00cc">Q</td>
- <td bgcolor="#ff0066">E</td>
- <td bgcolor="#ff0000">D</td>
- <td bgcolor="#ff3300">S</td>
- </tr>
- <tr>
- <td bgcolor="#ff6600">T</td>
- <td bgcolor="#ff9900">G</td>
- <td bgcolor="#ffcc00">P</td>
- <td bgcolor="#ffff00">C</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong><a name="taylor">Taylor</a></strong>
+ </p>
+ <p>These colours were invented by Willie Taylor and an
+ entertaining description of their birth can be found in Protein
+ Engineering, Vol 10 , 743-746 (1997)</p>
+ <div align="center">
+ <table width="400" border="1">
+ <tr>
+ <td bgcolor="#ccff00">A</td>
+ <td bgcolor="#99ff00">V</td>
+ <td bgcolor="#66ff00">I</td>
+ <td bgcolor="#33ff00">L</td>
+ </tr>
+ <tr>
+ <td bgcolor="#00ff00">M</td>
+ <td bgcolor="#00ff66">F</td>
+ <td bgcolor="#00ffcc">Y</td>
+ <td bgcolor="#00ccff">W</td>
+ </tr>
+ <tr>
+ <td bgcolor="#0066ff">H</td>
+ <td bgcolor="#0000ff">R</td>
+ <td bgcolor="#6600ff">K</td>
+ <td bgcolor="#cc00ff">N</td>
+ </tr>
+ <tr>
+ <td bgcolor="#ff00cc">Q</td>
+ <td bgcolor="#ff0066">E</td>
+ <td bgcolor="#ff0000">D</td>
+ <td bgcolor="#ff3300">S</td>
+ </tr>
+ <tr>
+ <td bgcolor="#ff6600">T</td>
+ <td bgcolor="#ff9900">G</td>
+ <td bgcolor="#ffcc00">P</td>
+ <td bgcolor="#ffff00">C</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head>
-Background Dependent Text Colour
+<head>Background Dependent Text Colour
</head>
<body>
-<strong>Background Dependent Text Colour</strong>
-<p>The <strong>Colour→Text Colour</strong> menu entry opens
-the <strong>"Adjust Foreground Text Colour Threshold"</strong>
-dialog box, allowing the colour of symbols rendered on dark or light
-backgrounds to be set for the current selection or the whole alignment.
-</p>
-<p><img src="textcolour.gif"></p>
-<p>The dialog box contains a slider, and two colour icons showing
-the text colour for dark backgrounds (left hand end of slider), and
-light backgrounds (right hand end of slider). Drag the slider to change
-the threshold for transitioning between dark and light background
-colours, and select either of the colour boxes to open a colour chooser
-to select a different text colour.</p>
+ <strong>Background Dependent Text Colour</strong>
+ <p>
+ The <strong>Colour→Text Colour</strong> menu entry opens the <strong>"Adjust
+ Foreground Text Colour Threshold"</strong> dialog box, allowing the
+ colour of symbols rendered on dark or light backgrounds to be set
+ for the current selection or the whole alignment.
+ </p>
+ <p>
+ <img src="textcolour.gif">
+ </p>
+ <p>The dialog box contains a slider, and two colour icons showing
+ the text colour for dark backgrounds (left hand end of slider), and
+ light backgrounds (right hand end of slider). Drag the slider to
+ change the threshold for transitioning between dark and light
+ background colours, and select either of the colour boxes to open a
+ colour chooser to select a different text colour.</p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Turn Colour Scheme</title>
+<head>
+<title>Turn Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Turn propensity</strong></p>
-<div align="center">
- <table width="400" border="1">
- <tr>
- <td bgcolor="#ff0000">N</td>
- <td bgcolor="#ff0000">G</td>
- <td bgcolor="#f60909">P</td>
- <td bgcolor="#f30c0c">B</td>
- <td bgcolor="#e81717">D</td>
- </tr>
- <tr>
- <td bgcolor="#e11e1e">S</td>
- <td bgcolor="#a85757">C</td>
- <td bgcolor="#9d6262">Y</td>
- <td bgcolor="#7e8181">K</td>
- <td bgcolor="#7c8383">X</td>
- </tr>
- <tr>
- <td bgcolor="#778888">Q</td>
- <td bgcolor="#738c8c">W</td>
- <td bgcolor="#738c8c">T</td>
- <td bgcolor="#708f8f">R</td>
- <td bgcolor="#708f8f">H</td>
- </tr>
- <tr>
- <td bgcolor="#5ba4a4">Z</td>
- <td bgcolor="#3fc0c0">E</td>
- <td bgcolor="#2cd3d3">A</td>
- <td bgcolor="#1ee1e1">F</td>
- <td bgcolor="#1ee1e1">M</td>
- </tr>
- <tr> </td>
- <td bgcolor="#1ce3e3">L</td>
- <td bgcolor="#07f8f8">V</td>
- <td bgcolor="#00ffff">I</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Turn propensity</strong>
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+ <tr>
+ <td bgcolor="#ff0000">N</td>
+ <td bgcolor="#ff0000">G</td>
+ <td bgcolor="#f60909">P</td>
+ <td bgcolor="#f30c0c">B</td>
+ <td bgcolor="#e81717">D</td>
+ </tr>
+ <tr>
+ <td bgcolor="#e11e1e">S</td>
+ <td bgcolor="#a85757">C</td>
+ <td bgcolor="#9d6262">Y</td>
+ <td bgcolor="#7e8181">K</td>
+ <td bgcolor="#7c8383">X</td>
+ </tr>
+ <tr>
+ <td bgcolor="#778888">Q</td>
+ <td bgcolor="#738c8c">W</td>
+ <td bgcolor="#738c8c">T</td>
+ <td bgcolor="#708f8f">R</td>
+ <td bgcolor="#708f8f">H</td>
+ </tr>
+ <tr>
+ <td bgcolor="#5ba4a4">Z</td>
+ <td bgcolor="#3fc0c0">E</td>
+ <td bgcolor="#2cd3d3">A</td>
+ <td bgcolor="#1ee1e1">F</td>
+ <td bgcolor="#1ee1e1">M</td>
+ </tr>
+ <tr>
+ </td>
+ <td bgcolor="#1ce3e3">L</td>
+ <td bgcolor="#07f8f8">V</td>
+ <td bgcolor="#00ffff">I</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>User Defined Colours</title></head>
+<head>
+<title>User Defined Colours</title>
+</head>
<body>
-<p><strong>User Defined Colours</strong></p>
-<p><img src="userDefined_java6.gif" width="815" height="402"> </p>
-<p>You may define any number of new colour schemes, each with a unique name. <br>
- <br>
- Each of the residues in a colour scheme may be assigned any chosen colour. <br>
- Select one or more residues, then select the desired colour.<br/>
- Use Ctrl-click to select multiple residues, or click then Shift-click to select a block.<br/>
- Note that the currently selected buttons are highlighted by a lighter text colour.
<p>
- The <strong>Case Sensitive</strong> option allows you to choose distinct colours for upper and
- lower case residue codes.
+ <strong>User Defined Colours</strong>
+ </p>
+ <p>
+ <img src="userDefined_java6.gif" width="815" height="402">
+ </p>
+ <p>
+ You may define any number of new colour schemes, each with a unique
+ name. <br> <br> Each of the residues in a colour scheme
+ may be assigned any chosen colour. <br> Select one or more
+ residues, then select the desired colour.<br /> Use Ctrl-click to
+ select multiple residues, or click then Shift-click to select a
+ block.<br /> Note that the currently selected buttons are
+ highlighted by a lighter text colour.
+ <p>
+ The <strong>Case Sensitive</strong> option allows you to choose
+ distinct colours for upper and lower case residue codes.
<p>
- Click <strong>Apply</strong> or <strong>OK</strong> to set your new colours on the active
- alignment window.<br/>
- Click <strong>Cancel</strong> to undo your changes if you pressed the <strong>Apply</strong>
- button.
+ Click <strong>Apply</strong> or <strong>OK</strong> to set your new
+ colours on the active alignment window.<br /> Click <strong>Cancel</strong>
+ to undo your changes if you pressed the <strong>Apply</strong>
+ button.
</p>
- If you save your colour scheme with a unique name, the colour scheme name will
- be added to the <strong>Colour</strong> menu on each new alignment window.<br>
+ If you save your colour scheme with a unique name, the colour scheme
+ name will be added to the
+ <strong>Colour</strong> menu on each new alignment window.
+ <br>
+ <br> Any saved colour schemes will be automatically loaded the
+ next time you use Jalview.
+ <br>
<br>
- Any saved colour schemes will be automatically loaded the next time you use
- Jalview.
- <br><br>
- <em>Note: the screenshot shows the appearance when running Java version 6. For Java 7 (from Jalview 2.8.2) only the Swatches colour chooser is
- currently supported (for reasons of available screen space).</em>
- <p/>
+ <em>Note: the screenshot shows the appearance when running Java
+ version 6. For Java 7 (from Jalview 2.8.2) only the Swatches colour
+ chooser is currently supported (for reasons of available screen
+ space).</em>
+ <p />
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Zappo Colour Scheme</title>
+<head>
+<title>Zappo Colour Scheme</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Zappo Colours</strong><br>
- <br>
- The residues are coloured according to their physicochemical properties as
- follows: </p>
-<div align="center">
- <table width="400" border="1">
- <tr>
- <td > Aliphatic/hydrophobic</td>
- <td bgcolor="#ffafaf">ILVAM </td>
- </tr>
- <tr>
- <td>Aromatic</td>
- <td bgcolor="#ffc800">FWY</td>
- </tr>
- <tr>
- <td>Positive</td>
- <td bgcolor="#6464ff">KRH</td>
- </tr>
- <tr>
- <td> Negative</td>
- <td bgcolor="#ff0000">DE</td>
- </tr>
- <tr>
- <td>Hydrophilic</td>
- <td bgcolor="#00ff00">STNQ</td>
- </tr>
- <tr>
- <td>conformationally special</td>
- <td bgcolor="#ff00ff">PG</td>
- </tr>
- <tr>
- <td>Cysteine</td>
- <td bgcolor="#ffff00">C</td>
- </tr>
- </table>
-</div>
+ <p>
+ <strong>Zappo Colours</strong><br> <br> The residues are
+ coloured according to their physicochemical properties as follows:
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+ <tr>
+ <td>Aliphatic/hydrophobic</td>
+ <td bgcolor="#ffafaf">ILVAM</td>
+ </tr>
+ <tr>
+ <td>Aromatic</td>
+ <td bgcolor="#ffc800">FWY</td>
+ </tr>
+ <tr>
+ <td>Positive</td>
+ <td bgcolor="#6464ff">KRH</td>
+ </tr>
+ <tr>
+ <td>Negative</td>
+ <td bgcolor="#ff0000">DE</td>
+ </tr>
+ <tr>
+ <td>Hydrophilic</td>
+ <td bgcolor="#00ff00">STNQ</td>
+ </tr>
+ <tr>
+ <td>conformationally special</td>
+ <td bgcolor="#ff00ff">PG</td>
+ </tr>
+ <tr>
+ <td>Cysteine</td>
+ <td bgcolor="#ffff00">C</td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Editing</title></head>
+<head>
+<title>Editing</title>
+</head>
<body>
-<p><strong>Editing</strong></p>
-<p>There are two major ways to edit alignments - in 'Normal mode',
-gaps are inserted and deleted at the mouse pointer in various ways by
-clicking the left mouse button and pressing a combination of either
-shift and control (or the alt, option or apple key on Macs) and dragging the mouse. Pressing
-<em>F2</em> toggles the alternative <a href="../features/cursorMode.html">'Cursor
-mode'</a> keyboard editing facility, where the space bar and delete
-keys add and remove gaps at the current editing position. The key
-strokes for both these modes are summarised in the <a
-href="../keys.html">keystrokes table</a>.</p>
-<p><strong>Tip:</strong> For large alignments, deselect "Calculate ->
- Autocalculate Consensus" to prevent the alignment performing lengthy calculations
- after every edit. </p>
-<p><em>Inserting / removing gaps</em> - hold down the
- "Shift" key. Click on a residue with the mouse and drag it
- to the left or right to insert gaps and remove gaps.<br>
- If the current selection is a group over all sequences in the
- alignment, or a group over some sequences or all columns in the
- alignment, then hold down either "Control"
- key (or the "Alt;" on OSX if "Control" does not work) and drag the residue left or right to edit all sequences in the defined
- group at once.</p>
-<p><em>Copy/paste/cut/delete</em> - any sequences which are in the current selection
- box (indicated in red) may be cut and / or copied to a new alignment or deleted.
-</p>
-<p><em>Undo / redo</em> - editing of sequences (insertion/removal of gaps, removal
- of sequences, trimming sequences etc) may be undone or redone at any time using
- the appropriate menu items from the edit menu. The undo history list only allows
- a maximum of 10 actions.
-<p><em>Trimming alignment</em> - First select a column by clicking the scale indicator
- (above the sequences) The alignment may then be trimmed to the left or right
- of this column. If multiple columns are selected, the alignment is trimmed to
- the right of the rightmost selected column (or to the left of the leftmost selected
- column)</p>
-<p><em>Remove gapped columns</em> - Removes columns within the alignment which
- contain only space characters ("-" or "." or " ")</p>
-<p><em>Removing gaps</em> - Removes all gaps from the alignment. Gaps are "-"
- or "." or " ".</p>
-<p><em>Set gap character</em> - Switches the gap character between "."
- and "-". If the "Render Gaps" option from the "View"
- menu is unticked all gaps will appear as blank spaces.</p>
-<p> </p>
-<p><strong>Editing In Selection Areas</strong></p>
-Editing can be restricted to the current selection area.
-This allows the user to "Lock" the alignment either side of the selection
-area. Any gap insertions or deletions will only affect the current selection area.
-<p><img src="editing.jpg" width="428" height="186" align="top"></p>
-<p>In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104,
- the same number of gaps will be inserted at position 116, (between M and L).
-</p>
-<p><em>Locked selection area based editing was introduced in Jalview 2.08</em></p>
-<p> </p>
+ <p>
+ <strong>Editing</strong>
+ </p>
+ <p>
+ There are two major ways to edit alignments - in 'Normal mode', gaps
+ are inserted and deleted at the mouse pointer in various ways by
+ clicking the left mouse button and pressing a combination of either
+ shift and control (or the alt, option or apple key on Macs) and
+ dragging the mouse. Pressing <em>F2</em> toggles the alternative <a
+ href="../features/cursorMode.html"
+ >'Cursor mode'</a> keyboard editing facility, where the space bar and
+ delete keys add and remove gaps at the current editing position. The
+ key strokes for both these modes are summarised in the <a
+ href="../keys.html"
+ >keystrokes table</a>.
+ </p>
+ <p>
+ <strong>Tip:</strong> For large alignments, deselect "Calculate
+ -> Autocalculate Consensus" to prevent the alignment
+ performing lengthy calculations after every edit.
+ </p>
+ <p>
+ <em>Inserting / removing gaps</em> - hold down the "Shift"
+ key. Click on a residue with the mouse and drag it to the left or
+ right to insert gaps and remove gaps.<br> If the current
+ selection is a group over all sequences in the alignment, or a group
+ over some sequences or all columns in the alignment, then hold down
+ either "Control" key (or the "Alt;" on OSX if
+ "Control" does not work) and drag the residue left or
+ right to edit all sequences in the defined group at once.
+ </p>
+ <p>
+ <em>Copy/paste/cut/delete</em> - any sequences which are in the
+ current selection box (indicated in red) may be cut and / or copied
+ to a new alignment or deleted.
+ </p>
+ <p>
+ <em>Undo / redo</em> - editing of sequences (insertion/removal of
+ gaps, removal of sequences, trimming sequences etc) may be undone or
+ redone at any time using the appropriate menu items from the edit
+ menu. The undo history list only allows a maximum of 10 actions.
+ <p>
+ <em>Trimming alignment</em> - First select a column by clicking the
+ scale indicator (above the sequences) The alignment may then be
+ trimmed to the left or right of this column. If multiple columns are
+ selected, the alignment is trimmed to the right of the rightmost
+ selected column (or to the left of the leftmost selected column)
+ </p>
+ <p>
+ <em>Remove gapped columns</em> - Removes columns within the
+ alignment which contain only space characters ("-" or
+ "." or " ")
+ </p>
+ <p>
+ <em>Removing gaps</em> - Removes all gaps from the alignment. Gaps
+ are "-" or "." or " ".
+ </p>
+ <p>
+ <em>Set gap character</em> - Switches the gap character between
+ "." and "-". If the "Render Gaps"
+ option from the "View" menu is unticked all gaps will
+ appear as blank spaces.
+ </p>
+ <p> </p>
+ <p>
+ <strong>Editing In Selection Areas</strong>
+ </p>
+ Editing can be restricted to the current selection area. This allows
+ the user to "Lock" the alignment either side of the
+ selection area. Any gap insertions or deletions will only affect the
+ current selection area.
+ <p>
+ <img src="editing.jpg" width="428" height="186" align="top">
+ </p>
+ <p>In this example, if Sequence IL2RA_MACMU has gaps removed from
+ position 98-104, the same number of gaps will be inserted at
+ position 116, (between M and L).</p>
+ <p>
+ <em>Locked selection area based editing was introduced in
+ Jalview 2.08</em>
+ </p>
+ <p> </p>
</body>
</html>
</head>
<body>
-<p><strong>The Alignment Annotations File</strong></p>
-<p>Alignment annotations can be imported onto an alignment since
-version 2.08 of Jalview, via an annotations file. It is a simple ASCII
-text file consisting of tab delimited records similar to the <a
- href="featuresFormat.html">Sequence Features File</a>, and introduced
-primarily for use with the Jalview applet.</p>
+ <p>
+ <strong>The Alignment Annotations File</strong>
+ </p>
+ <p>
+ Alignment annotations can be imported onto an alignment since
+ version 2.08 of Jalview, via an annotations file. It is a simple
+ ASCII text file consisting of tab delimited records similar to the <a
+ href="featuresFormat.html"
+ >Sequence Features File</a>, and introduced primarily for use with the
+ Jalview applet.
+ </p>
-<p><strong>Importing annotation files</strong><br/>
-Alignment annotations files are imported into Jalview in the
-following ways:<br/>
-<ul>
- <li>from the command line<strong><pre>
+ <p>
+ <strong>Importing annotation files</strong><br /> Alignment
+ annotations files are imported into Jalview in the following ways:<br />
+ <ul>
+ <li>from the command line<strong><pre>
-annotations <<em>Annotations filename</em>></pre></strong></li>
- <li>Dragging an annotations file onto an alignment window</li>
- <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
- menu of an alignment window.</li>
-</ul>
-</p>
-<p>
- <strong>Exporting annotation files</strong><br /> An annotation file
- can be created for any alignment view from the "Export
- Annotations ..." entry in the <strong>File</strong> menu of an
- alignment window.
-</p>
-<p><strong>THE ANNOTATION FILE FORMAT</strong>
-<br/>An annotation file consists of lines containing an instruction followed by
-tab delimited fields. Any lines starting with "#" are considered comments, and
-ignored. The sections below describe the structure of an annotation file.
-</p><ul>
-<li><a href="#annheader">JALVIEW_ANNOTATION</a> mandatory header</li>
-<li><a href="#annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a> to create annotation rows</li>
-<li><a href="#combine">COMBINE, COLOUR and GRAPHLINE</a> for thresholds and complex line graphs</li>
-<li><a href="#annrowprops">ROWPROPERTIES</a> control the display of individual annotation rows</li>
-<li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
-<li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>
-<li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for specifying target sequences and groups for annotation, reference sequence and column visibilty commands.</li>
- <li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS</a>
- for assigning the reference sequence on the alignment and hiding columns.</li>
- </ul>
- <p>
- At the end of this document, you can also find notes on <a
- href="#compatibility">compatibility</a> of annotation files across
- different versions of Jalview. An <a href="#exampleann">example
- annotation file</a> is also provided along with instructions on how to
- import it to Jalview.
- </p>
- <hr/>
-<p><strong><em><a name="annheader">Header line</a></em></strong><br/>The first non-commented out line of a valid Annotations file
-must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
-<hr/>
-<p><strong><em><a name="annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a></em></strong><br/>
-Labels, secondary structure, histograms and line graphs are added with a line like <strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Description</em> (optional)	<em>Values</em></pre></strong></p>
- <p>
- Here, the <em>GRAPH_TYPE</em> field in the first column defines the
- appearance of the annotation row when rendered by Jalview. The next
- field is the row <em>label</em> for the annotation. This may be
- followed by a <em>description</em> for the row, which is shown in a
- tooltip when the user mouses over the annotation row's label. Since
- Jalview 2.7, the description field may also contain HTML tags (in the same
- way as a <a href="featuresFile.html">sequence feature's</a> label),
- providing the text is enclosed in an <html/> tag.
-
- <ul><em>Please note: URL links embedded in HTML descriptions are not yet supported.</em>
- </ul>
- </p>
- <p>
- The final <em>Values</em> field contains a series of "|"
- separated value fields. Each value field is itself a comma separated
- list of fields of a particular type defined by the annotation row's <em>GRAPH_TYPE</em>.
- The allowed values of <em>GRAPH_TYPE</em> and corresponding
- interpretation of each <em>Value</em> are shown below:
-
- <ul>
- <li><strong>BAR_GRAPH</strong><br> Plots a histogram with
- labels below each bar.<br> <em>number</em>,<em>text
- character</em>,<em>Tooltip text</em></li>
- <li><strong>LINE_GRAPH</strong><br> Draws a line between
- values on the annotation row.<br> <em>number</em></li>
- <li><strong>NO_GRAPH</strong><br>For a row consisting of
- text labels and/or secondary structure symbols.<br> <em>{Secondary
- Structure Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br /> <br />The
- type of secondary structure symbol depends on the alignment being
- annotated being either Protein or RNA. <br />For proteins, structure
- symbols are <em>H</em> (for helix) and <em>E</em> (for strand)<br />
- <br />For RNA structures, VIENNA, WUSS, and extended notations can
- be used to specify paired positions.
- <ul>e.g. "(|(||)|)" or "|A|A|A|(|a|a|a|)")
- </ul></li>
- </ul>
- Any or all value fields may be left empty, as well as the BAR_GRAPH's
- text character field, and either or both of the text-label and
- secondary structure symbol fields of the NO_GRAPH type annotation rows.
- </p>
-<p>Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.
-</p>
-<hr/>
-<p><strong><a name="combine">COMBINE, COLOUR and GRAPHLINE</a> for line graphs</font></strong><br/>
-<em>LINE_GRAPH</em> type annotations can be given a colour
-(specified as 24 bit RGB triplet in hexadecimal or comma separated
-values), combined onto the same vertical axis, and have ordinate lines
-(horizontal lines at a particular vertical axis value) using the
-following commands (respectively):
-<pre>COLOUR	<em>graph_name</em>	<em>colour</em>
+ <li>Dragging an annotations file onto an alignment window</li>
+ <li>Via the "Load Features / Annotations" entry in
+ the <strong>File</strong> menu of an alignment window.
+ </li>
+ </ul>
+ </p>
+ <p>
+ <strong>Exporting annotation files</strong><br /> An annotation
+ file can be created for any alignment view from the "Export
+ Annotations ..." entry in the <strong>File</strong> menu of an
+ alignment window.
+ </p>
+ <p>
+ <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation file
+ consists of lines containing an instruction followed by tab
+ delimited fields. Any lines starting with "#" are
+ considered comments, and ignored. The sections below describe the
+ structure of an annotation file.
+ </p>
+ <ul>
+ <li><a href="#annheader">JALVIEW_ANNOTATION</a> mandatory
+ header</li>
+ <li><a href="#annrows">LINE_GRAPH, BAR_GRAPH and NO_GRAPH</a>
+ to create annotation rows</li>
+ <li><a href="#combine">COMBINE, COLOUR and GRAPHLINE</a> for
+ thresholds and complex line graphs</li>
+ <li><a href="#annrowprops">ROWPROPERTIES</a> control the
+ display of individual annotation rows</li>
+ <li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of
+ sequences for further annotation</li>
+ <li><a href="#groupprops">PROPERTIES</a> to set visualisation
+ properties for sequence groups</li>
+ <li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for
+ specifying target sequences and groups for annotation, reference
+ sequence and column visibilty commands.</li>
+ <li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and
+ HIDE_INSERTIONS</a> for assigning the reference sequence on the
+ alignment and hiding columns.</li>
+ </ul>
+ <p>
+ At the end of this document, you can also find notes on <a
+ href="#compatibility"
+ >compatibility</a> of annotation files across different versions of
+ Jalview. An <a href="#exampleann">example annotation file</a> is
+ also provided along with instructions on how to import it to
+ Jalview.
+ </p>
+ <hr />
+ <p>
+ <strong><em><a name="annheader">Header line</a></em></strong><br />The
+ first non-commented out line of a valid Annotations file must begin
+ with :<strong><pre>JALVIEW_ANNOTATION</pre></strong>
+ </p>
+ <hr />
+ <p>
+ <strong><em><a name="annrows">LINE_GRAPH,
+ BAR_GRAPH and NO_GRAPH</a></em></strong><br /> Labels, secondary structure,
+ histograms and line graphs are added with a line like <strong><pre>
+ <em>GRAPH_TYPE</em>	<em>Label</em>	<em>Description</em> (optional)	<em>Values</em>
+ </pre></strong>
+ </p>
+ <p>
+ Here, the <em>GRAPH_TYPE</em> field in the first column defines the
+ appearance of the annotation row when rendered by Jalview. The next
+ field is the row <em>label</em> for the annotation. This may be
+ followed by a <em>description</em> for the row, which is shown in a
+ tooltip when the user mouses over the annotation row's label. Since
+ Jalview 2.7, the description field may also contain HTML tags (in
+ the same way as a <a href="featuresFile.html">sequence feature's</a>
+ label), providing the text is enclosed in an <html/> tag.
+ <ul>
+ <em>Please note: URL links embedded in HTML descriptions are
+ not yet supported.</em>
+ </ul>
+ </p>
+ <p>
+ The final <em>Values</em> field contains a series of "|"
+ separated value fields. Each value field is itself a comma separated
+ list of fields of a particular type defined by the annotation row's
+ <em>GRAPH_TYPE</em>. The allowed values of <em>GRAPH_TYPE</em> and
+ corresponding interpretation of each <em>Value</em> are shown below:
+
+
+ <ul>
+ <li><strong>BAR_GRAPH</strong><br> Plots a histogram with
+ labels below each bar.<br> <em>number</em>,<em>text
+ character</em>,<em>Tooltip text</em></li>
+ <li><strong>LINE_GRAPH</strong><br> Draws a line between
+ values on the annotation row.<br> <em>number</em></li>
+ <li><strong>NO_GRAPH</strong><br>For a row consisting of
+ text labels and/or secondary structure symbols.<br> <em>{Secondary
+ Structure Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br />
+ <br />The type of secondary structure symbol depends on the
+ alignment being annotated being either Protein or RNA. <br />For
+ proteins, structure symbols are <em>H</em> (for helix) and <em>E</em>
+ (for strand)<br /> <br />For RNA structures, VIENNA, WUSS, and
+ extended notations can be used to specify paired positions.
+ <ul>e.g. "(|(||)|)" or
+ "|A|A|A|(|a|a|a|)")
+ </ul></li>
+ </ul>
+ Any or all value fields may be left empty, as well as the BAR_GRAPH's
+ text character field, and either or both of the text-label and
+ secondary structure symbol fields of the NO_GRAPH type annotation
+ rows.
+ </p>
+ <p>Color strings can be embedded in a value field by enclosing an
+ RGB triplet in square brackets to colour that position in an
+ annotation row.</p>
+ <hr />
+ <p>
+ <strong><a name="combine">COMBINE, COLOUR and GRAPHLINE</a>
+ for line graphs</font></strong><br /> <em>LINE_GRAPH</em> type annotations can be
+ given a colour (specified as 24 bit RGB triplet in hexadecimal or
+ comma separated values), combined onto the same vertical axis, and
+ have ordinate lines (horizontal lines at a particular vertical axis
+ value) using the following commands (respectively):
+ <pre>COLOUR	<em>graph_name</em>	<em>colour</em>
COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>
-</em></strong></pre>
-</p>
-<hr/>
-<p><strong><a name="annrowprops">ROWPROPERTIES</a></strong><br/>
-The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:</p>
-<pre>ROWPROPERTIES	<em>Row label</em>	<em>centrelabs=true( or false)</em>	<em>showalllabs=true(default is false)</em>	<em>scaletofit=true (default is false)</em></pre>
-<p>This sets the visual display properties according to the given values for all the annotation rows with labels matching <em>Row label</em>. The properties mostly affect the display of multi-character column labels, and are as follows:
-<ul><li><em>centrelabs</em> Centre each label on its column.</li>
-<li><em>showalllabs</em> Show every column label rather than only the first of a run of identical labels (setting this to true can have a drastic effect on secondary structure rows).</li>
-<li><em>scaletofit</em> Shrink each label's font size so that the label fits within the column. Useful when annotating an alignment with a specific column numbering system. (<em>Not available in Jalview applet due to AWT 1.1 limitations</em>)</li>
-</ul></p>
-<p><strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br/>
-Groups of sequences and column ranges can be defined using a tab delimited statement like:</p>
-<pre>SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	<em>Sequences</em></pre>
-<p>The sequences can be defined by alignment index and a range of sequences can
- be defined in a comma delimited field such as</p>
-<p>2-5,8-15,20,22</p>
-<p>Enter * to select all groups. </p>
-<p><strong>Note:</strong> If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list
-of sequence IDs. </p>
-<p>If a <a href="#seqgrprefs"><strong>SEQUENCE_REF</strong></a> has been defined, then <em>group_start</em> and <em>group_end</em> will be
- relative to the sequence residue numbering, otherwise the <em>group_start</em> and <em>group_end</em>
- will be alignment column indices. </p>
-<hr/>
-<p><strong><a name="groupprops">PROPERTIES</a></strong><br/>This statement allows various visualisation properties to be assigned to a named group. This takes a series of tab-delimited <em>key</em>=<em>value</em> pairs:</p>
-<pre>PROPERTIES	Group_name	tab_delimited_key_value_pairs
+</em></strong>
+ </pre>
+ </p>
+ <hr />
+ <p>
+ <strong><a name="annrowprops">ROWPROPERTIES</a></strong><br /> The
+ visual display properties for a set of annotation rows can be
+ modified using the following tab-delimited line:
+ </p>
+ <pre>ROWPROPERTIES	<em>Row label</em>	<em>centrelabs=true( or false)</em>	<em>showalllabs=true(default is false)</em>	<em>scaletofit=true (default is false)</em>
+ </pre>
+ <p>
+ This sets the visual display properties according to the given
+ values for all the annotation rows with labels matching <em>Row
+ label</em>. The properties mostly affect the display of multi-character
+ column labels, and are as follows:
+ <ul>
+ <li><em>centrelabs</em> Centre each label on its column.</li>
+ <li><em>showalllabs</em> Show every column label rather than
+ only the first of a run of identical labels (setting this to true
+ can have a drastic effect on secondary structure rows).</li>
+ <li><em>scaletofit</em> Shrink each label's font size so that
+ the label fits within the column. Useful when annotating an
+ alignment with a specific column numbering system. (<em>Not
+ available in Jalview applet due to AWT 1.1 limitations</em>)</li>
+ </ul>
+ </p>
+ <p>
+ <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br /> Groups
+ of sequences and column ranges can be defined using a tab delimited
+ statement like:
+ </p>
+ <pre>SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	<em>Sequences</em>
+ </pre>
+ <p>The sequences can be defined by alignment index and a range of
+ sequences can be defined in a comma delimited field such as</p>
+ <p>2-5,8-15,20,22</p>
+ <p>Enter * to select all groups.</p>
+ <p>
+ <strong>Note:</strong> If the alignment indices are not known, enter
+ -1, followed by a tab and then a tab delimited list of sequence IDs.
+ </p>
+ <p>
+ If a <a href="#seqgrprefs"><strong>SEQUENCE_REF</strong></a> has
+ been defined, then <em>group_start</em> and <em>group_end</em> will
+ be relative to the sequence residue numbering, otherwise the <em>group_start</em>
+ and <em>group_end</em> will be alignment column indices.
+ </p>
+ <hr />
+ <p>
+ <strong><a name="groupprops">PROPERTIES</a></strong><br />This
+ statement allows various visualisation properties to be assigned to
+ a named group. This takes a series of tab-delimited <em>key</em>=<em>value</em>
+ pairs:
+ </p>
+ <pre>PROPERTIES	Group_name	tab_delimited_key_value_pairs
</pre>
-<p>The currently supported set of sequence group key-value pairs that can be provided here are :</p>
-<table border="1">
-<tbody><tr><td width="50%">Key</td><td>Value</td></tr>
-<tr><td width="50%">description</td><td>Text - may include simple HTML tags</td></tr>
-<tr><td width="50%">colour</td><td>A string resolving to a valid Jalview colourscheme (e.g. Helix Propensity)</td></tr>
-<tr><td width="50%">pidThreshold</td><td>A number from 0-100 specifying the Percent Identity Threshold for colouring columns in the group or alignment</td></tr>
-<tr><td width="50%">consThreshold</td><td>A number from 0-100 specifying the degree of bleaching applied for conservation colouring</td></tr>
-<tr><td width="50%">outlineColour</td><td>Line colour used for outlining the group (default is red)</td></tr>
-<tr><td width="50%">displayBoxes</td><td>Boolean (default true) controlling display of shaded box for each alignment position</td></tr>
-<tr><td width="50%">displayText</td><td>Boolean (default true) controlling display of text for each alignment position</td></tr>
-<tr><td width="50%">colourText</td><td>Boolean (default false) specifying whether text should be shaded by applied colourscheme</td></tr>
-<tr><td width="50%">textCol1</td><td>Colour for text when shown on a light background</td></tr>
-<tr><td width="50%">textCol2</td><td>Colour for text when shown on a dark background</td></tr>
-<tr><td width="50%">textColThreshold</td><td>Number from 0-100 specifying switching threshold between light and dark background</td></tr>
-<tr><td width="50%">idColour</td><td>Colour for highlighting the Sequence ID labels for this group<br/>If <em>idColour</em> is given but <em>colour</em> is not, then idColor will also be used for the group background colour.</td></tr>
-<tr><td width="50%">showunconserved</td><td>Boolean (default false) indicating whether residues should only be shown that are different from current reference or consensus sequence</td></tr>
-<tr><td width="50%">hide</td><td>Boolean (default false) indicating whether the rows in this group should be marked as hidden.<br/><em>Note:</em> if the group is sequence associated (specified by SEQUENCE_REF), then all members will be hidden and marked as represented by the reference sequence.</td></tr>
-<!-- <tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr> --></tbody>
-</table>
+ <p>The currently supported set of sequence group key-value pairs
+ that can be provided here are :</p>
+ <table border="1">
+ <tbody>
+ <tr>
+ <td width="50%">Key</td>
+ <td>Value</td>
+ </tr>
+ <tr>
+ <td width="50%">description</td>
+ <td>Text - may include simple HTML tags</td>
+ </tr>
+ <tr>
+ <td width="50%">colour</td>
+ <td>A string resolving to a valid Jalview colourscheme
+ (e.g. Helix Propensity)</td>
+ </tr>
+ <tr>
+ <td width="50%">pidThreshold</td>
+ <td>A number from 0-100 specifying the Percent Identity
+ Threshold for colouring columns in the group or alignment</td>
+ </tr>
+ <tr>
+ <td width="50%">consThreshold</td>
+ <td>A number from 0-100 specifying the degree of bleaching
+ applied for conservation colouring</td>
+ </tr>
+ <tr>
+ <td width="50%">outlineColour</td>
+ <td>Line colour used for outlining the group (default is
+ red)</td>
+ </tr>
+ <tr>
+ <td width="50%">displayBoxes</td>
+ <td>Boolean (default true) controlling display of shaded
+ box for each alignment position</td>
+ </tr>
+ <tr>
+ <td width="50%">displayText</td>
+ <td>Boolean (default true) controlling display of text for
+ each alignment position</td>
+ </tr>
+ <tr>
+ <td width="50%">colourText</td>
+ <td>Boolean (default false) specifying whether text should
+ be shaded by applied colourscheme</td>
+ </tr>
+ <tr>
+ <td width="50%">textCol1</td>
+ <td>Colour for text when shown on a light background</td>
+ </tr>
+ <tr>
+ <td width="50%">textCol2</td>
+ <td>Colour for text when shown on a dark background</td>
+ </tr>
+ <tr>
+ <td width="50%">textColThreshold</td>
+ <td>Number from 0-100 specifying switching threshold
+ between light and dark background</td>
+ </tr>
+ <tr>
+ <td width="50%">idColour</td>
+ <td>Colour for highlighting the Sequence ID labels for this
+ group<br />If <em>idColour</em> is given but <em>colour</em>
+ is not, then idColor will also be used for the group
+ background colour.
+ </td>
+ </tr>
+ <tr>
+ <td width="50%">showunconserved</td>
+ <td>Boolean (default false) indicating whether residues
+ should only be shown that are different from current reference
+ or consensus sequence</td>
+ </tr>
+ <tr>
+ <td width="50%">hide</td>
+ <td>Boolean (default false) indicating whether the rows in
+ this group should be marked as hidden.<br />
+ <em>Note:</em> if the group is sequence associated (specified by
+ SEQUENCE_REF), then all members will be hidden and marked as
+ represented by the reference sequence.
+ </td>
+ </tr>
+ <!-- <tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr> -->
+ </tbody>
+ </table>
-<p><strong>Specifying colours in PROPERTIES key-value pairs</strong><br/>
-The <strong>colour</strong> property can take either a colour scheme name,
- or a single colour specification (either a colour name like 'red' or an RGB
- triplet like 'ff0066'). If a single colour is specified, then the group
- will be coloured with that colour.</p>
- <hr/>
- <p><strong><a name="seqgrprefs">SEQUENCE_REF and GROUP_REF</a></strong><br/>
- By
- default, annotation is associated with the alignment as a whole.
- However, it is also possible to have an annotation row associated with
- a specific sequence, or a sequence group. Clicking the annotation
- label for sequence or group associated annotation will highlight the
- associated rows in the alignment, and double clicking will select
- those rows, allowing further analysis. While group associated
- annotation remains associated with a particular alignment, sequence
- associated annotation can move with a sequence - so copying a sequence
- to another alignment will also copy its associated annotation.
- </p>
- <p>You can associate an annotation with a sequence by preceding its
-definition with the line:
-<pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre>
-All Annotations defined after a SEQUENCE_REF command will then be
-associated with that sequence, and the first field in the Value field
-list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
+ <p>
+ <strong>Specifying colours in PROPERTIES key-value pairs</strong><br />
+ The <strong>colour</strong> property can take either a colour scheme
+ name, or a single colour specification (either a colour name like
+ 'red' or an RGB triplet like 'ff0066'). If a single colour is
+ specified, then the group will be coloured with that colour.
+ </p>
+ <hr />
+ <p>
+ <strong><a name="seqgrprefs">SEQUENCE_REF and GROUP_REF</a></strong><br />
+ By default, annotation is associated with the alignment as a whole.
+ However, it is also possible to have an annotation row associated
+ with a specific sequence, or a sequence group. Clicking the
+ annotation label for sequence or group associated annotation will
+ highlight the associated rows in the alignment, and double clicking
+ will select those rows, allowing further analysis. While group
+ associated annotation remains associated with a particular
+ alignment, sequence associated annotation can move with a sequence -
+ so copying a sequence to another alignment will also copy its
+ associated annotation.
+ </p>
+ <p>You can associate an annotation with a sequence by preceding
+ its definition with the line:
+ <pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em>
+ </pre>
+ All Annotations defined after a SEQUENCE_REF command will then be
+ associated with that sequence, and the first field in the Value field
+ list will (optionally) be placed at the
+ <em>startIndex</em>'th column.
+ </p>
-<p>Sequence associations are turned off for subsequent annotation
-definitions by:
-<pre>SEQUENCE_REF	ALIGNMENT</pre>
-</p>
-<p>Similarly, since Jalview 2.5, group associated annotation can be defined by preceding the row definitions with the line:
-<pre>GROUP_REF	<em>group_name</em></pre>
-Group association is turned off for subsequent annotation rows by:
-<pre>GROUP_REF	<em>ALIGNMENT</em></pre>
-</p>
-<hr/>
+ <p>Sequence associations are turned off for subsequent annotation
+ definitions by:
+ <pre>SEQUENCE_REF	ALIGNMENT</pre>
+ </p>
+ <p>Similarly, since Jalview 2.5, group associated annotation can
+ be defined by preceding the row definitions with the line:
+ <pre>GROUP_REF	<em>group_name</em>
+ </pre>
+ Group association is turned off for subsequent annotation rows by:
+ <pre>GROUP_REF	<em>ALIGNMENT</em>
+ </pre>
+ </p>
+ <hr />
<p>
<strong><a name="refsandviews">VIEW_SETREF,
VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br /> Since Jalview 2.9, the
properties.
</p> -->
<p>
- <em>VIEW_SETREF</em><br />Marks the first sequence in the alignment,
- or alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
+ <em>VIEW_SETREF</em><br />Marks the first sequence in the
+ alignment, or alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
statement, as the <a href="../calculations/referenceseq.html">reference
sequence</a> for the alignment.
</p>
</p>
<hr />
- <p><strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br/>
- The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
- so that only annotation line graphs with the given names ands the same
- <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</p>
- <hr/>
+ <p>
+ <strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br />
+ The interpretation of the COMBINE statement in <em>Version
+ 2.8.1</em> was refined so that only annotation line graphs with the
+ given names ands the same <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong>
+ scope are grouped.
+ </p>
+ <hr />
-<p><strong><a name="exampleann">EXAMPLES</a></strong><br/>
-An example Annotation file is given below. Copy and paste the contents into a text file and load it onto the Jalview example protein alignment.</p>
-<pre>#Comment lines follow the hash symbol
+ <p>
+ <strong><a name="exampleann">EXAMPLES</a></strong><br /> An example
+ Annotation file is given below. Copy and paste the contents into a
+ text file and load it onto the Jalview example protein alignment.
+ </p>
+ <pre>#Comment lines follow the hash symbol
JALVIEW_ANNOTATION
SEQUENCE_REF	FER1_MESCR	5
BAR_GRAPH	Bar Graph 1	<html>an <em>html tooltip</em> for Bar graph 1.</html>	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
PROPERTIES	Group_B	outlineColour=red
PROPERTIES	Group_C	colour=Clustal
</pre>
-</p>
+ </p>
</body>
</html>
</p>
<p>
The BioJSON specification is published at <a
- href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/</a>.
+ href="http://jalview.github.io/biojson/"
+ >http://jalview.github.io/biojson/</a>.
</p>
<p>
<em>Import of BioJSON data from HTML pages</em>
</p>
<p>When importing embedded data in an HTML document, Jalview
- searches for a hidden (usually) input or div element named "seqData":</p>
+ searches for a hidden (usually) input or div element named
+ "seqData":</p>
<pre>
<code><div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div></code>
</pre>
<title>The Chimera PDB Viewer</title>
</head>
<body>
-<p><strong>The Chimera Viewer</strong></p>
-<p>Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a> (http://www.cgl.ucsf.edu/chimera/)
-has been integrated into Jalview for interactively viewing structures
-opened by entries in the <strong>"Structure"</strong> submenu in the <a href="../menus/popupMenu.html">sequence
-id pop-up menu</a> (if you can't see this, then you need to <a
- href="viewingpdbs.html">associate a PDB structure</a> with the
-sequence). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.</p>
-<p>You can set a default choice of Jmol or Chimera structure viewer in <a href="preferences.html#structure"> Preferences</a>.
-You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).
-<p>If you save your Jalview session as a project file, the state of any open Chimera windows will also be saved, and can be reopened by loading the project file on any machine with Chimera installed. <em>Since Jalview 2.9.</em>
-<!-- <p>The following menu entries are provided for viewing structure data<br>
+ <p>
+ <strong>The Chimera Viewer</strong>
+ </p>
+ <p>
+ Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
+ (http://www.cgl.ucsf.edu/chimera/) has been integrated into Jalview
+ for interactively viewing structures opened by entries in the <strong>"Structure"</strong>
+ submenu in the <a href="../menus/popupMenu.html">sequence id
+ pop-up menu</a> (if you can't see this, then you need to <a
+ href="viewingpdbs.html"
+ >associate a PDB structure</a> with the sequence). Chimera is
+ available from the Jalview desktop, provided Chimera has been
+ separately installed.
+ </p>
+ <p>
+ You can set a default choice of Jmol or Chimera structure viewer in
+ <a href="preferences.html#structure"> Preferences</a>. You can also
+ optionally specify the path to the Chimera program here (if it
+ differs from the standard paths searched by Jalview).
+ <p>
+ If you save your Jalview session as a project file, the state of any
+ open Chimera windows will also be saved, and can be reopened by
+ loading the project file on any machine with Chimera installed. <em>Since
+ Jalview 2.9.</em>
+ <!-- <p>The following menu entries are provided for viewing structure data<br>
<ul>
<li>The <strong>"Structure→View
Structure→</strong> submenu allows a single PDB structure to be chosen
</ul>
<br>
</p> -->
-<p><a name="align"><strong>Superposing structures based
-on their aligned sequences</strong></a><br>
-If several structures are available on the alignment, you may add
-additional structures to an existing Chimera view by selecting their entry
-in the appropriate pop-up menu. Jalview will ask you if you wish to add
-the structure to the existing alignment, and if you do, it will import
-and superimpose the new PDB file using the corresponding positions from
-the alignment. If the alignment is subsequently edited, you can use the
-<a href="#sAlign"><em>Chimera→Align</em></a> menu option from the
-menu bar of the structure view window to superpose the structures using
-the updated alignment.<br>
-</p>
-<p><strong>Chimera Controls</strong><br>
-The structure is by default rendered as a ribbon diagram. Moving the
-mouse over the structure brings up tooltips giving the residue name, PDB
-residue number and chain code
-([RES]Num:Chain). Moving the mouse over an
-associated residue in an alignment window highlights the associated
-atoms in the displayed structures. When residues are selected in the Chimera window, they are highlighted on the alignment. For comprehensive details of Chimera's commands, refer to the tool's Help menu.
-<p>Basic screen operations (see <a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a>
-at http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html for full details).
-<table border="1">
- <tr>
- <td><strong>Action</strong></td>
- <td><strong>Windows</strong></td>
- <td><strong>Unix</strong></td>
- <td><strong>Mac/OSX</strong></td>
- </tr>
- <tr>
- <td>Rotate View</td>
- <td>Left Click and Drag</td>
- <td>Left Click and Drag</td>
- <td>Left Click and Drag</td>
- </tr>
- <tr>
- <td>Zoom</td><td>Right Click<br>
- drag mouse up or down</td>
- <td>Right Click<br>drag mouse up or down</td>
- <td>cmd or Right + Click and drag mouse up or down, <br>or use mouse scroll button</td>
- </tr>
- <tr>
- <td>Move Origin</td>
- <td>Middle Button + Drag</td>
- <td>Middle Button and drag</td>
- <td>alt + Click<br>
- and drag</td>
- </tr>
- <tr>
- <td>Select Residues</td>
- <td>Ctrl + Click (and drag to select a region)</td>
- <td>Ctrl + Click (and drag)</td>
- <td>Ctrl + Click (and drag)</td>
- </tr>
-</table>
-</p>
-<p><strong>Jalview Controls</strong>
-<p>The Jalview Chimera View window has up to five menus:</p>
-<ul>
- <li><Strong>File<br>
- </strong>
- <ul>
- <li><strong>View Mapping<br>
- </strong><em> Opens a text window showing the alignment between the
- residues corresponding to alpha-carbon atoms in the PDB structure and
- the residues in the associated sequence.</em></li>
- </ul>
- </li>
- <li><strong>View</strong>
- <ul>
- <li><strong>Show Chains<br>
- </strong><em>Select which of the PDB file's chains (if more than one) are to be displayed.</em></li>
- <li><strong>Colour by ..<br></strong><em>Submenu allowing specific alignment views to be selected for colouring associated chains in the structure display. This menu contains all the alignment views associated with the structure view, with those used to colour the view indicated by ticks. Addditionally, it contains the following menu entries:</em>
- <ul><li><strong>Select many views<br></strong><em>When this option is enabled, selecting an alignment view adds it to the set used to colour the structures. Use this when colouring structures related to a number of alignments involving different domains or chains which are shown in the same structure view.</em>
- </li>
- <li><strong>Select all views<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will add all associated views to the set used to colour the structure display.</em>
- </li>
- <li><strong>Invert selection<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display.</em>
- </li></ul></li></ul>
- <li><strong>Colours<br>
- </strong>
- <ul>
- <li><strong>By Sequence<br>
- </strong><em> Colours each residue in the structure with the colour of its
- corresponding residue in the associated sequence as rendered in the
- associated alignment views, including any Uniprot sequence features or
- region colourings.<br/>Pick which of the associated alignment views are used to colour the structures using the <strong>View→Colour by ..</strong> sub menu.</em><br>
- Residues which only exist in the PDB structure are coloured white if
- they are insertions (relative to the associated sequence in the
- alignment) and grey if they are N or C terminal flanks outside the
- region mapped to the alignment window's sequence.</em></li>
- <li><strong>By Chain<br>
- </strong><em>Uses the Chimera 'rainbow chain' command to apply a different colour to each chain.</em></li>
- <li><strong>Charge & Cysteine<br>
- </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
- Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
- residues in blue.</em></li>
- <li><strong>Colour with Chimera<br></strong><em>Defers any colouring operations to Chimera. Select this if you want to use the
- Chimera scripting interface or menu to modify the view directly.</em></li>
- <li><strong>Standard and User Defined Jalview
- colourschemes.<br>
- </strong><em>The remaining entries apply the colourschemes available from
- the standard and user defined <a href="../colourSchemes/index.html">amino
- acid colours</a>.</em></li>
- </ul>
- </li>
- <li><strong>Chimera<br>
- </strong><em>This pulldown menu is only displayed if there are multiple
- structures shown in the Chimera window, and Jalview can also locate at
- least two of the structures in the currently associated alignment view.</em>
- <ul>
- <li><strong><a name="sAlign">Align</a> <br>
- </strong><em> When selected, the associated alignment will be used to
- superimpose all the structures in the view onto the first structure in
- the alignment. The regions used to calculate the superposition will be
- highlighted using the 'Cartoon' rendering style, and the remaining
- data shown as a chain trace.<br></em></li>
- </ul>
- </li>
- <li><strong>Help<br>
- </strong>
- <ul>
- <li><strong>Chimera Help<br>
- </strong><em>Access the Chimera Help documentation in a new browser window.</em></li>
- </ul>
- </li>
-</ul>
-<p><strong>Chimera and Windows Firewall</strong></p>
-Jalview and Chimera communicate using Chimera's <a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST service</a> (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).<br>
-Technically this requires both Chimera and Jalview to open ports on the local network, and this may be blocked by Windows Firewall with a warning message such as<br/>
-"Windows Firewall has blocked some features of this program" (where the program may be jp2launcher.exe for Jalview Webstart, or java.exe or javaw.exe for the InstallAnywhere version).<br/>
-To allow Jalview and Chimera to interact, you may need to add permission for the program to communicate over the network. This can be done from the warning dialogue, or in Control Panel, Firewall settings.
+ <p>
+ <a name="align"><strong>Superposing structures based on
+ their aligned sequences</strong></a><br> If several structures are
+ available on the alignment, you may add additional structures to an
+ existing Chimera view by selecting their entry in the appropriate
+ pop-up menu. Jalview will ask you if you wish to add the structure
+ to the existing alignment, and if you do, it will import and
+ superimpose the new PDB file using the corresponding positions from
+ the alignment. If the alignment is subsequently edited, you can use
+ the <a href="#sAlign"><em>Chimera→Align</em></a> menu option
+ from the menu bar of the structure view window to superpose the
+ structures using the updated alignment.<br>
+ </p>
+ <p>
+ <strong>Chimera Controls</strong><br> The structure is by
+ default rendered as a ribbon diagram. Moving the mouse over the
+ structure brings up tooltips giving the residue name, PDB residue
+ number and chain code ([RES]Num:Chain). Moving the mouse over an
+ associated residue in an alignment window highlights the associated
+ atoms in the displayed structures. When residues are selected in the
+ Chimera window, they are highlighted on the alignment. For
+ comprehensive details of Chimera's commands, refer to the tool's
+ Help menu.
+ <p>
+ Basic screen operations (see <a
+ href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html"
+ >Chimera help</a> at
+ http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html
+ for full details).
+ <table border="1">
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Zoom</td>
+ <td>Right Click<br> drag mouse up or down
+ </td>
+ <td>Right Click<br>drag mouse up or down
+ </td>
+ <td>cmd or Right + Click and drag mouse up or down, <br>or
+ use mouse scroll button
+ </td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Middle Button + Drag</td>
+ <td>Middle Button and drag</td>
+ <td>alt + Click<br> and drag
+ </td>
+ </tr>
+ <tr>
+ <td>Select Residues</td>
+ <td>Ctrl + Click (and drag to select a region)</td>
+ <td>Ctrl + Click (and drag)</td>
+ <td>Ctrl + Click (and drag)</td>
+ </tr>
+ </table>
+ </p>
+ <p>
+ <strong>Jalview Controls</strong>
+ <p>The Jalview Chimera View window has up to five menus:</p>
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>Show Chains<br>
+ </strong><em>Select which of the PDB file's chains (if more than
+ one) are to be displayed.</em></li>
+ <li><strong>Colour by ..<br></strong><em>Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:</em>
+ <ul>
+ <li><strong>Select many views<br></strong><em>When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.</em></li>
+ <li><strong>Select all views<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.</em></li>
+ <li><strong>Invert selection<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.</em></li>
+ </ul></li>
+ </ul>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ Uniprot sequence features or region colourings.<br />Pick
+ which of the associated alignment views are used to colour
+ the structures using the <strong>View→Colour
+ by ..</strong> sub menu.
+ </em><br> Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em>Uses the Chimera 'rainbow chain' command to apply a
+ different colour to each chain.</em></li>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong>Colour with Chimera<br></strong><em>Defers
+ any colouring operations to Chimera. Select this if you want
+ to use the Chimera scripting interface or menu to modify the
+ view directly.</em></li>
+ <li><strong>Standard and User Defined Jalview
+ colourschemes.<br>
+ </strong><em>The remaining entries apply the colourschemes available
+ from the standard and user defined <a
+ href="../colourSchemes/index.html"
+ >amino acid colours</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Chimera<br>
+ </strong><em>This pulldown menu is only displayed if there are multiple
+ structures shown in the Chimera window, and Jalview can also
+ locate at least two of the structures in the currently
+ associated alignment view.</em>
+ <ul>
+ <li><strong><a name="sAlign">Align</a> <br> </strong><em>
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ structure in the alignment. The regions used to calculate
+ the superposition will be highlighted using the 'Cartoon'
+ rendering style, and the remaining data shown as a chain
+ trace.<br>
+ </em></li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Chimera Help<br>
+ </strong><em>Access the Chimera Help documentation in a new browser
+ window.</em></li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong>Chimera and Windows Firewall</strong>
+ </p>
+ Jalview and Chimera communicate using Chimera's
+ <a
+ href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html"
+ >REST service</a>
+ (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
+ <br> Technically this requires both Chimera and Jalview to open
+ ports on the local network, and this may be blocked by Windows
+ Firewall with a warning message such as
+ <br /> "Windows Firewall has blocked some features of this program"
+ (where the program may be jp2launcher.exe for Jalview Webstart, or
+ java.exe or javaw.exe for the InstallAnywhere version).
+ <br /> To allow Jalview and Chimera to interact, you may need to add
+ permission for the program to communicate over the network. This can
+ be done from the warning dialogue, or in Control Panel, Firewall
+ settings.
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<title>Jalview Command Line Arguments
-</title>
+<title>Jalview Command Line Arguments</title>
<body>
- <p><strong>The Jalview Executable's Command Line
- Arguments</strong></p>
- See <a href="commandline.html">running Jalview from the command
- line</a> for more information.<br>
- <table width="100%" border="1" cellspacing="0" cellpadding="0">
- <tr >
- <td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
- </tr>
+ <p>
+ <strong>The Jalview Executable's Command Line Arguments</strong>
+ </p>
+ See
+ <a href="commandline.html">running Jalview from the command line</a>
+ for more information.
+ <br>
+ <table width="100%" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="27%"><div align="center">-nodisplay</div></td>
+ <td width="73%"><div align="left">Run Jalview without
+ User Interface. (automatically disables questionnaire, version
+ and usage stats checks)</div></td>
+ </tr>
- <tr>
- <td><div align="center">-props FILE/URL</div></td>
- <td><div align="left">Use the given Jalview properties file instead
- of users default.</div></td>
- </tr>
- <tr>
- <td><div align="center">-features FILE/URL</div></td>
- <td><div align="left">
- <p>Use the given file to add sequence features to an alignment.
- See <a href="featuresFormat.html" target="NEW">Features
- File</a> (Known as Groups file prior to 2.08) description. </p>
+ <tr>
+ <td><div align="center">-props FILE/URL</div></td>
+ <td><div align="left">Use the given Jalview properties
+ file instead of users default.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-features FILE/URL</div></td>
+ <td><div align="left">
+ <p>
+ Use the given file to add sequence features to an alignment.
+ See <a href="featuresFormat.html" target="NEW">Features
+ File</a> (Known as Groups file prior to 2.08) description.
+ </p>
- </div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-colour COLOURSCHEME</div>
- </td>
- <td>Set the colourscheme for the alignment. This can be any of
- the built-in colourschemes, a name of a predefined colourscheme
- (defined in the Jalview properties file), or an 'inline' colourscheme
- (see the applet's colour parameter for more information).</td>
- </tr>
- <tr>
- <td>
- <div align="center">-annotations FILE/URL</div>
- </td>
- <td>Add precalculated annotations to the alignment. See <a
- href="annotationsFormat.html" target="NEW">Annotation File</a>
- description.</td>
- </tr>
- <tr>
- <td>
- <div align="center">-tree FILE/URL</div>
- <td>
- <div align="left">Load the given newick format tree file onto
- the alignment</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-questionnaire URL</div>
- <td>
- <div align="left">Queries the given URL for information about
- any Jalview user questionnaires</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-noquestionnaire</div>
- <td>
- <div align="left">Turn off questionnaire check</div>
- </td>
- </tr>
- <tr><td>
- <div align="center">-nousagestats</div>
- <td>
- <div align="left">Turn off google analytics usage tracking</div>
- </td>
- </tr>
- <tr><td>
- <div align="center">-[no]sortbytree</div>
- <td>
- <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-dasserver nickname=URL</div>
- <td>
- <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments<br>
- Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
- <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-fetchfrom nickname</div>
- <td>
- <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
- and display them</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-groovy FILE/URL</div>
- <td>
- <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
- arguments have been processed</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-jabaws URL</div>
- <td>
- <div align="left">Specify the URL of the preferred JABAWS server</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
- <td>
- <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-vsess VAMSAS SESSION URL</div>
- <td>
- <div align="left">Join the given vamsas session<br>If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).<em>New in 2.5</em></div></div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-fasta FILE</div>
- </td>
+ </div></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-colour COLOURSCHEME</div>
+ </td>
+ <td>Set the colourscheme for the alignment. This can be any
+ of the built-in colourschemes, a name of a predefined
+ colourscheme (defined in the Jalview properties file), or an
+ 'inline' colourscheme (see the applet's colour parameter for
+ more information).</td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-annotations FILE/URL</div>
+ </td>
+ <td>Add precalculated annotations to the alignment. See <a
+ href="annotationsFormat.html" target="NEW"
+ >Annotation File</a> description.
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-tree FILE/URL</div>
+ <td>
+ <div align="left">Load the given newick format tree file
+ onto the alignment</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-questionnaire URL</div>
+ <td>
+ <div align="left">Queries the given URL for information
+ about any Jalview user questionnaires</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-noquestionnaire</div>
+ <td>
+ <div align="left">Turn off questionnaire check</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-nousagestats</div>
+ <td>
+ <div align="left">Turn off google analytics usage tracking</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-[no]sortbytree</div>
+ <td>
+ <div align="left">Enable or disable automatic sorting of
+ associated view when a new tree is displayed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-dasserver nickname=URL</div>
+ <td>
+ <div align="left">
+ Add and enable a <a href="dassettings.html">DAS server</a>
+ with given nickname (alphanumeric or underscores only) for
+ retrieval of features for all alignments<br> Sources that
+ also support the sequence command may be specified by
+ prepending the URL with 'sequence:'<br> <em>e.g.</em>
+ sequence:http://localdas.somewhere.org/das/source
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fetchfrom nickname</div>
+ <td>
+ <div align="left">
+ Query a <a href="dassettings.html">DAS source</a> called
+ nickname for features for the alignments and display them
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-groovy FILE/URL</div>
+ <td>
+ <div align="left">Execute groovy script in FILE (where
+ FILE may be 'STDIN' to read from the standard input) after all
+ other arguments have been processed</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-jabaws URL</div>
+ <td>
+ <div align="left">Specify the URL of the preferred JABAWS
+ server</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
+ <td>
+ <div align="left">
+ Import the given vamsas document into a new session.<br>
+ <em>New in 2.5</em>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-vsess VAMSAS SESSION URL</div>
+ <td>
+ <div align="left">
+ Join the given vamsas session<br>If a document was also
+ specified, this will be imported first and then committed as
+ new data from Jalview to the specified session (Experimental -
+ not yet enabled!).<em>New in 2.5</em>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fasta FILE</div>
+ </td>
- <td>
- <div align="left">Create alignment file FILE in Fasta format.</div>
- </td>
- </tr>
- <tr>
- <td><div align="center">-clustal FILE</div></td>
- <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-msf FILE</div></td>
+ <td>
+ <div align="left">Create alignment file FILE in Fasta
+ format.</div>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">-clustal FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Clustal format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-msf FILE</div></td>
- <td><div align="left">Create alignment file FILE in MSF format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pileup FILE</div></td>
- <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pir FILE</div></td>
+ <td><div align="left">Create alignment file FILE in MSF
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pileup FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Pileup format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pir FILE</div></td>
- <td><div align="left">Create alignment file FILE in PIR format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pfam FILE</div></td>
- <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-blc FILE</div></td>
- <td><div align="left">Create alignment file FILE in BLC format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-json FILE</div></td>
- <td><div align="left">Create alignment file FILE in JSON format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-jalview FILE</div></td>
+ <td><div align="left">Create alignment file FILE in PIR
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-pfam FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ PFAM format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-blc FILE</div></td>
+ <td><div align="left">Create alignment file FILE in BLC
+ format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ JSON format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-jalview FILE</div></td>
- <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-png FILE</div></td>
- <td><div align="left">Create PNG image FILE from alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-imgMap FILE</div></td>
+ <td><div align="left">Create alignment file FILE in
+ Jalview format.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-png FILE</div></td>
+ <td><div align="left">Create PNG image FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-imgMap FILE</div></td>
- <td><div align="left">Create HTML file FILE with image map of PNG
- image.</div></td>
- </tr>
- <tr>
- <td><div align="center">-eps FILE</div></td>
- <td><div align="left">Create EPS file FILE from alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-svg FILE</div></td>
- <td><div align="left">Create Scalable Vector Graphics file FILE from alignment.</div></td>
- </tr>
- </table>
+ <td><div align="left">Create HTML file FILE with image
+ map of PNG image.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-eps FILE</div></td>
+ <td><div align="left">Create EPS file FILE from
+ alignment.</div></td>
+ </tr>
+ <tr>
+ <td><div align="center">-svg FILE</div></td>
+ <td><div align="left">Create Scalable Vector Graphics
+ file FILE from alignment.</div></td>
+ </tr>
+ </table>
</body>
</html>
<title>DNA Sequence Coding Region Definition</title>
</head>
<body>
-<p><strong>DNA Sequence Coding Region Definition</strong></p>
-<p>Jalview includes the standard DNA codon translation table in
-order to be able to dynamically translate cDNA to its expressed
-protein sequence. DNA Sequence Coding Regions are sequence
-features that can be defined on any DNA sequence in order to
-mark stretches of cDNA that will be concatenated to form the
-series of codons that are translated by the <strong>"
-Calculate→Translate cDNA"</strong> menu function.
-</p>
+ <p>
+ <strong>DNA Sequence Coding Region Definition</strong>
+ </p>
+ <p>
+ Jalview includes the standard DNA codon translation table in order
+ to be able to dynamically translate cDNA to its expressed protein
+ sequence. DNA Sequence Coding Regions are sequence features that can
+ be defined on any DNA sequence in order to mark stretches of cDNA
+ that will be concatenated to form the series of codons that are
+ translated by the <strong>" Calculate→Translate
+ cDNA"</strong> menu function.
+ </p>
</body>
</html>
or hidden according to annotation rows on the alignment. The dialog
box is opened <em>via</em> "<strong>Select→Select/Hide
Columns by Annotation...</strong>", and different filters are
- presented dependent upon the data shown in the selected annotation row.
+ presented dependent upon the data shown in the selected annotation
+ row.
</p>
<table>
<tr>
</tr>
</table>
- <p>If an annotation with numeric values is selected, the
- threshold filter option is activated. For other types of annotation,
- use the text box and secondary structure check boxes (right). The
- radio buttons at the bottom of the dialog specify the action applied
- to columns matching the query.</p>
+ <p>If an annotation with numeric values is selected, the threshold
+ filter option is activated. For other types of annotation, use the
+ text box and secondary structure check boxes (right). The radio
+ buttons at the bottom of the dialog specify the action applied to
+ columns matching the query.</p>
<ul>
<li><strong>Search Filter</strong>
<ul>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Running Jalview from the command line</title></head>
+<head>
+<title>Running Jalview from the command line</title>
+</head>
<body>
- <p><strong>Running Jalview from the command line</strong></p>
- <p>Jalview is most easily run from the command line if you have built
- it from source, or via the 'Jalview' executable created from the
- InstallAnywhere Jalview installation. Both of these mechanisms allow
- true command line execution of Jalview - allowing you to provide
- additional options.</p><p>
-The Java Webstart version of
- Jalview can be executed from the command line using something like
- :
- <pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open
- <em>yourFileName</em></pre>
- But, this is not guaranteed to work on all versions of webstart on all
- operating systems, and doesn't let you execute Jalview with any
- additional parameters.
- <p><strong>Running Jalview from the InstallAnywhere
- installation</strong></p>
- <p>If you install with InstallAnywhere you can use several more commands.
- However, if you call the application with the link provided by InstallAnywhere
- any output from the application will be sent to output.txt, not standard
- out.<br>
- The Jalview application also requires a number of additional
- libraries on the class path. The command line below adds the Jalview
- installation's 'lib' directory to the list of directories that are
- searched for jars to be added to the classpath:</p>
-<pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>
- <p>Use '-help' to get more information on the <a
- href="clarguments.html">command line arguments</a> that Jalview
- accepts.</p>
- <p> </p>
- <p> </p>
- </body>
- </html>
+ <p>
+ <strong>Running Jalview from the command line</strong>
+ </p>
+ <p>Jalview is most easily run from the command line if you have
+ built it from source, or via the 'Jalview' executable created from
+ the InstallAnywhere Jalview installation. Both of these mechanisms
+ allow true command line execution of Jalview - allowing you to
+ provide additional options.</p>
+ <p>The Java Webstart version of Jalview can be executed from the
+ command line using something like :
+ <pre>javaws http://www.jalview.org/webstart/jalview.jnlp -open
+ <em>yourFileName</em>
+ </pre>
+ But, this is not guaranteed to work on all versions of webstart on all
+ operating systems, and doesn't let you execute Jalview with any
+ additional parameters.
+ <p>
+ <strong>Running Jalview from the InstallAnywhere
+ installation</strong>
+ </p>
+ <p>
+ If you install with InstallAnywhere you can use several more
+ commands. However, if you call the application with the link
+ provided by InstallAnywhere any output from the application will be
+ sent to output.txt, not standard out.<br> The Jalview
+ application also requires a number of additional libraries on the
+ class path. The command line below adds the Jalview installation's
+ 'lib' directory to the list of directories that are searched for
+ jars to be added to the classpath:
+ </p>
+ <pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>
+ <p>
+ Use '-help' to get more information on the <a
+ href="clarguments.html"
+ >command line arguments</a> that Jalview accepts.
+ </p>
+ <p> </p>
+ <p> </p>
+</body>
+</html>
<title>Creating Sequence Features</title>
</head>
<body>
-<strong>Creating Sequence Features</strong>
-<p>Jalview can create sequence features from the matches of a <a
- href="search.html">regular expression search</a>, or from the currently
-selected area via the <strong>"selection→Create
-sequence feature"</strong> entry in the <a href="../menus/popupMenu.html">selection area popup menu</a>. In both
-cases, the <strong>Create Features</strong> dialog box will then be
-opened:</p>
-<p><img src="crnewfeature.gif"></p>
-<p>Select or enter the attributes for the features being created,
-and then press OK to create the new features.</p>
-<p>Each attribute is described below:
-<ul>
- <li><strong>Sequence Feature Name</strong>
- <p>Either give the new features a new name or use the menu to
- re-use an existing feature name.</p>
- </li>
- <li><strong>Feature group</strong>
- <p>Enter a new group name, or re-use an existing group from the
- pull-down menu.</p>
- </li>
- <li><strong>Feature Colour</strong>
- <p>Keep the existing colour for this feature's name and group, or
- select the colour box to open a colour chooser to pick a different one.</p>
- </li>
- <li><strong>Description</strong>
- <p>Enter a description for all the features being created. Each
- feature defined on a sequence may have its own description that will be
- displayed in the tooltip for the feature in that region.</p>
- </li>
-</ul>
-</p><p><em>Sequence Feature Creation was introduced in Jalview Version 2.2</em></p>
+ <strong>Creating Sequence Features</strong>
+ <p>
+ Jalview can create sequence features from the matches of a <a
+ href="search.html"
+ >regular expression search</a>, or from the currently selected area
+ via the <strong>"selection→Create sequence
+ feature"</strong> entry in the <a href="../menus/popupMenu.html">selection
+ area popup menu</a>. In both cases, the <strong>Create
+ Features</strong> dialog box will then be opened:
+ </p>
+ <p>
+ <img src="crnewfeature.gif">
+ </p>
+ <p>Select or enter the attributes for the features being created,
+ and then press OK to create the new features.</p>
+ <p>Each attribute is described below:
+ <ul>
+ <li><strong>Sequence Feature Name</strong>
+ <p>Either give the new features a new name or use the menu to
+ re-use an existing feature name.</p></li>
+ <li><strong>Feature group</strong>
+ <p>Enter a new group name, or re-use an existing group from
+ the pull-down menu.</p></li>
+ <li><strong>Feature Colour</strong>
+ <p>Keep the existing colour for this feature's name and group,
+ or select the colour box to open a colour chooser to pick a
+ different one.</p></li>
+ <li><strong>Description</strong>
+ <p>Enter a description for all the features being created.
+ Each feature defined on a sequence may have its own description
+ that will be displayed in the tooltip for the feature in that
+ region.</p></li>
+ </ul>
+ </p>
+ <p>
+ <em>Sequence Feature Creation was introduced in Jalview Version
+ 2.2</em>
+ </p>
</body>
</html>
<title>Cursor Mode</title>
</head>
<body>
-<p><strong>Cursor Mode</strong></p>
-<p>Cursor mode is a new feature in Jalview 2.08, and allows more
-precise selection and editing of alignments through the use of the
-keyboard for both navigation and the input of editing and selection commands.</p>
-<p><em>F2</em> Toggles between normal and cursor editing modes. When
-in cursor mode, a black cursor appears in the residue area of the
-alignment, and any mouse clicks on that area will move the cursor to
-that position (this means that the region selection menu is
-unavailable in cursor mode).</p>
-<p><b>Navigation</b>
-<ul>
- <li>Cursor keys - Move cursor around the alignment.</li>
-</ul>
-<ul>
- <li>S - Type a number x then press 'S' to jump to sequence x.</li>
-</ul>
-<ul>
- <li>C - Type a number x then press 'C' to jump to column x.</li>
-</ul>
-<ul>
- <li>P - Type a number x then press 'P' to jump to position x in current sequence.</li>
-</ul>
-<ul>
- <li>65,82<return> - Quick jump to column 65, sequence 82</li>
-</ul>
-</p>
-<p><b>Defining Regions</b>
-<ul>
- <li>Q - Define the top left corner of the selection area</li>
-</ul>
-<ul>
- <li>M - Define the bottom right corner of the selection area<br>
- </li>
-</ul>
-<p><b>Editing The Alignment</b>
-<ul>
- <li>Space - Insert a gap at the cursor position. <br>
- To insert 12 spaces at the current cursor, type 12 before pressing Space.<br>
- To group insert, hold control or shift together with space.</li>
-</ul>
-<ul>
- <li>Delete (or backspace) - Delete a gap at the cursor position.<br>
- To delete 12 spaces at the current cursor, type 12 before pressing
- Delete (or backspace).<br>
- To group delete, hold down control or shift together with Delete
- (or backspace).</li>
-</ul>
-</p>
+ <p>
+ <strong>Cursor Mode</strong>
+ </p>
+ <p>Cursor mode is a new feature in Jalview 2.08, and allows more
+ precise selection and editing of alignments through the use of the
+ keyboard for both navigation and the input of editing and selection
+ commands.</p>
+ <p>
+ <em>F2</em> Toggles between normal and cursor editing modes. When in
+ cursor mode, a black cursor appears in the residue area of the
+ alignment, and any mouse clicks on that area will move the cursor to
+ that position (this means that the region selection menu is
+ unavailable in cursor mode).
+ </p>
+ <p>
+ <b>Navigation</b>
+ <ul>
+ <li>Cursor keys - Move cursor around the alignment.</li>
+ </ul>
+ <ul>
+ <li>S - Type a number x then press 'S' to jump to sequence x.</li>
+ </ul>
+ <ul>
+ <li>C - Type a number x then press 'C' to jump to column x.</li>
+ </ul>
+ <ul>
+ <li>P - Type a number x then press 'P' to jump to position x in
+ current sequence.</li>
+ </ul>
+ <ul>
+ <li>65,82<return> - Quick jump to column 65, sequence 82</li>
+ </ul>
+ </p>
+ <p>
+ <b>Defining Regions</b>
+ <ul>
+ <li>Q - Define the top left corner of the selection area</li>
+ </ul>
+ <ul>
+ <li>M - Define the bottom right corner of the selection area<br>
+ </li>
+ </ul>
+ <p>
+ <b>Editing The Alignment</b>
+ <ul>
+ <li>Space - Insert a gap at the cursor position. <br> To
+ insert 12 spaces at the current cursor, type 12 before pressing
+ Space.<br> To group insert, hold control or shift together
+ with space.
+ </li>
+ </ul>
+ <ul>
+ <li>Delete (or backspace) - Delete a gap at the cursor
+ position.<br> To delete 12 spaces at the current cursor, type
+ 12 before pressing Delete (or backspace).<br> To group
+ delete, hold down control or shift together with Delete (or
+ backspace).
+ </li>
+ </ul>
+ </p>
</body>
</html>
</head>
<body>
-<p><strong>DAS Sequence Feature Retrieval</strong></p>
-<p>Jalview includes a client for retrieving sequences and their features via
-the <a href="http://www.biodas.org">Distributed Annotation System</a>.</p>
-<ol>
- <li>Open the Feature Settings panel by selecting "View ->
- Feature Settings..."</li>
- <li>Click on the "<a href="dassettings.html">DAS Settings</a>"
- tabbed pane.</li>
- <li>Select the sources to use for DAS feature retrieval, then
- click the "Fetch DAS Features" button.
- <ul>
- <li>Cancelling Feature Retrieval<br>
- Press the <strong>Cancel Fetch</strong> button to immediately stop
- feature retrieval. This will not remove any features already added to
- the alignment, but will halt any outstanding DAS requests.<em>The
- cancel fetch button is of particular use when one or more DAS
- annotation servers are not responding!</em>
- </ul>
- </li>
-</ol>
-<p>If your DAS source selection contains sources which use Uniprot
-accession ids, you will be asked whether Jalview should find Uniprot
-Accession ids for the given sequence names. It is important to realise
-that many DAS sources only use Uniprot accession ids, rather than
-Swissprot/Uniprot sequence names.<br>
-The <a href="../webServices/dbreffetcher.html">database reference
-fetcher</a> documentation describes how Jalview discovers what database
-references are appropriate for the sequences in the alignment.
-<ul>
- <li><em>Note</em><br>
- Please remember to save your alignment if either the start/end
- numbering, or the sequence IDs were updated during the ID
- retrieval process.</li>
-</ul>
-<p>
-<p><em>DAS support was introduced in Jalview Version 2.1.</em></p>
-<p>
+ <p>
+ <strong>DAS Sequence Feature Retrieval</strong>
+ </p>
+ <p>
+ Jalview includes a client for retrieving sequences and their
+ features via the <a href="http://www.biodas.org">Distributed
+ Annotation System</a>.
+ </p>
+ <ol>
+ <li>Open the Feature Settings panel by selecting "View
+ -> Feature Settings..."</li>
+ <li>Click on the "<a href="dassettings.html">DAS
+ Settings</a>" tabbed pane.
+ </li>
+ <li>Select the sources to use for DAS feature retrieval, then
+ click the "Fetch DAS Features" button.
+ <ul>
+ <li>Cancelling Feature Retrieval<br> Press the <strong>Cancel
+ Fetch</strong> button to immediately stop feature retrieval. This
+ will not remove any features already added to the alignment,
+ but will halt any outstanding DAS requests.<em>The cancel
+ fetch button is of particular use when one or more DAS
+ annotation servers are not responding!</em>
+ </ul>
+ </li>
+ </ol>
+ <p>
+ If your DAS source selection contains sources which use Uniprot
+ accession ids, you will be asked whether Jalview should find Uniprot
+ Accession ids for the given sequence names. It is important to
+ realise that many DAS sources only use Uniprot accession ids, rather
+ than Swissprot/Uniprot sequence names.<br> The <a
+ href="../webServices/dbreffetcher.html"
+ >database reference fetcher</a> documentation describes how Jalview
+ discovers what database references are appropriate for the sequences
+ in the alignment.
+ <ul>
+ <li><em>Note</em><br> Please remember to save your
+ alignment if either the start/end numbering, or the sequence IDs
+ were updated during the ID retrieval process.</li>
+ </ul>
+ <p>
+ <p>
+ <em>DAS support was introduced in Jalview Version 2.1.</em>
+ </p>
+ <p>
</body>
</html>
</head>
<body>
-<p><strong>DAS Settings</strong></p>
-<p>Jalview can retrieve sequences and features from many <a
- href="http://biodas.org/">DAS</a> sources. The DAS sources that
-it uses are discovered and selected <em>via</em> the DAS settings panel,
-opened either from the <a href="featuresettings.html">View→Feature
-Settings</a> dialog box from the alignment window's menu bar, or the <a
- href="featuresettings.html">Tools→Preferences</a> dialog box
-opened from the Desktop menu bar.</p>
-<p><img src="das.gif">
-<p>The available sources are listed in the table using each source's
-Nickname as its identifier. Clicking on a source's entry in the table
-reveals more information about that service in the panel to the right.
-Select the tickbox in the "Use Source" column for a source to
-add it to the set Jalview queries for alignment and sequence features.</p>
-<p>You can filter the visible DAS sources by authority, type and
-"label". You should read the DAS documentation to understand
-more about these values.
-<p><strong>Updating the list of sources</strong></p>
-<p>When the DAS Settings panel is first opened, and when the <strong>'Refresh
-source'</strong> buton is pressed, a list of DAS sources is retrieved from the
-DAS registry URL. Note that the registry hosted at http://www.dasregistry.org/das/ was retired at the start of 2015.
-An alternative service is currently hosted at http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this service, ensure your .jalview_properties file includes the following line:<br>
-<b>DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/</b>
-</p>
-<p><strong>Adding your own DAS Sources</strong></p>
-<p>You can add your own DAS source to the list by clicking the
-"Add Local Source" button. Enter the URL and nickname of your
-additional service. It should be noted that Jalview 2.1 will not query
-additional sources for more information, but this will be implemented in
-future editions.
-<p>
+ <p>
+ <strong>DAS Settings</strong>
+ </p>
+ <p>
+ Jalview can retrieve sequences and features from many <a
+ href="http://biodas.org/"
+ >DAS</a> sources. The DAS sources that it uses are discovered and
+ selected <em>via</em> the DAS settings panel, opened either from the
+ <a href="featuresettings.html">View→Feature Settings</a>
+ dialog box from the alignment window's menu bar, or the <a
+ href="featuresettings.html"
+ >Tools→Preferences</a> dialog box opened from the Desktop menu
+ bar.
+ </p>
+ <p>
+ <img src="das.gif">
+ <p>The available sources are listed in the table using each
+ source's Nickname as its identifier. Clicking on a source's entry in
+ the table reveals more information about that service in the panel
+ to the right. Select the tickbox in the "Use Source"
+ column for a source to add it to the set Jalview queries for
+ alignment and sequence features.</p>
+ <p>You can filter the visible DAS sources by authority, type and
+ "label". You should read the DAS documentation to
+ understand more about these values.
+ <p>
+ <strong>Updating the list of sources</strong>
+ </p>
+ <p>
+ When the DAS Settings panel is first opened, and when the <strong>'Refresh
+ source'</strong> buton is pressed, a list of DAS sources is retrieved from
+ the DAS registry URL. Note that the registry hosted at
+ http://www.dasregistry.org/das/ was retired at the start of 2015. An
+ alternative service is currently hosted at
+ http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this
+ service, ensure your .jalview_properties file includes the following
+ line:<br> <b>DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/</b>
+ </p>
+ <p>
+ <strong>Adding your own DAS Sources</strong>
+ </p>
+ <p>You can add your own DAS source to the list by clicking the
+ "Add Local Source" button. Enter the URL and nickname of
+ your additional service. It should be noted that Jalview 2.1 will
+ not query additional sources for more information, but this will be
+ implemented in future editions.
+ <p>
</body>
</html>
<title>Amending or Deleting Sequence Features</title>
</head>
<body>
-<strong>Amending or Deleting Sequence Features</strong>
-<p>Double clicking a position in the alignment with one or more
-displayed sequence features opens the <strong>"Amend/Delete
-Features"</strong> dialog box.</p>
-<p><img src="amendfeature.gif"></p>
-<p>The dialog box only allows one of the features at the
-double-clicked position to be edited or deleted at a time, and it will
-also be highlighted in black in the alignment window.</p>
-<p>Choose which feature is to be modified by selecting it from the <strong>Sequence
-Feature Name</strong> <!-- and <strong>Feature Group</strong> --> pull down
-menu. In addition to the Name, group, colour and description attributes
-described for the <a href="creatinFeatures.html">new feature dialog
-box</a>, a feature's start and end position can be changed either by
-entering a new position directly or by using the adjacent up and down
-buttons.</p>
-<p>Select <strong>Amend</strong> to update the feature, <strong>Delete</strong>
-to remove the selected feature, or <strong>Cancel</strong> to leave the
-feature unchanged.</p>
-<p><em>Sequence feature editing was implemented in Jalview 2.2</em></p>
+ <strong>Amending or Deleting Sequence Features</strong>
+ <p>
+ Double clicking a position in the alignment with one or more
+ displayed sequence features opens the <strong>"Amend/Delete
+ Features"</strong> dialog box.
+ </p>
+ <p>
+ <img src="amendfeature.gif">
+ </p>
+ <p>The dialog box only allows one of the features at the
+ double-clicked position to be edited or deleted at a time, and it
+ will also be highlighted in black in the alignment window.</p>
+ <p>
+ Choose which feature is to be modified by selecting it from the <strong>Sequence
+ Feature Name</strong>
+ <!-- and <strong>Feature Group</strong> -->
+ pull down menu. In addition to the Name, group, colour and
+ description attributes described for the <a
+ href="creatinFeatures.html"
+ >new feature dialog box</a>, a feature's start and end position can be
+ changed either by entering a new position directly or by using the
+ adjacent up and down buttons.
+ </p>
+ <p>
+ Select <strong>Amend</strong> to update the feature, <strong>Delete</strong>
+ to remove the selected feature, or <strong>Cancel</strong> to leave
+ the feature unchanged.
+ </p>
+ <p>
+ <em>Sequence feature editing was implemented in Jalview 2.2</em>
+ </p>
</body>
</html>
<title>Sequence Features File</title>
</head>
<body>
-<p><strong>Sequence Features File</strong><p>
-<p>
-The Sequence features file (which used to be known as the
-"Groups file" prior to version 2.08) is a simple way of getting
-your own sequence annotations into Jalview. It was introduced to
-allow sequence features to be rendered in the Jalview applet, and
-so is intentionally lightweight and minimal because the applet is
-often used in situations where data file size must be kept to a
-minimum, and no XML parser is available.</p>
-
-<p>Features files are imported into Jalview in the following
-ways:<br>
-
-<ul>
-<li>from the command line
-
-<pre>
+ <p>
+ <strong>Sequence Features File</strong>
+ <p>
+ <p>The Sequence features file (which used to be known as the
+ "Groups file" prior to version 2.08) is a simple way of getting your
+ own sequence annotations into Jalview. It was introduced to allow
+ sequence features to be rendered in the Jalview applet, and so is
+ intentionally lightweight and minimal because the applet is often
+ used in situations where data file size must be kept to a minimum,
+ and no XML parser is available.</p>
+
+ <p>
+ Features files are imported into Jalview in the following ways:<br>
+ <ul>
+ <li>from the command line <pre>
<strong> -features <<em>Features filename</em>></strong>
</pre>
-</li>
-
-<li>Dragging a features file onto an alignment window</li>
-
-<li>Via the "Load Features / Annotations" entry in the
-<strong>File</strong> menu of an alignment window.</li>
-</ul>
-
-</p>
-
-<p><strong>Sequence Features File Format</strong></p>
-<p>
-A features file is a simple ASCII text file, where each line
-contains tab separated text fields. <strong>No comments are
-allowed</strong>.</p>
-<p>
-The first set of lines contain type definitions:
-
-<pre>
+ </li>
+
+ <li>Dragging a features file onto an alignment window</li>
+
+ <li>Via the "Load Features / Annotations" entry in
+ the <strong>File</strong> menu of an alignment window.
+ </li>
+ </ul>
+
+ </p>
+
+ <p>
+ <strong>Sequence Features File Format</strong>
+ </p>
+ <p>
+ A features file is a simple ASCII text file, where each line
+ contains tab separated text fields. <strong>No comments are
+ allowed</strong>.
+ </p>
+ <p>The first set of lines contain type definitions:
+ <pre>
<strong><em>Feature label</em>	<em>Feature Colour</em>
<!-- 	<em>Feature links</em> --></strong>
</pre>
-A feature type has a text label, and a colour specification. This
-can be either:
+ A feature type has a text label, and a colour specification. This can
+ be either:
-<ul>
-<li>A single colour specified as either a red,green,blue 24 bit
-triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
-(ranging from 0 to 255))</li>
+ <ul>
+ <li>A single colour specified as either a red,green,blue 24 bit
+ triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
+ (ranging from 0 to 255))</li>
-<li>A <a href="featureschemes.html">graduated colourscheme</a>
-specified as a "|" separated list of fields:
-
-<pre>
+ <li>A <a href="featureschemes.html">graduated colourscheme</a>
+ specified as a "|" separated list of fields: <pre>
[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
-</pre>
-
-The fields are as follows:
-
-<ul>
-<li><em>label</em><br>
- Indicate that the feature description should be used to create a
-colour for features of this type.<br>
-<em>Note: if no threshold value is needed then the final '|' may be
-ommitted.<br>
-This keyword was added in Jalview 2.6</em></li>
-
-<li><em>mincolor</em> and <em>maxcolor</em><br>
- Colour triplets specified as hexadecimal or comma separated values
-(may be left blank for a <em>label</em> style colourscheme, but
-remember to specify the remaining fields)</li>
-
-<li><em>absolute</em><br>
- An optional switch indicating that the <em>minvalue</em> and
-<em>maxvalue</em> parameters should be left as is, rather than
-rescaled according to the range of scores for this feature
-type.</li>
-
-<li><em>minvalue</em> and <em>maxvalue</em><br>
- Minimum and maximum values defining the range of scores for which
-the colour range will be defined over. If minvalue is greater than
-maxvalue then the linear mapping will have negative gradient.</li>
-
-<li><em>thresholdtype</em><br>
- Either "none", "below", or "above". <em>below</em> and
-<em>above</em> require an additional <em>threshold value</em> which
-is used to control the display of features with a score either
-below or above the value.</li>
-</ul>
-</li>
-</ul>
-</p>
-
-<p>The remaining lines in the file are the sequence annotation
-definitions, where the now defined features are attached to regions
-on particular sequences. Each feature can optionally include some descriptive text
-which is displayed in a tooltip when the mouse is near the feature on that
-sequence (and can also be used to generate a colour the feature).</p>
-
-<p>If your sequence annotation is already available in GFF Format (see <a href="http://www.sanger.ac.uk/resources/software/gff/spec.html">http://www.sanger.ac.uk/resources/software/gff/spec.html</a>),
-then you can leave it as is, after first adding a line containing
-only 'GFF' after any Jalview feature colour definitions (<em>this mixed format capability was added in Jalview 2.6</em>). Alternately, you can use Jalview's own sequence feature
-annotation format, which additionally allows HTML and URLs to be
-directly attached to each piece of annotation.</p>
-
-<p><strong>Jalview's sequence feature annotation format</strong></p>
-<p>
-Each feature is specified as a tab-separated series of columns as defined below:
-<pre>
+</pre> The fields are as follows:
+
+ <ul>
+ <li><em>label</em><br> Indicate that the feature
+ description should be used to create a colour for features of
+ this type.<br> <em>Note: if no threshold value is
+ needed then the final '|' may be ommitted.<br> This
+ keyword was added in Jalview 2.6
+ </em></li>
+
+ <li><em>mincolor</em> and <em>maxcolor</em><br> Colour
+ triplets specified as hexadecimal or comma separated values
+ (may be left blank for a <em>label</em> style colourscheme,
+ but remember to specify the remaining fields)</li>
+
+ <li><em>absolute</em><br> An optional switch
+ indicating that the <em>minvalue</em> and <em>maxvalue</em>
+ parameters should be left as is, rather than rescaled
+ according to the range of scores for this feature type.</li>
+
+ <li><em>minvalue</em> and <em>maxvalue</em><br>
+ Minimum and maximum values defining the range of scores for
+ which the colour range will be defined over. If minvalue is
+ greater than maxvalue then the linear mapping will have
+ negative gradient.</li>
+
+ <li><em>thresholdtype</em><br> Either
+ "none", "below", or "above". <em>below</em>
+ and <em>above</em> require an additional <em>threshold
+ value</em> which is used to control the display of features with
+ a score either below or above the value.</li>
+ </ul>
+ </li>
+ </ul>
+ </p>
+
+ <p>The remaining lines in the file are the sequence annotation
+ definitions, where the now defined features are attached to regions
+ on particular sequences. Each feature can optionally include some
+ descriptive text which is displayed in a tooltip when the mouse is
+ near the feature on that sequence (and can also be used to generate
+ a colour the feature).</p>
+
+ <p>
+ If your sequence annotation is already available in GFF Format (see
+ <a href="http://www.sanger.ac.uk/resources/software/gff/spec.html">http://www.sanger.ac.uk/resources/software/gff/spec.html</a>),
+ then you can leave it as is, after first adding a line containing
+ only 'GFF' after any Jalview feature colour definitions (<em>this
+ mixed format capability was added in Jalview 2.6</em>). Alternately,
+ you can use Jalview's own sequence feature annotation format, which
+ additionally allows HTML and URLs to be directly attached to each
+ piece of annotation.
+ </p>
+
+ <p>
+ <strong>Jalview's sequence feature annotation format</strong>
+ </p>
+ <p>Each feature is specified as a tab-separated series of columns
+ as defined below:
+ <pre>
<em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em>	<em>score (optional)</em>
</pre>
-This format allows two alternate ways of referring to a sequence, either by
-its text ID, or its index in an associated alignment. Normally, sequence features are associated with sequences rather
-than alignments, and the sequenceIndex field is given as "-1". In
-order to specify a sequence by its index in a particular alignment,
-the sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the
-sequenceId field will be used in preference to the sequenceIndex
-field.
-</p>
-
-
-<p>The description may contain simple HTML document body tags if
-enclosed by "<html></html>" and these will be rendered
-as formatted tooltips in the Jalview Application (the Jalview
-applet is not capable of rendering HTML tooltips, so all formatting
-tags will be removed).<br>
-<em>Attaching Links to Sequence Features</em><br>
-Any anchor tags in an html formatted description line will be
-translated into URL links. A link symbol will be displayed adjacent
-to any feature which includes links, and these are made available
-from the <a href="../menus/popupMenu.html#sqid.popup">links
-submenu</a> of the popup menu which is obtained by right-clicking
-when a link symbol is displayed in the tooltip.<br>
-<em>Non-positional features</em><br>
-Specify the <em>start</em> and <em>end</em> for a feature to be
-<strong>0</strong> in order to attach it to the whole sequence.
-Non-positional features are shown in a tooltip when the mouse
-hovers over the sequence ID panel, and any embedded links can be
-accessed from the popup menu.<br/> <em>Scores</em><br>
-Scores can be associated with sequence features, and used to sort
-sequences or shade the alignment (this was added in Jalview 2.5).
-The score field is optional, and malformed scores will be
-ignored.</p>
-
-<p>Feature annotations can be collected into named groups by
-prefixing definitions with lines of the form:
-
-<pre>
+ This format allows two alternate ways of referring to a sequence,
+ either by its text ID, or its index in an associated alignment.
+ Normally, sequence features are associated with sequences rather than
+ alignments, and the sequenceIndex field is given as "-1". In
+ order to specify a sequence by its index in a particular alignment,
+ the sequenceId should be given as "ID_NOT_SPECIFIED",
+ otherwise the sequenceId field will be used in preference to the
+ sequenceIndex field.
+ </p>
+
+
+ <p>
+ The description may contain simple HTML document body tags if
+ enclosed by "<html></html>" and these will be
+ rendered as formatted tooltips in the Jalview Application (the
+ Jalview applet is not capable of rendering HTML tooltips, so all
+ formatting tags will be removed).<br> <em>Attaching Links
+ to Sequence Features</em><br> Any anchor tags in an html formatted
+ description line will be translated into URL links. A link symbol
+ will be displayed adjacent to any feature which includes links, and
+ these are made available from the <a
+ href="../menus/popupMenu.html#sqid.popup"
+ >links submenu</a> of the popup menu which is obtained by
+ right-clicking when a link symbol is displayed in the tooltip.<br>
+ <em>Non-positional features</em><br> Specify the <em>start</em>
+ and <em>end</em> for a feature to be <strong>0</strong> in order to
+ attach it to the whole sequence. Non-positional features are shown
+ in a tooltip when the mouse hovers over the sequence ID panel, and
+ any embedded links can be accessed from the popup menu.<br /> <em>Scores</em><br>
+ Scores can be associated with sequence features, and used to sort
+ sequences or shade the alignment (this was added in Jalview 2.5).
+ The score field is optional, and malformed scores will be ignored.
+ </p>
+
+ <p>Feature annotations can be collected into named groups by
+ prefixing definitions with lines of the form:
+ <pre>
<strong>startgroup groupname</strong>
</pre>
-.. and subsequently post-fixing the group with:
+ .. and subsequently post-fixing the group with:
-<pre>
+ <pre>
<strong>endgroup groupname</strong>
</pre>
-Feature grouping was introduced in version 2.08, and used to
-control whether a set of features are either hidden or shown
-together in the <a href="seqfeatures.html">sequence Feature
-settings dialog box</a>.</p>
-
+ Feature grouping was introduced in version 2.08, and used to control
+ whether a set of features are either hidden or shown together in the
+ <a href="seqfeatures.html">sequence Feature settings dialog box</a>.
+ </p>
+
-<p>A complete example is shown below :
-<pre>
+ <p>A complete example is shown below :
+ <pre>
domain	red
metal ion-binding site	00ff00
transit peptide	0,105,215
</head>
<body>
-<p><strong>Sequence feature colour schemes</strong></p>
-<p>Jalview can visualize annotation present on parts of a sequence by
-overlaying colours according to the annotation present at each position.
-It allows features to be colored either according to type, or for a
-particular type, according to an individual feature's associated label
-or score. The <a href="featuresettings.html">Feature Settings dialog
-box</a> controls the order and display of each sequence annotation type, and
-also allows the colour scheme used for the the feature to be changed <em>via</em>
-the 'Graduated Colour' option in the sequence feature pop-up menu
-(obtained by right-clicking on a sequence feature).</p>
+ <p>
+ <strong>Sequence feature colour schemes</strong>
+ </p>
+ <p>
+ Jalview can visualize annotation present on parts of a sequence by
+ overlaying colours according to the annotation present at each
+ position. It allows features to be colored either according to type,
+ or for a particular type, according to an individual feature's
+ associated label or score. The <a href="featuresettings.html">Feature
+ Settings dialog box</a> controls the order and display of each
+ sequence annotation type, and also allows the colour scheme used for
+ the the feature to be changed <em>via</em> the 'Graduated Colour'
+ option in the sequence feature pop-up menu (obtained by
+ right-clicking on a sequence feature).
+ </p>
-<center><img src="featurecoloursettings.gif"><br/>Graduated
-feature colour scheme settings dialog box</img></center>
-<p>The Graduated Feature Colour dialog box has the following
-controls:
-<ul>
- <li><em>Colour by Label</em> - when checked this derives a colour
- for each feature based on the label text.</li>
- <li><em>Min and Max Color boxes</em> - Click on these boxes to set
- the minimum and maximum colours used to shade features by their
- associated score.</li>
- <li><em>Threshold type combo box</em> - Allows features to be
- hidden features if their score is below or above a given threshold.<br />
- <em>Set the threshold using the slider or type it in to the text
- box. The threshold cannot be set outside the available range of feature
- scores.</em>
- </li>
- <li><em>Threshold is Min/Max</em> - When checked, the threshold
- will be used as the upper or lower limit when shading the features
- according to their score using the Min and Max colour.</li>
-</ul>
-</p>
-<p><strong>Icon styles for graduated feature styles</strong><br/>
-<p>When a graduated colourscheme is applied to a feature, it is indicated in the feature settings or amend feature dialog box by the following types of icon:<br/>
-<center><table width="50%" border="1">
-<tr><td><strong>Type of Colouring</strong></td><td><strong>Icon</strong></td></tr>
-<tr><td><em>Graduated colour by Feature Score</em></td><td><img src="fcsminmax.gif"/></td></tr>
-<tr><td><em>Graduated colour thresholded (less than) by feature Score</em></td><td><img src="fcsltthan.gif"/></td></tr>
-<tr><td><em>Graduated colour thresholded (greater than) by feature Score</em></td><td><img src="fcsgtthan.gif"/></td></tr>
-<tr><td><em>Colour by Feature Label (may also be thresholded)</em></td><td><img src="fcsntlabel.gif"/></td></tr>
-<tr>
- <td align="center" colspan="2">
- <em>
- <strong>The current threshold is given in the
- icon's tooltip.</strong>
- </em>
- </td></tr></table></center></p>
-<em>Graduated feature colours were introduced in Jalview 2.5</em>
+ <center>
+ <img src="featurecoloursettings.gif"><br />Graduated feature
+ colour scheme settings dialog box</img>
+ </center>
+ <p>The Graduated Feature Colour dialog box has the following
+ controls:
+ <ul>
+ <li><em>Colour by Label</em> - when checked this derives a
+ colour for each feature based on the label text.</li>
+ <li><em>Min and Max Color boxes</em> - Click on these boxes to
+ set the minimum and maximum colours used to shade features by
+ their associated score.</li>
+ <li><em>Threshold type combo box</em> - Allows features to be
+ hidden features if their score is below or above a given
+ threshold.<br /> <em>Set the threshold using the slider or
+ type it in to the text box. The threshold cannot be set outside
+ the available range of feature scores.</em></li>
+ <li><em>Threshold is Min/Max</em> - When checked, the threshold
+ will be used as the upper or lower limit when shading the features
+ according to their score using the Min and Max colour.</li>
+ </ul>
+ </p>
+ <p>
+ <strong>Icon styles for graduated feature styles</strong><br />
+ <p>
+ When a graduated colourscheme is applied to a feature, it is
+ indicated in the feature settings or amend feature dialog box by the
+ following types of icon:<br />
+ <center>
+ <table width="50%" border="1">
+ <tr>
+ <td><strong>Type of Colouring</strong></td>
+ <td><strong>Icon</strong></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour by Feature Score</em></td>
+ <td><img src="fcsminmax.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour thresholded (less than) by
+ feature Score</em></td>
+ <td><img src="fcsltthan.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Graduated colour thresholded (greater than) by
+ feature Score</em></td>
+ <td><img src="fcsgtthan.gif" /></td>
+ </tr>
+ <tr>
+ <td><em>Colour by Feature Label (may also be
+ thresholded)</em></td>
+ <td><img src="fcsntlabel.gif" /></td>
+ </tr>
+ <tr>
+ <td align="center" colspan="2"><em> <strong>The
+ current threshold is given in the icon's tooltip.</strong>
+ </em></td>
+ </tr>
+ </table>
+ </center>
+ </p>
+ <em>Graduated feature colours were introduced in Jalview 2.5</em>
</body>
</html>
<title>Sequence Feature Settings Dialog Box</title>
</head>
<body>
-<p><strong>Sequence Feature Settings Dialog Box</strong></p>
-<p>Select <strong>View→Feature Settings...</strong> menu entry
-in an alignment window to open the feature settings dialog box, which
-allows you to precisely control the presence and appearance of sequence
-features for the current alignment.</p>
-<center><img src="featureSettings.gif" width="400" height="452">
-<br>
-Sequence Feature Settings for the Jalview Application</img></center>
-<p>The top section of the dialog box lists all the sequence feature
-groups, along with a tickbox for each that controls whether its features
-are displayed. The table in the middle lists all the features in the
-currently selected groups, along with their display style and whether
-they are currently being displayed (only the ticked features and groups
-are displayed). <strong><em>You can change the colour or
-shading style used for a feature in the associated alignment by clicking
-on its colour box.</em></strong></p>
- <p>
- <a name="selectbyfeature"><strong><em>Selecting
- alignment columns by feature</em></strong></a><br> <strong>Double-clicking
- a feature type</strong> in the <strong>Feature
- Settings</strong> dialog allows you to select columns in the
- alignment that contain (or do not contain) features of that type. If a
- region of the alignment is currently selected, then only features in
- the current selection will be searched. The following keys affect the
- way in which selections are made:<ul>
- <li>Hold down <strong>Alt</strong> to select columns not
- containing features of a particular type.
- </li>
- <li>Hold down <strong>Shift</strong> to add columns to the
- current selection.
- </li>
- <li>Press <strong>Command/Windows key</strong> to toggle column
- selection state (XOR)
- </li>
- </ul>
- Options are also provided in the feature's pop-up menu (see below).
- <br />
- <em>Select columns by feature was added in Jalview 2.8.1</em>
- </p>
- <p><strong><em>Feature settings pop-up menu</em></strong><br>
-<strong>Right-click</strong> on a feature to open a pop-up menu that
-allows you to sort the alignment or current selection using that feature
-type (see below), or toggle the type of colouring used for the feature.
-Features may be highlighted with either a single colour or a <a
- href="featureschemes.html">feature colourscheme</a> based on either the
-scores associated with that feature or from the feature's description
-(e.g. to distinguish different names associated with a DOMAIN feature).</p>
-<p><strong>Ordering alignment by features</strong><br>
-The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the
-alignment based on the average score or total number of currently active
-features and groups on each sequence. To order the alignment using a
-specific feature type, use the <em>sort by ..</em> entries in the pop-up
-menu for that type.<br>
-<em>Feature sorting and graduated feature colouring were introduced
-in Jalview 2.5</em></p>
+ <p>
+ <strong>Sequence Feature Settings Dialog Box</strong>
+ </p>
+ <p>
+ Select <strong>View→Feature Settings...</strong> menu entry in
+ an alignment window to open the feature settings dialog box, which
+ allows you to precisely control the presence and appearance of
+ sequence features for the current alignment.
+ </p>
+ <center>
+ <img src="featureSettings.gif" width="400" height="452"> <br>
+ Sequence Feature Settings for the Jalview Application</img>
+ </center>
+ <p>
+ The top section of the dialog box lists all the sequence feature
+ groups, along with a tickbox for each that controls whether its
+ features are displayed. The table in the middle lists all the
+ features in the currently selected groups, along with their display
+ style and whether they are currently being displayed (only the
+ ticked features and groups are displayed). <strong><em>You
+ can change the colour or shading style used for a feature in the
+ associated alignment by clicking on its colour box.</em></strong>
+ </p>
+ <p>
+ <a name="selectbyfeature"><strong><em>Selecting
+ alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+ a feature type</strong> in the <strong>Feature Settings</strong> dialog
+ allows you to select columns in the alignment that contain (or do
+ not contain) features of that type. If a region of the alignment is
+ currently selected, then only features in the current selection will
+ be searched. The following keys affect the way in which selections
+ are made:
+ <ul>
+ <li>Hold down <strong>Alt</strong> to select columns not
+ containing features of a particular type.
+ </li>
+ <li>Hold down <strong>Shift</strong> to add columns to the
+ current selection.
+ </li>
+ <li>Press <strong>Command/Windows key</strong> to toggle column
+ selection state (XOR)
+ </li>
+ </ul>
+ Options are also provided in the feature's pop-up menu (see below).
+ <br />
+ <em>Select columns by feature was added in Jalview 2.8.1</em>
+ </p>
+ <p>
+ <strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
+ on a feature to open a pop-up menu that allows you to sort the
+ alignment or current selection using that feature type (see below),
+ or toggle the type of colouring used for the feature. Features may
+ be highlighted with either a single colour or a <a
+ href="featureschemes.html"
+ >feature colourscheme</a> based on either the scores associated with
+ that feature or from the feature's description (e.g. to distinguish
+ different names associated with a DOMAIN feature).
+ </p>
+ <p>
+ <strong>Ordering alignment by features</strong><br> The 'Seq
+ Sort by Score' and 'Seq Sort by Density' buttons will sort the
+ alignment based on the average score or total number of currently
+ active features and groups on each sequence. To order the alignment
+ using a specific feature type, use the <em>sort by ..</em> entries
+ in the pop-up menu for that type.<br> <em>Feature sorting
+ and graduated feature colouring were introduced in Jalview 2.5</em>
+ </p>
-<p><strong>Transparency and Feature Ordering</strong></p>
-<p>It is important to realise that sequence features are often not
-distinct and often overlap (for example, a metal binding site feature
-may be attached to one position along a stretch of sequence marked with
-a secondary structure feature).</p>
-<p>The ordering of the sequence features in the dialog box list is
-the order used by Jalview for rendering sequence features. A feature at
-the bottom of the list is rendered <em>below</em> a feature higher up in
-the list.<br>
-<em><strong>You can change the order of a feature by
-dragging it up and down the list with the mouse</strong></em>.</p>
-<p>The <strong><em>Optimise order</em></strong> button (currently
-only available in the application) will re-order the feature render
-ordering based on the average length of each feature type.</p>
-<p>The <strong><em>transparency slider setting</em></strong>
-(currently only available in the application version) controls the
-visibility of features rendered below other features. Reducing the
-transparency will mean that features at the top of the list can obscure
-features lower down, and increasing it allows the user to 'see through'
-the upper layers of a set of features.</p>
-<p><strong><em>You can save all features, with their
-current colours and visibility in a Jalview format file. </em></strong></p>
+ <p>
+ <strong>Transparency and Feature Ordering</strong>
+ </p>
+ <p>It is important to realise that sequence features are often not
+ distinct and often overlap (for example, a metal binding site
+ feature may be attached to one position along a stretch of sequence
+ marked with a secondary structure feature).</p>
+ <p>
+ The ordering of the sequence features in the dialog box list is the
+ order used by Jalview for rendering sequence features. A feature at
+ the bottom of the list is rendered <em>below</em> a feature higher
+ up in the list.<br> <em><strong>You can change
+ the order of a feature by dragging it up and down the list with
+ the mouse</strong></em>.
+ </p>
+ <p>
+ The <strong><em>Optimise order</em></strong> button (currently only
+ available in the application) will re-order the feature render
+ ordering based on the average length of each feature type.
+ </p>
+ <p>
+ The <strong><em>transparency slider setting</em></strong> (currently
+ only available in the application version) controls the visibility
+ of features rendered below other features. Reducing the transparency
+ will mean that features at the top of the list can obscure features
+ lower down, and increasing it allows the user to 'see through' the
+ upper layers of a set of features.
+ </p>
+ <p>
+ <strong><em>You can save all features, with their
+ current colours and visibility in a Jalview format file. </em></strong>
+ </p>
</body>
</html>
<title>Groovy Shell</title>
</head>
<body>
- <p>
- <strong>The Groovy Shell</strong>
- </p>
- <p>
- <a href="http://groovy.codehaus.org/">Groovy</a> is an "<em>agile
- and dynamic language for the Java platform</em>". The groovy
- scripting language makes it extremely easy to programmatically
- interact with Java programs, in much the same way that Javascript is
- used to generate and interact with applets and other objects on the
- page.
- </p>
- <p>
- <strong><em>Getting Groovy...</em>
- </strong><br> Jalview Groovy support is only possible if the core groovy
- jars which include the GroovyShell are present on the CLASSPATH when
- Jalview is started.
- </p>
- <p>
- The jars are obtained from the <em>embedded</em> directory within the
- <a href="http://dist.codehaus.org/groovy/distributions">groovy
- distribution</a>. The easiest way of adding them to the Jalview classpath
- is to download and build Jalview from its source distribution, and
- then add the groovy-all-*.jar to the lib directory whose path is given
- in the java.ext.dirs property.
- </p>
- <p>
- <strong>Opening Jalview's Groovy Console</strong><br>If groovy is
- available, then the <strong>Tools→Groovy Console...</strong>
- menu entry will be available from the Jalview Desktop's drop-down
- menu. Selecting this will open the <a
- href="http://groovy.codehaus.org/Groovy+Console">Groovy Console</a>
- which allows you to interactively execute Groovy scripts within the
- Jalview run-time environment.
- </p>
- <p>
- <strong>Executing groovy scripts on Jalview startup</strong><br>
- The -groovy <script> option on the <a href="commandline.html">
- Jalview command line</a> will execute the contents of <script>.
- <script> may be a file, a URL, or alternatively if it is
- "STDIN" then the standard input will be used.<br>
- <em>Note: The groovy script will be executed <strong>after</strong>
- any data is loaded, and <strong>before</strong> images or any output
- files are written. This allows you to perform customised Jalview
- analysis workflows with groovy.</em>
- </p>
- <p>
- <strong>Access to Jalview's functions from Groovy Scripts</strong><br>
- There is as yet no properly defined scripting interface to Jalview,
- but all the public methods of the jalview class hierarchy can be
- called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
- object defined in the groovy environent which corresponds to the
- <pre>jalview.gui.Desktop</pre>
- object which manages all the Jalview windows.
- Here's an example to get you started:
- <br>
- <ul>
- <li>Getting the title, alignment and first sequence from the
- current alignFrame<br> <pre>
+ <p>
+ <strong>The Groovy Shell</strong>
+ </p>
+ <p>
+ <a href="http://groovy.codehaus.org/">Groovy</a> is an "<em>agile
+ and dynamic language for the Java platform</em>". The groovy
+ scripting language makes it extremely easy to programmatically
+ interact with Java programs, in much the same way that Javascript is
+ used to generate and interact with applets and other objects on the
+ page.
+ </p>
+ <p>
+ <strong><em>Getting Groovy...</em> </strong><br> Jalview Groovy
+ support is only possible if the core groovy jars which include the
+ GroovyShell are present on the CLASSPATH when Jalview is started.
+ </p>
+ <p>
+ The jars are obtained from the <em>embedded</em> directory within
+ the <a href="http://dist.codehaus.org/groovy/distributions">groovy
+ distribution</a>. The easiest way of adding them to the Jalview
+ classpath is to download and build Jalview from its source
+ distribution, and then add the groovy-all-*.jar to the lib directory
+ whose path is given in the java.ext.dirs property.
+ </p>
+ <p>
+ <strong>Opening Jalview's Groovy Console</strong><br>If groovy
+ is available, then the <strong>Tools→Groovy
+ Console...</strong> menu entry will be available from the Jalview Desktop's
+ drop-down menu. Selecting this will open the <a
+ href="http://groovy.codehaus.org/Groovy+Console"
+ >Groovy Console</a> which allows you to interactively execute Groovy
+ scripts within the Jalview run-time environment.
+ </p>
+ <p>
+ <strong>Executing groovy scripts on Jalview startup</strong><br>
+ The -groovy <script> option on the <a href="commandline.html">
+ Jalview command line</a> will execute the contents of <script>.
+ <script> may be a file, a URL, or alternatively if it is
+ "STDIN" then the standard input will be used.<br> <em>Note:
+ The groovy script will be executed <strong>after</strong> any data
+ is loaded, and <strong>before</strong> images or any output files
+ are written. This allows you to perform customised Jalview
+ analysis workflows with groovy.
+ </em>
+ </p>
+ <p>
+ <strong>Access to Jalview's functions from Groovy Scripts</strong><br>
+ There is as yet no properly defined scripting interface to Jalview,
+ but all the public methods of the jalview class hierarchy can be
+ called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
+ object defined in the groovy environent which corresponds to the
+ <pre>jalview.gui.Desktop</pre>
+ object which manages all the Jalview windows. Here's an example to get
+ you started:
+ <br>
+ <ul>
+ <li>Getting the title, alignment and first sequence from the
+ current alignFrame<br> <pre>
def alf = Jalview.getAlignFrames();
print alf[0].getTitle();
def alignment = alf[0].viewport.alignment;
def seq = alignment.getSequenceAt(0);
-</pre></li>
-<li>When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:<br><pre>
+</pre>
+ </li>
+ <li>When running a groovy script from the command line, the
+ alignment that was just loaded can be referred to like so:<br>
+ <pre>
print currentAlFrame.getTitle();</pre>
- </ul>
-If you have downloaded the InstallAnywhere version of Jalview, you can find additional groovy scripts in the examples/groovy subfolder of the installation directory.
+ </ul>
+ If you have downloaded the InstallAnywhere version of Jalview, you can
+ find additional groovy scripts in the examples/groovy subfolder of the
+ installation directory.
</body>
</html>
<title>Hidden Regions</title>
</head>
<body>
-<p><strong>Hidden Regions</strong></p>
-<p>Use the keyboard key "H" to hide / reveal selected
-columns and sequences. To hide / reveal only selected sequences, use
-"Shift H", to hide / reveal only selected columns, use
-"Control H". You can also use "Shift" and
-"Control" together to hide everything but the currently
-selected region.</p>
-<p><strong><em>Hiding Sequences</em></strong><br>
-To hide selected sequences in an alignment, use the <strong>"View
--> Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide
-Sequences"</strong> from the Popup menu after a right click on the sequence
-Ids.</p>
-<p>Hidden sequences will not be used in any calculations, editing or
-web service alignments performed on visible sequences.</p>
-<p><strong><em>Hidden Sequences Representatives</em></strong><br>
-A more advanced hide involves a right-mouse click on a sequence, then
-selecting <strong>"SequenceID -> Represent Group with
-SequenceId"</strong>. Using this method of hiding sequences, any edits
-performed on the visible group representative will be propagated to all
-the sequences in that group. <br>
-The hidden representative sequences will not be used in any calculations
-or web service alignments (<em>nb. this may change in the future</em>).
-<p><strong><em>Hidden Sequence Representatives and
-Multiple Views</em></strong><br>
-<em>A word of warning: hidden representative sequence groups are
-(still) only partly implemented in the Jalview 2.5 release, and we hope
-to deal with the following issues in the future.</em><br>
-Currently, represented hidden groups are only made correctly if there is
-just one alignment view. When multiple views on an alignment exist, then
-the represented group will be displayed correctly in the view in which
-it was made, but in other views, both representative and hidden
-sequences will be visible, but will behave as if they are grouped. <br>
-Hidden representatives are propagated correctly to a new view if they
-exist in the current view. However, if the represented sequences are
-revealed in any one view, then in all other views they will simply be
-marked as hidden, and their association with the representative sequence
-will be lost.<br>
-</blockquote>
-</p>
-<p><strong><em>Hiding Columns</em></strong><br>
-To hide selected columns in an alignment, use the <strong>"View
--> Hide -> Selected Columns"</strong> menu item, or right click within
-a region of selected columns in the scale above the alignment (only
-available in non wrapped mode) and select <strong>"Hide
-Columns"</strong>.</p>
-<p>When an alignment view contains hidden columns, certain
-constraints apply:
-<ul>
- <li>Editing the alignment is bound by the hidden columns, <em>i.e.</em>
- you cannot move residues across a hidden column boundary.</li>
- <li><strong><a href="../calculations/tree.html">Tree</a></strong>,
- <strong><a href="../calculations/pairwise.html">pairwise
- alignment</a></strong> and <strong><a href="../calculations/pca.html">PCA</a></strong>
- calculations will only be performed using the <em>visible</em> parts of
- the alignment.</li>
- <li><a href="../webServices/msaclient.html">Multiple Sequence
- Alignments</a> are performed locally on on each visible chunk of the input,
- and concatenated with the hidden regions to form the final result.
-</p>
-</li>
-</ul>
-<p><strong>Column Separability</strong><br>
-Calculations where hidden columns are excluded, and a single analysis
-performed on the result, are termed <em>column-separable</em>. The
-simple Tree and PCA calculations are column separable because
-essentially the same results would be obtained if the excluded hidden
-columns were replaced by gaps as the input to the calculation.</p>
-<p>Multiple Sequence alignment and secondary structure prediction
-are both non-column-separable, and so the exclusion of hidden regions
-leads to only 'locally optimal' results - sometimes different to that
-obtained when using the full alignment.</p>
-<p> </p>
-<p> </p>
-<p> </p>
+ <p>
+ <strong>Hidden Regions</strong>
+ </p>
+ <p>Use the keyboard key "H" to hide / reveal selected
+ columns and sequences. To hide / reveal only selected sequences, use
+ "Shift H", to hide / reveal only selected columns, use
+ "Control H". You can also use "Shift" and
+ "Control" together to hide everything but the currently
+ selected region.</p>
+ <p>
+ <strong><em>Hiding Sequences</em></strong><br> To hide selected
+ sequences in an alignment, use the <strong>"View ->
+ Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide
+ Sequences"</strong> from the Popup menu after a right click on the
+ sequence Ids.
+ </p>
+ <p>Hidden sequences will not be used in any calculations, editing
+ or web service alignments performed on visible sequences.</p>
+ <p>
+ <strong><em>Hidden Sequences Representatives</em></strong><br>
+ A more advanced hide involves a right-mouse click on a sequence,
+ then selecting <strong>"SequenceID -> Represent
+ Group with SequenceId"</strong>. Using this method of hiding
+ sequences, any edits performed on the visible group representative
+ will be propagated to all the sequences in that group. <br> The
+ hidden representative sequences will not be used in any calculations
+ or web service alignments (<em>nb. this may change in the
+ future</em>).
+ <p>
+ <strong><em>Hidden Sequence Representatives and
+ Multiple Views</em></strong><br> <em>A word of warning: hidden
+ representative sequence groups are (still) only partly implemented
+ in the Jalview 2.5 release, and we hope to deal with the following
+ issues in the future.</em><br> Currently, represented hidden
+ groups are only made correctly if there is just one alignment view.
+ When multiple views on an alignment exist, then the represented
+ group will be displayed correctly in the view in which it was made,
+ but in other views, both representative and hidden sequences will be
+ visible, but will behave as if they are grouped. <br> Hidden
+ representatives are propagated correctly to a new view if they exist
+ in the current view. However, if the represented sequences are
+ revealed in any one view, then in all other views they will simply
+ be marked as hidden, and their association with the representative
+ sequence will be lost.<br>
+ </blockquote>
+ </p>
+ <p>
+ <strong><em>Hiding Columns</em></strong><br> To hide selected
+ columns in an alignment, use the <strong>"View ->
+ Hide -> Selected Columns"</strong> menu item, or right click within
+ a region of selected columns in the scale above the alignment (only
+ available in non wrapped mode) and select <strong>"Hide
+ Columns"</strong>.
+ </p>
+ <p>When an alignment view contains hidden columns, certain
+ constraints apply:
+ <ul>
+ <li>Editing the alignment is bound by the hidden columns, <em>i.e.</em>
+ you cannot move residues across a hidden column boundary.
+ </li>
+ <li><strong><a href="../calculations/tree.html">Tree</a></strong>,
+ <strong><a href="../calculations/pairwise.html">pairwise
+ alignment</a></strong> and <strong><a
+ href="../calculations/pca.html"
+ >PCA</a></strong> calculations will only be performed using the <em>visible</em>
+ parts of the alignment.</li>
+ <li><a href="../webServices/msaclient.html">Multiple
+ Sequence Alignments</a> are performed locally on on each visible
+ chunk of the input, and concatenated with the hidden regions to
+ form the final result.
+ </p></li>
+ </ul>
+ <p>
+ <strong>Column Separability</strong><br> Calculations where
+ hidden columns are excluded, and a single analysis performed on the
+ result, are termed <em>column-separable</em>. The simple Tree and
+ PCA calculations are column separable because essentially the same
+ results would be obtained if the excluded hidden columns were
+ replaced by gaps as the input to the calculation.
+ </p>
+ <p>Multiple Sequence alignment and secondary structure prediction
+ are both non-column-separable, and so the exclusion of hidden
+ regions leads to only 'locally optimal' results - sometimes
+ different to that obtained when using the full alignment.</p>
+ <p> </p>
+ <p> </p>
+ <p> </p>
</body>
</html>
</head>
<body>
-<p><strong>Jalview Project Archives</strong>
-</p>
+ <p>
+ <strong>Jalview Project Archives</strong>
+ </p>
-<p>These are java archives of an XML file containing alignments, trees and Jalview
- display information. A data exchange standard is currently being developed,
- so there is no stable schema yet, but Jalview web services will soon make use
- of the same interchange format.</p>
-<p>For those who want to know...<br>
- Jalview uses java classes automatically created using <a href="http://www.castor.org">Castor</a>.
- Jalview 2.08 uses descriptor classes which significantly increase the speed
- of marshalling / unmarshalling java objects into XML. Files created prior to
- Jalview 2.08 can still be read in, but they will be saved in the new format.
-</p>
+ <p>These are java archives of an XML file containing alignments,
+ trees and Jalview display information. A data exchange standard is
+ currently being developed, so there is no stable schema yet, but
+ Jalview web services will soon make use of the same interchange
+ format.</p>
+ <p>
+ For those who want to know...<br> Jalview uses java classes
+ automatically created using <a href="http://www.castor.org">Castor</a>.
+ Jalview 2.08 uses descriptor classes which significantly increase
+ the speed of marshalling / unmarshalling java objects into XML.
+ Files created prior to Jalview 2.08 can still be read in, but they
+ will be saved in the new format.
+ </p>
</body>
</html>
<title>The Jmol PDB Viewer</title>
</head>
<body>
-<p><strong>The Jmol PDB Viewer</strong></p>
-<p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
-has been integrated into Jalview for interactively viewing structures
-opened by entries in the <strong>"Structure"</strong> submenu in the <a href="../menus/popupMenu.html">sequence
-id pop-up menu</a> (if you can't see this, then you need to <a
- href="viewingpdbs.html">associate a PDB structure</a> with the
-sequence). Jmol is available from the Jalview desktop and should also
-run in the JalviewLite applet, providing the browser supports Java 1.5.
-If Jmol is not available, then the original <a href="pdbviewer.html">internal
-pdb viewer</a> will be used as a fallback.</p>
-<!-- <p>The following menu entries are provided for viewing structure data<br>
+ <p>
+ <strong>The Jmol PDB Viewer</strong>
+ </p>
+ <p>
+ Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
+ has been integrated into Jalview for interactively viewing
+ structures opened by entries in the <strong>"Structure"</strong>
+ submenu in the <a href="../menus/popupMenu.html">sequence id
+ pop-up menu</a> (if you can't see this, then you need to <a
+ href="viewingpdbs.html"
+ >associate a PDB structure</a> with the sequence). Jmol is available
+ from the Jalview desktop and should also run in the JalviewLite
+ applet, providing the browser supports Java 1.5. If Jmol is not
+ available, then the original <a href="pdbviewer.html">internal
+ pdb viewer</a> will be used as a fallback.
+ </p>
+ <!-- <p>The following menu entries are provided for viewing structure data<br>
<ul>
<li>The <strong>"Structure→View
Structure→</strong> submenu allows a single PDB structure to be chosen
</ul>
<br>
</p> -->
-<p><a name="align"><strong>Superposing structures based
-on their aligned sequences</strong></a><br>
-If several structures are available on the alignment, you may add
-additional structures to an existing Jmol view by selecting their entry
-in the appropriate pop-up menu. Jalview will ask you if you wish to add
-the structure to the existing alignment, and if you do, it will import
-and superimpose the new PDB file using the corresponding positions from
-the alignment. If the alignment is subsequently edited, you can use the
-<a href="#sAlign"><em>Jmol→Align</em></a> menu option from the
-menu bar of the structure view window to superpose the structures using
-the updated alignment.<br>
-<em>Sequence based structure superposition was added in Jalview 2.6</em>
-</p>
-<p><strong>Controls</strong><br>
-The structure is by default rendered as a ribbon diagram. Moving the
-mouse over the structure brings up tooltips giving the residue name, PDB
-residue number and chain code, atom name and number
-([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue
-in any associated sequences, then this will be highlighted in each one's
-alignment window. The converse also occurs - moving the mouse over an
-associated residue in an alignment window highlights the associated
-atoms in the displayed structures.</p>
-<p>Selecting a residue highlights its associated sequence residue
-and alpha carbon location. Double clicking an atom allows distances to
-be measured from it to any other atom in the structure.</p>
-<p>
-<table border="1">
- <tr>
- <td><strong>Action</strong></td>
- <td><strong>Windows</strong></td>
- <td><strong>Unix</strong></td>
- <td><strong>Mac/OSX</strong></td>
- </tr>
- <tr>
- <td>Rotate View</td>
- <td>Left Click and Drag</td>
- <td>Left Click and Drag</td>
- <td>Click and Drag</td>
- </tr>
- <tr>
- <td>Zoom</td>
- <td>Shift + Left Click<br>
- drag mouse up or down</td>
- <td>Shift + Left Click<br>
- or middle button<br>
- drag mouse up or down</td>
- <td>Left-Alt + Click and drag mouse up or down</td>
- </tr>
- <tr>
- <td>Select/<br>
- Deselect<br>
- Residue</td>
- <td>Left Click</td>
- <td>Left Click</td>
- <td>Click</td>
- </tr>
- <tr>
- <td>Roll View</td>
- <td>Shift + Left Click<br>
- drag mouse to left or right</td>
- <td>Shift + Left Click<br>
- or middle button<br>
- drag mouse to left or right</td>
- <td>Left-Alt + Click and drag mouse to left or right</td>
- </tr>
- <tr>
- <td>Move Origin</td>
- <td>Shift+Control+Left Click<br>
- or Middle Button<br>
- + Drag</td>
- <td>Middle-Button<br>
- and<br>
- drag</td>
- <td>Shift+Control+Left Click<br>
- or Middle Button<br>
- and drag</td>
- </tr>
- <tr>
- <td>Jmol Menu</td>
- <td>Right-Click</td>
- <td>Right-Click</td>
- <td>Apple-Click</td>
- </tr>
-</table>
-</p>
-<p>The window has up to five menus:
-<ul>
- <li><Strong>File<br>
- </strong>
- <ul>
- <li><strong>Save As<br>
- </strong><em>Save the displayed PDB File, or the current view as an EPS or
- PNG file.</em></li>
- <li><strong>View Mapping<br>
- </strong><em> Opens a text window showing the alignment between the
- residues corresponding to alpha-carbon atoms in the PDB structure and
- the residues in the associated sequence.</em></li>
- </ul>
- </li>
- <li><strong>View</strong>
- <ul>
- <li><strong>Show Chains<br>
- </strong><em>Select which of the PDB file's chains are to be displayed.</em></li>
- <li><strong>Colour by ..<br></strong><em>Submenu allowing specific alignment views to be selected for colouring associated chains in the structure display. This menu contains all the alignment views associated with the structure view, with those used to colour the view indicated by ticks. Addditionally, it contains the following menu entries:</em>
- <ul><li><strong>Select many views<br></strong><em>When this option is enabled, selecting an alignment view adds it to the set used to colour the structures. Use this when colouring structures related to a number of alignments involving different domains or chains which are shown in the same structure view.</em>
- </li>
- <li><strong>Select all views<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will add all associated views to the set used to colour the structure display.</em>
- </li>
- <li><strong>Invert selection<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display.</em>
- </li></ul></li></ul>
- <li><strong>Colours<br>
- </strong>
- <ul>
- <li><strong>By Sequence<br>
- </strong><em> Colours each residue in the structure with the colour of its
- corresponding residue in the associated sequence as rendered in the
- associated alignment views, including any Uniprot sequence features or
- region colourings.<br/>Pick which of the associated alignment views are used to colour the structures using the <strong>View→Colour by ..</strong> sub menu.</em><br>
- Residues which only exist in the PDB structure are coloured white if
- they are insertions (relative to the associated sequence in the
- alignment) and grey if they are N or C terminal flanks outside the
- region mapped to the alignment window's sequence.</em></li>
- <li><strong>By Chain<br>
- </strong><em> Assigns a random colour to each PDB chain.</em>
- <li><strong>Charge & Cysteine<br>
- </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
- Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
- residues in blue.</em></li>
- <li><strong>Colour with Jmol<br></strong><em>Defers any colouring operations to Jmol. Select this if you want to use the Jmol scripting interface or menu to modify the view directly.</em></li>
- <li><strong>Standard and User Defined Jalview
- colourschemes.<br>
- </strong><em>The remaining entries apply the colourschemes available from
- the standard and user defined <a href="../colourSchemes/index.html">amino
- acid colours</a>.</em></li>
- </ul>
- </li>
- <li><strong>Jmol<br>
- </strong><em>This pulldown menu is only displayed if there are multiple
- structures shown in the Jmol window, and Jalview can also locate at
- least two of the structures in the currently associated alignment view.</em>
- <ul>
- <li><strong><a name="sAlign">Align</a> <br>
- </strong><em> When selected, the associated alignment will be used to
- superimpose all the structures in the view onto the first structure in
- the alignment. The regions used to calculate the superposition will be
- highlighted using the 'Cartoon' rendering style, and the remaining
- data shown as a chain trace.<br>
- (This option was introduced in Jalview 2.6)</em></li>
- </ul>
- </li>
- <li><strong>Help<br>
- </strong>
- <ul>
- <li><strong>Jmol Help<br>
- </strong><em>Access the Jmol Help documentation in a new browser window.</em></li>
- </ul>
- </li>
-</ul>
-</p>
-<p><strong>Functionality provided by Jmol</strong></p>
-<p>Jmol's own functions are accessed by clicking the 'Jmol' logo or
-right-clicking in the structure display area. Either way will open the
-Jmol pop-up menu, which provides access to a number of features for
-controlling the colour and display of molecules, adding measurements and
-labels, plotting surfaces, and display animation. The 'Set Picking' menu
-controls the behaviour of single and double mouse clicking on the
-structure, and the 'Console' option opens the Jmol scripting console.</p>
-<p>The state of each Jmol display is stored within <a
- href="jalarchive.html">Jalview archives</a> as a Jmol state recovery
-script file. This means that any Jmol visualization effects that you add
-beyond those provided by Jalview will be able to be stored and recovered
-along with the displayed alignments in Jalview.</p>
-<p><strong>More Information</strong></p>
-<p>Jmol is a sophisticated program in its own right, with its own
-command console and scripting language. Only the essentials have been
-described here - the interested reader is referred to <a
- href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive
-online documentation</a>.</p>
-</p>
+ <p>
+ <a name="align"><strong>Superposing structures based on
+ their aligned sequences</strong></a><br> If several structures are
+ available on the alignment, you may add additional structures to an
+ existing Jmol view by selecting their entry in the appropriate
+ pop-up menu. Jalview will ask you if you wish to add the structure
+ to the existing alignment, and if you do, it will import and
+ superimpose the new PDB file using the corresponding positions from
+ the alignment. If the alignment is subsequently edited, you can use
+ the <a href="#sAlign"><em>Jmol→Align</em></a> menu option from
+ the menu bar of the structure view window to superpose the
+ structures using the updated alignment.<br> <em>Sequence
+ based structure superposition was added in Jalview 2.6</em>
+ </p>
+ <p>
+ <strong>Controls</strong><br> The structure is by default
+ rendered as a ribbon diagram. Moving the mouse over the structure
+ brings up tooltips giving the residue name, PDB residue number and
+ chain code, atom name and number
+ ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a
+ residue in any associated sequences, then this will be highlighted
+ in each one's alignment window. The converse also occurs - moving
+ the mouse over an associated residue in an alignment window
+ highlights the associated atoms in the displayed structures.
+ </p>
+ <p>Selecting a residue highlights its associated sequence residue
+ and alpha carbon location. Double clicking an atom allows distances
+ to be measured from it to any other atom in the structure.</p>
+ <p>
+ <table border="1">
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Zoom</td>
+ <td>Shift + Left Click<br> drag mouse up or down
+ </td>
+ <td>Shift + Left Click<br> or middle button<br>
+ drag mouse up or down
+ </td>
+ <td>Left-Alt + Click and drag mouse up or down</td>
+ </tr>
+ <tr>
+ <td>Select/<br> Deselect<br> Residue
+ </td>
+ <td>Left Click</td>
+ <td>Left Click</td>
+ <td>Click</td>
+ </tr>
+ <tr>
+ <td>Roll View</td>
+ <td>Shift + Left Click<br> drag mouse to left or right
+ </td>
+ <td>Shift + Left Click<br> or middle button<br>
+ drag mouse to left or right
+ </td>
+ <td>Left-Alt + Click and drag mouse to left or right</td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Shift+Control+Left Click<br> or Middle Button<br>
+ + Drag
+ </td>
+ <td>Middle-Button<br> and<br> drag
+ </td>
+ <td>Shift+Control+Left Click<br> or Middle Button<br>
+ and drag
+ </td>
+ </tr>
+ <tr>
+ <td>Jmol Menu</td>
+ <td>Right-Click</td>
+ <td>Right-Click</td>
+ <td>Apple-Click</td>
+ </tr>
+ </table>
+ </p>
+ <p>The window has up to five menus:
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>Save As<br>
+ </strong><em>Save the displayed PDB File, or the current view as an
+ EPS or PNG file.</em></li>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>Show Chains<br>
+ </strong><em>Select which of the PDB file's chains are to be
+ displayed.</em></li>
+ <li><strong>Colour by ..<br></strong><em>Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:</em>
+ <ul>
+ <li><strong>Select many views<br></strong><em>When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.</em></li>
+ <li><strong>Select all views<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.</em></li>
+ <li><strong>Invert selection<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.</em></li>
+ </ul></li>
+ </ul>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ Uniprot sequence features or region colourings.<br />Pick
+ which of the associated alignment views are used to colour
+ the structures using the <strong>View→Colour
+ by ..</strong> sub menu.
+ </em><br> Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em> Assigns a random colour to each PDB chain.</em>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong>Colour with Jmol<br></strong><em>Defers
+ any colouring operations to Jmol. Select this if you want to
+ use the Jmol scripting interface or menu to modify the view
+ directly.</em></li>
+ <li><strong>Standard and User Defined Jalview
+ colourschemes.<br>
+ </strong><em>The remaining entries apply the colourschemes available
+ from the standard and user defined <a
+ href="../colourSchemes/index.html"
+ >amino acid colours</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Jmol<br>
+ </strong><em>This pulldown menu is only displayed if there are multiple
+ structures shown in the Jmol window, and Jalview can also locate
+ at least two of the structures in the currently associated
+ alignment view.</em>
+ <ul>
+ <li><strong><a name="sAlign">Align</a> <br> </strong><em>
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ structure in the alignment. The regions used to calculate
+ the superposition will be highlighted using the 'Cartoon'
+ rendering style, and the remaining data shown as a chain
+ trace.<br> (This option was introduced in Jalview 2.6)
+ </em></li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Jmol Help<br>
+ </strong><em>Access the Jmol Help documentation in a new browser
+ window.</em></li>
+ </ul></li>
+ </ul>
+ </p>
+ <p>
+ <strong>Functionality provided by Jmol</strong>
+ </p>
+ <p>Jmol's own functions are accessed by clicking the 'Jmol' logo
+ or right-clicking in the structure display area. Either way will
+ open the Jmol pop-up menu, which provides access to a number of
+ features for controlling the colour and display of molecules, adding
+ measurements and labels, plotting surfaces, and display animation.
+ The 'Set Picking' menu controls the behaviour of single and double
+ mouse clicking on the structure, and the 'Console' option opens the
+ Jmol scripting console.</p>
+ <p>
+ The state of each Jmol display is stored within <a
+ href="jalarchive.html"
+ >Jalview archives</a> as a Jmol state recovery script file. This means
+ that any Jmol visualization effects that you add beyond those
+ provided by Jalview will be able to be stored and recovered along
+ with the displayed alignments in Jalview.
+ </p>
+ <p>
+ <strong>More Information</strong>
+ </p>
+ <p>
+ Jmol is a sophisticated program in its own right, with its own
+ command console and scripting language. Only the essentials have
+ been described here - the interested reader is referred to <a
+ href="http://jmol.sourceforge.net/docs/"
+ >Jmol's own comprehensive online documentation</a>.
+ </p>
+ </p>
</body>
</html>
<title>Multiple Alignment Views</title>
</head>
<body>
-<p><strong>Multiple Alignment Views</strong></p>
-<p>Multiple alignment views allow the same alignment to be viewed
-independently in many different ways simultaneously. Each view is an
-independent visualization of the same alignment, so each may have a
-different ordering, colouring, row and column hiding and sequence
-feature and annotation display setting, but alignment, feature and
-annotation edits are common to all, since this affects the underlying
-data.</p>
-<p>Create a new view using the <strong>"View→New
-View"</strong> menu item, or by pressing <strong>Control+T</strong>. A newly
-created view will be identical to the view it was created from, but any
-changes to the way the alignment is coloured or displayed will only
-affect the new view.</p>
-<!-- TODO sharing selections between views -->
-<p>A particular view may focus on some specific aspect of an
-alignment - for example, hiding all but the region of an alignment
-containing a particular domain. <strong>Right-clicking</strong> a view's
-tab opens the View Name dialog box, allowing it to be renamed to
-something more meaningful.</p>
-<p><strong>Viewing Multiple Views Simultaneously</strong></p>
-<p>Multiple views of an alignment are, by default, gathered together
-as tabs within a single alignment window. They can be viewed
-simultanously by pressing <strong>X</strong> (or via <strong>"View→Expand"</strong>)
-to expand each view into its own linked alignment window. Expanded views
-are gathered back into a single tabbed alignment window by pressing
-<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>.
-</p>
-<p><strong>Hidden Sequence Representatives and Multiple
-Views</strong></p>
-<p>There are some unexpected interactions between hidden sequence
-representatives and their display in multiple views. See the
-corresponding entry in the <a href="hiddenRegions.html">documentation
-for hidden regions</a>.</p>
-<p><strong>Structure and Analysis Viewers and Multiple
-Views</strong></p>
-<p>A tree calculated on a particular view, or loaded onto it, is by
-default associated with just that view. However, the <a
- href="../calculations/treeviewer.html">Tree Viewer's</a> <strong>"View→Associate
-leaves"</strong> submenu allows a tree's view association to be changed to
-to any or all other views.</p>
-<p>The results of a <a href="../calculations/pca.html">PCA
-calculation</a> on a particular view may also be associated with other
-views, using the PCA Viewer's <strong>"View→Associate
-Nodes"</strong> submenu.</p>
-<p><a href="jmol.html">PDB Structure Viewers</a>
-opened on a structure associated with a sequence in a particular view are now (as of Jalview 2.3) associated with the same sequence in all views. This means that when 'Colour by Sequence' is selected in the structure view, the colour will be updated to the colours given in the view with the current input focus.
-<!--
+ <p>
+ <strong>Multiple Alignment Views</strong>
+ </p>
+ <p>Multiple alignment views allow the same alignment to be viewed
+ independently in many different ways simultaneously. Each view is an
+ independent visualization of the same alignment, so each may have a
+ different ordering, colouring, row and column hiding and sequence
+ feature and annotation display setting, but alignment, feature and
+ annotation edits are common to all, since this affects the
+ underlying data.</p>
+ <p>
+ Create a new view using the <strong>"View→New
+ View"</strong> menu item, or by pressing <strong>Control+T</strong>. A
+ newly created view will be identical to the view it was created
+ from, but any changes to the way the alignment is coloured or
+ displayed will only affect the new view.
+ </p>
+ <!-- TODO sharing selections between views -->
+ <p>
+ A particular view may focus on some specific aspect of an alignment
+ - for example, hiding all but the region of an alignment containing
+ a particular domain. <strong>Right-clicking</strong> a view's tab
+ opens the View Name dialog box, allowing it to be renamed to
+ something more meaningful.
+ </p>
+ <p>
+ <strong>Viewing Multiple Views Simultaneously</strong>
+ </p>
+ <p>
+ Multiple views of an alignment are, by default, gathered together as
+ tabs within a single alignment window. They can be viewed
+ simultanously by pressing <strong>X</strong> (or via <strong>"View→Expand"</strong>)
+ to expand each view into its own linked alignment window. Expanded
+ views are gathered back into a single tabbed alignment window by
+ pressing <strong>G</strong>, or by selecting <strong>"View→Gather"</strong>.
+ </p>
+ <p>
+ <strong>Hidden Sequence Representatives and Multiple Views</strong>
+ </p>
+ <p>
+ There are some unexpected interactions between hidden sequence
+ representatives and their display in multiple views. See the
+ corresponding entry in the <a href="hiddenRegions.html">documentation
+ for hidden regions</a>.
+ </p>
+ <p>
+ <strong>Structure and Analysis Viewers and Multiple Views</strong>
+ </p>
+ <p>
+ A tree calculated on a particular view, or loaded onto it, is by
+ default associated with just that view. However, the <a
+ href="../calculations/treeviewer.html"
+ >Tree Viewer's</a> <strong>"View→Associate
+ leaves"</strong> submenu allows a tree's view association to be
+ changed to to any or all other views.
+ </p>
+ <p>
+ The results of a <a href="../calculations/pca.html">PCA
+ calculation</a> on a particular view may also be associated with other
+ views, using the PCA Viewer's <strong>"View→Associate
+ Nodes"</strong> submenu.
+ </p>
+ <p>
+ <a href="jmol.html">PDB Structure Viewers</a> opened on a structure
+ associated with a sequence in a particular view are now (as of
+ Jalview 2.3) associated with the same sequence in all views. This
+ means that when 'Colour by Sequence' is selected in the structure
+ view, the colour will be updated to the colours given in the view
+ with the current input focus.
+ <!--
also, by default, only be associated
with the sequence as it is displayed in that view. The
"View→Associate View" submenu allows the association of
alternative views.</p> -->
-<p><em>Multiple Views were introduced in Jalview 2.2</em></p>
+ <p>
+ <em>Multiple Views were introduced in Jalview 2.2</em>
+ </p>
</body>
</html>
-->
<title>New Key Strokes and Menus</title>
<body>
-<strong>New Key Strokes and Menus</strong>
-<p>Many new <a href="../keys.html">keyboard shortcuts</a> have been
-added in Jalview 2.2 to make editing, selecting and navigating an
-alignment even easier. The selection commands in the <strong>Edit</strong>
-menu, and the alignment formatting controls within the <strong>View</strong>
-menu have also been moved into their own respective <strong>Select</strong>
-and <strong>Format</strong> menus.</p>
-<p>Some of the more important new keystrokes are shown below :
-<ul>
- <li><strong>Page Up</strong> and <strong>Page Down</strong>
- scrolls through the alignment view.</li>
- <li><strong>Control I</strong> inverts the currently selected
- sequence set, and <strong>Control Alt I</strong> will invert the
- currently selected set of columns.
- <li><strong>Control V</strong> will paste the contents of the
- clipboard to the current alignment window, and <strong>Control
- Shift V</strong> pastes the data to a new window.</li>
- <li><strong>Control O</strong> opens the file browser for loading
- a new alignment or Jalview archive.</li>
- <li><strong>Control S</strong> saves the alignment with the
- current filename and format, and <strong>Control Shift S</strong> opens
- the <strong>Save As...</strong> dialog box.</li>
- <li><strong>Control T</strong> creates a new alignment view, and <strong>Control
- W</strong> closes the current view, or if none remain, then the whole alignment.</li>
- <li><strong>Control E</strong> will remove gapped columns in the alignment.</li>
- <li><strong>Control D</strong> opens the <strong>Remove Redundancy</strong> dialog box.</li>
-</ul>
-</p>
+ <strong>New Key Strokes and Menus</strong>
+ <p>
+ Many new <a href="../keys.html">keyboard shortcuts</a> have been
+ added in Jalview 2.2 to make editing, selecting and navigating an
+ alignment even easier. The selection commands in the <strong>Edit</strong>
+ menu, and the alignment formatting controls within the <strong>View</strong>
+ menu have also been moved into their own respective <strong>Select</strong>
+ and <strong>Format</strong> menus.
+ </p>
+ <p>Some of the more important new keystrokes are shown below :
+ <ul>
+ <li><strong>Page Up</strong> and <strong>Page Down</strong>
+ scrolls through the alignment view.</li>
+ <li><strong>Control I</strong> inverts the currently selected
+ sequence set, and <strong>Control Alt I</strong> will invert the
+ currently selected set of columns.
+ <li><strong>Control V</strong> will paste the contents of the
+ clipboard to the current alignment window, and <strong>Control
+ Shift V</strong> pastes the data to a new window.</li>
+ <li><strong>Control O</strong> opens the file browser for
+ loading a new alignment or Jalview archive.</li>
+ <li><strong>Control S</strong> saves the alignment with the
+ current filename and format, and <strong>Control Shift S</strong>
+ opens the <strong>Save As...</strong> dialog box.</li>
+ <li><strong>Control T</strong> creates a new alignment view,
+ and <strong>Control W</strong> closes the current view, or if none
+ remain, then the whole alignment.</li>
+ <li><strong>Control E</strong> will remove gapped columns in
+ the alignment.</li>
+ <li><strong>Control D</strong> opens the <strong>Remove
+ Redundancy</strong> dialog box.</li>
+ </ul>
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Overview Window</title></head>
+<head>
+<title>Overview Window</title>
+</head>
<body>
-<p><strong>View→Overview window</strong></p>
-<p>Select the overview window menu item to get a navigable image of the whole alignment.
-</p>
-<p>The red box indicates the currently viewed region of the alignment, this
- may be moved by clicking and dragging with the mouse.</p>
-<p><img src="overview.gif" width="407" height="137"></p>
-<p> </p>
+ <p>
+ <strong>View→Overview window</strong>
+ </p>
+ <p>Select the overview window menu item to get a navigable image
+ of the whole alignment.</p>
+ <p>The red box indicates the currently viewed region of the
+ alignment, this may be moved by clicking and dragging with the
+ mouse.</p>
+ <p>
+ <img src="overview.gif" width="407" height="137">
+ </p>
+ <p> </p>
</body>
</html>
</head>
<body>
- <strong>The PDB Sequence Fetcher</strong>
- <p>Jalview provides a specialised interface that allows fast and efficient discovery and retrieval of data from the PDB
- database, based on the EMBL-EBI's PDBe BioSOLR query interface. It allows interactive querying of PDB metadata with free text and structured queries, so structures can be located without prior knowledge of their database accessions,
- or <em>via</em> manual cross-referencing with other bioinformatics websites.</p>
+ <strong>The PDB Sequence Fetcher</strong>
<p>
- To open the PDB Sequence Fetcher, select PDB as the database from any <a
- href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em> <strong>"File
- →Fetch Sequences"</strong>).
+ Jalview provides a specialised interface that allows fast and
+ efficient discovery and retrieval of data from the PDB database,
+ based on the EMBL-EBI's PDBe BioSOLR query interface. It allows
+ interactive querying of PDB metadata with free text and structured
+ queries, so structures can be located without prior knowledge of
+ their database accessions, or <em>via</em> manual cross-referencing
+ with other bioinformatics websites.
</p>
- <img src="pdbseqfetcher.png" align="left"
- alt="PDB sequence fetcher (introduced in Jalview 2.9)"/>
+ <p>
+ To open the PDB Sequence Fetcher, select PDB as the database from
+ any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
+ <strong>"File →Fetch Sequences"</strong>).
+ </p>
+ <img src="pdbseqfetcher.png" align="left"
+ alt="PDB sequence fetcher (introduced in Jalview 2.9)"
+ />
- <p><strong>Searching the PDB Database</strong></p>
+ <p>
+ <strong>Searching the PDB Database</strong>
+ </p>
<p>
To search the PDB, begin typing in the text box. The results of your
query are shown in the search results tab, which updates every time
keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
button to retrieve and view them in Jalview.
</p>
- <p>
- <ul><li><strong>Searching a specific PDB field</strong><br/>If you want to find structures based on a specific PDB metadata field, you can select it from the drop-down menu.</li>
- <li><strong>Retrieving a unique chain for a PDB entry</strong><br>To
- retrieve a specific chain for a PDB entry, append the PDB ID with a
- colon followed by the chain code in the search box.<br/> e.g 1xyz:A
- </li>
+ <p>
+ <ul>
+ <li><strong>Searching a specific PDB field</strong><br />If you
+ want to find structures based on a specific PDB metadata field,
+ you can select it from the drop-down menu.</li>
+ <li><strong>Retrieving a unique chain for a PDB entry</strong><br>To
+ retrieve a specific chain for a PDB entry, append the PDB ID with
+ a colon followed by the chain code in the search box.<br /> e.g
+ 1xyz:A</li>
<li><strong>Bulk PDB retrieval</strong><br>Multiple PDB
- IDs can be specified by separating them with a semi-colon.<br/> e.g.
- 1xyz;2xyz;3xyz<br />Hitting Return or OK will automatically fetch
- those IDs, like the default Sequence Fetcher interface.</li>
+ IDs can be specified by separating them with a semi-colon.<br />
+ e.g. 1xyz;2xyz;3xyz<br />Hitting Return or OK will automatically
+ fetch those IDs, like the default Sequence Fetcher interface.</li>
<li><strong>Wild card searching</strong><br>The following
wild cards are supported by the EMBL-EBI PDBe query service:
search string te?t would match both test and text.</li>
<li><strong>*</strong> matches multiple characters<br />The
search string: tes* - would match test, testing, and tester.</li>
- </ul>
- <em>Note:</em> you can use wildcard characters anywhere in a query
- string.<br />For example: te*t - would match test and text. *est -
- would match pest and test.</li>
+ </ul> <em>Note:</em> you can use wildcard characters anywhere in a
+ query string.<br />For example: te*t - would match test and text.
+ *est - would match pest and test.</li>
<li><strong>Structured queries</strong><br />The PDBe SOLR
interface supports boolean query syntax, allowing quoted search
strings to be combined with AND, OR, and NOT. Currently, no
special support for constructing these queries is provided in the
query dialog box.</li>
</ul>
- <p>
- <strong>Customising The PDB Sequence Fetcher</strong></p><p>To change the
- displayed meta-data in the search result, click the 'Configure
- Displayed Columns' tab, and select the fields you'd like displayed.
- These fields can also be configured
- <em>via</em> the Structure tab of the <a
- href="preferences.html#structure">Jalview Desktop Preferences</a>.
+ <p>
+ <strong>Customising The PDB Sequence Fetcher</strong>
+ </p>
+ <p>
+ To change the displayed meta-data in the search result, click the
+ 'Configure Displayed Columns' tab, and select the fields you'd like
+ displayed. These fields can also be configured <em>via</em> the
+ Structure tab of the <a href="preferences.html#structure">Jalview
+ Desktop Preferences</a>.
</p>
<p>
<em>The PDB Sequence Fetcher interface was introduced in
<title>PDB Viewer</title>
</head>
<body>
-<p><strong>The Jalview internal PDB Viewer</strong><br>
-Since Jalview 2.3, the <a href="jmol.html">Jmol PDB Viewer</a> is
-the main method for <a href="viewingpdbs.html">viewing PDB
-structures</a>. The documentation below concerns the original Jalview
-PDB viewer, which is only used in situations where Jmol is unavailable
-or cannot operate.</p>
-<p><strong>The PDB Viewer Window</strong>
-<p>This interactive structure viewing window is opened by selecting
-entries from the <strong>"Structure→"</strong> submenu
- of the <a href="../menus/popupMenu.html">sequence
- id pop-up menu</a>. The internal PDB viewer is not able to show
- superpositions, so no other options are provided. Structures can only
- be viewed for sequences which have an <a href="viewingpdbs.html">associated
-PDB structure</a>, and the PDB Viewer will only be associated with the
-particular alignment view from which it was opened.</p>
-<p><strong>Controls</strong></p>
-<p>The structure is rendered as an alpha-carbon trace. Moving the
-mouse over the structure brings up tooltips with a residue name and PDB
-sequence position. If a mapping exists to a residue in the associated
-sequence, then this will be highlighted in the associated view in its
-alignment window, and vice versa for viewing the coordinates associated
-with a particular residue in the sequence in a particular view on the
-alignment.</p>
-<p>Selecting a residue highlights its associated sequence residue
-and alpha carbon location.</p>
-<p>
-<table>
- <tr>
- <td><strong>Action</strong></td>
- <td><strong>Windows</strong></td>
- <td><strong>Unix</strong></td>
- <td><strong>Mac/OSX</strong></td>
- </tr>
- <tr>
- <td>Select/<br>
- Deselect<br>
- Residue</td>
- <td>Left Click</td>
- <td>Left Click</td>
- <td>Click</td>
- </tr>
- <tr>
- <td>Rotate View</td>
- <td>Left Click and Drag</td>
- <td>Left Click and Drag</td>
- <td>Click and Drag</td>
- </tr>
- <tr>
- <td>Roll View</td>
- <td>Right Click and drag</td>
- <td>Right Click and Drag</td>
- <td>TODO</td>
- </tr>
- <tr>
- <td>Move Origin</td>
- <td>Middle-Button and Drag</td>
- <td>Middle-Button and Drag</td>
- <td>TODO</td>
- </tr>
- <tr>
- <td>Zoom In</td>
- <td>Up Arrow</td>
- <td>Up Arrow</td>
- <td>Up Arrow</td>
- </tr>
- <tr>
- <td>Zoom Out</td>
- <td>Down Arrow</td>
- <td>Down Arrow</td>
- <td>Down Arrow</td>
- </tr>
-</table>
-</p>
-<p>There are three menus:
-<ul>
- <li><Strong>File<br>
- </strong>
- <ul>
- <li><strong>Save As<br>
- </strong><em>Saves the current view as an EPS or PNG file.</em></li>
- <li><strong>View Mapping<br>
- </strong><em> Opens a text window showing the alignment between the
- residues corresponding to alpha-carbon atoms in the PDB structure and
- the residues in the associated sequence.</em></li>
- </ul>
- </li>
- <li><strong>Colours<br>
- </strong>
- <ul>
- <li><strong>By Sequence<br>
- </strong><em> Colours each residue in the structure with the colour of its
- corresponding residue in the associated sequence as rendered in the
- associated alignment view, including any Uniprot sequence features or
- region colourings.<br>
- Residues which only exist in the PDB structure are coloured white if
- they are insertions (relative to the associated sequence in the
- alignment) and grey if they are N or C terminal flanks outside the
- region mapped to the alignment window's sequence.</em></li>
- <li><strong>By Chain<br>
- </strong><em> Assigns a random colour to each PDB chain.</em>
- <li><strong>Charge & Cysteine<br>
- </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
- Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
- residues in blue.</em></li>
- <li><strong><em>Standard and User Defined Jalview
- colourschemes.<br>
- </em></strong> The remaining entries apply the colourschemes available from the
- standard and user defined <a href="../colourSchemes/index.html">amino
- acid colours</a>.</em></li>
- </ul>
- </li>
- <li><strong>View<br>
- </strong><em> These options can be turned off to improve performance when
- viewing large structures, some at the expense of visual clarity.</em>
- <ul>
- <li><strong>Wireframe<br>
- </strong><em> Draws thin lines rather than thick lines for the
- alpha-carbon trace.</em></li>
- <li><strong>Depthcue<br>
- </strong><em>Shades the structure so parts of the structure near the front
- of the view are brighter than those further away.</em></li>
- <li><strong>Z Buffering<br>
- </strong><em> Applies depth sorting to correctly render occluded regions
- of the backbone trace.</em></li>
- <li><strong>Show All Chains<br>
- </strong><em> When turned on, shows all chains in the PDB file, not just
- the one associated with a sequence in the alignment window.</em></li>
- <!-- NOT YET IMPLEMENTED <li><strong>Associate View</strong><br>
+ <p>
+ <strong>The Jalview internal PDB Viewer</strong><br> Since
+ Jalview 2.3, the <a href="jmol.html">Jmol PDB Viewer</a> is the main
+ method for <a href="viewingpdbs.html">viewing PDB structures</a>.
+ The documentation below concerns the original Jalview PDB viewer,
+ which is only used in situations where Jmol is unavailable or cannot
+ operate.
+ </p>
+ <p>
+ <strong>The PDB Viewer Window</strong>
+ <p>
+ This interactive structure viewing window is opened by selecting
+ entries from the <strong>"Structure→"</strong>
+ submenu of the <a href="../menus/popupMenu.html">sequence id
+ pop-up menu</a>. The internal PDB viewer is not able to show
+ superpositions, so no other options are provided. Structures can
+ only be viewed for sequences which have an <a
+ href="viewingpdbs.html"
+ >associated PDB structure</a>, and the PDB Viewer will only be
+ associated with the particular alignment view from which it was
+ opened.
+ </p>
+ <p>
+ <strong>Controls</strong>
+ </p>
+ <p>The structure is rendered as an alpha-carbon trace. Moving the
+ mouse over the structure brings up tooltips with a residue name and
+ PDB sequence position. If a mapping exists to a residue in the
+ associated sequence, then this will be highlighted in the associated
+ view in its alignment window, and vice versa for viewing the
+ coordinates associated with a particular residue in the sequence in
+ a particular view on the alignment.</p>
+ <p>Selecting a residue highlights its associated sequence residue
+ and alpha carbon location.</p>
+ <p>
+ <table>
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Select/<br> Deselect<br> Residue
+ </td>
+ <td>Left Click</td>
+ <td>Left Click</td>
+ <td>Click</td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Roll View</td>
+ <td>Right Click and drag</td>
+ <td>Right Click and Drag</td>
+ <td>TODO</td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Middle-Button and Drag</td>
+ <td>Middle-Button and Drag</td>
+ <td>TODO</td>
+ </tr>
+ <tr>
+ <td>Zoom In</td>
+ <td>Up Arrow</td>
+ <td>Up Arrow</td>
+ <td>Up Arrow</td>
+ </tr>
+ <tr>
+ <td>Zoom Out</td>
+ <td>Down Arrow</td>
+ <td>Down Arrow</td>
+ <td>Down Arrow</td>
+ </tr>
+ </table>
+ </p>
+ <p>There are three menus:
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>Save As<br>
+ </strong><em>Saves the current view as an EPS or PNG file.</em></li>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment view, including any
+ Uniprot sequence features or region colourings.<br>
+ Residues which only exist in the PDB structure are coloured
+ white if they are insertions (relative to the associated
+ sequence in the alignment) and grey if they are N or C
+ terminal flanks outside the region mapped to the alignment
+ window's sequence.
+ </em></li>
+ <li><strong>By Chain<br>
+ </strong><em> Assigns a random colour to each PDB chain.</em>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong><em>Standard and User Defined
+ Jalview colourschemes.<br>
+ </em></strong> The remaining entries apply the colourschemes available from
+ the standard and user defined <a
+ href="../colourSchemes/index.html"
+ >amino acid colours</a>.</em></li>
+ </ul></li>
+ <li><strong>View<br>
+ </strong><em> These options can be turned off to improve performance
+ when viewing large structures, some at the expense of visual
+ clarity.</em>
+ <ul>
+ <li><strong>Wireframe<br>
+ </strong><em> Draws thin lines rather than thick lines for the
+ alpha-carbon trace.</em></li>
+ <li><strong>Depthcue<br>
+ </strong><em>Shades the structure so parts of the structure near the
+ front of the view are brighter than those further away.</em></li>
+ <li><strong>Z Buffering<br>
+ </strong><em> Applies depth sorting to correctly render occluded
+ regions of the backbone trace.</em></li>
+ <li><strong>Show All Chains<br>
+ </strong><em> When turned on, shows all chains in the PDB file, not
+ just the one associated with a sequence in the alignment
+ window.</em></li>
+ <!-- NOT YET IMPLEMENTED <li><strong>Associate View</strong><br>
Change which view on the associated sequence's alignment is to be
associated with the PDB viewer.-->
- </ul>
- </li>
-</ul>
-</p>
-<p><strong>Notes for PDB Viewing in the Jalview Applet</strong>
-<p>The applet can only load PDB files by copying and pasting the
-text into the popup window which appears when "Show PDB
-Structure" is selected after right clicking on a sequence name.</p>
+ </ul></li>
+ </ul>
+ </p>
+ <p>
+ <strong>Notes for PDB Viewing in the Jalview Applet</strong>
+ <p>The applet can only load PDB files by copying and pasting the
+ text into the popup window which appears when "Show PDB
+ Structure" is selected after right clicking on a sequence name.</p>
</body>
</html>
</head>
<body>
-<p><strong>Preferences</strong></p>
-<p>The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong> menu.</p>
-<p>There are eight tabs in the Preferences dialog box:
-<ul>
- <li>The <a href="#visual"><strong>"Visual"</strong>
- Preferences</a> tab allows you to configure the default display for a new
- alignment window.</li>
- <li>The <a href="#colours"><strong>"Colours"</strong>
- Preferences</a> tab allows you to configure default colourschemes for a new
- alignment window.</li>
- <li>The <a href="#structure"><strong>"Structure"</strong>
- Preferences</a> tab allows you to configure options for obtaining and displaying structure information.</li>
- <li>The <a href="#connections"><strong>"Connections"</strong>
- Preferences</a> tab allows you to change the links made from Jalview to
- your default web browser.</li>
- <li>The <a href="#output"><strong>"Output"</strong>
- Preferences</a> tab contains settings affecting the export of sequence
- alignments and EPS files.</li>
- <li>The <a href="#editing"><strong>"Editing"</strong>
- Preferences</a> tab contains settings affecting the export of sequence
- alignments and EPS files.</li>
- <li>The <a href="dassettings.html"><strong>"DAS
- Settings"</strong> Preferences</a> tab allows you to select which DAS sources
- to use when fetching DAS Features.</li>
- <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web Service"</strong> Preferences</a> tab allows you to configure the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a> servers that Jalview uses, and change the layout of the alignment's Web Services menu.</li>
-</ul>
-</p>
-<p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
-<p><em>Maximise Window</em> - If this is selected, a new alignment
-window will stretch to fit the available space.</p>
-<p><em>Open Overview Window</em> - When this is selected, the <a
- href="overview.html">alignment overview</a> panel is opened by default
-for a new alignment window.</p>
-<p><em>Show Annotations</em> - If this is selected the new window
-will display an annotation panel below the sequences. This annotation
-panel may have several rows describing the whole alignment. The 3
-standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
-for the alignment may be shown or hidden by default using the checkboxes
-below.</p>
-<p><em>Show group: Conservation and Consensus</em> controls the
-display of per-group automatic annotation.</p>
-<p><em>Consensus: Histogram and Logo</em> checkboxes control the
-display of the consensus histogram and sequence logo for consensus
-annotation rows.</p>
-<p><em>Full Sequence ID</em> - If selected the ID panel will display
-the name of a sequence plus the start and end residues in the format
-name/start-end. If not selected, the displayed ID will be the name of
-the sequence.</p>
-<p><em>Right Align IDs</em> - select to align all sequence IDs to
-the left-hand edge of the sequence alignment, rather than the left-hand
-edge of the alignment display window.</p>
-<p><em>Font</em> - The default font name, size and style can be set
-for a new alignment window.</p>
-<p><em>Sequence ID Tooltip</em>: Control the display of Database
-References and Non-positional annotation in the tooltip displayed when
-the mouse is over a sequence's ID.</p>
-<p><em>Show Unconserved</em> - When this is selected, all consensus sequence
-symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.</p>
-<p><em>Sequence Name Italics</em> - select to apply the italicised
-version of the font to sequence labels.</p>
-<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
-rendering of the alignment.</p>
-<p><em>Gap Symbol</em> - The default gap symbol may be set to either
-"-" or "."</p>
-<p><em>Wrap Alignment</em> - Select whether to open new alignment
-windows in wrapped mode or not.</p>
-<p><em>Sort alignment by</em> - When the alignment is loaded in, it can
-be ordered as read (No sort), or sorted by Id or pairwise identity.</p>
-<p><em>Sort annotations by</em> - Annotations can be unsorted, sorted by the order of the related sequences in
-the alignment, or by label. Autocalculated annotations (e.g. Consensus) can be shown either last (below sequence
-annotations) or first (above sequence annotations). <em>Since Jalview 2.8.2.</em></p>
-<p><em>Open file</em> - If this is selected then the default
-alignment file will be opened when Jalview is started. You can change
-the default file by clicking on file name and either typing in the file
-path or selecting it from the file chooser window.<br/><em>Note: The default example alignment is updated periodically to demonstrate new features in Jalview.</em></p>
-<p><a name="colours"><strong>"Colours" Preferences tab</strong></p>
-<p><em>Alignment Colour</em> - The default colour scheme for a new alignment
-window. If the chosen option is "User Defined" then the last
-User Defined Colour loaded or saved via the User Defined Colours panel
-will be loaded.</p>
- <p>
- <em>Annotation Shading Default</em> - set the default minimum
- and maximum colours used when <a
- href="../colourSchemes/annotationColouring.html">Colour by
- Annotation...</a> is selected from the alignment window's colours menu.
- </p>
-<p><a name="structure"><strong>"Structure"
-Preferences tab</strong></a><em> added in Jalview 2.8.2</em></p>
-<p><em>Process secondary structure from PDB</em> - if selected, then structure information
-read from PDB will be processed and annotation added to associated sequences.
-<p><em>Use RNAView for secondary structure</em> - if selected, the pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>) will be
-called to derive secondary structure information for RNA chains.
-<p><em>Add secondary structure annotation to alignment</em> - if selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's implementation DSSP</a> will be used to add annotation to polypeptide chains in the structure.
-<p><em>Add Temperature Factor annotation to alignment</em> - if selected, values extracted from the Temperature Factor
-column for the backbone atoms in the PDB file will be extracted as annotation lines shown on the alignment.
-<p><em>Default structure viewer</em> - choose JMOL or CHIMERA for viewing 3D structures.
-<p><em>Path to Chimera program</em> - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS.
-If you have installed Chimera in a non-standard location, you can specify it here, by entering the full path to the Chimera executable program.
-Double-click this field to open a file chooser dialog.
-
-<p><a name="connections"><strong>"Connections"
-Preferences tab</strong></a></p>
-<p><em>URL Link From Sequence ID</em><br>
-These definitions are used to generate URLs from a sequence's ID or
-database cross references. Read more about <a
- href="../webServices/urllinks.html#urllinks">configuring URL links
-here</a>.</p>
-<p><em>Default Browser (Unix)</em><br>
-Its difficult in Java to detect the default web browser for Unix users.
-If Jalview can't find your default web browser, enter the name or full
-path to your web browser application.</p>
-<p><em>Proxy Server</em><br>
-If you normally use a proxy server for using the internet, you must tick
-the box "Use a Proxy Server" and enter the address and port
-details as necessary. Web Services will not work if you are using a
-proxy server and do not enter the settings here.</p>
-<p><em>Usage statistics, Questionnaire and Version checks</em><br>
-Uncheck these options to prevent Jalview from submitting usage
-statistics to google analytics, checking for Jalview questionnaires or
-retrieving details of the latest release version (at www.jalview.org).
-See the <a href="../privacy.html">user privacy statement</a> for more
-information.</p>
-<p><a name="output"><strong>Output Preferences tab</strong></a></p>
-<p><em>EPS Rendering Style</em><br>
-This is a selection box which allows the user to set a default rendering
-style for EPS export:
-<ul>
- <li>"Prompt each time"<br>
- Choose this to be asked select between Lineart and Text each time you
- make an EPS file.</li>
- <li>"Lineart"<br>
- EPS files will accurately reproduce the alignment view in Jalview and
- all characters will be converted into line art. Files generated in this
- way are large and are not easily editable, but have no font table
- dependencies.</li>
- <li>"Text"<br>
- EPS files will be a mixture of text and lineart. This produces compact
- files that can be edited easily in programs like Microsoft Word and
- Adobe Illustrator, but can be problematic if the fonts available to
- Jalview are not accessible by the program reading the EPS file.
-</ul>
-<p><em>Automatically set ID width</em><br>
-When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.</p>
-<p><em>Figure ID column width</em><br>
-Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if <em>"Automatically set ID width"</em> is set.
-</p>
-<p><em>Sequence//Start-End Numbering</em><br>
-The output tab also has a group of checkboxes for each file format. If
-these are ticked, then Jalview will write files with the start and end
-sequence positions appended to each sequence id: <pre>
+ <p>
+ <strong>Preferences</strong>
+ </p>
+ <p>
+ The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong>
+ menu.
+ </p>
+ <p>There are eight tabs in the Preferences dialog box:
+ <ul>
+ <li>The <a href="#visual"><strong>"Visual"</strong>
+ Preferences</a> tab allows you to configure the default display for
+ a new alignment window.
+ </li>
+ <li>The <a href="#colours"><strong>"Colours"</strong>
+ Preferences</a> tab allows you to configure default colourschemes
+ for a new alignment window.
+ </li>
+ <li>The <a href="#structure"><strong>"Structure"</strong>
+ Preferences</a> tab allows you to configure options for obtaining
+ and displaying structure information.
+ </li>
+ <li>The <a href="#connections"><strong>"Connections"</strong>
+ Preferences</a> tab allows you to change the links made from Jalview
+ to your default web browser.
+ </li>
+ <li>The <a href="#output"><strong>"Output"</strong>
+ Preferences</a> tab contains settings affecting the export of
+ sequence alignments and EPS files.
+ </li>
+ <li>The <a href="#editing"><strong>"Editing"</strong>
+ Preferences</a> tab contains settings affecting the export of
+ sequence alignments and EPS files.
+ </li>
+ <li>The <a href="dassettings.html"><strong>"DAS
+ Settings"</strong> Preferences</a> tab allows you to select which DAS
+ sources to use when fetching DAS Features.
+ </li>
+ <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
+ Service"</strong> Preferences</a> tab allows you to configure the <a
+ href="http://www.compbio.dundee.ac.uk/jabaws"
+ >JABAWS</a> servers that Jalview uses, and change the layout of the
+ alignment's Web Services menu.
+ </li>
+ </ul>
+ </p>
+ <p>
+ <strong><a name="visual">Visual</a> Preferences tab</strong>
+ </p>
+ <p>
+ <em>Maximise Window</em> - If this is selected, a new alignment
+ window will stretch to fit the available space.
+ </p>
+ <p>
+ <em>Open Overview Window</em> - When this is selected, the <a
+ href="overview.html"
+ >alignment overview</a> panel is opened by default for a new alignment
+ window.
+ </p>
+ <p>
+ <em>Show Annotations</em> - If this is selected the new window will
+ display an annotation panel below the sequences. This annotation
+ panel may have several rows describing the whole alignment. The 3
+ standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
+ for the alignment may be shown or hidden by default using the
+ checkboxes below.
+ </p>
+ <p>
+ <em>Show group: Conservation and Consensus</em> controls the display
+ of per-group automatic annotation.
+ </p>
+ <p>
+ <em>Consensus: Histogram and Logo</em> checkboxes control the
+ display of the consensus histogram and sequence logo for consensus
+ annotation rows.
+ </p>
+ <p>
+ <em>Full Sequence ID</em> - If selected the ID panel will display
+ the name of a sequence plus the start and end residues in the format
+ name/start-end. If not selected, the displayed ID will be the name
+ of the sequence.
+ </p>
+ <p>
+ <em>Right Align IDs</em> - select to align all sequence IDs to the
+ left-hand edge of the sequence alignment, rather than the left-hand
+ edge of the alignment display window.
+ </p>
+ <p>
+ <em>Font</em> - The default font name, size and style can be set for
+ a new alignment window.
+ </p>
+ <p>
+ <em>Sequence ID Tooltip</em>: Control the display of Database
+ References and Non-positional annotation in the tooltip displayed
+ when the mouse is over a sequence's ID.
+ </p>
+ <p>
+ <em>Show Unconserved</em> - When this is selected, all consensus
+ sequence symbols will be rendered as a '.', highlighting mutations
+ in highly conserved alignments.
+ </p>
+ <p>
+ <em>Sequence Name Italics</em> - select to apply the italicised
+ version of the font to sequence labels.
+ </p>
+ <p>
+ <em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
+ rendering of the alignment.
+ </p>
+ <p>
+ <em>Gap Symbol</em> - The default gap symbol may be set to either
+ "-" or "."
+ </p>
+ <p>
+ <em>Wrap Alignment</em> - Select whether to open new alignment
+ windows in wrapped mode or not.
+ </p>
+ <p>
+ <em>Sort alignment by</em> - When the alignment is loaded in, it can
+ be ordered as read (No sort), or sorted by Id or pairwise identity.
+ </p>
+ <p>
+ <em>Sort annotations by</em> - Annotations can be unsorted, sorted
+ by the order of the related sequences in the alignment, or by label.
+ Autocalculated annotations (e.g. Consensus) can be shown either last
+ (below sequence annotations) or first (above sequence annotations).
+ <em>Since Jalview 2.8.2.</em>
+ </p>
+ <p>
+ <em>Open file</em> - If this is selected then the default alignment
+ file will be opened when Jalview is started. You can change the
+ default file by clicking on file name and either typing in the file
+ path or selecting it from the file chooser window.<br />
+ <em>Note: The default example alignment is updated periodically
+ to demonstrate new features in Jalview.</em>
+ </p>
+ <p>
+ <a name="colours"><strong>"Colours"
+ Preferences tab</strong>
+ </p>
+ <p>
+ <em>Alignment Colour</em> - The default colour scheme for a new
+ alignment window. If the chosen option is "User Defined"
+ then the last User Defined Colour loaded or saved via the User
+ Defined Colours panel will be loaded.
+ </p>
+ <p>
+ <em>Annotation Shading Default</em> - set the default minimum and
+ maximum colours used when <a
+ href="../colourSchemes/annotationColouring.html"
+ >Colour by Annotation...</a> is selected from the alignment window's
+ colours menu.
+ </p>
+ <p>
+ <a name="structure"><strong>"Structure"
+ Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
+ </p>
+ <p>
+ <em>Process secondary structure from PDB</em> - if selected, then
+ structure information read from PDB will be processed and annotation
+ added to associated sequences.
+ <p>
+ <em>Use RNAView for secondary structure</em> - if selected, the
+ pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>)
+ will be called to derive secondary structure information for RNA
+ chains.
+ <p>
+ <em>Add secondary structure annotation to alignment</em> - if
+ selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's
+ implementation DSSP</a> will be used to add annotation to polypeptide
+ chains in the structure.
+ <p>
+ <em>Add Temperature Factor annotation to alignment</em> - if
+ selected, values extracted from the Temperature Factor column for
+ the backbone atoms in the PDB file will be extracted as annotation
+ lines shown on the alignment.
+ <p>
+ <em>Default structure viewer</em> - choose JMOL or CHIMERA for
+ viewing 3D structures.
+ <p>
+ <em>Path to Chimera program</em> - Optional, as Jalview will search
+ standard installation paths for Windows, Linux or MacOS. If you have
+ installed Chimera in a non-standard location, you can specify it
+ here, by entering the full path to the Chimera executable program.
+ Double-click this field to open a file chooser dialog.
+ <p>
+ <a name="connections"><strong>"Connections"
+ Preferences tab</strong></a>
+ </p>
+ <p>
+ <em>URL Link From Sequence ID</em><br> These definitions are
+ used to generate URLs from a sequence's ID or database cross
+ references. Read more about <a
+ href="../webServices/urllinks.html#urllinks"
+ >configuring URL links here</a>.
+ </p>
+ <p>
+ <em>Default Browser (Unix)</em><br> Its difficult in Java to
+ detect the default web browser for Unix users. If Jalview can't find
+ your default web browser, enter the name or full path to your web
+ browser application.
+ </p>
+ <p>
+ <em>Proxy Server</em><br> If you normally use a proxy server
+ for using the internet, you must tick the box "Use a Proxy
+ Server" and enter the address and port details as necessary.
+ Web Services will not work if you are using a proxy server and do
+ not enter the settings here.
+ </p>
+ <p>
+ <em>Usage statistics, Questionnaire and Version checks</em><br>
+ Uncheck these options to prevent Jalview from submitting usage
+ statistics to google analytics, checking for Jalview questionnaires
+ or retrieving details of the latest release version (at
+ www.jalview.org). See the <a href="../privacy.html">user privacy
+ statement</a> for more information.
+ </p>
+ <p>
+ <a name="output"><strong>Output Preferences tab</strong></a>
+ </p>
+ <p>
+ <em>EPS Rendering Style</em><br> This is a selection box which
+ allows the user to set a default rendering style for EPS export:
+ <ul>
+ <li>"Prompt each time"<br> Choose this to be
+ asked select between Lineart and Text each time you make an EPS
+ file.
+ </li>
+ <li>"Lineart"<br> EPS files will accurately
+ reproduce the alignment view in Jalview and all characters will be
+ converted into line art. Files generated in this way are large and
+ are not easily editable, but have no font table dependencies.
+ </li>
+ <li>"Text"<br> EPS files will be a mixture of
+ text and lineart. This produces compact files that can be edited
+ easily in programs like Microsoft Word and Adobe Illustrator, but
+ can be problematic if the fonts available to Jalview are not
+ accessible by the program reading the EPS file.
+ </ul>
+ <p>
+ <em>Automatically set ID width</em><br> When enabled, the
+ column containing sequence and annotation labels at the left hand
+ side of an exported figure will be made large enough to display each
+ sequence ID and annotation label in its own line. Enable this if you
+ have particularly long sequence IDs and need to generate EPS or PNG
+ figures or web pages.
+ </p>
+ <p>
+ <em>Figure ID column width</em><br> Manually specify the width
+ of the left hand column where sequence IDs and annotation labels
+ will be rendered in exported alignment figures. This setting will be
+ ignored if <em>"Automatically set ID width"</em> is set.
+ </p>
+ <p>
+ <em>Sequence//Start-End Numbering</em><br> The output tab also
+ has a group of checkboxes for each file format. If these are ticked,
+ then Jalview will write files with the start and end sequence
+ positions appended to each sequence id:
+ <pre>
>ID/1-10
AACDEAAFEA
</pre>
-<p>If the boxes are left unchecked for a particular format, the
-sequence limits will not be appended to the sequence id.</p>
-<p><em>Embed BioJSON to HTML export</em></p>
-<p>When this option is enabled, Jalview embeds <a href="bioJsonFormat.html">BioJSON</a> data within
-HTML files exported from Jalview at generation time. This enables the exported HTML files
-to be extracted and imported back into the Jalview desktop application at a later time.
-
-<p><em>Use Modeller Output</em></p>
-<p>This option only applies to PIR format output. Jalview
-automatically reads PIR files with sequence descriptions compatible with
-the program <a href="http://salilab.org/modeller/">Modeller</a>. If this
-option is selected <a href="../io/modellerpir.html">Jalview will
-write Modeller style PIR files</a> with correct start/end numbering and PDB
-file association (if available). The Jalview id/start-end option is
-ignored if Modeller output is selected.
-
-<p><a name="editing"><strong>Editing Preferences tab</strong></a></p>
-<p>There are currently three options available which can be selected /
-deselected.</p>
-<p><em>AutoCalculate Consensus</em> - For large alignments it can be
-useful to deselect "Autocalculate Consensus" when editing.
-This prevents lengthy calculations which are performed after each
-sequence edit. New alignment windows will have their "Autocalculate
-Consensus" option set according to this setting.</p>
-<p><em>Pad Gaps when Editing</em> - New alignment windows will
-"Pad Gaps" according to this setting.</p>
-<p><em>Sort with New Tree</em> - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.</p>
-<p> </p>
-<p> </p>
+ <p>If the boxes are left unchecked for a particular format, the
+ sequence limits will not be appended to the sequence id.</p>
+ <p>
+ <em>Embed BioJSON to HTML export</em>
+ </p>
+ <p>
+ When this option is enabled, Jalview embeds <a
+ href="bioJsonFormat.html"
+ >BioJSON</a> data within HTML files exported from Jalview at
+ generation time. This enables the exported HTML files to be
+ extracted and imported back into the Jalview desktop application at
+ a later time.
+ <p>
+ <em>Use Modeller Output</em>
+ </p>
+ <p>
+ This option only applies to PIR format output. Jalview automatically
+ reads PIR files with sequence descriptions compatible with the
+ program <a href="http://salilab.org/modeller/">Modeller</a>. If this
+ option is selected <a href="../io/modellerpir.html">Jalview will
+ write Modeller style PIR files</a> with correct start/end numbering
+ and PDB file association (if available). The Jalview id/start-end
+ option is ignored if Modeller output is selected.
+ <p>
+ <a name="editing"><strong>Editing Preferences tab</strong></a>
+ </p>
+ <p>There are currently three options available which can be
+ selected / deselected.</p>
+ <p>
+ <em>AutoCalculate Consensus</em> - For large alignments it can be
+ useful to deselect "Autocalculate Consensus" when editing.
+ This prevents lengthy calculations which are performed after each
+ sequence edit. New alignment windows will have their
+ "Autocalculate Consensus" option set according to this
+ setting.
+ </p>
+ <p>
+ <em>Pad Gaps when Editing</em> - New alignment windows will
+ "Pad Gaps" according to this setting.
+ </p>
+ <p>
+ <em>Sort with New Tree</em> - When selected, any trees calculated or
+ loaded onto the alignment will automatically sort the alignment.
+ </p>
+ <p> </p>
+ <p> </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Search</title>
+<head>
+<title>Search</title>
<style type="text/css">
<!--
td {
</head>
<body>
-<p><strong>Search</strong></p>
-<p>The search box is displayed by pressing Control and F or
- selecting "Find..." from the "Search" menu.</p>
-<img src="search.gif" width="339" height="110">
-<p>"Find next" will find the next occurence of the specified and adjust
- the alignment window view to show it, and "Find all" highlights all
- matches for a pattern. The "New Feature" is a quick way to highlight
- and group residues matching the specified search pattern throughout the alignment.
-<ul>
- <li>The search uses regular expressions. (understands a mixture of posix and
- perl style regex - see below for a summary)</li>
- <li>Gaps are ignored when matching the query to the sequences in the alignment.</li>
- <li>The search is applied to both sequences and their IDs.</li>
- <li>If a region is selected, then search will <strong>only</strong> be performed
- on that region. </li>
- <li>To quickly clear the current selection, press the "Escape" key.</li>
- <li>Tick the "Match Case" box to perform a case sensitive search.</li>
-</ul>
-<p><strong>Creating Features from Search Results</strong></p>
-<p>
- If "New Feature" is selected, the feature can be given a name from
- a popup input box. Use the "Feature Settings" under the "View"
- menu to change the visibility and colour of the new sequence feature.</p>
-<p><strong>A quick Regular Expression Guide</strong></p>
-<p>A regular expression is not just a simple text query - although it
-can be used like one, the query is not parsed literally, but
-interpreted like a series of instructions defining the features of the
-match. For example, a simple query like "ACDED" would
-match all occurences of that string, but "ACD+ED" matches
-both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query
-"[ILGVMA]{;5,}" would find stretches of small,
-hydrophobic amino acids of at least five residues in length.
-</p>
-<p> The table
-below describes some of the regular expression syntax:<br></p>
-<table width="100%" border="1">
- <tr>
- <td width="24%">Regular Expression Element</td>
- <td width="76%">Effect</td>
- </tr>
- <tr>
- <td width="24%">.</td>
- <td width="76%">Matches any single character</td>
- </tr>
- <tr>
- <td>[]</td>
- <td>Matches any one of the characters in the brackets</td>
- </tr>
- <tr>
- <td>^</td>
- <td>Matches at the start of an ID or sequence</td>
- </tr>
- <tr>
- <td>$</td>
- <td>Matches at the end of an ID or sequence</td>
- </tr>
- <tr>
- <td>*</td>
- <td>Matches if the preceding element matches zero or more times</td>
- </tr>
- <tr>
- <td>?</td>
- <td>Matches if the preceding element matched once or not at all</td>
- </tr>
- <tr>
- <td>+</td>
- <td>Matches if the preceding element matched at least once</td>
- </tr>
- <tr>
- <td>{count}</td>
- <td>Matches if the preceding element matches a specified number of
- times
- </td>
- </tr>
- <tr>
- <td>{min,}</td>
- <td> Matches of the preceding element matched at least the
- specified number of times</td>
- </tr>
- <tr>
- <td>{min,max} </td>
- <td>Matches if the preceding element matches min or at most max
- number of times</td>
- </tr>
-</table>
+ <p>
+ <strong>Search</strong>
+ </p>
+ <p>The search box is displayed by pressing Control and F or
+ selecting "Find..." from the "Search" menu.</p>
+ <img src="search.gif" width="339" height="110">
+ <p>"Find next" will find the next occurence of the
+ specified and adjust the alignment window view to show it, and
+ "Find all" highlights all matches for a pattern. The
+ "New Feature" is a quick way to highlight and group
+ residues matching the specified search pattern throughout the
+ alignment.
+ <ul>
+ <li>The search uses regular expressions. (understands a mixture
+ of posix and perl style regex - see below for a summary)</li>
+ <li>Gaps are ignored when matching the query to the sequences
+ in the alignment.</li>
+ <li>The search is applied to both sequences and their IDs.</li>
+ <li>If a region is selected, then search will <strong>only</strong>
+ be performed on that region.
+ </li>
+ <li>To quickly clear the current selection, press the
+ "Escape" key.</li>
+ <li>Tick the "Match Case" box to perform a case
+ sensitive search.</li>
+ </ul>
+ <p>
+ <strong>Creating Features from Search Results</strong>
+ </p>
+ <p>If "New Feature" is selected, the feature can be
+ given a name from a popup input box. Use the "Feature
+ Settings" under the "View" menu to change the
+ visibility and colour of the new sequence feature.</p>
+ <p>
+ <strong>A quick Regular Expression Guide</strong>
+ </p>
+ <p>A regular expression is not just a simple text query - although
+ it can be used like one, the query is not parsed literally, but
+ interpreted like a series of instructions defining the features of
+ the match. For example, a simple query like "ACDED" would
+ match all occurences of that string, but "ACD+ED" matches
+ both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query
+ "[ILGVMA]{;5,}" would find stretches of small, hydrophobic
+ amino acids of at least five residues in length.</p>
+ <p>
+ The table below describes some of the regular expression syntax:<br>
+ </p>
+ <table width="100%" border="1">
+ <tr>
+ <td width="24%">Regular Expression Element</td>
+ <td width="76%">Effect</td>
+ </tr>
+ <tr>
+ <td width="24%">.</td>
+ <td width="76%">Matches any single character</td>
+ </tr>
+ <tr>
+ <td>[]</td>
+ <td>Matches any one of the characters in the brackets</td>
+ </tr>
+ <tr>
+ <td>^</td>
+ <td>Matches at the start of an ID or sequence</td>
+ </tr>
+ <tr>
+ <td>$</td>
+ <td>Matches at the end of an ID or sequence</td>
+ </tr>
+ <tr>
+ <td>*</td>
+ <td>Matches if the preceding element matches zero or more
+ times</td>
+ </tr>
+ <tr>
+ <td>?</td>
+ <td>Matches if the preceding element matched once or not at
+ all</td>
+ </tr>
+ <tr>
+ <td>+</td>
+ <td>Matches if the preceding element matched at least once</td>
+ </tr>
+ <tr>
+ <td>{count}</td>
+ <td>Matches if the preceding element matches a specified
+ number of times</td>
+ </tr>
+ <tr>
+ <td>{min,}</td>
+ <td>Matches of the preceding element matched at least the
+ specified number of times</td>
+ </tr>
+ <tr>
+ <td>{min,max}</td>
+ <td>Matches if the preceding element matches min or at most
+ max number of times</td>
+ </tr>
+ </table>
</body>
</html>
<title>Sequence Features</title>
</head>
<body>
-<p><strong>Sequence Features</strong></p>
-<p>Jalview can colour parts of a sequence based on the presence of
-sequence features - which may be retrieved from database records (such
-as Uniprot), the result of <a href="search.html">sequence motif
-searches</a> or simply read from a <a href="featuresFormat.html">sequence
-features file</a>. You can also <a href="creatinFeatures.html">create
-features</a> from the results of searches or the current selection, and <a
- href="editingFeatures.html">edit features</a> by double clicking on
-them.</p>
-<p><strong>Sequence Feature Colouring Styles</strong></p>
-<p>By default, Jalview will assign a color to each feature based on
-its type. These colours can be changed from the <a
- href="featuresettings.html">feature settings</a> and <a
- href="editingFeatures.html">amend features</a> dialog boxes. Since
-Jalview 2.5, it is also possible to define <a href="featureschemes.html">feature
-colourschemes</a> to shade features based on their associated scores or text
-labels.</p>
-<p><strong>Sequence Feature Groups</strong></p>
-<p>Since Jalview 2.08, sequence features assigned to a sequence can
-be organised into groups, which may indicate that the features were all
-retrieved from the same database (such as Uniprot features), or
-generated by the same analysis process (as might be specified in a <a
- href="featuresFormat.html">sequence features file</a>).</p>
-<p><strong>Sequence Feature Inheritance</strong></p>
-<p>Since Jalview 2.08, sequence features are <em>global</em> to a
-set of sequences appearing (independently or together) in many different
-alignments. Practically, this means features loaded onto one alignment
-can be viewed in any alignments involving the same sequences. The same
-sequence appears in different alignments when a new alignment is
-generated by submitting an existing set of sequences to one of the
-alignment or prediction web services, and when sequences are copied and
-pasted into other alignment windows.</p>
-<p><strong>View→Show Sequence Features</strong></p>
-<p>Toggle the display of sequence features in this alignment. If
-feature retrieval has not already been carried out, then Jalview will
-automatically try to fetch sequence features (as described below).</p>
-<p><strong>View→Sequence Feature Settings...</strong></p>
-<p>Once sequence features have been loaded, their display can be
-fully controlled using the alignment window's <a
- href="featuresettings.html">Sequence Feature Settings</a> dialog box.
-Feature colour schemes and display parameters are unique to a particular
-alignment, so it is possible to colour the same sequence features
-differently in different alignment views.<br>
-Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS
-features</a> to an alignment via the DAS tabbed pane of the feature settings
-window.</p>
-<p><strong>View→Sequence ID Tooltip→Show
-Non-Positional features</strong><br>
-<em>Only available in application</em></br>
-</p>
-<p>Toggles the display of non-positional features in the sequence ID
-tooltip, and whether they will be included when sequence features are
-exported using "File→Export Features".</p>
-<p>Precalculated Sequence Features may be added to an alignment from
-the command line, drag and drop, or from the "File→Load
-Features / Annotations" menu item. See the <a
- href="featuresFormat.html">Features File Format</a> for more details.</p>
+ <p>
+ <strong>Sequence Features</strong>
+ </p>
+ <p>
+ Jalview can colour parts of a sequence based on the presence of
+ sequence features - which may be retrieved from database records
+ (such as Uniprot), the result of <a href="search.html">sequence
+ motif searches</a> or simply read from a <a href="featuresFormat.html">sequence
+ features file</a>. You can also <a href="creatinFeatures.html">create
+ features</a> from the results of searches or the current selection,
+ and <a href="editingFeatures.html">edit features</a> by double
+ clicking on them.
+ </p>
+ <p>
+ <strong>Sequence Feature Colouring Styles</strong>
+ </p>
+ <p>
+ By default, Jalview will assign a color to each feature based on its
+ type. These colours can be changed from the <a
+ href="featuresettings.html"
+ >feature settings</a> and <a href="editingFeatures.html">amend
+ features</a> dialog boxes. Since Jalview 2.5, it is also possible to
+ define <a href="featureschemes.html">feature colourschemes</a> to
+ shade features based on their associated scores or text labels.
+ </p>
+ <p>
+ <strong>Sequence Feature Groups</strong>
+ </p>
+ <p>
+ Since Jalview 2.08, sequence features assigned to a sequence can be
+ organised into groups, which may indicate that the features were all
+ retrieved from the same database (such as Uniprot features), or
+ generated by the same analysis process (as might be specified in a <a
+ href="featuresFormat.html"
+ >sequence features file</a>).
+ </p>
+ <p>
+ <strong>Sequence Feature Inheritance</strong>
+ </p>
+ <p>
+ Since Jalview 2.08, sequence features are <em>global</em> to a set
+ of sequences appearing (independently or together) in many different
+ alignments. Practically, this means features loaded onto one
+ alignment can be viewed in any alignments involving the same
+ sequences. The same sequence appears in different alignments when a
+ new alignment is generated by submitting an existing set of
+ sequences to one of the alignment or prediction web services, and
+ when sequences are copied and pasted into other alignment windows.
+ </p>
+ <p>
+ <strong>View→Show Sequence Features</strong>
+ </p>
+ <p>Toggle the display of sequence features in this alignment. If
+ feature retrieval has not already been carried out, then Jalview
+ will automatically try to fetch sequence features (as described
+ below).</p>
+ <p>
+ <strong>View→Sequence Feature Settings...</strong>
+ </p>
+ <p>
+ Once sequence features have been loaded, their display can be fully
+ controlled using the alignment window's <a
+ href="featuresettings.html"
+ >Sequence Feature Settings</a> dialog box. Feature colour schemes and
+ display parameters are unique to a particular alignment, so it is
+ possible to colour the same sequence features differently in
+ different alignment views.<br> Since Jalview 2.1, it is
+ possible to add <a href="dassettings.html">DAS features</a> to an
+ alignment via the DAS tabbed pane of the feature settings window.
+ </p>
+ <p>
+ <strong>View→Sequence ID Tooltip→Show
+ Non-Positional features</strong><br> <em>Only available in
+ application</em></br>
+ </p>
+ <p>Toggles the display of non-positional features in the sequence
+ ID tooltip, and whether they will be included when sequence features
+ are exported using "File→Export Features".</p>
+ <p>
+ Precalculated Sequence Features may be added to an alignment from
+ the command line, drag and drop, or from the "File→Load
+ Features / Annotations" menu item. See the <a
+ href="featuresFormat.html"
+ >Features File Format</a> for more details.
+ </p>
</body>
</html>
<title>Sequence Fetcher</title>
</head>
<body>
-<p><strong>Sequence Fetcher</strong></p>
-<p>Jalview can retrieve sequences from certain databases using either the
-DBFetch service provided by the EMBL European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
- <img src="seqfetcher.gif" align="center"
- alt="The Jalview Sequence Fetcher Dialog Box">
- <p>The Sequence Fetcher dialog box can be opened via the "File"
- menu on the main desktop in order to retrieve sequences as a new
- alignment, or opened via the "File" menu of an existing alignment
- to import additional sequences. There may be a short delay when the sequence fetcher is first opened,
- whilst Jalview compiles the list of available sequence datasources from the
- currently defined DAS server registry.
-</p>
- <p>First, <strong>select the database you want to retrieve sequences from</strong>
- by clicking the button labeled 'Select database retrieval source'. If
- a database source is already selected, then the button's label will
- change to show the currently selected database.</p>
- <img src="selectfetchdb.gif" align="left" alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
- <p>Since Jalview 2.8, the
- available databases are shown as a tree in a popup dialog box. The
- databases are ordered alphabetically, and if there are many sources
- for the same type of sequence identifier, they will be grouped
- together in a sub-branch branch labeled with the identifier.</p>
- <p>Once you have selected the sequence database using the popup dialog box, <strong>enter
- one or more accession ids</strong> (as a semi-colon separated list), or press the
- "Example" button to paste the example accession for the currently selected database into the retrieval box.
- Finally, press "OK" to initiate the retrieval.</p>
+ <p>
+ <strong>Sequence Fetcher</strong>
+ </p>
+ <p>
+ Jalview can retrieve sequences from certain databases using either
+ the DBFetch service provided by the EMBL European Bioinformatics
+ Institute, or, since Jalview 2.4, DAS servers capable of the <em>sequence</em>
+ command (configured in <a href="dassettings.html">DAS settings</a>).
+ </p>
+ <img src="seqfetcher.gif" align="center"
+ alt="The Jalview Sequence Fetcher Dialog Box"
+ >
+ <p>The Sequence Fetcher dialog box can be opened via the
+ "File" menu on the main desktop in order to retrieve
+ sequences as a new alignment, or opened via the "File"
+ menu of an existing alignment to import additional sequences. There
+ may be a short delay when the sequence fetcher is first opened,
+ whilst Jalview compiles the list of available sequence datasources
+ from the currently defined DAS server registry.</p>
+ <p>
+ First, <strong>select the database you want to retrieve
+ sequences from</strong> by clicking the button labeled 'Select database
+ retrieval source'. If a database source is already selected, then
+ the button's label will change to show the currently selected
+ database.
+ </p>
+ <img src="selectfetchdb.gif" align="left"
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)"
+ >
+ <p>Since Jalview 2.8, the available databases are shown as a tree
+ in a popup dialog box. The databases are ordered alphabetically, and
+ if there are many sources for the same type of sequence identifier,
+ they will be grouped together in a sub-branch branch labeled with
+ the identifier.</p>
+ <p>
+ Once you have selected the sequence database using the popup dialog
+ box, <strong>enter one or more accession ids</strong> (as a
+ semi-colon separated list), or press the "Example" button
+ to paste the example accession for the currently selected database
+ into the retrieval box. Finally, press "OK" to initiate
+ the retrieval.
+ </p>
<p>
<strong>Fetching from The PDB with the EMBL-EBI PDBe Search
Interface</strong>
Jalview 2.8</em>
</p>
- <p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PFAM, and RFAM)
- in work for publication, please cite:</p>
-<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
- S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>
- SOAP-based services provided by the European Bioinformatics Institute.<br>
- Nucleic Acids Res. 33(1):W25-W28 (2005) <br>
- <br>
+ <p>If you use the WSDBFetch sequence fetcher services (EMBL,
+ Uniprot, PFAM, and RFAM) in work for publication, please cite:</p>
+ <p>
+ Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
+ J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
+ R. <br> SOAP-based services provided by the European
+ Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
+ (2005) <br> <br>
</p>
</body>
</html>
<title>Mapping Between Different Sequences</title>
</head>
<body>
-<p><strong>Mapping Between Different Sequences</strong></p>
-<p>A new feature in Jalview 2.3 is the ability to map between sequences in different
- domains, based on alignment, or by the use of explicit mappings provided by
- databases. </p>
-<p>The most familiar mapping is the one used to identify
-the coordinates corresponding to a displayed sequence when
-viewing a PDB file associated with a sequence (see
-<a href="viewingpdbs.html">"Viewing PDB Files"</a>
-for more information.</p>
-<p>The newest form of mapping supported by Jalview is the
-correspondence between DNA and protein sequences. This mapping
-can be imported directly from EMBL and EMBLCDS database records
-retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>,
-and allows sequence features to be mapped directly from Uniprot
-das sources to their coding region on EMBL sequence records.
+ <p>
+ <strong>Mapping Between Different Sequences</strong>
+ </p>
+ <p>A new feature in Jalview 2.3 is the ability to map between
+ sequences in different domains, based on alignment, or by the use of
+ explicit mappings provided by databases.</p>
+ <p>
+ The most familiar mapping is the one used to identify the
+ coordinates corresponding to a displayed sequence when viewing a PDB
+ file associated with a sequence (see <a href="viewingpdbs.html">"Viewing
+ PDB Files"</a> for more information.
+ </p>
+ <p>
+ The newest form of mapping supported by Jalview is the
+ correspondence between DNA and protein sequences. This mapping can
+ be imported directly from EMBL and EMBLCDS database records
+ retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>, and
+ allows sequence features to be mapped directly from Uniprot das
+ sources to their coding region on EMBL sequence records.
</body>
</html>
<title>Split Frame Views</title>
</head>
<body>
-<p><strong>Split Frame Views</strong></p>
+ <p>
+ <strong>Split Frame Views</strong>
+ </p>
<p>
Jalview provides a special viewing mode to show Coding DNA (cDNA)
and protein product alignments as a split view, with cDNA above and
protein below. The two alignments are linked, allowing editing and
analysis to be performed at both the peptide and nucleotide level.
- Linked protein alignments also have an additional
- <strong>cDNA Consensus</strong> annotation row, showing the
- distribution of codons at each column
- of the protein alignment.
+ Linked protein alignments also have an additional <strong>cDNA
+ Consensus</strong> annotation row, showing the distribution of codons at
+ each column of the protein alignment.
</p>
<p>
- Split Frame views can be <a
- href="#opensplit">created in a number of ways</a>. In the Jalview
- Desktop, Split Frame views are saved in Jalview Projects, like any
- other alignment view.
+ Split Frame views can be <a href="#opensplit">created in a
+ number of ways</a>. In the Jalview Desktop, Split Frame views are
+ saved in Jalview Projects, like any other alignment view.
</p>
- <p><strong>Operations supported in Split Frame Mode</strong></p>
-<p>Split Frame views allow the following:
-
+ <p>
+ <strong>Operations supported in Split Frame Mode</strong>
+ </p>
+ <p>Split Frame views allow the following:
<ul>
<li>Mouseover or scrolling of either alignment is followed by
the other (unless you turn off <strong><a
- href="../menus/alwview.html">"View→Automatic
- Scrolling"</a></strong>)
+ href="../menus/alwview.html"
+ >"View→Automatic Scrolling"</a></strong>)
</li>
<li>On selecting rows, columns or regions in one alignment, the
corresponding selection is made in the other</li>
<li>Sequence ordering in one alignment (using the cursor, or <strong><a
- href="../calculate/sorting.html">"Calculate→Sort")</a></strong> is
- also applied to the other
+ href="../calculate/sorting.html"
+ >"Calculate→Sort")</a></strong> is also applied to the other
</li>
<li>Editing (gap insertion / deletion) in the protein alignment
is reflected in the cDNA (but not vice versa)</li>
<li>Any trees imported or created with <strong><a
- href="../calculations/tree.html">"Calculate Tree"</a></strong> on one of
- the views allow both cDNA and Protein views to be grouped,
- coloured or sorted.
+ href="../calculations/tree.html"
+ >"Calculate Tree"</a></strong> on one of the views allow both cDNA and
+ Protein views to be grouped, coloured or sorted.
</li>
<li>To allow for the different widths in cDNA and Protein
alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
View / Expand Views / Gather Views"</strong></a> behave as for a normal
alignment window, but always create new views as Split Frames</li>
</ul>
- <p>An alignment annotation row on the protein alignment shows the <strong><a href="../calculations/consensus.html">cDNA consensus</a></strong> for each peptide column.<br/>
-This consensus may reveal variation in nucleotides coding for conserved protein residues.</p>
-
-<a name="opensplit"/><p><strong>Opening a Split Frame View</strong></p>
-<p>A Split Frame View can be opened in one of the following ways:</p>
-<p><strong><em>Add Sequences</em></strong></p>
-<p>If you add (coding) DNA sequences to an open peptide alignment, or vice versa, <em>and</em> at least one DNA sequence translates to one of the
-peptide sequences, then the option to open in a split window is offered. The DNA may include start and/or stop codons, but no non-coding (intron)
-sequence.<br>
-If more than one cDNA variant is present in the alignment, Jalview will first try to match these to protein sequences based on any retrieved cross-references, and failing that, pairwise as they are ordered in the alignments.
+ <p>
+ An alignment annotation row on the protein alignment shows the <strong><a
+ href="../calculations/consensus.html"
+ >cDNA consensus</a></strong> for each peptide column.<br /> This consensus may
+ reveal variation in nucleotides coding for conserved protein
+ residues.
+ </p>
-<p>This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox).
-The additional options below apply to Jalview Desktop only.</p>
+ <a name="opensplit" />
+ <p>
+ <strong>Opening a Split Frame View</strong>
+ </p>
+ <p>A Split Frame View can be opened in one of the following ways:</p>
+ <p>
+ <strong><em>Add Sequences</em></strong>
+ </p>
+ <p>
+ If you add (coding) DNA sequences to an open peptide alignment, or
+ vice versa, <em>and</em> at least one DNA sequence translates to one
+ of the peptide sequences, then the option to open in a split window
+ is offered. The DNA may include start and/or stop codons, but no
+ non-coding (intron) sequence.<br> If more than one cDNA variant
+ is present in the alignment, Jalview will first try to match these
+ to protein sequences based on any retrieved cross-references, and
+ failing that, pairwise as they are ordered in the alignments.
+ <p>This option is available in Jalview Desktop (when adding
+ sequences by any supported method), and Jalview applet (adding from
+ textbox). The additional options below apply to Jalview Desktop
+ only.</p>
-<p><strong><em>Translate as cDNA</em></strong></p>
-<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Translate as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this option shows the DNA and its
-calculated protein product in a Split Frame view.</p>
+ <p>
+ <strong><em>Translate as cDNA</em></strong>
+ </p>
+ <p>
+ Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Translate
+ as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this
+ option shows the DNA and its calculated protein product in a Split
+ Frame view.
+ </p>
-<p><strong><em>Get Cross-References</em></strong></p>
-<p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Get Cross-References"</a></strong> is available for fetched sequences which have cross-references to other databases.
-On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.</p>
+ <p>
+ <strong><em>Get Cross-References</em></strong>
+ </p>
+ <p>
+ Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Get
+ Cross-References"</a></strong> is available for fetched sequences which have
+ cross-references to other databases. On selecting protein
+ cross-references (for a cDNA alignment), or DNA xrefs (for peptide),
+ a Split Frame view is opened showing cDNA and peptide.
+ </p>
-<p><strong><em>Realign a Split View</em></strong></p>
+ <p>
+ <strong><em>Realign a Split View</em></strong>
+ </p>
<p>If you invoke a web service to realign either half of a Split
Frame, then the resulting realignment is displayed in a new Split
- Frame.
- </p>
+ Frame.</p>
<ul>
<li>the alignment you chose to realign (for example, peptide)
is displayed as aligned by the external web service</li>
this case, cDNA) by inserting gaps in the corresponding positions</li>
</ul>
<p>
- <a name="reconalignment" /><strong>Reconstructed Alignments</strong>
+ <a name="reconalignment" /><strong>Reconstructed
+ Alignments</strong>
</p>
<p>
Reconstructed alignments are typically <em>not</em> the same as the
kinds of molecular evolution analysis.
</p>
<p>
- <em>Split Frame Views were introduced in Jalview 2.9</em>
- </p>
+ <em>Split Frame Views were introduced in Jalview 2.9</em>
+ </p>
</body>
</html>
</head>
<body>
- <p>
- <strong>Structure Chooser</strong>
- </p>
+ <p>
+ <strong>Structure Chooser</strong>
+ </p>
- The Structure Chooser interface provides a smart technique for
- selecting PDB structures to view in Jalview by querying readily
- available meta-data of structures. The Interface can be invoked by selecting
- the
- <strong>"3D Structure Data.."</strong> option from a sequence's
- <a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
- features it provides are listed below:
- <ul>
- <li>Automatic discovery, retrieval and association of PDB entries
- for an alignment's sequences</li>
- <li>Visualisation of discovered structures' meta-data</li>
- <li>Ability to configure the meta-data entries to visualise</li>
- <li>Auto-selection of the best structure via filtering by the
- available metric parameters in the meta-data (i.e. resolution,
- quality etc).</li>
- <li>Selection of multiple structures in a single operation</li>
- </ul>
- Additionally, the Structure Chooser retains the following contemporary
- features of Jalview:
- <ul>
- <li>Manual association of PDB entries via entering the PDB Id or
- From File</li>
- <li>Ability to view cached PDB entries</li>
- </ul>
+ The Structure Chooser interface provides a smart technique for
+ selecting PDB structures to view in Jalview by querying readily
+ available meta-data of structures. The Interface can be invoked by
+ selecting the
+ <strong>"3D Structure Data.."</strong> option from a sequence's
+ <a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
+ features it provides are listed below:
+ <ul>
+ <li>Automatic discovery, retrieval and association of PDB
+ entries for an alignment's sequences</li>
+ <li>Visualisation of discovered structures' meta-data</li>
+ <li>Ability to configure the meta-data entries to visualise</li>
+ <li>Auto-selection of the best structure via filtering by the
+ available metric parameters in the meta-data (i.e. resolution,
+ quality etc).</li>
+ <li>Selection of multiple structures in a single operation</li>
+ </ul>
+ Additionally, the Structure Chooser retains the following contemporary
+ features of Jalview:
+ <ul>
+ <li>Manual association of PDB entries via entering the PDB Id
+ or From File</li>
+ <li>Ability to view cached PDB entries</li>
+ </ul>
- <strong>Associating PDB files with Sequences</strong><br>
- Discovery/Association of PDB entries to a sequence now happens
- automatically during the initialisation of the Structure Chooser
- Interface. Jalview uses the sequence's ID to query the PDB Rest API
- provided by the EBI to discover PDB Ids associated with the sequence.
+ <strong>Associating PDB files with Sequences</strong>
+ <br> Discovery/Association of PDB entries to a sequence now
+ happens automatically during the initialisation of the Structure
+ Chooser Interface. Jalview uses the sequence's ID to query the PDB
+ Rest API provided by the EBI to discover PDB Ids associated with the
+ sequence.
-<br><br>
- <strong>Configuring displayed meta-data for Structures</strong><br>
- To configure the visible meta-data displayed for the discovered structures, click the 'Configure Displayed Columns' tab, then tick the options which you intend to make visible.
+ <br>
+ <br>
+ <strong>Configuring displayed meta-data for Structures</strong>
+ <br> To configure the visible meta-data displayed for the
+ discovered structures, click the 'Configure Displayed Columns' tab,
+ then tick the options which you intend to make visible.
-<br><br>
- <strong>Auto-selection of best Structures</strong>
- <br> Jalview can automatically filter and select the best structures using various metric categories avaialble from the meta-data
- of the structures. To perform this simply select any of the following options from the drop-down menu in the Structure
- Chooser interface: Best Uniprot coverage, Higest Resolution,
- Best Quality, Highest Protein Chain etc. When the 'Invert' option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.<p>
-
- <img src="schooser_main.png" style="width: 464px; height: 369px;">
- <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
+ <br>
+ <br>
+ <strong>Auto-selection of best Structures</strong>
+ <br> Jalview can automatically filter and select the best
+ structures using various metric categories avaialble from the
+ meta-data of the structures. To perform this simply select any of the
+ following options from the drop-down menu in the Structure Chooser
+ interface: Best Uniprot coverage, Higest Resolution, Best Quality,
+ Highest Protein Chain etc. When the 'Invert' option is selected,
+ Jalview returns an inverse result for the current selected option in
+ the drop-down menu.
+ <p>
+
+ <img src="schooser_main.png" style="width: 464px; height: 369px;">
+ <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
<p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
<p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
<p><img src="schooser_cached.png"> -->
- <br>The screenshot above shows the Structure Chooser interface
- along with the meta-data of auto-discovered structures for the sample
- alignment. Note however that if no structures were auto-discovered, a
- different interface for manual association will be invoked as seen in
- the screenshot below.
- <p>
- <img src="schooser_enter-id.png" style="width: 464px; height: 369px;">
- <p>
- <strong>Manual selection/association of PDB files with Sequences</strong>
- </p>
- <p>To manually associate PDB files with a sequence, select any of
- the follwing options listed below from the drop-down menu in the
- interface:
- <ul>
- <li><strong>From File</strong> - You can load a PDB file from the
- local machine or network and associate it with the selected sequence.
- PDB files associated in this way will also be saved in the <a
- href="jalarchive.html">Jalview Archive file</a>.<br></li>
- <li><strong>Enter PDB Id</strong> - Jalview will use the PDB Rest
- API, provided by the EBI, to fetch the PDB file with the entered Id.<br>
- </li>
- <li><strong>Cached PDB Entries</strong> - You can view PDB structures which have previously been downloaded/viewed using this option. Jalview caches previously downloaded PDB entries in the computer memory. However, if the project is saved before exiting Jalview, Jalview will serialize the cached entries to the file system. </li>
- </ul>
+ <br>The screenshot above shows the Structure Chooser interface
+ along with the meta-data of auto-discovered structures for the
+ sample alignment. Note however that if no structures were
+ auto-discovered, a different interface for manual association will
+ be invoked as seen in the screenshot below.
+ <p>
+ <img src="schooser_enter-id.png"
+ style="width: 464px; height: 369px;"
+ >
+ <p>
+ <strong>Manual selection/association of PDB files with
+ Sequences</strong>
+ </p>
+ <p>To manually associate PDB files with a sequence, select any of
+ the follwing options listed below from the drop-down menu in the
+ interface:
+ <ul>
+ <li><strong>From File</strong> - You can load a PDB file from
+ the local machine or network and associate it with the selected
+ sequence. PDB files associated in this way will also be saved in
+ the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
+ <li><strong>Enter PDB Id</strong> - Jalview will use the PDB
+ Rest API, provided by the EBI, to fetch the PDB file with the
+ entered Id.<br></li>
+ <li><strong>Cached PDB Entries</strong> - You can view PDB
+ structures which have previously been downloaded/viewed using this
+ option. Jalview caches previously downloaded PDB entries in the
+ computer memory. However, if the project is saved before exiting
+ Jalview, Jalview will serialize the cached entries to the file
+ system.</li>
+ </ul>
- <p>
- <em>The Structure Chooser interface was introduced in Jalview 2.9.
- </em>
- </p>
+ <p>
+ <em>The Structure Chooser interface was introduced in Jalview
+ 2.9. </em>
+ </p>
</body>
</html>
\ No newline at end of file
<title>The VARNA RNA Viewer</title>
</head>
<body>
-<p><strong>The VARNA RNA Viewer</strong></p>
-<p><a href="http://varna.lri.fr/index.html">VARNA</a> was
-integrated into Jalview 2.8 to allow interactive viewing of RNA secondary structure annotation. It is opened by
-selecting the <strong>"Structure→View
-Structure:"</strong> option in
-the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if
-you can't see this, then no RNA structure is associated with your
-sequence or alignment). In the pop-up menu all structures that
-are associated with this sequence and all sequences that are
-associated with the alignment are available.
-<p>Saving a Jalview session as a project file includes the state of any Varna viewers, which are reopened when the project is reloaded <em>(since Jalview 2.9)</em>.
+ <p>
+ <strong>The VARNA RNA Viewer</strong>
+ </p>
+ <p>
+ <a href="http://varna.lri.fr/index.html">VARNA</a> was integrated
+ into Jalview 2.8 to allow interactive viewing of RNA secondary
+ structure annotation. It is opened by selecting the <strong>"Structure→View
+ Structure:"</strong> option in the <a href="../menus/popupMenu.html">sequence
+ id pop-up menu</a> (if you can't see this, then no RNA structure is
+ associated with your sequence or alignment). In the pop-up menu all
+ structures that are associated with this sequence and all sequences
+ that are associated with the alignment are available.
+ <p>
+ Saving a Jalview session as a project file includes the state of any
+ Varna viewers, which are reopened when the project is reloaded <em>(since
+ Jalview 2.9)</em>.
+ <p>
+ <strong>Different structures</strong>
+ </p>
+ <ul>
+ <li><b>Alignment structures</b>: Structures associated with the
+ alignment are marked by having "consensus" attached to
+ their name. VARNA contains two different entries for consensus
+ structures.
+ <ul>
+ <li>Consensus structure: the individual sequence folded
+ into the consensus structure</li>
+ <li>Trimmed consensus structure: the individual sequence
+ folded into the the gap-free consensus structure. That means
+ all columns that contained gaps in the individual sequence
+ were removed. If this breaks a base-pair the pairing is
+ removed also. This can be considered as an approximation for
+ the individual structure.
+ </ul></li>
+ <li><b>Individual structures</b>: this is a structure
+ associated with the individual sequence and therefore not related
+ to the alignment</li>
+ </ul>
+ <p>
+ <strong>Controls</strong><br>
+ <ul>
+ <li>Rotate view - Left Click and drag</li>
+ <li>Zoom in - Press '+'</li>
+ <li>Zoom out - Press '-'</li>
+ <li>Choose a different structure - Left click on structure in
+ the left hand panel</li>
+ <li>Highlighting bases - Move mouse over columns in the Jalview
+ alignment panel</li>
+ </ul>
-<p><strong>Different structures</strong></p>
-<ul>
- <li>
- <b>Alignment structures</b>:
- Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
- <ul>
- <li>Consensus structure: the individual sequence folded into the consensus structure</li>
- <li>Trimmed consensus structure: the individual sequence
- folded into the the gap-free consensus structure. That means all
- columns that contained gaps in the individual sequence were
- removed. If this breaks a base-pair the pairing is removed also.
- This can be considered as an approximation for the individual structure.
- </ul>
- </li>
- <li>
- <b>Individual structures</b>:
- this is a structure associated with the individual sequence and therefore not related to the alignment
- </li>
-</ul>
-<p><strong>Controls</strong><br>
-<ul>
-<li>Rotate view - Left Click and drag</li>
-<li>Zoom in - Press '+'</li>
-<li>Zoom out - Press '-'</li>
-<li>Choose a different structure - Left click on structure in the left hand panel</li>
-<li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>
-</ul>
-
-<p><strong>Functionality provided by VARNA</strong></p>
-<p>VARNA's own functions are accessed by right-clicking in the
-structure display area. That will open the VARNA pop-up menu,
-which provides access to a number of features like different draw algorithm, color highlighting or annotations.
-</p>
-<p><strong>More Information</strong></p>
-<p>VARNA is a very powerful RNA viewer on its own. Only the
-essentials have been described here - the interested reader is
-referred to <a href="http://varna.lri.fr/index.php?page=manual&css=varna">VARNA's own
-comprehensive online documentation</a>.</p>
+ <p>
+ <strong>Functionality provided by VARNA</strong>
+ </p>
+ <p>VARNA's own functions are accessed by right-clicking in the
+ structure display area. That will open the VARNA pop-up menu, which
+ provides access to a number of features like different draw
+ algorithm, color highlighting or annotations.</p>
+ <p>
+ <strong>More Information</strong>
+ </p>
+ <p>
+ VARNA is a very powerful RNA viewer on its own. Only the essentials
+ have been described here - the interested reader is referred to <a
+ href="http://varna.lri.fr/index.php?page=manual&css=varna"
+ >VARNA's own comprehensive online documentation</a>.
+ </p>
</body>
</html>
<title>PDB Viewing</title>
</head>
<body>
- <p>
- <strong>Viewing PDB Structures</strong>
- </p>
- Jalview can be used to view protein structures by following the steps below:
- <ol>
- <li>Select the <strong>"3D Structure Data..."</strong> option from a
- sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to open the <a href="structurechooser.html">Structure Chooser</a> dialog box.
- <ul>
- <li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
- dialog will open with them listed in the results pane.</li>
- <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface will present options for manual association of PDB structures.</li>
- </ul>
- </li>
+ <p>
+ <strong>Viewing PDB Structures</strong>
+ </p>
+ Jalview can be used to view protein structures by following the steps
+ below:
+ <ol>
+ <li>Select the <strong>"3D Structure Data..."</strong> option
+ from a sequence's <a href="../menus/popupMenu.html">pop-up
+ menu</a> to open the <a href="structurechooser.html">Structure
+ Chooser</a> dialog box.
+ <ul>
+ <li>If one or more structures exists for the given
+ sequence, the <a href="structurechooser.html">Structure
+ Chooser</a> dialog will open with them listed in the results
+ pane.
+ </li>
+ <li>However, if no structure was found, the <a
+ href="structurechooser.html"
+ >Structure Chooser</a> interface will present options for manual
+ association of PDB structures.
+ </li>
+ </ul>
+ </li>
<li><strong>Selecting Structures</strong><br /> If structures
have been discovered, then some will already be selected according
to predefined selection criteria, such as structures with the
</li>
</ol>
- The
- <a href="jmol.html">Jmol viewer</a> has been included since Jalview
- 2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>, provided it is
- installed and can be launched by Jalview. The default viewer can be
- configured in the
- <a href="preferences.html#structure">Structure tab</a> in the
- <strong>Tools→Preferences</strong> dialog box.
- <p>
- Structure data imported into Jalview can also be processed to display
- secondary structure and temperature factor annotation. See the <a
- href="xsspannotation.html">Annotation from Structure</a> page for
- more information.
- </p>
+ The
+ <a href="jmol.html">Jmol viewer</a> has been included since Jalview
+ 2.3. Jalview 2.8.2 included support for
+ <a href="chimera.html">Chimera</a>, provided it is installed and can
+ be launched by Jalview. The default viewer can be configured in the
+ <a href="preferences.html#structure">Structure tab</a> in the
+ <strong>Tools→Preferences</strong> dialog box.
+ <p>
+ Structure data imported into Jalview can also be processed to
+ display secondary structure and temperature factor annotation. See
+ the <a href="xsspannotation.html">Annotation from Structure</a> page
+ for more information.
+ </p>
-<p>If a <strong>single</strong> PDB
-structure is selected, one of the following will happen:</p>
+ <p>
+ If a <strong>single</strong> PDB structure is selected, one of the
+ following will happen:
+ </p>
-<ul>
- <li>If no structures are open, then an interactive display of the
- structure will be opened in a new window.</li>
+ <ul>
+ <li>If no structures are open, then an interactive display of
+ the structure will be opened in a new window.</li>
- <li>If another structure is already shown for the current
- alignment, then you will be asked if you want to add and <a
- href="jmol.html#align">align this structure</a> to the structure in
- the existing view. (<em>new feature in Jalview 2.6</em>).</li>
+ <li>If another structure is already shown for the current
+ alignment, then you will be asked if you want to add and <a
+ href="jmol.html#align"
+ >align this structure</a> to the structure in the existing view. (<em>new
+ feature in Jalview 2.6</em>).
+ </li>
- <li>If the structure is already shown, then you will be prompted
- to associate the sequence with an existing view of the selected
- structure. This is useful when working with multi-domain or multi-chain PDB files.</li>
+ <li>If the structure is already shown, then you will be
+ prompted to associate the sequence with an existing view of the
+ selected structure. This is useful when working with multi-domain
+ or multi-chain PDB files.</li>
- <li style="list-style: none">See the <a href="jmol.html">Jmol
- </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
-</ul>
+ <li style="list-style: none">See the <a href="jmol.html">Jmol
+ </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
+ more information about the display.
+ </li>
+ </ul>
-<p><strong>Importing PDB Entries or files in PDB format</strong><br>
-You can retrieve sequences from the PDB using the <a
- href="pdbsequencefetcher.html">Sequence Fetcher</a>. Any sequences retrieved with
-this service are automatically associated with their source database
-entry. For PDB sequences, simply select PDB as the database and enter
-your known PDB id (appended with ':' and a chain code, if desired).<br>
-Jalview will also read PDB files directly. Simply load in the file as
-you would an alignment file. The sequences of any protein or nucleotide chains will be
-extracted from the file and viewed in the alignment window.</p>
+ <p>
+ <strong>Importing PDB Entries or files in PDB format</strong><br>
+ You can retrieve sequences from the PDB using the <a
+ href="pdbsequencefetcher.html"
+ >Sequence Fetcher</a>. Any sequences retrieved with this service are
+ automatically associated with their source database entry. For PDB
+ sequences, simply select PDB as the database and enter your known
+ PDB id (appended with ':' and a chain code, if desired).<br>
+ Jalview will also read PDB files directly. Simply load in the file
+ as you would an alignment file. The sequences of any protein or
+ nucleotide chains will be extracted from the file and viewed in the
+ alignment window.
+ </p>
-<p>
-<strong>Associating a large number of PDB files to sequences
-in an alignment</strong><br /> It is often the case when working with
-structure alignments that you will have a directory of PDB files, and
-an alignment involving one or more of the structures. If you drag a
-number of PDB files onto an alignment in the Jalview desktop, Jalview
-will give you the option of associating PDB files with sequences that
-have the same filename. This means, for example, you can automatically
-associate PDB files with names like '1gaq.pdb' with sequences that
-have an ID like '1gaq'.
-<br/><em>Note: This feature was added in Jalview 2.7</em>
-</p>
-<p><em>Note for Jalview applet users:<br>
-Due to the applet security constraints, PDB Files can currently only be
-imported by cut and paste of the PDB file text into the text box opened
-by the 'From File' entry of the structure menu.</em></p>
+ <p>
+ <strong>Associating a large number of PDB files to
+ sequences in an alignment</strong><br /> It is often the case when working
+ with structure alignments that you will have a directory of PDB
+ files, and an alignment involving one or more of the structures. If
+ you drag a number of PDB files onto an alignment in the Jalview
+ desktop, Jalview will give you the option of associating PDB files
+ with sequences that have the same filename. This means, for example,
+ you can automatically associate PDB files with names like '1gaq.pdb'
+ with sequences that have an ID like '1gaq'. <br />
+ <em>Note: This feature was added in Jalview 2.7</em>
+ </p>
+ <p>
+ <em>Note for Jalview applet users:<br> Due to the applet
+ security constraints, PDB Files can currently only be imported by
+ cut and paste of the PDB file text into the text box opened by the
+ 'From File' entry of the structure menu.
+ </em>
+ </p>
-<p><strong>Viewing the PDB Residue Numbering</strong><br>
-Sequences which have PDB entry or PDB file associations are annotated
-with sequence features from a group named with the associated PDB
-accession number or file name. Each feature gives the corresponding PDB
-Residue Number for each mapped residue in the sequence. The display of
-these features is controlled through the <strong>"View→Sequence
-Features"</strong> menu item and the <a href="featuresettings.html">Feature
-Settings dialog box</a>.</p>
+ <p>
+ <strong>Viewing the PDB Residue Numbering</strong><br>
+ Sequences which have PDB entry or PDB file associations are
+ annotated with sequence features from a group named with the
+ associated PDB accession number or file name. Each feature gives the
+ corresponding PDB Residue Number for each mapped residue in the
+ sequence. The display of these features is controlled through the <strong>"View→Sequence
+ Features"</strong> menu item and the <a href="featuresettings.html">Feature
+ Settings dialog box</a>.
+ </p>
-<p><em><strong>Outstanding problem with cut'n'pasted
-files in Jalview 2.6 and Jalview 2.7</strong><br>
-Structures imported via the cut'n'paste dialog box will not be correctly
-highlighted or coloured when they are displayed in structure views,
-especially if they contain more than one PDB structure. See the bug
-report at http://issues.jalview.org/browse/JAL-623 for news on this problem.</em></p>
+ <p>
+ <em><strong>Outstanding problem with cut'n'pasted
+ files in Jalview 2.6 and Jalview 2.7</strong><br> Structures
+ imported via the cut'n'paste dialog box will not be correctly
+ highlighted or coloured when they are displayed in structure
+ views, especially if they contain more than one PDB structure. See
+ the bug report at http://issues.jalview.org/browse/JAL-623 for
+ news on this problem.</em>
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Wrap Alignment</title></head>
+<head>
+<title>Wrap Alignment</title>
+</head>
<body>
-<p><strong>View→Wrap alignment </strong></p>
-<p>Use this feature to wrap an alignment to the screen width. </p>
-<p>All output (HTML, Printing, JPG etc) will also be in this wrapped format.</p>
-<p>This is most useful when looking at alignments with less than 20 sequences.
-</p>
-<table width="480" border="1">
- <tr><td>
+ <p>
+ <strong>View→Wrap alignment </strong>
+ </p>
+ <p>Use this feature to wrap an alignment to the screen width.</p>
+ <p>All output (HTML, Printing, JPG etc) will also be in this
+ wrapped format.</p>
+ <p>This is most useful when looking at alignments with less than
+ 20 sequences.</p>
+ <table width="480" border="1">
+ <tr>
+ <td>
-<table border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td colspan="6"> </td>
- <td colspan="9">10<br>
- |</td>
- <td></td>
- <td colspan="9">20<br>
- |</td>
- <td></td>
- </tr>
- <tr>
- <td nowrap>ADHR_DROPS/7-107 </td>
- <td bgcolor="#e6331a">K</td>
- <td bgcolor="#1ab3b3">H</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">C</td>
- <td bgcolor="#1ab3b3">Y</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">A</td>
- <td>D</td>
- <td bgcolor="#80b3e6">C</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#80b3e6">I</td>
- <td>A</td>
- <td bgcolor="#80b3e6">L</td>
- <td>E</td>
- <td bgcolor="#1acc1a">T</td>
- <td bgcolor="#1acc1a">S</td>
- <td bgcolor="#e6331a">K</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#80b3e6">M</td>
- <td>T</td>
- <td bgcolor="#e6331a">K</td>
- <td>N</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">A</td>
- </tr>
- <tr>
- <td nowrap>ADH_DROHE/5-105 </td>
- <td>S</td>
- <td>N</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">F</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#cc4dcc">D</td>
- <td bgcolor="#1acc1a">T</td>
- <td bgcolor="#1acc1a">S</td>
- <td bgcolor="#e6331a">R</td>
- <td>E</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">V</td>
- <td>K</td>
- <td>S</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#cccc00">P</td>
- <td>K</td>
- </tr>
- <tr>
- <td nowrap>PGDH_HUMAN/6-106 </td>
- <td bgcolor="#e6331a">K</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#1acc1a">T</td>
- <td bgcolor="#e6994d">G</td>
- <td>A</td>
- <td bgcolor="#80b3e6">A</td>
- <td>Q</td>
- <td bgcolor="#e6994d">G</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#e6994d">G</td>
- <td>R</td>
- <td>A</td>
- <td>F</td>
- <td>A</td>
- <td bgcolor="#cc4dcc">E</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#80b3e6">L</td>
- <td>L</td>
- <td bgcolor="#e6331a">K</td>
- <td bgcolor="#e6994d">G</td>
- <td>.</td>
- <td bgcolor="#80b3e6">A</td>
- </tr>
- <tr>
- <td height="5"></td>
- </tr>
- <tr>
- <td colspan="6"> </td>
- <td colspan="9">36<br>
- |</td>
- <td></td>
- <td colspan="9">46<br>
- |</td>
- <td></td>
- </tr>
- <tr>
- <td nowrap>ADHR_DROPS/7-107 </td>
- <td bgcolor="#e6331a">K</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">L</td>
- <td>Q</td>
- <td>S</td>
- <td bgcolor="#80b3e6">V</td>
- <td>E</td>
- <td bgcolor="#1acc1a">N</td>
- <td bgcolor="#cccc00">P</td>
- <td bgcolor="#cccc00">P</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>A</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#1acc1a">Q</td>
- <td bgcolor="#80b3e6">L</td>
- <td>Q</td>
- </tr>
- <tr>
- <td nowrap>ADH_DROHE/5-105 </td>
- <td>N</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#cc4dcc">D</td>
- <td>R</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#cc4dcc">D</td>
- <td bgcolor="#1acc1a">N</td>
- <td bgcolor="#cccc00">P</td>
- <td bgcolor="#80b3e6">A</td>
- <td>A</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#cc4dcc">E</td>
- <td bgcolor="#80b3e6">L</td>
- <td>K</td>
- </tr>
- <tr>
- <td nowrap>PGDH_HUMAN/6-106 </td>
- <td bgcolor="#e6331a">K</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#cc4dcc">D</td>
- <td>W</td>
- <td>N</td>
- <td>L</td>
- <td>E</td>
- <td bgcolor="#80b3e6">A</td>
- <td bgcolor="#e6994d">G</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>V</td>
- <td>Q</td>
- <td bgcolor="#80b3e6">C</td>
- <td>K</td>
- <td>A</td>
- <td bgcolor="#80b3e6">A</td>
- <td>L</td>
- </tr>
- <tr>
- <td height="5"></td>
- </tr>
- <tr>
- <td colspan="6"> </td>
- <td colspan="9">62<br>
- |</td>
- <td></td>
- <td colspan="9">72<br>
- |</td>
- <td></td>
- </tr>
- <tr>
- <td nowrap>ADHR_DROPS/7-107 </td>
- <td>S</td>
- <td bgcolor="#80b3e6">I</td>
- <td>K</td>
- <td bgcolor="#1ab3b3">H</td>
- <td>S</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>T</td>
- <td>Q</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#80b3e6">F</td>
- <td bgcolor="#80b3e6">F</td>
- <td bgcolor="#80b3e6">W</td>
- <td>T</td>
- <td bgcolor="#80b3e6">F</td>
- <td bgcolor="#cc4dcc">D</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#1acc1a">T</td>
- <td bgcolor="#80b3e6">M</td>
- <td bgcolor="#80b3e6">A</td>
- <td>R</td>
- <td bgcolor="#cc4dcc">E</td>
- <td bgcolor="#cc4dcc">E</td>
- <td>M</td>
- </tr>
- <tr>
- <td nowrap>ADH_DROHE/5-105 </td>
- <td>A</td>
- <td bgcolor="#80b3e6">L</td>
- <td>N</td>
- <td bgcolor="#cccc00">P</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>K</td>
- <td>V</td>
- <td>T</td>
- <td bgcolor="#80b3e6">I</td>
- <td bgcolor="#1acc1a">T</td>
- <td bgcolor="#80b3e6">F</td>
- <td bgcolor="#1ab3b3">Y</td>
- <td bgcolor="#cccc00">P</td>
- <td bgcolor="#1ab3b3">Y</td>
- <td bgcolor="#cc4dcc">D</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#1acc1a">T</td>
- <td bgcolor="#80b3e6">V</td>
- <td bgcolor="#cccc00">P</td>
- <td>L</td>
- <td>A</td>
- <td bgcolor="#cc4dcc">E</td>
- <td>T</td>
- </tr>
- <tr>
- <td nowrap>PGDH_HUMAN/6-106 </td>
- <td>D</td>
- <td>E</td>
- <td>Q</td>
- <td bgcolor="#80b3e6">F</td>
- <td>E</td>
- <td bgcolor="#cccc00">P</td>
- <td>.</td>
- <td>.</td>
- <td>.</td>
- <td>Q</td>
- <td>K</td>
- <td bgcolor="#1acc1a">T</td>
- <td bgcolor="#80b3e6">L</td>
- <td bgcolor="#80b3e6">F</td>
- <td bgcolor="#80b3e6">I</td>
- <td>Q</td>
- <td bgcolor="#80b3e6">C</td>
- <td bgcolor="#cc4dcc">D</td>
- <td bgcolor="#80b3e6">V</td>
- <td>A</td>
- <td>D</td>
- <td>Q</td>
- <td>Q</td>
- <td bgcolor="#1acc1a">Q</td>
- <td>L</td>
- <td>.</td>
- </tr>
- <tr>
- <td height="5"></td>
- </tr>
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr>
+ <td colspan="6"> </td>
+ <td colspan="9">10<br> |
+ </td>
+ <td></td>
+ <td colspan="9">20<br> |
+ </td>
+ <td></td>
+ </tr>
+ <tr>
+ <td nowrap>ADHR_DROPS/7-107 </td>
+ <td bgcolor="#e6331a">K</td>
+ <td bgcolor="#1ab3b3">H</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">C</td>
+ <td bgcolor="#1ab3b3">Y</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td>D</td>
+ <td bgcolor="#80b3e6">C</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td>A</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td>E</td>
+ <td bgcolor="#1acc1a">T</td>
+ <td bgcolor="#1acc1a">S</td>
+ <td bgcolor="#e6331a">K</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#80b3e6">M</td>
+ <td>T</td>
+ <td bgcolor="#e6331a">K</td>
+ <td>N</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">A</td>
+ </tr>
+ <tr>
+ <td nowrap>ADH_DROHE/5-105 </td>
+ <td>S</td>
+ <td>N</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">F</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#cc4dcc">D</td>
+ <td bgcolor="#1acc1a">T</td>
+ <td bgcolor="#1acc1a">S</td>
+ <td bgcolor="#e6331a">R</td>
+ <td>E</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td>K</td>
+ <td>S</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#cccc00">P</td>
+ <td>K</td>
+ </tr>
+ <tr>
+ <td nowrap>PGDH_HUMAN/6-106 </td>
+ <td bgcolor="#e6331a">K</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#1acc1a">T</td>
+ <td bgcolor="#e6994d">G</td>
+ <td>A</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td>Q</td>
+ <td bgcolor="#e6994d">G</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#e6994d">G</td>
+ <td>R</td>
+ <td>A</td>
+ <td>F</td>
+ <td>A</td>
+ <td bgcolor="#cc4dcc">E</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td>L</td>
+ <td bgcolor="#e6331a">K</td>
+ <td bgcolor="#e6994d">G</td>
+ <td>.</td>
+ <td bgcolor="#80b3e6">A</td>
+ </tr>
+ <tr>
+ <td height="5"></td>
+ </tr>
+ <tr>
+ <td colspan="6"> </td>
+ <td colspan="9">36<br> |
+ </td>
+ <td></td>
+ <td colspan="9">46<br> |
+ </td>
+ <td></td>
+ </tr>
+ <tr>
+ <td nowrap>ADHR_DROPS/7-107 </td>
+ <td bgcolor="#e6331a">K</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td>Q</td>
+ <td>S</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td>E</td>
+ <td bgcolor="#1acc1a">N</td>
+ <td bgcolor="#cccc00">P</td>
+ <td bgcolor="#cccc00">P</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>A</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#1acc1a">Q</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td>Q</td>
+ </tr>
+ <tr>
+ <td nowrap>ADH_DROHE/5-105 </td>
+ <td>N</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#cc4dcc">D</td>
+ <td>R</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#cc4dcc">D</td>
+ <td bgcolor="#1acc1a">N</td>
+ <td bgcolor="#cccc00">P</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td>A</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#cc4dcc">E</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td>K</td>
+ </tr>
+ <tr>
+ <td nowrap>PGDH_HUMAN/6-106 </td>
+ <td bgcolor="#e6331a">K</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#cc4dcc">D</td>
+ <td>W</td>
+ <td>N</td>
+ <td>L</td>
+ <td>E</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td bgcolor="#e6994d">G</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>V</td>
+ <td>Q</td>
+ <td bgcolor="#80b3e6">C</td>
+ <td>K</td>
+ <td>A</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td>L</td>
+ </tr>
+ <tr>
+ <td height="5"></td>
+ </tr>
+ <tr>
+ <td colspan="6"> </td>
+ <td colspan="9">62<br> |
+ </td>
+ <td></td>
+ <td colspan="9">72<br> |
+ </td>
+ <td></td>
+ </tr>
+ <tr>
+ <td nowrap>ADHR_DROPS/7-107 </td>
+ <td>S</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td>K</td>
+ <td bgcolor="#1ab3b3">H</td>
+ <td>S</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>T</td>
+ <td>Q</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#80b3e6">F</td>
+ <td bgcolor="#80b3e6">F</td>
+ <td bgcolor="#80b3e6">W</td>
+ <td>T</td>
+ <td bgcolor="#80b3e6">F</td>
+ <td bgcolor="#cc4dcc">D</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#1acc1a">T</td>
+ <td bgcolor="#80b3e6">M</td>
+ <td bgcolor="#80b3e6">A</td>
+ <td>R</td>
+ <td bgcolor="#cc4dcc">E</td>
+ <td bgcolor="#cc4dcc">E</td>
+ <td>M</td>
+ </tr>
+ <tr>
+ <td nowrap>ADH_DROHE/5-105 </td>
+ <td>A</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td>N</td>
+ <td bgcolor="#cccc00">P</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>K</td>
+ <td>V</td>
+ <td>T</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td bgcolor="#1acc1a">T</td>
+ <td bgcolor="#80b3e6">F</td>
+ <td bgcolor="#1ab3b3">Y</td>
+ <td bgcolor="#cccc00">P</td>
+ <td bgcolor="#1ab3b3">Y</td>
+ <td bgcolor="#cc4dcc">D</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#1acc1a">T</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td bgcolor="#cccc00">P</td>
+ <td>L</td>
+ <td>A</td>
+ <td bgcolor="#cc4dcc">E</td>
+ <td>T</td>
+ </tr>
+ <tr>
+ <td nowrap>PGDH_HUMAN/6-106 </td>
+ <td>D</td>
+ <td>E</td>
+ <td>Q</td>
+ <td bgcolor="#80b3e6">F</td>
+ <td>E</td>
+ <td bgcolor="#cccc00">P</td>
+ <td>.</td>
+ <td>.</td>
+ <td>.</td>
+ <td>Q</td>
+ <td>K</td>
+ <td bgcolor="#1acc1a">T</td>
+ <td bgcolor="#80b3e6">L</td>
+ <td bgcolor="#80b3e6">F</td>
+ <td bgcolor="#80b3e6">I</td>
+ <td>Q</td>
+ <td bgcolor="#80b3e6">C</td>
+ <td bgcolor="#cc4dcc">D</td>
+ <td bgcolor="#80b3e6">V</td>
+ <td>A</td>
+ <td>D</td>
+ <td>Q</td>
+ <td>Q</td>
+ <td bgcolor="#1acc1a">Q</td>
+ <td>L</td>
+ <td>.</td>
+ </tr>
+ <tr>
+ <td height="5"></td>
+ </tr>
- </table>
-</table>
+ </table>
+ </table>
</body>
<title>Annotation from 3D structure data</title>
</head>
<body>
- <p>
- <strong>Working with annotation from 3D structure data</strong>
- </p>
- <p>
- Jalview can process PDB data associated with sequences to display
- values extracted from the <em>Temperature Factor</em> column for
- corresponding sites, and secondary structure from DSSP or RNAView (as
- appropriate).
- </p>
- <p>
- <strong>Extracting data from PDB files<br /></strong>Annotation is
- created for structure files retrieved directly from the PDB loaded
- from the file system (via the <strong>Structure→Associate
- Structure...→From file</strong> option, or when displayed via the View
- Structures Menu.<br /> Structure annotation is not automatically
- added to an alignment, but any available structure annotation rows for
- the current selection or a particular sequence can be added via the <strong>Add
- Reference Annotation</strong> in the <strong>Selection</strong> and <strong>Sequence
- ID</strong> sub-menus of the Sequence ID Panel's popup menu.<br/> <em>Please
- note:</em>Protein structures are analysed
- <em>in situ</em>, but Jalview employs a web service to process RNA
- structures which can cause long delays if your internet connection is
- slow.
- </p>
- <p>
- The <a href="../menus/alwannotation.html"><em>Annotations</em>
- alignment menu</a> provides settings useful for controlling the display
- of secondary structure annotation.
- </p>
- <p>
- <strong>Shading sequences by associated structure annotation<br /></strong>The
- annotation colouring dialog (opened by the <strong>Colour→By
- Annotation</strong> option) allows sequences with associated secondary
- structure data to be shaded according to secondary structure type.
- Once the dialog is opened, select the <em>Per Sequence</em> option and
- then choose <em>Secondary structure</em> from the dropdown menu.<br />When
- colouring alignments by secondary structure, two modes can be
- employed. The default is to shade sequences with the same colour as
- the secondary structure glyph. If, however, <em>original colours</em>
- is selected and another colourscheme has already been applied, then
- only portions of the sequence with defined secondary structure will be
- shaded with the previously applied scheme.<br />
- </p>
- <p>
- <strong>Configuration options for processing PDB files<br /></strong>
- Occasionally, you may wish to disable secondary structure processing.
- Configuration options in the <strong>Structure</strong> tab in the <strong>Tools→Preferences</strong>
- dialog allow the processing of structure data to be disabled, or
- selectively enabled. For more information, take a look at the <a href="preferences.html#structure">documentation for the structure panel</a>.
- </p>
- <p>
- <em>The display of secondary structure data was introduced in
- Jalview 2.8.2, and is made possible by Jalview's use of <a
- href="jmol.html">Jmol's DSSP implementation</a>, based on the
- original <a href="http://www.ncbi.nlm.nih.gov/pubmed/6667333">Kabsch
- and Sander algorithm</a> ported by <a
- href="http://swift.cmbi.ru.nl/gv/dssp/">Robbie P. Joosten and
- colleagues</a>, and a client for <a
- href="https://github.com/fjossinet/PyRNA">Fabrice Jossinet's
- pyRNA services</a> that was developed by Anne Menard, Jim Procter and
- Yann Ponty as part of the Jalview Summer of Code 2012.
- </em>
- </p>
+ <p>
+ <strong>Working with annotation from 3D structure data</strong>
+ </p>
+ <p>
+ Jalview can process PDB data associated with sequences to display
+ values extracted from the <em>Temperature Factor</em> column for
+ corresponding sites, and secondary structure from DSSP or RNAView
+ (as appropriate).
+ </p>
+ <p>
+ <strong>Extracting data from PDB files<br /></strong>Annotation is
+ created for structure files retrieved directly from the PDB loaded
+ from the file system (via the <strong>Structure→Associate
+ Structure...→From file</strong> option, or when displayed via the View
+ Structures Menu.<br /> Structure annotation is not automatically
+ added to an alignment, but any available structure annotation rows
+ for the current selection or a particular sequence can be added via
+ the <strong>Add Reference Annotation</strong> in the <strong>Selection</strong>
+ and <strong>Sequence ID</strong> sub-menus of the Sequence ID
+ Panel's popup menu.<br /> <em>Please note:</em>Protein structures
+ are analysed <em>in situ</em>, but Jalview employs a web service to
+ process RNA structures which can cause long delays if your internet
+ connection is slow.
+ </p>
+ <p>
+ The <a href="../menus/alwannotation.html"><em>Annotations</em>
+ alignment menu</a> provides settings useful for controlling the
+ display of secondary structure annotation.
+ </p>
+ <p>
+ <strong>Shading sequences by associated structure
+ annotation<br />
+ </strong>The annotation colouring dialog (opened by the <strong>Colour→By
+ Annotation</strong> option) allows sequences with associated secondary
+ structure data to be shaded according to secondary structure type.
+ Once the dialog is opened, select the <em>Per Sequence</em> option
+ and then choose <em>Secondary structure</em> from the dropdown menu.<br />When
+ colouring alignments by secondary structure, two modes can be
+ employed. The default is to shade sequences with the same colour as
+ the secondary structure glyph. If, however, <em>original
+ colours</em> is selected and another colourscheme has already been
+ applied, then only portions of the sequence with defined secondary
+ structure will be shaded with the previously applied scheme.<br />
+ </p>
+ <p>
+ <strong>Configuration options for processing PDB files<br /></strong>
+ Occasionally, you may wish to disable secondary structure
+ processing. Configuration options in the <strong>Structure</strong>
+ tab in the <strong>Tools→Preferences</strong> dialog allow the
+ processing of structure data to be disabled, or selectively enabled.
+ For more information, take a look at the <a
+ href="preferences.html#structure"
+ >documentation for the structure panel</a>.
+ </p>
+ <p>
+ <em>The display of secondary structure data was introduced in
+ Jalview 2.8.2, and is made possible by Jalview's use of <a
+ href="jmol.html"
+ >Jmol's DSSP implementation</a>, based on the original <a
+ href="http://www.ncbi.nlm.nih.gov/pubmed/6667333"
+ >Kabsch and Sander algorithm</a> ported by <a
+ href="http://swift.cmbi.ru.nl/gv/dssp/"
+ >Robbie P. Joosten and colleagues</a>, and a client for <a
+ href="https://github.com/fjossinet/PyRNA"
+ >Fabrice Jossinet's pyRNA services</a> that was developed by Anne
+ Menard, Jim Procter and Yann Ponty as part of the Jalview Summer
+ of Code 2012.
+ </em>
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Jalview Documentation</title></head>
+<head>
+<title>Jalview Documentation</title>
+</head>
<body>
-<IMG src="Jalview_Logo.png">
-<p><strong>Welcome to Jalview's built in documentation.</strong></p>
-<p>Here are some good places to start:</p><ul>
-<li><a href="whatsNew.html">What's New</a> summarises the new features in this release of Jalview.</li>
-<li>Learn how to <a href="editing/index.html">edit alignments</a> with Jalview.</li>
-<li><a href="features/seqfeatures.html">Import and display sequence features on your alignment</a></li>
-<li>Use <a href="features/viewingpdbs.html">Jmol to view and superpose 3D structures</a> associated with sequences in the alignment</li>
-</ul>
- <p>
- For more information, you might also want to take a look at the
- documentation section of the Jalview website (<a
- href="http://www-test.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
- </p>
- <p>
- If you are using the Jalview Desktop application and are looking for
- something specific, then try the search box (next to the print icon).
- If you're already viewing this in your web browser, then google the
- online version of these pages. If you don't find what you are looking
- for, or want to report a bug or make a feature request, then get in
- contact over at <a href="http://www.jalview.org/community">http://www.jalview.org/community</a>
- </p>
+ <IMG src="Jalview_Logo.png">
+ <p>
+ <strong>Welcome to Jalview's built in documentation.</strong>
+ </p>
+ <p>Here are some good places to start:</p>
+ <ul>
+ <li><a href="whatsNew.html">What's New</a> summarises the new
+ features in this release of Jalview.</li>
+ <li>Learn how to <a href="editing/index.html">edit
+ alignments</a> with Jalview.
+ </li>
+ <li><a href="features/seqfeatures.html">Import and display
+ sequence features on your alignment</a></li>
+ <li>Use <a href="features/viewingpdbs.html">Jmol to view
+ and superpose 3D structures</a> associated with sequences in the
+ alignment
+ </li>
+ </ul>
+ <p>
+ For more information, you might also want to take a look at the
+ documentation section of the Jalview website (<a
+ href="http://www-test.jalview.org/about/documentation"
+ >http://www.jalview.org/about/documentation</a>).
+ </p>
+ <p>
+ If you are using the Jalview Desktop application and are looking for
+ something specific, then try the search box (next to the print
+ icon). If you're already viewing this in your web browser, then
+ google the online version of these pages. If you don't find what you
+ are looking for, or want to report a bug or make a feature request,
+ then get in contact over at <a
+ href="http://www.jalview.org/community"
+ >http://www.jalview.org/community</a>
+ </p>
- <p><strong>Citing Jalview</strong><br/>If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
-<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
- "Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"<br>
- <em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>
- <p><strong>The Jalview Authors</strong><br/>
- The following people have contributed to Jalview's development:
- <ul>
- <li>Jalview 1
- <ul><li>Michele Clamp</li>
- <li>James Cuff</li>
- <li>Steve Searle</li>
- <li>David Martin</li>
- <li>Geoff Barton</li>
- </ul>
- </li><li>Jalview 2<ul>
- <li>Jim Procter</li>
- <li>Andrew Waterhouse</li>
- <li>Mungo Carstairs</li>
- <li>Tochukwu 'Charles' Ofoegbu</li>
- <li>Jan Engelhardt</li>
- <li>Lauren Lui</li>
- <li>Anne Menard</li>
- <li>Natasha Sherstnev</li>
- <li>Daniel Barton</li>
- <li>David Roldan-Martinez</li>
- <li>David Martin</li>
- <li>Geoff Barton</li>
- </ul>
- </li>
- </ul>
- </p>
+ <p>
+ <strong>Citing Jalview</strong><br />If you use Jalview in your
+ work, please cite the Jalview 2 paper in Bioinformatics:
+ </p>
+ <p>
+ Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton,
+ G.J (2009), <br> "Jalview version 2: A Multiple Sequence
+ Alignment and Analysis Workbench,"<br> <em>Bioinformatics</em>
+ <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
+ </p>
+ <p>
+ <strong>The Jalview Authors</strong><br /> The following people have
+ contributed to Jalview's development:
+ <ul>
+ <li>Jalview 1
+ <ul>
+ <li>Michele Clamp</li>
+ <li>James Cuff</li>
+ <li>Steve Searle</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li>
+ <li>Jalview 2
+ <ul>
+ <li>Jim Procter</li>
+ <li>Andrew Waterhouse</li>
+ <li>Mungo Carstairs</li>
+ <li>Tochukwu 'Charles' Ofoegbu</li>
+ <li>Jan Engelhardt</li>
+ <li>Lauren Lui</li>
+ <li>Anne Menard</li>
+ <li>Natasha Sherstnev</li>
+ <li>Daniel Barton</li>
+ <li>David Roldan-Martinez</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li>
+ </ul>
+ </p>
</body>
</html>
<body>
<p>
<strong>Exporting alignments as graphics and lineart<a
- name="export"></a></strong>
+ name="export"
+ ></a></strong>
</p>
<p>
The alignment view can be printed using <strong>File→Print</strong>,
or exported in a number of ways via the <strong>File→Export</strong>
menu:
-
<ul>
- <li>HTML<br>
- <em>for viewing in a web browser</em>
+ <li>HTML<br> <em>for viewing in a web browser</em>
</li>
- <li>PNG - a Portable Networks Graphics image<br>
- <em>For low quality diagrams and powerpoint presentations</em>
+ <li>PNG - a Portable Networks Graphics image<br> <em>For
+ low quality diagrams and powerpoint presentations</em>
</li>
- <li>EPS - an Encapsulated Postscript Document<br>
- <em>For high quality diagrams and publications.</em>
- <li>SVG - a Scalable Vector Graphics document<br>
- <em>For high quality diagrams in publications and on the web.</em>
+ <li>EPS - an Encapsulated Postscript Document<br> <em>For
+ high quality diagrams and publications.</em>
+ <li>SVG - a Scalable Vector Graphics document<br> <em>For
+ high quality diagrams in publications and on the web.</em>
</li>
<li>BioJS MSA - A JavaScript based multiple sequence alignment
viewer. <br> <em>For interactive alignment data
<a name="htmlexport" />
<p>
<strong>Exporting alignments as Web Pages</strong>
-
<p>
In Jalview 2.9, new HTML exporting options were introduced. The
standard HTML export option displays alignments as SVG documents
provides a range of interactive analysis capabiltiies.
</p>
<p>
-
-<p><strong>Tips for working with EPS Files</strong></p>
-<li>The EPS file generated by Jalview contains vector graphics which are directly
- editable in graphics applications such as Adobe Illustrator.</li>
-<li>EPS files can be produced as "Text" or "Lineart". Use
- "Text" if you want the final document to be MUCH smaller in diskspace
- and be able to search, edit and select text. Use "Lineart" if you
- want an exact image of the alignment as displayed in Jalview. This is useful
- if a 3rd Party EPS viewer does not have the same Font which the EPS file was
- created with.</li>
-<li>When importing an EPS file into a Microsoft office document, a snapshot image of the
- file will be displayed which often looks blurred. Right-click the
- image and choose "Edit image." to convert it to word
- drawing objects which give a truer WYSIWIG representation.
- </li>
- <li>
- Mac OSX users will find that eps files are automatically converted into
- PDF files.
- </li>
-</p>
+ <p>
+ <strong>Tips for working with EPS Files</strong>
+ </p>
+ <li>The EPS file generated by Jalview contains vector graphics
+ which are directly editable in graphics applications such as Adobe
+ Illustrator.</li>
+ <li>EPS files can be produced as "Text" or
+ "Lineart". Use "Text" if you want the final
+ document to be MUCH smaller in diskspace and be able to search, edit
+ and select text. Use "Lineart" if you want an exact image
+ of the alignment as displayed in Jalview. This is useful if a 3rd
+ Party EPS viewer does not have the same Font which the EPS file was
+ created with.</li>
+ <li>When importing an EPS file into a Microsoft office document,
+ a snapshot image of the file will be displayed which often looks
+ blurred. Right-click the image and choose "Edit image." to
+ convert it to word drawing objects which give a truer WYSIWIG
+ representation.</li>
+ <li>Mac OSX users will find that eps files are automatically
+ converted into PDF files.</li>
+ </p>
</body>
</html>
<title>Viewing and exporting sequence annotation reports</title>
</head>
<body>
-<p><strong>Viewing and exporting sequence annotation reports</strong>
-<br/>
-Much of the information retrieved by Jalview about a sequence is visualized on the alignment.
-Often, however, there are a huge number of ontology terms, cross-references, links to publications and other kinds of data shown
- in the sequence ID tooltip that cannot be examined. In this case, you can view and export the information shown in a sequence's ID tooltip by right-clicking and
-selecting the <strong>"<em>(sequence's name)</em></em>→Sequence Details ..."</strong> entry from the <a href="../menus/popupMenu.html">pop-up menu</a>.
-</p>
-<p><strong>Annotation Reports for a range of sequences</strong><br/>
-If you would like to view the tooltips for a number of sequences, simply select them all and then use the <strong>Selection→Sequence Details ...</strong> entry in the <a href="../menus/popupMenu.html">pop-up menu</a>.
-</p>
-<img src="seqreport.gif" alt="Sequence Annotation is displayed as HTML in a report window"/>
-<p><strong>Copying and pasting annotation to other programs</strong><br>
-The <strong>File→Save</strong> option in the sequence annotation report window allows the report to be saved as HTML, which will preserve links and any other metadata. It is also possible to copy and paste the text to other programs, but in some cases, the HTML will not be preserved. In that case, you can toggle the display of HTML source code with the <strong>Edit→Show HTML Source</strong> drop down menu entry.
-</p>
+ <p>
+ <strong>Viewing and exporting sequence annotation reports</strong> <br />
+ Much of the information retrieved by Jalview about a sequence is
+ visualized on the alignment. Often, however, there are a huge number
+ of ontology terms, cross-references, links to publications and other
+ kinds of data shown in the sequence ID tooltip that cannot be
+ examined. In this case, you can view and export the information
+ shown in a sequence's ID tooltip by right-clicking and selecting the
+ <strong>"<em>(sequence's name)</em></em>→Sequence
+ Details ..."
+ </strong> entry from the <a href="../menus/popupMenu.html">pop-up menu</a>.
+ </p>
+ <p>
+ <strong>Annotation Reports for a range of sequences</strong><br />
+ If you would like to view the tooltips for a number of sequences,
+ simply select them all and then use the <strong>Selection→Sequence
+ Details ...</strong> entry in the <a href="../menus/popupMenu.html">pop-up
+ menu</a>.
+ </p>
+ <img src="seqreport.gif"
+ alt="Sequence Annotation is displayed as HTML in a report window"
+ />
+ <p>
+ <strong>Copying and pasting annotation to other programs</strong><br>
+ The <strong>File→Save</strong> option in the sequence
+ annotation report window allows the report to be saved as HTML,
+ which will preserve links and any other metadata. It is also
+ possible to copy and paste the text to other programs, but in some
+ cases, the HTML will not be preserved. In that case, you can toggle
+ the display of HTML source code with the <strong>Edit→Show
+ HTML Source</strong> drop down menu entry.
+ </p>
</body>
</html>
</head>
<body>
-<p><strong>Alignment File Formats</strong>
-<p>Jalview understands a wide range of sequence alignment formats. In
-order to determine which format has been used for an alignment,
-Jalview tries to detect some text or formatting unique to one of the formats:
-</p>
-<table width="100%" border="1">
-<tr><td width="17%">Format</td>
-<td width="60%">Unique File Feature</td>
-<td width="23%">File Extension</td>
-<tr>
-<td width="17%">FASTA</td>
-<td width="60%">>SequenceName<br>
-THISISASEQUENCE<br></td>
-<td width="23%">.fa, .fasta</td>
-</tr><tr><td width="17%">MSF</td>
-<td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br>
-<em>..</em><br>
-//<br></td>
-<td width="23%">.msf</td>
-</tr><tr><td width="17%">CLUSTALW</td>
-<td width="60%">CLUSTAL</td>
-<td width="23%">.aln</td>
-</tr><tr><td width="17%">PILEUP</td>
-<td width="60%">PileUp</td>
-<td width="23%"></td>
-</tr><tr><td width="17%">PIR</td>
-<td width="60%">>P1;</td>
-<td width="23%">.pir</td>
-</tr><tr><td width="17%">BLC</td>
-<td width="60%">>Seq1<br>
->Seq2</td>
-<td width="23%">.blc</td>
-</tr><tr><td width="17%">PFAM</td>
-<td width="60%">SequenceName THISISASEQUENCE</td>
-<td width="23%">.pfam</td>
-</tr><tr>
-<td width="17%">Stockholm</td>
-<td width="60%"># STOCKHOLM VersionNumber<br>
-<em>...</em><br>//</td>
-<td width="23%">.stk, .sto</td>
-</tr><tr>
-<td width="17%">Phylip</td>
-<td width="60%">Line starts with two numbers separated by white space<br>
-<em>...</em><br>//</td>
-<td width="23%">.phy</td>
-</tr>
-<tr>
-<td width="17%">JSON</td>
-<td width="60%">Data starts with '{' <br>Data ends with '}' <br><br>See <a href="../features/bioJsonFormat.html">BioJSON</a> for more infomation about the Jalview JSON format <br></td>
-<td width="23%">.json</td>
-</tr>
+ <p>
+ <strong>Alignment File Formats</strong>
+ <p>Jalview understands a wide range of sequence alignment formats.
+ In order to determine which format has been used for an alignment,
+ Jalview tries to detect some text or formatting unique to one of the
+ formats:</p>
+ <table width="100%" border="1">
+ <tr>
+ <td width="17%">Format</td>
+ <td width="60%">Unique File Feature</td>
+ <td width="23%">File Extension</td>
+ <tr>
+ <td width="17%">FASTA</td>
+ <td width="60%">>SequenceName<br> THISISASEQUENCE<br></td>
+ <td width="23%">.fa, .fasta</td>
+ </tr>
+ <tr>
+ <td width="17%">MSF</td>
+ <td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br> <em>..</em><br>
+ //<br></td>
+ <td width="23%">.msf</td>
+ </tr>
+ <tr>
+ <td width="17%">CLUSTALW</td>
+ <td width="60%">CLUSTAL</td>
+ <td width="23%">.aln</td>
+ </tr>
+ <tr>
+ <td width="17%">PILEUP</td>
+ <td width="60%">PileUp</td>
+ <td width="23%"></td>
+ </tr>
+ <tr>
+ <td width="17%">PIR</td>
+ <td width="60%">>P1;</td>
+ <td width="23%">.pir</td>
+ </tr>
+ <tr>
+ <td width="17%">BLC</td>
+ <td width="60%">>Seq1<br> >Seq2
+ </td>
+ <td width="23%">.blc</td>
+ </tr>
+ <tr>
+ <td width="17%">PFAM</td>
+ <td width="60%">SequenceName THISISASEQUENCE</td>
+ <td width="23%">.pfam</td>
+ </tr>
+ <tr>
+ <td width="17%">Stockholm</td>
+ <td width="60%"># STOCKHOLM VersionNumber<br> <em>...</em><br>//
+ </td>
+ <td width="23%">.stk, .sto</td>
+ </tr>
+ <tr>
+ <td width="17%">Phylip</td>
+ <td width="60%">Line starts with two numbers separated by
+ white space<br> <em>...</em><br>//
+ </td>
+ <td width="23%">.phy</td>
+ </tr>
+ <tr>
+ <td width="17%">JSON</td>
+ <td width="60%">Data starts with '{' <br>Data ends with
+ '}' <br>
+ <br>See <a href="../features/bioJsonFormat.html">BioJSON</a>
+ for more infomation about the Jalview JSON format <br></td>
+ <td width="23%">.json</td>
+ </tr>
-</table>
-<p>The file extensions are used to associate Jalview alignment icons
-with alignment files: <img src="file.png" width=12 height=12 >
-</p>
+ </table>
+ <p>
+ The file extensions are used to associate Jalview alignment icons
+ with alignment files: <img src="file.png" width=12 height=12>
+ </p>
</body>
</html>
<title>Input/Output</title>
</head>
<body>
-<p><strong>Input</strong></p>
-<p>Jalview can read alignment files in any of the following standard
-formats:</p>
-<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
-NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em></p>
-<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
-of these file formats.</p>
-<p>Additionally, whole sets of coloured and annotated alignments and
-trees can be read from a <a href="../features/jalarchive.html">Jalview
-(jar) format</a> file using <strong>Desktop→Load Project</strong>.</p>
-<p>Press "Control O" to open a file browser, or use
-the <strong>Desktop→Input Alignment</strong> menu to read in
-alignments from:</p>
-<ul>
- <li><strong>From File</strong>: the local file system</li>
- <li><strong>From URL</strong>: the web (please use the full url)</li>
- <li><strong>from Textbox</strong>: a copy and paste into the
- "Cut & Paste" text window</li>
-</ul>
-<p>Jalview will try to recognise the file type automatically (using
-some special <a href="fileformats.html">features</a>). If a file is of
-an unknown format or there is any other error reading the alignment file
-then you will be given an error message. If you think Jalview really
-should be able to read your file, then send an email containing the
-problem file to help@jalview.org.</p>
-<p>Jalview can also read Jalview specific files for <a
- href="../features/featuresFormat.html">sequence features</a> and <a
- href="../features/annotationsFormat.html">alignment annotation</a>.</p>
-<p><strong>Output</strong></p>
-<p>Each alignment, whether it is the original or an edited version
-may be saved in the standard formats using <strong>File→Save
-As</strong></p>
-<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
-NBRF/PIR, Pfam/Stockholm</em></p>
-Jalview will by default append the sequence start and end to each
-sequence name, in the format /start-end. If you do not want this
-behaviour for a particular file output, open the "Output" tab
-on the
-<a href="../features/preferences.html">Preferences</a>
-window where you can select which file formats you want to append the
-start and end sequence positions for. In the case of PIR format, the
-output tab also contains a switch for turning on the output of Modeller
-style structured description lines.
-<p>Quantitative and symbolic <a href="../features/annotation.html">alignment
-annotation</a> can be exported as a comma separated value file by right
-clicking on an annotation row under the alignment.</p>
-<p>You can also save the current set of alignments and their
-colours, annotations and trees in a Jalview archive file using <strong>Desktop→Save
-project</strong>.<br>The project data includes the state of any open structure viewers (Jmol, and <em>since Jalview 2.9</em> also Chimera and Varna).</p>
-<p> </p>
+ <p>
+ <strong>Input</strong>
+ </p>
+ <p>Jalview can read alignment files in any of the following
+ standard formats:</p>
+ <p>
+ <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
+ NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
+ </p>
+ <p>
+ The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
+ of these file formats.
+ </p>
+ <p>
+ Additionally, whole sets of coloured and annotated alignments and
+ trees can be read from a <a href="../features/jalarchive.html">Jalview
+ (jar) format</a> file using <strong>Desktop→Load
+ Project</strong>.
+ </p>
+ <p>
+ Press "Control O" to open a file browser, or use the <strong>Desktop→Input
+ Alignment</strong> menu to read in alignments from:
+ </p>
+ <ul>
+ <li><strong>From File</strong>: the local file system</li>
+ <li><strong>From URL</strong>: the web (please use the full
+ url)</li>
+ <li><strong>from Textbox</strong>: a copy and paste into the
+ "Cut & Paste" text window</li>
+ </ul>
+ <p>
+ Jalview will try to recognise the file type automatically (using
+ some special <a href="fileformats.html">features</a>). If a file is
+ of an unknown format or there is any other error reading the
+ alignment file then you will be given an error message. If you think
+ Jalview really should be able to read your file, then send an email
+ containing the problem file to help@jalview.org.
+ </p>
+ <p>
+ Jalview can also read Jalview specific files for <a
+ href="../features/featuresFormat.html"
+ >sequence features</a> and <a
+ href="../features/annotationsFormat.html"
+ >alignment annotation</a>.
+ </p>
+ <p>
+ <strong>Output</strong>
+ </p>
+ <p>
+ Each alignment, whether it is the original or an edited version may
+ be saved in the standard formats using <strong>File→Save
+ As</strong>
+ </p>
+ <p>
+ <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
+ NBRF/PIR, Pfam/Stockholm</em>
+ </p>
+ Jalview will by default append the sequence start and end to each
+ sequence name, in the format /start-end. If you do not want this
+ behaviour for a particular file output, open the "Output"
+ tab on the
+ <a href="../features/preferences.html">Preferences</a> window where
+ you can select which file formats you want to append the start and end
+ sequence positions for. In the case of PIR format, the output tab also
+ contains a switch for turning on the output of Modeller style
+ structured description lines.
+ <p>
+ Quantitative and symbolic <a href="../features/annotation.html">alignment
+ annotation</a> can be exported as a comma separated value file by
+ right clicking on an annotation row under the alignment.
+ </p>
+ <p>
+ You can also save the current set of alignments and their colours,
+ annotations and trees in a Jalview archive file using <strong>Desktop→Save
+ project</strong>.<br>The project data includes the state of any open
+ structure viewers (Jmol, and <em>since Jalview 2.9</em> also Chimera
+ and Varna).
+ </p>
+ <p> </p>
</body>
</html>
<title>Modeller PIR Format IO</title>
</head>
<body>
-<p><strong>Modeller PIR Format IO</strong></p>
-<p>The homology modelling program, <a
-href="http://salilab.org/modeller/">Modeller</a> uses a special form
-of the PIR format where information about sequence numbering and chain
-codes are written into the 'description' line between the PIR protein
-tag and the protein alignment entry:</p>
-<pre>>P1;Q93Z60_ARATH
+ <p>
+ <strong>Modeller PIR Format IO</strong>
+ </p>
+ <p>
+ The homology modelling program, <a
+ href="http://salilab.org/modeller/"
+ >Modeller</a> uses a special form of the PIR format where information
+ about sequence numbering and chain codes are written into the
+ 'description' line between the PIR protein tag and the protein
+ alignment entry:
+ </p>
+ <pre>>P1;Q93Z60_ARATH
sequence:Q93Z60_ARATH:1:.:118:.:.
----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSD------QSFLD-D-------------
EV-CPVDCFY----EGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEK
KDPLPDAEDWDGVKGKLQHLE*
</pre>
-<p>Jalview will attempt to parse any PIR entries conforming to the
-Modeller/PIR format, in order to extract the sequence start and end
-numbering and (possibly) a PDB file reference. The description line
-information is always stored in the sequence description string - so
-no information is lost if this parsing process fails.</p>
-<p>The 'Modeller Output' flag in the 'Output' tab of the Jalview <a href="../features/preferences.html">Preferences dialog
-box</a> controls whether Jalview will also output MODELLER style PIR
-files. In this case, any existing 'non-modeller PIR' header
-information in the description string of an alignment is appended to
-an automatically generated modeller description line for that
-sequence.</p>
-<p>The general format used for generating the Modeller/PIR sequence
-description line is shown below :
-<pre>>P1;<em>Primary_Sequence_ID</em>
+ <p>Jalview will attempt to parse any PIR entries conforming to the
+ Modeller/PIR format, in order to extract the sequence start and end
+ numbering and (possibly) a PDB file reference. The description line
+ information is always stored in the sequence description string - so
+ no information is lost if this parsing process fails.</p>
+ <p>
+ The 'Modeller Output' flag in the 'Output' tab of the Jalview <a
+ href="../features/preferences.html"
+ >Preferences dialog box</a> controls whether Jalview will also output
+ MODELLER style PIR files. In this case, any existing 'non-modeller
+ PIR' header information in the description string of an alignment is
+ appended to an automatically generated modeller description line for
+ that sequence.
+ </p>
+ <p>The general format used for generating the Modeller/PIR
+ sequence description line is shown below :
+ <pre>>P1;<em>Primary_Sequence_ID</em>
<em>sequence or structureX</em>:<em>pdb-reference if
available</em>:<em>start residue</em>:<em>start chain code</em>:<em>end
- residue</em>:<em>end chain code</em>:. <em>description text</em></pre>
-The first field is either sequence or structureX, depending upon the
-presence of a PDB database ID for the sequence. If the protein has no
-PDB reference, then the chain code is not specified, unless one
-already existed when the sequence was imported into Jalview.
+ residue</em>:<em>end chain code</em>:. <em>description text</em>
+ </pre>
+ The first field is either sequence or structureX, depending upon the
+ presence of a PDB database ID for the sequence. If the protein has no
+ PDB reference, then the chain code is not specified, unless one
+ already existed when the sequence was imported into Jalview.
</body>
</html>
<title>T-COFFEE Annotation Scores</title>
</head>
<body>
-<p><strong>Loading and viewing T-COFFEE Annotation Scores</strong></p>
-<p>T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can be displayed on the alignment using the <strong><em>Colours→T-COFFEE Scores</em></strong>
-or <strong><em>Colour → <a href="../colourSchemes/annotationColouring.html">Colour by Annotation</a></em></strong> options.</p>
-<img src="../colourSchemes/colbytcoffee.png"/>
-<p><strong><a name="tcoffeeeg">Example T-COFFEE Score file</a></strong><br/>
-T-COFFEE score files like the one below can be dropped directly onto the corresponding alignment to visualize alignment confidence scores.
-</p>
-<pre>
+ <p>
+ <strong>Loading and viewing T-COFFEE Annotation Scores</strong>
+ </p>
+ <p>
+ T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can
+ be displayed on the alignment using the <strong><em>Colours→T-COFFEE
+ Scores</em></strong> or <strong><em>Colour → <a
+ href="../colourSchemes/annotationColouring.html"
+ >Colour by Annotation</a></em></strong> options.
+ </p>
+ <img src="../colourSchemes/colbytcoffee.png" />
+ <p>
+ <strong><a name="tcoffeeeg">Example T-COFFEE Score file</a></strong><br />
+ T-COFFEE score files like the one below can be dropped directly onto
+ the corresponding alignment to visualize alignment confidence
+ scores.
+ </p>
+ <pre>
T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
Cedric Notredame
CPU TIME:0 sec.
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Key Strokes</title></head>
+<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>
+ <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>Left Arrow</strong></td>
- <td>Normal </td>
- <td>Slides selected sequence(s) left. Press Alt key to slide in cursor mode</td>
- </tr>
- <tr>
- <td><strong>Right Arrow</strong></td>
- <td>Normal</td>
- <td>Slides selected sequence(s) right. Press Alt key to slide in cursor mode</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>Page Up</strong></td>
- <td>Both</td>
- <td>Scroll up the alignment view</td>
- </tr>
- <tr>
- <td><strong>Page Down</strong></td>
- <td>Both</td>
- <td>Scroll down the alignment view</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
+ <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>Left Arrow</strong></td>
+ <td>Normal</td>
+ <td>Slides selected sequence(s) left. Press Alt key to slide
+ in cursor mode</td>
+ </tr>
+ <tr>
+ <td><strong>Right Arrow</strong></td>
+ <td>Normal</td>
+ <td>Slides selected sequence(s) right. Press Alt key to slide
+ in cursor mode</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>Page Up</strong></td>
+ <td>Both</td>
+ <td>Scroll up the alignment view</td>
+ </tr>
+ <tr>
+ <td><strong>Page Down</strong></td>
+ <td>Both</td>
+ <td>Scroll down the alignment view</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 + Shift 'H'</strong></td>
- <td>Both</td>
- <td>Hides everything but the current selection</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>
+ </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 + Shift 'H'</strong></td>
+ <td>Both</td>
+ <td>Hides everything but the current selection</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>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Memory Settings</title></head>
+<head>
+<title>Memory Settings</title>
+</head>
<body>
-<h2>
- <center>
- <strong>Memory Usage Settings for Jalview</strong>
- </center>
-</h2>
-<p>Jalview sometimes runs out of memory. This is because of the way that Java
- runs on a computer - what is actually run is a program called a virtual machine
- (the JVM) which executes the java instructions. The JVM has limits on the memory
- that can be allocated to the java program - and you might need to increase them
- if you are working with particularly large datasets.<br>
- If Jalview has not explicitly told you that it has run out of memory, then a
- common sign is that a function that normally works seems to have no effect when
- working with a larger set of sequences (this might include open dialog boxes
- for saving PNG files, or when interpreting the result of a web service calculation).</p>
- <p><em>Jalview Memory Usage Monitor</em>: If you are concerned about memory, or think that things might be behaving
- strangely because of a shortage of memory, then you can check this by enabling the
- memory usage monitor. This is done by selecting the <strong>Tools→Show Memory Usage</strong>
- option. Once enabled, the memory usage monitor displays the currently
- available memory, the total memory, and the percentage free at the
- bottom left hand side of the Jalview Desktop window's background.</p>
-<p><em>Increasing the memory available to Jalview</em><br>
-The way you increase the memory settings for the JVM depends on which installation
- of Jalview you use:</p>
-<ul>
- <li><em><font size="3">Web Start Version</font></em>
- <p>
- JavaWS sets the JVM parameters through special tags in the JNLP
- file. You can obtain a JNLP file with modified memory settings from
- our service with the following link (replace 2G with desired memory
- in G or M):<br /> <a
- href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
- </p>
- <p>
- Alternatively, if you want to create your own JNLP file then please
- download the latest JNLP file from <a
- href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
- and modify the max-heap-size parameter for the j2se tag in the
- <resources> element. e.g.
- <pre>
+ <h2>
+ <center>
+ <strong>Memory Usage Settings for Jalview</strong>
+ </center>
+ </h2>
+ <p>
+ Jalview sometimes runs out of memory. This is because of the way
+ that Java runs on a computer - what is actually run is a program
+ called a virtual machine (the JVM) which executes the java
+ instructions. The JVM has limits on the memory that can be allocated
+ to the java program - and you might need to increase them if you are
+ working with particularly large datasets.<br> If Jalview has
+ not explicitly told you that it has run out of memory, then a common
+ sign is that a function that normally works seems to have no effect
+ when working with a larger set of sequences (this might include open
+ dialog boxes for saving PNG files, or when interpreting the result
+ of a web service calculation).
+ </p>
+ <p>
+ <em>Jalview Memory Usage Monitor</em>: If you are concerned about
+ memory, or think that things might be behaving strangely because of
+ a shortage of memory, then you can check this by enabling the memory
+ usage monitor. This is done by selecting the <strong>Tools→Show
+ Memory Usage</strong> option. Once enabled, the memory usage monitor
+ displays the currently available memory, the total memory, and the
+ percentage free at the bottom left hand side of the Jalview Desktop
+ window's background.
+ </p>
+ <p>
+ <em>Increasing the memory available to Jalview</em><br> The way
+ you increase the memory settings for the JVM depends on which
+ installation of Jalview you use:
+ </p>
+ <ul>
+ <li><em><font size="3">Web Start Version</font></em>
+ <p>
+ JavaWS sets the JVM parameters through special tags in the JNLP
+ file. You can obtain a JNLP file with modified memory settings
+ from our service with the following link (replace 2G with
+ desired memory in G or M):<br /> <a
+ href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G"
+ >http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
+ </p>
+ <p>
+ Alternatively, if you want to create your own JNLP file then
+ please download the latest JNLP file from <a
+ href="http://www.jalview.org/webstart/jalview.jnlp"
+ >http://www.jalview.org/webstart/jalview.jnlp</a> and modify the
+ max-heap-size parameter for the j2se tag in the
+ <resources> element. e.g.
+ <pre>
<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
-</pre> In both cases, you should save your new jnlp file somewhere and
- then either point your web browser at the file's url, launch it from
- your file browser, or from a terminal window run javaws (located in
- your Java installation's bin directory) with the file location as its
- argument. The file's url is something like :<br> <pre>
+</pre> In both cases, you should save your new jnlp file somewhere and then
+ either point your web browser at the file's url, launch it from
+ your file browser, or from a terminal window run javaws (located
+ in your Java installation's bin directory) with the file location
+ as its argument. The file's url is something like :<br> <pre>
file://<full path to file>
</pre> If Jalview doesn't start up, see <a href="#memsetting">below</a>.
- You'll have to edit the above settings in the JNLP file using a text
- editor, save it, and try starting Jalview with it once more.
- </p></li>
- <li><em><font size="3">Install Anywhere version</font></em>
- <p> You need to change the InstallAnywhere configuration settings for the
- application. These are found in different places depending upon which operating
- system you have :
- <ul>
- <li><em>Unix/Windows</em>
- <p> Take a look inside the Jalview program installation directory (this
- might be in C:\Program Files\Jalview on windows). You should find a
- file called 'Jalview.lax' in it - make a backup, and then add the following
- lines to the end of the original file :
- <pre>
+ You'll have to edit the above settings in the JNLP file using a
+ text editor, save it, and try starting Jalview with it once more.
+ </p></li>
+ <li><em><font size="3">Install Anywhere version</font></em>
+ <p>You need to change the InstallAnywhere configuration
+ settings for the application. These are found in different
+ places depending upon which operating system you have :
+ <ul>
+ <li><em>Unix/Windows</em>
+ <p>Take a look inside the Jalview program installation
+ directory (this might be in C:\Program Files\Jalview on
+ windows). You should find a file called 'Jalview.lax' in it
+ - make a backup, and then add the following lines to the end
+ of the original file :
+ <pre>
lax.nl.java.option.java.heap.size.max=1000m
lax.nl.java.option.java.heap.size.initial=500m
-</pre>
- Case and (lack of) spaces are important here! Do not add any spaces after
- the m in each line, and do not put any spaces before 'lax'.<br>
- Also there MUST be a carriage return after the final line.
- <p></p>
- </li>
- <li><em>Mac OSX</em>
- <p>The lines you need to change are in the <em>Info.plist</em> file inside
- the <em>Jalview.app/Contents</em> directory (which is where the installAnywhere
- installation was made) :
- <pre>
+</pre> Case and (lack of) spaces are important here! Do not add any spaces
+ after the m in each line, and do not put any spaces before
+ 'lax'.<br> Also there MUST be a carriage return after the
+ final line.
+ <p></p></li>
+ <li><em>Mac OSX</em>
+ <p>
+ The lines you need to change are in the <em>Info.plist</em>
+ file inside the <em>Jalview.app/Contents</em> directory
+ (which is where the installAnywhere installation was made) :
+
+ <pre>
<key&ht;VMOptions</key&ht;
<array>
! <string>-Xms2M</string>
! <string>-Xmx64M</string>
</array>
-</pre>
- Exchange the above two string tags for :
- <pre>
+</pre> Exchange the above two string tags for : <pre>
<string>-Xms500M</string>
<string>-Xmx1000M</string>
</pre>
- <p></p>
- </li>
- </ul>
- <li><font size="3"><em>In all cases</em></font><br>
- Save the file and try to start Jalview in the normal way. If it doesn't start,
- see below... </li>
-</ul>
-<font size="3"><em>Jalview doesn't start... What do the memory settings mean ?<a name="memsetting"></a></em></font>
-<p> The 1000m value corresponds to the maximum number of megabytes of space that
- java objects can occupy. The 500m is the initial heap size that java will run
- in - increasing this can speed up memory allocation if you know you will need
- 500 meg of memory to begin with (ie it should speed up loading large alignments).
-</p>
-<p> If, after setting the initial and maximum heap size to some large value, you
- cannot actually start Jalview, then the max and initial sizes are too big for
- your machine (there seems to be a physical limit related to physical RAM - email
- the usual address to enlighten us if you know better!). Our experiments found
- 1000m to be the biggest setting that could be used on a 1GB machine. Just try
- reducing the sizes until Jalview starts up properly! </p>
-<p> </p>
+ <p></p></li>
+ </ul>
+ <li><font size="3"><em>In all cases</em></font><br> Save
+ the file and try to start Jalview in the normal way. If it doesn't
+ start, see below...</li>
+ </ul>
+ <font size="3"><em>Jalview doesn't start... What do the
+ memory settings mean ?<a name="memsetting"></a>
+ </em></font>
+ <p>The 1000m value corresponds to the maximum number of megabytes
+ of space that java objects can occupy. The 500m is the initial heap
+ size that java will run in - increasing this can speed up memory
+ allocation if you know you will need 500 meg of memory to begin with
+ (ie it should speed up loading large alignments).</p>
+ <p>If, after setting the initial and maximum heap size to some
+ large value, you cannot actually start Jalview, then the max and
+ initial sizes are too big for your machine (there seems to be a
+ physical limit related to physical RAM - email the usual address to
+ enlighten us if you know better!). Our experiments found 1000m to be
+ the biggest setting that could be used on a 1GB machine. Just try
+ reducing the sizes until Jalview starts up properly!</p>
+ <p> </p>
</body>
</html>
<strong>Alignment Window Menus</strong>
</p>
<ul>
- <li><strong>File</strong>
- <ul>
- <li><strong>Fetch Sequence</strong><br> <em>Shows a
- dialog window in which you can retrieve known ids from Uniprot,
- EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
- European Bioinformatics Institute. See <a
- href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
- <li><strong>Add Sequences</strong><em><br> Add
- sequences to the visible alignment from file, URL, or cut &
- paste window </em>
- </li>
- <li><strong>Reload</strong><em><br> Reloads the
- alignment from the original file, if available.<br> <strong>Warning:
- This will delete any edits, analyses and colourings applied since
- the alignment was last saved, and cannot be undone.</strong> </em>
- </li>
- <li><strong>Save (Control S)</strong><em><br> Saves
- the alignment to the file it was loaded from (if available), in
- the same format, updating the original in place. </em>
- </li>
- <li><strong>Save As (Control Shift S)<br> </strong><em>Save
- the alignment to local file. A file selection window will open,
- use the "Files of type:" selection box to determine
- which <a href="../io/index.html">alignment format</a> to save as.</em>
- </li>
- <li><strong>Output to Textbox<br> </strong><em>The
- alignment will be displayed in plain text in a new window, which
- you can "Copy and Paste" using the pull down menu, or
- your standard operating system copy and paste keys. The output
- window also has a <strong>"New Window"</strong> button
- to import the (possibly edited) text as a new alignment.<br>
- Select the format of the text by selecting one of the following
- menu items.</em>
- <ul>
- <li><strong>FASTA</strong> </li>
- <li><strong>MSF</strong></li>
- <li><strong>CLUSTAL</strong></li>
- <li><strong>BLC</strong></li>
- <li><strong>PIR</strong></li>
- <li><strong>PFAM</strong></li>
- <li><strong>PileUp</strong></li>
- <li><strong>AMSA</strong></li>
- <li><strong>STH</strong></li>
- <li><strong>Phylip</strong></li>
- <li><strong>JSON</strong></li>
- </ul></li>
-<li><strong>Page Setup ...</strong><br>
- <em>Open the printing system's Page Setup dialog box, to
- control page size, layout and orientation.</em></li>
- <li><strong>Print (Control P)<br>
- </strong><em>Jalview will print the alignment using the current fonts and
- colours of your alignment. If the alignment has annotations visible,
- these will be printed below the alignment. If the alignment is wrapped
- the number of residues per line of your alignment will depend on the
- paper width or your alignment window width, whichever is the smaller. </em></li>
- <li><strong>Export Image</strong> <em><br>
- Creates an alignment graphic with the current view's annotation,
- alignment background colours and group colours. If the alignment is <a
- href="../features/wrap.html">wrapped</a>, the output will also be
- wrapped and will have the same visible residue width as the open
- alignment. </em>
- <ul>
- <li><strong>HTML<br>
- </strong><em>Create a <a href="../io/export.html">web page</a> from your
- alignment.</em></li>
- <li><strong>EPS<br>
- </strong><em>Create an <a href="../io/export.html">Encapsulated
- Postscript</a> file from your alignment.</em></li>
- <li><strong>PNG<br>
- </strong><em>Create a <a href="../io/export.html">Portable Network
- Graphics</a> file from your alignment.</em></li>
- <li><strong>SVG<br>
- </strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
- <li><strong>BioJS<br>
- </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
- </ul>
- </li>
+ <li><strong>File</strong>
+ <ul>
+ <li><strong>Fetch Sequence</strong><br> <em>Shows
+ a dialog window in which you can retrieve known ids from
+ Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+ Web Services provided by the European Bioinformatics
+ Institute. See <a href="../features/seqfetch.html">Sequence
+ Fetcher</a>
+ </em>.</li>
+ <li><strong>Add Sequences</strong><em><br> Add
+ sequences to the visible alignment from file, URL, or cut
+ & paste window </em></li>
+ <li><strong>Reload</strong><em><br> Reloads the
+ alignment from the original file, if available.<br> <strong>Warning:
+ This will delete any edits, analyses and colourings
+ applied since the alignment was last saved, and cannot be
+ undone.</strong> </em></li>
+ <li><strong>Save (Control S)</strong><em><br>
+ Saves the alignment to the file it was loaded from (if
+ available), in the same format, updating the original in
+ place. </em></li>
+ <li><strong>Save As (Control Shift S)<br>
+ </strong><em>Save the alignment to local file. A file selection
+ window will open, use the "Files of type:"
+ selection box to determine which <a href="../io/index.html">alignment
+ format</a> to save as.
+ </em></li>
+ <li><strong>Output to Textbox<br>
+ </strong><em>The alignment will be displayed in plain text in a new
+ window, which you can "Copy and Paste" using the
+ pull down menu, or your standard operating system copy and
+ paste keys. The output window also has a <strong>"New
+ Window"</strong> button to import the (possibly edited) text
+ as a new alignment.<br> Select the format of the text
+ by selecting one of the following menu items.
+ </em>
+ <ul>
+ <li><strong>FASTA</strong></li>
+ <li><strong>MSF</strong></li>
+ <li><strong>CLUSTAL</strong></li>
+ <li><strong>BLC</strong></li>
+ <li><strong>PIR</strong></li>
+ <li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>Phylip</strong></li>
+ <li><strong>JSON</strong></li>
+ </ul></li>
+ <li><strong>Page Setup ...</strong><br> <em>Open
+ the printing system's Page Setup dialog box, to control page
+ size, layout and orientation.</em></li>
+ <li><strong>Print (Control P)<br>
+ </strong><em>Jalview will print the alignment using the current
+ fonts and colours of your alignment. If the alignment has
+ annotations visible, these will be printed below the
+ alignment. If the alignment is wrapped the number of
+ residues per line of your alignment will depend on the paper
+ width or your alignment window width, whichever is the
+ smaller. </em></li>
+ <li><strong>Export Image</strong> <em><br>
+ Creates an alignment graphic with the current view's
+ annotation, alignment background colours and group colours.
+ If the alignment is <a href="../features/wrap.html">wrapped</a>,
+ the output will also be wrapped and will have the same
+ visible residue width as the open alignment. </em>
+ <ul>
+ <li><strong>HTML<br>
+ </strong><em>Create a <a href="../io/export.html">web page</a>
+ from your alignment.
+ </em></li>
+ <li><strong>EPS<br>
+ </strong><em>Create an <a href="../io/export.html">Encapsulated
+ Postscript</a> file from your alignment.
+ </em></li>
+ <li><strong>PNG<br>
+ </strong><em>Create a <a href="../io/export.html">Portable
+ Network Graphics</a> file from your alignment.
+ </em></li>
+ <li><strong>SVG<br>
+ </strong><em>Create a <a href="../io/export.html">Scalable
+ Vector Graphics</a> file from your alignment for embedding
+ in web pages.
+ </em></li>
+ <li><strong>BioJS<br>
+ </strong><em>Create a <a href="../io/export.html">BioJS MSA
+ Viewer HTML </a> file from your alignment.
+ </em></li>
+ </ul></li>
<li><strong>Export Features</strong><em><br> All
- features visible on the alignment can be saved to file or
- displayed in a textbox in either Jalview or GFF format</em>
- </li>
- <li><strong>Export Annotations</strong><em><br> All
- annotations visible on the alignment can be saved to file or
- displayed in a textbox in Jalview annotations format. </em>
- </li>
- <li><strong>Load Associated Tree<br> </strong><em>Jalview
- can <a href="../calculations/treeviewer.html">view trees</a>
- stored in the Newick file format, and associate them with the
- alignment. Note: the ids of the tree file and your alignment MUST
- be the same.</em></li>
- <li><strong>Load Features / Annotations<br> </strong><em>Load
- files describing precalculated <a
- href="../features/featuresFormat.html">sequence features</a> or <a
- href="../features/annotationsFormat.html">alignment
- annotations</a>.</em></li>
- <li><strong>Close (Control W)</strong><br> <em>Close
- the alignment window. Make sure you have saved your alignment
- before you close - either from the Desktop's <strong>Save Project</strong> File menu option, or by using the <strong>Save
- As</strong> menu.</em>
- </li>
- </ul></li>
- <li><strong>Edit</strong>
- <ul>
- <li><strong>Undo (Control Z)</strong><em><br> This
- will undo any edits you make to the alignment. This applies to
- insertion or deletion of gaps, cutting residues or sequences from
- the alignment or pasting sequences to the current alignment or
- sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
- colour changes, adjustments to group sizes, or changes to the
- annotation panel. </em>
- </li>
- <li><strong>Redo (Control Y)<br> </strong><em>Any
- actions which you undo can be redone using redo. </em>
- </li>
- <li><strong>Cut (Control X)<br> </strong><em>This
- will make a copy of the currently selected residues before
- removing them from your alignment. Click on a sequence name if you
- wish to select a whole sequence. <br> Use <CTRL> and X
- (<APPLE> and X on MacOSX) to cut.</em>
- </li>
- <li><strong>Copy (Control C)</strong><br> <em>Copies
- the currently selected residues to the system clipboard - you can
- also do this by pressing <CTRL> and C (<APPLE> and C
- on MacOSX). <br> If you try to paste the clipboard contents
- to a text editor, you will see the format of the copied residues
- FASTA.</em></li>
- <li><strong>Paste </strong>
- <ul>
- <li><strong>To New Alignment (Control Shift V)<br>
- </strong><em>A new alignment window will be created from sequences
- previously copied or cut to the system clipboard. <br> Use
- <CTRL> and <SHIFT> and V(<APPLE> and
- <SHIFT;> and and V on MacOSX) to paste.</em>
- </li>
- <li><strong>Add To This Alignment (Control V)<br>
- </strong><em>Copied sequences from another alignment window can be
- added to the current Jalview alignment. </em>
- </li>
- </ul></li>
- <li><strong>Delete (Backspace)<br> </strong><em>This
- will delete the currently selected residues without copying them
- to the clipboard. Like the other edit operations, this can be
- undone with <strong>Undo</strong>.</em>
- </li>
- <li><strong>Remove Left (Control L)<br> </strong><em>If
- the alignment has marked columns, the alignment will be trimmed to
- the left of the leftmost marked column. To mark a column, mouse
- click the scale bar above the alignment. Click again to unmark a
- column, or select "Deselect All" to deselect all
- columns.</em></li>
- <li><strong>Remove Right (Control R)<br> </strong><em>If
- the alignment has marked columns, the alignment will be trimmed to
- the left of the leftmost marked column. To mark a column, mouse
- click the scale bar above the alignment. Click again to unmark a
- column, or select "Deselect All" to deselect all
- columns.</em></li>
- <li><strong>Remove Empty Columns (Control E)<br>
- </strong><em>All columns which only contain gap characters
- ("-", ".") will be deleted.<br> You may
- set the default gap character in <a
- href="../features/preferences.html">preferences</a>. </em>
- </li>
- <li><strong>Remove All Gaps (Control Shift E)</strong><br>
- <em>Gap characters ("-", ".") will be
- deleted from the selected area of the alignment. If no selection
- is made, ALL the gaps in the alignment will be removed.<br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>. </em>
- </li>
- <li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
- this option brings up a window asking you to select a threshold.
- If the percentage identity between any two sequences (under the
- current alignment) exceeds this value then one of the sequences
- (the shorter) is discarded. Press the "Apply" button to
- remove redundant sequences. The "Undo" button will undo
- the last redundancy deletion.</em>
- </li>
- <li><strong>Pad Gaps<br> </strong><em>When selected,
- the alignment will be kept at minimal width (so there are no empty
- columns before or after the first or last aligned residue) and all
- sequences will be padded with gap characters before and
- after their terminating residues.<br> This switch is useful
- when making a tree using unaligned sequences and when working with
- alignment analysis programs which require 'properly aligned
- sequences' to be all the same length.<br> You may set the
- default for <strong>Pad Gaps</strong> in the <a
- href="../features/preferences.html">preferences</a>. </em>
- </li>
- </ul></li>
- <li><strong>Select</strong>
- <ul>
- <li><a href="../features/search.html"><strong>Find... (Control F)</strong></a><br>
- <em>Opens the Find dialog box to search for residues, sequence name or residue
- position within the alignment and create new sequence features from the queries.
- </em>
- <li><strong>Select All (Control A)</strong><strong><br>
- </strong><em>Selects all the sequences and residues in the alignment. <br>
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></em></li>
- <li><strong>Deselect All (Escape)<br>
- </strong><em>Removes the current selection box (red dashed box) from the
- alignment window. All selected sequences, residues and marked columns
- will be deselected. </em><em> <br>
- Use <ESCAPE> to deselect all.</em></li>
- <li><strong>Invert Sequence Selection (Control I)<br>
- </strong><em>Any sequence ids currently not selected will replace the
- current selection. </em></li>
- <li><strong>Invert Column Selection (Control Alt I)<br>
- </strong><em>Any columns currently not selected will replace the current
- column selection. </em></li>
- <li><strong>Create Group (Control G)<br></strong>
- <em>Create a group containing the currently selected sequences.</em></li>
- <li><strong>Remove Group (Shift Control G)<br></strong>
- <em>Ungroup the currently selected sequence group.</em></li>
- <li><strong>Make Groups for selection<br /></strong> <em>The
- currently selected groups of the alignment will be subdivided
- according to the contents of the currently selected region. <br />Use
- this to subdivide an alignment based on the different combinations
- of residues at marked columns.
- </em></li>
- <li><strong>Undefine Groups (Control U)<br>
- </strong><em>The alignment will be reset with no defined groups.<br>
- <strong>WARNING</strong>: This cannot be undone.</em></li>
- <li><strong><a
- href="../features/columnFilterByAnnotation.html">Select/Hide Columns by Annotation</a></strong> <br />
- <em>Select or Hide columns in the alignment according to
- secondary structure, labels and values shown in alignment
- annotation rows. </em></li>
- </ul></li>
- <li><strong>View</strong>
- <ul>
- <li><strong>New View (Control T)</strong><em><br>
- Creates a new view from the current alignment view. </em>
- </li>
- <li><strong>Expand Views (X)</strong><em><br> Display
- each view associated with the alignment in its own alignment
- window, allowing several views to be displayed simultaneously. </em>
- </li>
- <li><strong>Gather Views (G)</strong><em><br> Each
- view associated with the alignment will be displayed within its
- own tab on the current alignment window. </em>
- </li>
- <li><strong>Show→(all Columns / Sequences /
- Sequences and Columns)</strong><em><br> All hidden Columns /
- Sequences / Sequences and Columns will be revealed. </em>
- </li>
- <li><strong>Hide→(all Columns / Sequences /
- Selected Region / All but Selected Region )</strong><em><br>
- Hides the all the currently selected Columns / Sequences / Region
- or everything but the selected Region.</em>
- </li>
- <li><strong>Automatic Scrolling<br> </strong><em>When
- selected, the view will automatically scroll to display the
- highlighted sequence position corresponding to the position under
- the mouse pointer in a linked alignment or structure view.</em></li>
- <li><strong>Show Sequence Features</strong><br> <em>Show
- or hide sequence features on this alignment.</em>
- </li>
- <li><strong><a href="../features/featuresettings.html">Sequence
- Feature Settings...</a> </strong><em><br> <em>Opens the
- Sequence Feature Settings dialog box to control the colour and
- display of sequence features on the alignment, and configure and
- retrieve features from DAS annotation servers.</em>
- </li>
- <li><strong>Sequence ID Tooltip</strong><em> (application
- only) <br>This submenu's options allow the inclusion or
- exclusion of non-positional sequence features or database cross
- references from the tooltip shown when the mouse hovers over the
- sequence ID panel.</em>
- </li>
- <li><strong>Alignment Properties...<br /> </strong><em>Displays
- some simple statistics computed for the current alignment view and
- any named properties defined on the whole alignment.</em>
- </li>
- <li><strong><a href="../features/overview.html">Overview
- Window</a><br> </strong><em>A scaled version of the alignment will
- be displayed in a small window. A red box will indicate the
- currently visible area of the alignment. Move the visible region
- using the mouse. </em>
- </li>
- </ul></li>
- <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
- <ul>
- <li><strong>Show Annotations<br> </strong><em>If this
- is selected the "Annotation Panel" will be displayed
- below the alignment. The default setting is to display the
- conservation calculation, quality calculation and consensus values
- as bar charts. </em>
- </li>
- <li><strong>Show Alignment Related</strong><em><br>
- Show all annotations that are for the alignment as a whole (for example, Consensus,
- or secondary structure prediction from alignment).</em></li>
- <li><strong>Hide Alignment Related</strong><em><br>
- Hide all annotations that are for the alignment as a whole.</em></li>
- <li><strong>Show Sequence Related</strong><em><br>
- Show all annotations that are for individual sequences.</em></li>
- <li><strong>Hide Sequence Related</strong><em><br>
- Hide all annotations that are for individual sequences.</em></li>
- <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
- or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
- <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
- (and within that, by label).</em></li>
- <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
- (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
- allowing you to make a manual ordering of the annotations.</em></li>
- <li><strong>Autocalculated Annotation<br> </strong><em>Settings
- for the display of autocalculated annotation.</em>
- <ul>
- <li><strong>Show first<br></strong><em>
- Show autocalculated annotations above sequence-specific annotations.
- Note this also applies to other annotations for the alignment, for example secondary
- structure prediction from alignment.</em></li>
- <li><strong>Show last<br></strong><em>
- Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, any modification to the current settings will be applied
- to all autocalculated annotation.</em></li>
- <li><strong>Show Consensus Histogram<br> </strong><em>
- Enable or disable the display of the histogram above the
- consensus sequence.</em></li>
- <li><strong>Show Consensus Logo<br> </strong><em> Enable
- or disable the display of the Consensus Logo above the consensus
- sequence.</em></li>
- <li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.</em></li>
- <li><strong>Group Conservation<br> </strong><em> When
- ticked, display a conservation row for all groups (only available
- for protein alignments).</em></li>
- <li><strong>Group Consensus<br> </strong><em> When
- ticked, display a consensus row for all groups.</em></li>
- </ul>
- </li>
- </ul>
- </li>
- <li><strong>Alignment Window Format Menu</strong>
- <ul>
- <li><strong>Font...<br> </strong><em>Opens the
- "Choose Font" dialog box, in order to change the font of
- the display and enable or disable 'smooth fonts' (anti-aliasing)
- for faster alignment rendering. </em></li>
- <li><strong>Wrap<br> </strong><em>When ticked, the
- alignment display is "<a href="../features/wrap.html">wrapped</a>"
- to the width of the alignment window. This is useful if your
- alignment has only a few sequences to view its full width at once.</em><br>
- Additional options for display of sequence numbering and scales are
- also visible in wrapped layout mode:<br>
- <ul>
- <li><strong>Scale Above</strong><br><em> Show the alignment
- column position scale.</em></li>
- <li><strong>Scale Left</strong><br><em> Show the sequence
- position for the first aligned residue in each row in the left
- column of the alignment.</em></li>
- <li><strong>Scale Right</strong><br><em> Show the sequence
- position for the last aligned residue in each row in the
- right-most column of the alignment.</em></li>
- <li><strong>Show Sequence Limits<br> </strong><em>If
- this box is selected the sequence name will have the start and
- end position of the sequence appended to the name, in the format
- NAME/START-END</em>
- </li>
- <li><strong>Right Align Sequence ID<br> </strong><em>If
- this box is selected then the sequence names displayed in the
- sequence label area will be aligned against the left-hand edge
- of the alignment display, rather than the left-hand edge of the
- alignment window.
- </li>
- <li><strong>Show Hidden Markers<br> </strong><em>When
- this box is selected, positions in the alignment where rows and
- columns are hidden will be marked by blue arrows.
- </li>
- <li><strong>Boxes</strong><em><br> If this is
- selected the background of a residue will be coloured using the
- selected background colour. Useful if used in conjunction with
- "Colour Text." </em>
- </li>
- <li><strong>Text<br> </strong><em>If this is
- selected the residues will be displayed using the standard 1
- character amino acid alphabet.</em>
- </li>
- <li><strong>Colour Text<br> </strong><em>If this is
- selected the residues will be coloured according to the
- background colour associated with that residue. The colour is
- slightly darker than background so the amino acid symbol remains
- visible. </em>
- </li>
- <li><strong>Show Gaps<br> </strong><em>When this is
- selected, gap characters will be displayed as "." or
- "-". If unselected, then gap characters will appear as
- blank spaces. <br> You may set the default gap character in
- <a href="../features/preferences.html">preferences</a>.</em>
- </li>
- <li><strong>Centre Annotation Labels<br> </strong><em>Select
- this to center labels along an annotation row relative to their
- associated column (default is off, i.e. left-justified).</em>
- </li>
- <li><strong>Show Unconserved<br> </strong><em>When
- this is selected, all consensus sequence symbols will be
- rendered as a '.', highlighting mutations in highly conserved
- alignments. </em>
- </li>
+ features visible on the alignment can be saved to file or
+ displayed in a textbox in either Jalview or GFF format</em></li>
+ <li><strong>Export Annotations</strong><em><br>
+ All annotations visible on the alignment can be saved to
+ file or displayed in a textbox in Jalview annotations
+ format. </em></li>
+ <li><strong>Load Associated Tree<br>
+ </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
+ trees</a> stored in the Newick file format, and associate them
+ with the alignment. Note: the ids of the tree file and your
+ alignment MUST be the same.
+ </em></li>
+ <li><strong>Load Features / Annotations<br>
+ </strong><em>Load files describing precalculated <a
+ href="../features/featuresFormat.html"
+ >sequence features</a> or <a
+ href="../features/annotationsFormat.html"
+ >alignment annotations</a>.
+ </em></li>
+ <li><strong>Close (Control W)</strong><br> <em>Close
+ the alignment window. Make sure you have saved your
+ alignment before you close - either from the Desktop's <strong>Save
+ Project</strong> File menu option, or by using the <strong>Save
+ As</strong> menu.
+ </em></li>
+ </ul></li>
+ <li><strong>Edit</strong>
+ <ul>
+ <li><strong>Undo (Control Z)</strong><em><br>
+ This will undo any edits you make to the alignment. This
+ applies to insertion or deletion of gaps, cutting residues
+ or sequences from the alignment or pasting sequences to the
+ current alignment or sorting the alignment. <strong>NOTE:</strong>
+ It DOES NOT undo colour changes, adjustments to group sizes,
+ or changes to the annotation panel. </em></li>
+ <li><strong>Redo (Control Y)<br>
+ </strong><em>Any actions which you undo can be redone using redo. </em></li>
+ <li><strong>Cut (Control X)<br>
+ </strong><em>This will make a copy of the currently selected
+ residues before removing them from your alignment. Click on
+ a sequence name if you wish to select a whole sequence. <br>
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to
+ cut.
+ </em></li>
+ <li><strong>Copy (Control C)</strong><br> <em>Copies
+ the currently selected residues to the system clipboard -
+ you can also do this by pressing <CTRL> and C
+ (<APPLE> and C on MacOSX). <br> If you try to
+ paste the clipboard contents to a text editor, you will see
+ the format of the copied residues FASTA.
+ </em></li>
+ <li><strong>Paste </strong>
+ <ul>
+ <li><strong>To New Alignment (Control Shift V)<br>
+ </strong><em>A new alignment window will be created from
+ sequences previously copied or cut to the system
+ clipboard. <br> Use <CTRL> and <SHIFT>
+ and V(<APPLE> and <SHIFT;> and and V on
+ MacOSX) to paste.
+ </em></li>
+ <li><strong>Add To This Alignment (Control V)<br>
+ </strong><em>Copied sequences from another alignment window can
+ be added to the current Jalview alignment. </em></li>
+ </ul></li>
+ <li><strong>Delete (Backspace)<br>
+ </strong><em>This will delete the currently selected residues
+ without copying them to the clipboard. Like the other edit
+ operations, this can be undone with <strong>Undo</strong>.
+ </em></li>
+ <li><strong>Remove Left (Control L)<br>
+ </strong><em>If the alignment has marked columns, the alignment will
+ be trimmed to the left of the leftmost marked column. To
+ mark a column, mouse click the scale bar above the
+ alignment. Click again to unmark a column, or select
+ "Deselect All" to deselect all columns.</em></li>
+ <li><strong>Remove Right (Control R)<br>
+ </strong><em>If the alignment has marked columns, the alignment will
+ be trimmed to the left of the leftmost marked column. To
+ mark a column, mouse click the scale bar above the
+ alignment. Click again to unmark a column, or select
+ "Deselect All" to deselect all columns.</em></li>
+ <li><strong>Remove Empty Columns (Control E)<br>
+ </strong><em>All columns which only contain gap characters
+ ("-", ".") will be deleted.<br> You
+ may set the default gap character in <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ <li><strong>Remove All Gaps (Control Shift E)</strong><br>
+ <em>Gap characters ("-", ".") will be
+ deleted from the selected area of the alignment. If no
+ selection is made, ALL the gaps in the alignment will be
+ removed.<br> You may set the default gap character in <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ <li><strong>Remove Redundancy (Control D)<br>
+ </strong><em>Selecting this option brings up a window asking you to
+ select a threshold. If the percentage identity between any
+ two sequences (under the current alignment) exceeds this
+ value then one of the sequences (the shorter) is discarded.
+ Press the "Apply" button to remove redundant
+ sequences. The "Undo" button will undo the last
+ redundancy deletion.</em></li>
+ <li><strong>Pad Gaps<br>
+ </strong><em>When selected, the alignment will be kept at minimal
+ width (so there are no empty columns before or after the
+ first or last aligned residue) and all sequences will be
+ padded with gap characters before and after their
+ terminating residues.<br> This switch is useful when
+ making a tree using unaligned sequences and when working
+ with alignment analysis programs which require 'properly
+ aligned sequences' to be all the same length.<br> You
+ may set the default for <strong>Pad Gaps</strong> in the <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Select</strong>
+ <ul>
+ <li><a href="../features/search.html"><strong>Find...
+ (Control F)</strong></a><br> <em>Opens the Find dialog box to
+ search for residues, sequence name or residue position
+ within the alignment and create new sequence features from
+ the queries. </em>
+ <li><strong>Select All (Control A)</strong><strong><br>
+ </strong><em>Selects all the sequences and residues in the
+ alignment. <br> Use <CTRL> and A (<APPLE>
+ and A on a MacOSX) to select all.
+ </em></em></li>
+ <li><strong>Deselect All (Escape)<br>
+ </strong><em>Removes the current selection box (red dashed box) from
+ the alignment window. All selected sequences, residues and
+ marked columns will be deselected. </em><em> <br> Use
+ <ESCAPE> to deselect all.
+ </em></li>
+ <li><strong>Invert Sequence Selection (Control I)<br>
+ </strong><em>Any sequence ids currently not selected will replace
+ the current selection. </em></li>
+ <li><strong>Invert Column Selection (Control Alt
+ I)<br>
+ </strong><em>Any columns currently not selected will replace the
+ current column selection. </em></li>
+ <li><strong>Create Group (Control G)<br></strong> <em>Create
+ a group containing the currently selected sequences.</em></li>
+ <li><strong>Remove Group (Shift Control G)<br></strong>
+ <em>Ungroup the currently selected sequence group.</em></li>
+ <li><strong>Make Groups for selection<br /></strong> <em>The
+ currently selected groups of the alignment will be
+ subdivided according to the contents of the currently
+ selected region. <br />Use this to subdivide an alignment
+ based on the different combinations of residues at marked
+ columns.
+ </em></li>
+ <li><strong>Undefine Groups (Control U)<br>
+ </strong><em>The alignment will be reset with no defined groups.<br>
+ <strong>WARNING</strong>: This cannot be undone.
+ </em></li>
+ <li><strong><a
+ href="../features/columnFilterByAnnotation.html"
+ >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select
+ or Hide columns in the alignment according to secondary
+ structure, labels and values shown in alignment annotation
+ rows. </em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>New View (Control T)</strong><em><br>
+ Creates a new view from the current alignment view. </em></li>
+ <li><strong>Expand Views (X)</strong><em><br>
+ Display each view associated with the alignment in its own
+ alignment window, allowing several views to be displayed
+ simultaneously. </em></li>
+ <li><strong>Gather Views (G)</strong><em><br>
+ Each view associated with the alignment will be displayed
+ within its own tab on the current alignment window. </em></li>
+ <li><strong>Show→(all Columns / Sequences /
+ Sequences and Columns)</strong><em><br> All hidden Columns
+ / Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences /
+ Selected Region / All but Selected Region )</strong><em><br>
+ Hides the all the currently selected Columns / Sequences /
+ Region or everything but the selected Region.</em></li>
+ <li><strong>Automatic Scrolling<br>
+ </strong><em>When selected, the view will automatically scroll to
+ display the highlighted sequence position corresponding to
+ the position under the mouse pointer in a linked alignment
+ or structure view.</em></li>
+ <li><strong>Show Sequence Features</strong><br> <em>Show
+ or hide sequence features on this alignment.</em></li>
+ <li><strong><a
+ href="../features/featuresettings.html"
+ >Sequence Feature Settings...</a> </strong><em><br> <em>Opens
+ the Sequence Feature Settings dialog box to control the
+ colour and display of sequence features on the alignment,
+ and configure and retrieve features from DAS annotation
+ servers.</em></li>
+ <li><strong>Sequence ID Tooltip</strong><em>
+ (application only) <br>This submenu's options allow the
+ inclusion or exclusion of non-positional sequence features
+ or database cross references from the tooltip shown when the
+ mouse hovers over the sequence ID panel.
+ </em></li>
+ <li><strong>Alignment Properties...<br />
+ </strong><em>Displays some simple statistics computed for the
+ current alignment view and any named properties defined on
+ the whole alignment.</em></li>
+ <li><strong><a href="../features/overview.html">Overview
+ Window</a><br> </strong><em>A scaled version of the alignment
+ will be displayed in a small window. A red box will indicate
+ the currently visible area of the alignment. Move the
+ visible region using the mouse. </em></li>
+ </ul></li>
+ <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+ <ul>
+ <li><strong>Show Annotations<br>
+ </strong><em>If this is selected the "Annotation Panel"
+ will be displayed below the alignment. The default setting
+ is to display the conservation calculation, quality
+ calculation and consensus values as bar charts. </em></li>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole
+ (for example, Consensus, or secondary structure prediction
+ from alignment).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><em>You can also selectively show or hide
+ annotations from the <a href="./popupMenu.html">Popup</a> or
+ <a href="../features/annotation.html">Annotation</a> menus.
+ </em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort
+ sequence-specific annotations by sequence order in the
+ alignment (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort
+ sequence-specific annotations by label (and within that, by
+ sequence order). If neither sort order is selected, no
+ sorting is applied, allowing you to make a manual ordering
+ of the annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br>
+ </strong><em>Settings for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em> Show
+ autocalculated annotations above sequence-specific
+ annotations. Note this also applies to other annotations
+ for the alignment, for example secondary structure
+ prediction from alignment.</em></li>
+ <li><strong>Show last<br></strong><em> Show
+ autocalculated / alignment annotations below
+ sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br>
+ </strong><em> When ticked, any modification to the current
+ settings will be applied to all autocalculated
+ annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br>
+ </strong><em> Enable or disable the display of the histogram
+ above the consensus sequence.</em></li>
+ <li><strong>Show Consensus Logo<br>
+ </strong><em> Enable or disable the display of the Consensus
+ Logo above the consensus sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same
+ height, making it easier to compare symbol diversity in
+ highly variable regions.</em></li>
+ <li><strong>Group Conservation<br>
+ </strong><em> When ticked, display a conservation row for all
+ groups (only available for protein alignments).</em></li>
+ <li><strong>Group Consensus<br>
+ </strong><em> When ticked, display a consensus row for all
+ groups.</em></li>
+ </ul></li>
+ </ul></li>
+ <li><strong>Alignment Window Format Menu</strong>
+ <ul>
+ <li><strong>Font...<br>
+ </strong><em>Opens the "Choose Font" dialog box, in order
+ to change the font of the display and enable or disable
+ 'smooth fonts' (anti-aliasing) for faster alignment
+ rendering. </em></li>
+ <li><strong>Wrap<br>
+ </strong><em>When ticked, the alignment display is "<a
+ href="../features/wrap.html"
+ >wrapped</a>" to the width of the alignment window. This is
+ useful if your alignment has only a few sequences to view
+ its full width at once.
+ </em><br> Additional options for display of sequence numbering
+ and scales are also visible in wrapped layout mode:<br>
+ <ul>
+ <li><strong>Scale Above</strong><br>
+ <em> Show the alignment column position scale.</em></li>
+ <li><strong>Scale Left</strong><br>
+ <em> Show the sequence position for the first aligned
+ residue in each row in the left column of the alignment.</em></li>
+ <li><strong>Scale Right</strong><br>
+ <em> Show the sequence position for the last aligned
+ residue in each row in the right-most column of the
+ alignment.</em></li>
+ <li><strong>Show Sequence Limits<br>
+ </strong><em>If this box is selected the sequence name will have
+ the start and end position of the sequence appended to
+ the name, in the format NAME/START-END</em></li>
+ <li><strong>Right Align Sequence ID<br>
+ </strong><em>If this box is selected then the sequence names
+ displayed in the sequence label area will be aligned
+ against the left-hand edge of the alignment display,
+ rather than the left-hand edge of the alignment window.
+ </li>
+ <li><strong>Show Hidden Markers<br>
+ </strong><em>When this box is selected, positions in the
+ alignment where rows and columns are hidden will be
+ marked by blue arrows. </li>
+ <li><strong>Boxes</strong><em><br> If this is
+ selected the background of a residue will be coloured
+ using the selected background colour. Useful if used in
+ conjunction with "Colour Text." </em></li>
+ <li><strong>Text<br>
+ </strong><em>If this is selected the residues will be displayed
+ using the standard 1 character amino acid alphabet.</em></li>
+ <li><strong>Colour Text<br>
+ </strong><em>If this is selected the residues will be coloured
+ according to the background colour associated with that
+ residue. The colour is slightly darker than background
+ so the amino acid symbol remains visible. </em></li>
+ <li><strong>Show Gaps<br>
+ </strong><em>When this is selected, gap characters will be
+ displayed as "." or "-". If
+ unselected, then gap characters will appear as blank
+ spaces. <br> You may set the default gap character
+ in <a href="../features/preferences.html">preferences</a>.
+ </em></li>
+ <li><strong>Centre Annotation Labels<br>
+ </strong><em>Select this to center labels along an annotation
+ row relative to their associated column (default is off,
+ i.e. left-justified).</em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all consensus sequence
+ symbols will be rendered as a '.', highlighting
+ mutations in highly conserved alignments. </em></li>
- </ul></li>
- </ul>
- </li>
+ </ul></li>
+ </ul></li>
- </ul>
- </li>
+ </ul>
+ </li>
- <li><strong>Colour</strong>
- <ul>
- <li><strong>Apply Colour To All Groups<br> </strong><em>If
- this is selected, any changes made to the background colour will
- be applied to all currently defined groups.<br> </em>
- </li>
- <li><strong><a href="../colourSchemes/textcolour.html">Colour
- Text...</a> </strong><em><br> Opens the Colour Text dialog box to
- set a different text colour for light and dark background, and the
- intensity threshold for transition between them. </em>
- </li>
- <li>Colour Scheme options: <strong>None, ClustalX,
- Blosum62 Score, Percentage Identity, Zappo, Taylor,
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn
- Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
- <a href="../colourSchemes/index.html">colours</a> for a
- description of all colour schemes.</em><br></li>
- <li><strong>By Conservation<br> </strong><em>See <a
- href="../colourSchemes/conservation.html">Colouring by
- Conservation</a>.</em><br></li>
- <li><strong>Modify Conservation Threshold<br> </strong><em>Use
- this to display the conservation threshold slider window. Useful
- if the window has been closed, or if the 'by conservation' option
- appears to be doing nothing!</em><br></li>
- <li><strong>Above Identity Threshold<br> </strong><em>See
- <a href="../colourSchemes/abovePID.html">Above Percentage
- Identity</a> </em><strong>.<br> </strong>
- </li>
- <li><strong>Modify Identity Threshold<br> </strong><em>Use
- this to set the threshold value for colouring above Identity.
- Useful if the window has been closed.<br> </em>
- </li>
- <li><strong>By Annotation</strong><br> <em>Colours
- the alignment on a per-column value from a specified annotation.
- See <a href="../colourSchemes/annotationColouring.html">Annotation
- Colouring</a>.</em><br></li>
- <li><strong>By RNA Helices</strong><br>
- <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
- <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
- Colouring</a>.</em><br>
- </li>
- </ul></li>
- <li><strong>Calculate</strong>
- <ul>
- <li><strong>Sort </strong>
- <ul>
- <li><strong>by ID</strong><em><br> This will sort
- the sequences according to sequence name. If the sort is
- repeated, the order of the sorted sequences will be inverted. </em>
- </li>
- <li><strong>by Length</strong><em><br> This will
- sort the sequences according to their length (excluding gap
- characters). If the sort is repeated, the order of the sorted
- sequences will be inverted. </em></li>
- <li><strong>by Group</strong><strong><br> </strong><em>This
- will sort the sequences according to sequence name. If the sort
- is repeated, the order of the sorted sequences will be inverted.
- </em><strong></strong></li>
- <li><strong>by Pairwise Identity<br> </strong><em>This
- will sort the selected sequences by their percentage identity to
- the consensus sequence. The most similar sequence is put at the
- top. </em></li>
- <li><em>The <a href="../calculations/sorting.html">Sort
- menu</a> will have some additional options if you have just done a
- multiple alignment calculation, or opened a tree viewer window.</em><br>
- </li>
- </ul>
- </li>
+ <li><strong>Colour</strong>
+ <ul>
+ <li><strong>Apply Colour To All Groups<br>
+ </strong><em>If this is selected, any changes made to the background
+ colour will be applied to all currently defined groups.<br>
+ </em></li>
+ <li><strong><a
+ href="../colourSchemes/textcolour.html"
+ >Colour Text...</a> </strong><em><br> Opens the Colour Text
+ dialog box to set a different text colour for light and dark
+ background, and the intensity threshold for transition between
+ them. </em></li>
+ <li>Colour Scheme options: <strong>None, ClustalX,
+ Blosum62 Score, Percentage Identity, Zappo, Taylor,
+ Hydrophobicity, Helix Propensity, Strand Propensity, Turn
+ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+ Defined<br>
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
+ for a description of all colour schemes.
+ </em><br></li>
+ <li><strong>By Conservation<br>
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+ by Conservation</a>.
+ </em><br></li>
+ <li><strong>Modify Conservation Threshold<br>
+ </strong><em>Use this to display the conservation threshold slider
+ window. Useful if the window has been closed, or if the 'by
+ conservation' option appears to be doing nothing!</em><br></li>
+ <li><strong>Above Identity Threshold<br>
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above
+ Percentage Identity</a>
+ </em><strong>.<br>
+ </strong></li>
+ <li><strong>Modify Identity Threshold<br>
+ </strong><em>Use this to set the threshold value for colouring above
+ Identity. Useful if the window has been closed.<br>
+ </em></li>
+ <li><strong>By Annotation</strong><br> <em>Colours
+ the alignment on a per-column value from a specified
+ annotation. See <a
+ href="../colourSchemes/annotationColouring.html"
+ >Annotation Colouring</a>.
+ </em><br></li>
+ <li><strong>By RNA Helices</strong><br> <em>Colours
+ the helices of an RNA alignment loaded from a Stockholm file.
+ See <a href="../colourSchemes/rnahelicesColouring.html">RNA
+ Helices Colouring</a>.
+ </em><br></li>
+ </ul></li>
+ <li><strong>Calculate</strong>
+ <ul>
+ <li><strong>Sort </strong>
+ <ul>
+ <li><strong>by ID</strong><em><br> This will
+ sort the sequences according to sequence name. If the sort
+ is repeated, the order of the sorted sequences will be
+ inverted. </em></li>
+ <li><strong>by Length</strong><em><br> This
+ will sort the sequences according to their length
+ (excluding gap characters). If the sort is repeated, the
+ order of the sorted sequences will be inverted. </em></li>
+ <li><strong>by Group</strong><strong><br> </strong><em>This
+ will sort the sequences according to sequence name. If the
+ sort is repeated, the order of the sorted sequences will
+ be inverted. </em><strong></strong></li>
+ <li><strong>by Pairwise Identity<br>
+ </strong><em>This will sort the selected sequences by their
+ percentage identity to the consensus sequence. The most
+ similar sequence is put at the top. </em></li>
+ <li><em>The <a href="../calculations/sorting.html">Sort
+ menu</a> will have some additional options if you have just
+ done a multiple alignment calculation, or opened a tree
+ viewer window.
+ </em><br></li>
+ </ul></li>
<li><strong>Calculate Tree </strong> <br> <em>Functions
for calculating trees on the alignment or the currently
selected region. See <a href="../calculations/tree.html">calculating
</ul> <strong>Note: Since Version 2.8.1, a number of
additional similarity measures for tree calculation are
provided in this menu.</strong></li>
- <li><strong>Pairwise Alignments</strong><br> <em>Applies
- Smith and Waterman algorithm to selected sequences. See <a
- href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
- </li>
- <li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on similarity scores calculated with
- the alignment. See <a href="../calculations/pca.html">Principal
- Component Analysis</a>.</em> <br>
- </li>
- <li><strong>Extract Scores ... (optional)</strong><br> <em>This
- option is only visible if Jalview detects one or more white-space
- separated values in the description line of the alignment
- sequences.<br> When selected, these numbers are parsed into
- sequence associated annotation which can then be used to sort the
- alignment via the Sort by→Score menu.</em> <br>
- </li>
- <li><strong>Autocalculate Consensus</strong><br> <em>For
- large alignments it can be useful to deselect "Autocalculate
- Consensus" when editing. This prevents the sometimes lengthy
- calculations performed after each sequence edit.</em> <br>
- </li>
- <li><strong>Sort With New Tree</strong><br> <em>When
- enabled, Jalview will automatically sort the alignment when a new
- tree is calculated or loaded onto it.</em> <br></li>
- <li><strong>Show Flanking Regions</strong><br> <em>Opens
- a new alignment window showing any additional sequence data either
- side of the current alignment. Useful in conjunction with 'Fetch
- Database References' when the 'Trim Retrieved Sequences' option is
- disabled to retrieve full length sequences for a set of aligned
- peptides. </em></li>
- </ul></li>
+ <li><strong>Pairwise Alignments</strong><br> <em>Applies
+ Smith and Waterman algorithm to selected sequences. See <a
+ href="../calculations/pairwise.html"
+ >pairwise alignments</a>.
+ </em><br></li>
+ <li><strong>Principal Component Analysis</strong><br> <em>Shows
+ a spatial clustering of the sequences based on similarity
+ scores calculated with the alignment. See <a
+ href="../calculations/pca.html"
+ >Principal Component Analysis</a>.
+ </em> <br></li>
+ <li><strong>Extract Scores ... (optional)</strong><br> <em>This
+ option is only visible if Jalview detects one or more
+ white-space separated values in the description line of the
+ alignment sequences.<br> When selected, these numbers are
+ parsed into sequence associated annotation which can then be
+ used to sort the alignment via the Sort by→Score menu.
+ </em> <br></li>
+ <li><strong>Autocalculate Consensus</strong><br> <em>For
+ large alignments it can be useful to deselect
+ "Autocalculate Consensus" when editing. This
+ prevents the sometimes lengthy calculations performed after
+ each sequence edit.</em> <br></li>
+ <li><strong>Sort With New Tree</strong><br> <em>When
+ enabled, Jalview will automatically sort the alignment when a
+ new tree is calculated or loaded onto it.</em> <br></li>
+ <li><strong>Show Flanking Regions</strong><br> <em>Opens
+ a new alignment window showing any additional sequence data
+ either side of the current alignment. Useful in conjunction
+ with 'Fetch Database References' when the 'Trim Retrieved
+ Sequences' option is disabled to retrieve full length
+ sequences for a set of aligned peptides. </em></li>
+ </ul></li>
- <li><strong>Web Service Menu</strong><br /> <em>This menu
- is dynamic, and may contain user-defined web service entries in
- addition to any of the following ones:</em>
- <ul>
- <li><strong>Fetch DB References</strong><br> <em>This
- submenu contains options for accessing any of the database services
- that Jalview is aware of (e.g. DAS sequence servers and the
- WSDBFetch service provided by the EBI) to verify sequence start/end
- positions and retrieve all database cross references and PDB ids
- associated with all or just the selected sequences in the alignment.
+ <li><strong>Web Service Menu</strong><br /> <em>This menu
+ is dynamic, and may contain user-defined web service entries in
+ addition to any of the following ones:</em>
+ <ul>
+ <li><strong>Fetch DB References</strong><br> <em>This
+ submenu contains options for accessing any of the database
+ services that Jalview is aware of (e.g. DAS sequence servers
+ and the WSDBFetch service provided by the EBI) to verify
+ sequence start/end positions and retrieve all database cross
+ references and PDB ids associated with all or just the
+ selected sequences in the alignment.
+ <ul>
+ <li>'Trim Retrieved Sequences' - when checked, Jalview
+ will discard any additional sequence data for accessions
+ associated with sequences in the alignment. <br> <strong>Note:
+ Disabling this could cause out of memory errors when
+ working with genomic sequence records !</strong><br> <strong>Added
+ in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against
+ the EBI databases plus any active DAS sequence sources<</li>
+ </ul> Other sub-menus allow you to pick a specific source to query
+ - sources are listed alphabetically according to their
+ nickname.
+ </em><br></li>
+ </ul>
+ <p>Selecting items from the following submenus will start a
+ remote service on compute facilities at the University of Dundee,
+ or elsewhere. You need a continuous network connection in order to
+ use these services through Jalview.</p>
+ <ul>
+ <li><strong>Alignment</strong><br />
+ <em> Align the currently selected sequences or all sequences
+ in the alignment, or re-align unaligned sequences to the
+ aligned sequences. Entries in this menu provide access to the
+ various alignment programs supported by <a
+ href="../webServices/JABAWS.html"
+ >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
+ Sequence Alignment webservice client</a> entry for more
+ information.
+ </em></li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <ul>
+ <li><strong>JPred Secondary Structure Prediction</strong><br>
+ <em>Secondary structure prediction by network
+ consensus. See the <a href="../webServices/jnet.html">Jpred3</a>
+ client entry for more information. The behaviour of this
+ calculation depends on the current selection:
+ <ul>
+ <li>If nothing is selected, and the displayed
+ sequences appear to be aligned, then a JNet prediction
+ will be run for the first sequence in the alignment,
+ using the current alignment. Otherwise the first
+ sequence will be submitted for prediction.</li>
+ <li>If just one sequence (or a region on one
+ sequence) has been selected, it will be submitted to
+ the automatic JNet prediction server for homolog
+ detection and prediction.</li>
+ <li>If a set of sequences are selected, and they
+ appear to be aligned, then the alignment will be used
+ for a Jnet prediction on the <strong>first</strong>
+ sequence in the set (that is, the one that appears
+ first in the alignment window).
+ </li>
+ </ul>
+ </em>
+ </ul></li>
+ <li><strong>Analysis</strong><br />
<ul>
- <li>'Trim Retrieved Sequences' - when checked, Jalview will
- discard any additional sequence data for accessions associated with
- sequences in the alignment. <br> <strong>Note: Disabling this
- could cause out of memory errors when working with genomic
- sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
- </li>
- <li>'Standard Databases' will check sequences against the EBI
- databases plus any active DAS sequence sources<</li>
- </ul> Other sub-menus allow you to pick a specific source to query -
- sources are listed alphabetically according to their nickname.
- </em><br></li>
- </ul>
- <p>Selecting items from the following submenus will start a
- remote service on compute facilities at the University of Dundee, or
- elsewhere. You need a continuous network connection in order to use
- these services through Jalview.
- </p>
- <ul>
- <li><strong>Alignment</strong><br /><em> Align the currently
- selected sequences or all sequences in the alignment, or re-align
- unaligned sequences to the aligned sequences. Entries in this menu
- provide access to the various alignment programs supported by <a
- href="../webServices/JABAWS.html">JABAWS</a>. See the <a
- href="../webServices/msaclient.html">Multiple Sequence
- Alignment webservice client</a> entry for more information.</em></li>
- <li><strong>Secondary Structure Prediction</strong>
- <ul>
- <li><strong>JPred Secondary Structure Prediction</strong><br>
- <em>Secondary structure prediction by network consensus. See
- the <a href="../webServices/jnet.html">Jpred3</a> client entry for
- more information. The behaviour of this calculation depends on
- the current selection:
- <ul>
- <li>If nothing is selected, and the displayed sequences
- appear to be aligned, then a JNet prediction will be run for
- the first sequence in the alignment, using the current
- alignment. Otherwise the first sequence will be submitted for
- prediction.</li>
- <li>If just one sequence (or a region on one sequence) has
- been selected, it will be submitted to the automatic JNet
- prediction server for homolog detection and prediction.</li>
- <li>If a set of sequences are selected, and they appear to
- be aligned, then the alignment will be used for a Jnet
- prediction on the <strong>first</strong> sequence in the set
- (that is, the one that appears first in the alignment window).
- </li>
- </ul> </em>
- </ul></li>
- <li><strong>Analysis</strong><br />
- <ul>
- <li><strong>Multi-Harmony</strong><br> <em>Performs
- functional residue analysis on a protein family alignment with
- sub-families defined on it. See the <a
- href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
- information.</em>
- </li>
- </ul></li>
- </ul></li>
- </ul>
+ <li><strong>Multi-Harmony</strong><br> <em>Performs
+ functional residue analysis on a protein family alignment
+ with sub-families defined on it. See the <a
+ href="../webServices/shmr.html"
+ >Multi-Harmony service</a> entry for more information.
+ </em></li>
+ </ul></li>
+ </ul></li>
+ </ul>
</body>
</html>
</head>
<body>
-<p><strong>Alignment Window Annotations Menu</strong> (Since Jalview 2.8.2)</p>
-<ul>
- <li><strong>Show Alignment Related</strong><em><br>
- Show all annotations that are for the alignment as a whole (for example, Consensus,
- or secondary structure prediction from alignment)).</em></li>
- <li><strong>Hide Alignment Related</strong><em><br>
- Hide all annotations that are for the alignment as a whole.</em></li>
- <li><strong>Show Sequence Related</strong><em><br>
- Show all annotations that are for individual sequences.</em></li>
- <li><strong>Hide Sequence Related</strong><em><br>
- Hide all annotations that are for individual sequences.</em></li>
- <li><strong>Show Alignment Related</strong><em><br>
- Show all annotations that are for the alignment as a whole (for example, Consensus).</em></li>
- <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
- or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
- <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
- (and within that, by label).</em></li>
- <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
- (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
- allowing you to make a manual ordering of the annotations.</em></li>
- <li><strong>Autocalculated Annotation<br> </strong><em>Settings
- for the display of autocalculated annotation.</em>
- <ul>
- <li><strong>Show first<br></strong><em>
- Show autocalculated annotations above sequence-specific annotations.
- Note this also applies to other annotations for the alignment, for example secondary
- structure prediction from alignment.</em></li>
- <li><strong>Show last<br></strong><em>
- Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, any modification to the current settings will be applied
- to all autocalculated annotation.</em></li>
- <li><strong>Show Consensus Histogram<br> </strong><em>
- Enable or disable the display of the histogram above the
- consensus sequence.</em></li>
- <li><strong>Show Consensus Logo<br> </strong><em> Enable
- or disable the display of the Consensus Logo above the consensus
- sequence.</em></li>
- <li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.</em></li>
- <li><strong>Group Conservation<br> </strong><em> When
- ticked, display a conservation row for all groups (only available
- for protein alignments).</em></li>
- <li><strong>Group Consensus<br> </strong><em> When
- ticked, display a consensus row for all groups.</em></li>
- </ul>
- </li>
-</ul>
-<p> </p>
+ <p>
+ <strong>Alignment Window Annotations Menu</strong> (Since Jalview
+ 2.8.2)
+ </p>
+ <ul>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for
+ example, Consensus, or secondary structure prediction from
+ alignment)).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for
+ example, Consensus).</em></li>
+ <li><em>You can also selectively show or hide annotations
+ from the <a href="./popupMenu.html">Popup</a> or <a
+ href="../features/annotation.html"
+ >Annotation</a> menus.
+ </em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort
+ sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort
+ sequence-specific annotations by label (and within that, by
+ sequence order). If neither sort order is selected, no sorting
+ is applied, allowing you to make a manual ordering of the
+ annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br>
+ </strong><em>Settings for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em> Show
+ autocalculated annotations above sequence-specific
+ annotations. Note this also applies to other annotations for
+ the alignment, for example secondary structure prediction
+ from alignment.</em></li>
+ <li><strong>Show last<br></strong><em> Show
+ autocalculated / alignment annotations below
+ sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br>
+ </strong><em> When ticked, any modification to the current settings
+ will be applied to all autocalculated annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br>
+ </strong><em> Enable or disable the display of the histogram above
+ the consensus sequence.</em></li>
+ <li><strong>Show Consensus Logo<br>
+ </strong><em> Enable or disable the display of the Consensus Logo
+ above the consensus sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same
+ height, making it easier to compare symbol diversity in
+ highly variable regions.</em></li>
+ <li><strong>Group Conservation<br>
+ </strong><em> When ticked, display a conservation row for all groups
+ (only available for protein alignments).</em></li>
+ <li><strong>Group Consensus<br>
+ </strong><em> When ticked, display a consensus row for all groups.</em></li>
+ </ul></li>
+ </ul>
+ <p> </p>
</body>
</html>
<title>Annotation Panel Menus</title>
</head>
<body>
-<p><strong>Annotation Panel Menus</strong></p>
-<ul>
- <li> <strong>Annotation Label Popup Menu</strong><br>
- <em>This menu is opened by clicking anywhere on the annotation row labels
- area (below the sequence ID area).</em>
- <ul>
- <li><strong>Add New Row</strong><br>
- <em>Adds a new, named annotation row (a dialog box will pop up for you
- to enter the label for the new row). </em> </li>
- <li><strong>Edit Label/Description</strong><br>
- <em>This opens a dialog where you can change the name (displayed label), or the description
- (as shown on the label tooltip) of the clicked annotation. </em> </li>
- <li><strong>Hide This Row</strong><br>
- <em>Hides the annotation row whose label was clicked in order to bring up
- the menu.</em> </li>
- <li><strong>Hide All <em><label></em></strong><br>
- <em>Hides all annotation rows whose label matches the one clicked.
- (This option is only shown for annotations that relate to individual sequences,
- not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
- <li><strong>Delete Row</strong><br>
- <em>Deletes the annotation row whose label was clicked in order to bring
- up the menu.</em> </li>
- <li><strong>Show All Hidden Rows</strong><br>
- <em>Shows all hidden annotation rows.</em> </li>
- <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
- <em>Annotations can be saved to file or output to a text window in either the
- Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
- <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
- <em>Opens a text box with a list of comma-separated values corresponding
- to the annotation (numerical or otherwise) at each position in the row.
- This is useful to export alignment quality measurements for further analysis.</em>
- </li>
- </ul>
- <em>The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:</em>
- <ul>
-
- <li><strong>Ignore Gaps in Consensus</strong><br>
- If this checkbox is selected, all consensus calculations performed in
- the current Alignment window will be done without counting gaps as a consensus
- character.</li>
+ <p>
+ <strong>Annotation Panel Menus</strong>
+ </p>
+ <ul>
+ <li><strong>Annotation Label Popup Menu</strong><br> <em>This
+ menu is opened by clicking anywhere on the annotation row labels
+ area (below the sequence ID area).</em>
+ <ul>
+ <li><strong>Add New Row</strong><br> <em>Adds a
+ new, named annotation row (a dialog box will pop up for you
+ to enter the label for the new row). </em></li>
+ <li><strong>Edit Label/Description</strong><br> <em>This
+ opens a dialog where you can change the name (displayed
+ label), or the description (as shown on the label tooltip)
+ of the clicked annotation. </em></li>
+ <li><strong>Hide This Row</strong><br> <em>Hides
+ the annotation row whose label was clicked in order to bring
+ up the menu.</em></li>
+ <li><strong>Hide All <em><label></em></strong><br>
+ <em>Hides all annotation rows whose label matches the one
+ clicked. (This option is only shown for annotations that
+ relate to individual sequences, not for whole alignment
+ annotations. Since Jalview 2.8.2.)</em></li>
+ <li><strong>Delete Row</strong><br> <em>Deletes
+ the annotation row whose label was clicked in order to bring
+ up the menu.</em></li>
+ <li><strong>Show All Hidden Rows</strong><br> <em>Shows
+ all hidden annotation rows.</em></li>
+ <li><strong>Export Annotation</strong> <em>(Application
+ only)</em><br> <em>Annotations can be saved to file or
+ output to a text window in either the Jalview annotations
+ format or as a spreadsheet style set of comma separated
+ values (CSV). </em></li>
+ <li><strong>Show Values in Text Box</strong> <em>(applet
+ only)</em><br> <em>Opens a text box with a list of
+ comma-separated values corresponding to the annotation
+ (numerical or otherwise) at each position in the row. This
+ is useful to export alignment quality measurements for
+ further analysis.</em></li>
+ </ul> <em>The following additional entries are available when the
+ popup menu is opened on a consensus sequence annotation row:</em>
+ <ul>
+
+ <li><strong>Ignore Gaps in Consensus</strong><br> If
+ this checkbox is selected, all consensus calculations
+ performed in the current Alignment window will be done without
+ counting gaps as a consensus character.</li>
<li><strong>Show Consensus Histogram<br></strong>
- Enable or disable the display of the histogram above the consensus sequence.
- </li>
- <li>
- <strong>Show Consensus Logo<br></strong>
- Enable or disable the display of the sequence logo above the consensus sequence.
- </li>
+ Enable or disable the display of the histogram above the
+ consensus sequence.</li>
+ <li><strong>Show Consensus Logo<br></strong> Enable or
+ disable the display of the sequence logo above the consensus
+ sequence.</li>
<li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.</em></li>
+ </strong><em>When enabled, scales all logo stacks to the same
+ height, making it easier to compare symbol diversity in
+ highly variable regions.</em></li>
<li>
- <li><strong>Copy Consensus Sequence</strong><br>
- Copies the consensus sequence to the clipboard in Fasta format, to allow
- the consensus sequence to be added to an alignment. Note the copied sequence
- is not accessible to other programs if Jalview is running as an applet
- in a web page.</li>
- </ul>
- </li>
- <li><strong>Annotation Popup Menu<br>
- </strong><em>This menu is opened when right-clicking on the selected positions
- of an annotation.</em>
- <ul>
- <li><strong>Helix</strong><br>
- <em>Mark selected positions with a helix glyph (a red oval), and optional
- text label (see below). Consecutive ovals will be rendered as an unbroken
- red line.</em> </li>
- <li><strong>Sheet</strong><br>
- <em>Mark selected positions with a sheet glyph (a green arrow oriented
- from left to right), and optional text label (see below). Consecutive
- arrows will be joined together to form a single green arrow.</em> </li>
- <li><strong>Label</strong><br>
- <em>Sets the text label at the selected positions. If more that one consecutive
- position is marked with the same label, only the first position's label
- will be rendered.</em> </li>
- <li><strong>Colour</strong><br>
- <em>Changes the colour of the annotation text label.</em> </li>
- <li><strong>Remove Annotation</strong><br>
- <em>Blanks any annotation at the selected positions on the row. Note:
- <strong>This cannot be undone</strong></em> </li>
- </ul>
- </li>
-</ul>
+ <li><strong>Copy Consensus Sequence</strong><br>
+ Copies the consensus sequence to the clipboard in Fasta
+ format, to allow the consensus sequence to be added to an
+ alignment. Note the copied sequence is not accessible to other
+ programs if Jalview is running as an applet in a web page.</li>
+ </ul></li>
+ <li><strong>Annotation Popup Menu<br>
+ </strong><em>This menu is opened when right-clicking on the selected
+ positions of an annotation.</em>
+ <ul>
+ <li><strong>Helix</strong><br> <em>Mark selected
+ positions with a helix glyph (a red oval), and optional text
+ label (see below). Consecutive ovals will be rendered as an
+ unbroken red line.</em></li>
+ <li><strong>Sheet</strong><br> <em>Mark selected
+ positions with a sheet glyph (a green arrow oriented from
+ left to right), and optional text label (see below).
+ Consecutive arrows will be joined together to form a single
+ green arrow.</em></li>
+ <li><strong>Label</strong><br> <em>Sets the text
+ label at the selected positions. If more that one
+ consecutive position is marked with the same label, only the
+ first position's label will be rendered.</em></li>
+ <li><strong>Colour</strong><br> <em>Changes the
+ colour of the annotation text label.</em></li>
+ <li><strong>Remove Annotation</strong><br> <em>Blanks
+ any annotation at the selected positions on the row. Note: <strong>This
+ cannot be undone</strong>
+ </em></li>
+ </ul></li>
+ </ul>
</body>
</html>
</head>
<body>
- <p>
- <strong>Alignment Window Calculate Menu</strong>
- </p>
- <ul>
- <li><strong>Sort </strong>
- <ul>
- <li><strong>By ID</strong><em><br> This will sort the
- sequences according to sequence name. If the sort is repeated, the
- order of the sorted sequences will be inverted. </em>
- </li>
- <li><strong>By Length</strong><em><br> This will sort
- the sequences according to their length (excluding gap
- characters). If the sort is repeated, the order of the sorted
- sequences will be inverted. </em>
- </li>
- <li><strong>By Group</strong><strong><br> </strong><em>This
- will sort the sequences according to sequence name. If the sort is
- repeated, the order of the sorted sequences will be inverted. </em><strong></strong>
- </li>
- <li><strong>By Pairwise Identity<br> </strong><em>This
- will sort the selected sequences by their percentage identity to
- the consensus sequence. The most similar sequence is put at the
- top. </em>
- </li>
- <li><em>The <a href="../calculations/sorting.html">Sort
- menu</a> will have some additional options if the alignment has any
- associated score annotation, or you have just done a multiple
- alignment calculation or opened a tree viewer window.</em><br></li>
- </ul></li>
+ <p>
+ <strong>Alignment Window Calculate Menu</strong>
+ </p>
+ <ul>
+ <li><strong>Sort </strong>
+ <ul>
+ <li><strong>By ID</strong><em><br> This will sort
+ the sequences according to sequence name. If the sort is
+ repeated, the order of the sorted sequences will be
+ inverted. </em></li>
+ <li><strong>By Length</strong><em><br> This will
+ sort the sequences according to their length (excluding gap
+ characters). If the sort is repeated, the order of the
+ sorted sequences will be inverted. </em></li>
+ <li><strong>By Group</strong><strong><br> </strong><em>This
+ will sort the sequences according to sequence name. If the
+ sort is repeated, the order of the sorted sequences will be
+ inverted. </em><strong></strong></li>
+ <li><strong>By Pairwise Identity<br>
+ </strong><em>This will sort the selected sequences by their
+ percentage identity to the consensus sequence. The most
+ similar sequence is put at the top. </em></li>
+ <li><em>The <a href="../calculations/sorting.html">Sort
+ menu</a> will have some additional options if the alignment
+ has any associated score annotation, or you have just done a
+ multiple alignment calculation or opened a tree viewer
+ window.
+ </em><br></li>
+ </ul></li>
<li><strong>Calculate Tree </strong> <br> <em>Functions
for calculating trees on the alignment or the currently selected
region. See <a href="../calculations/tree.html">calculating
<li><strong>Average Distance Using % Identity</strong></li>
</ul></li>
<li><strong>Pairwise Alignments</strong><br> <em>Applies
- Smith and Waterman algorithm to selected sequences. See <a
- href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
- </li>
- <li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on similarity scores calculated over the alignment.. See <a href="../calculations/pca.html">Principal
- Component Analysis</a>.</em> <br></li>
- <li><strong>Extract Scores ... (optional)</strong><br> <em>This
- option is only visible if Jalview detects one or more white-space
- separated values in the description line of the alignment sequences.<br>
- When selected, these numbers are parsed into sequence associated
- annotation which can then be used to sort the alignment via the Sort
- by→Score menu.</em> <br></li>
- <li><strong>Translate as cDNA</strong> (not applet)<br><em>This option is visible for nucleotide alignments.
- Selecting this option shows the DNA's calculated protein product in a new <a href="../features/splitView.html">split frame</a> window. Note that the
- translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
- standard <a href="../misc/geneticCode.html">genetic code</a> (any incomplete final codon is discarded).
- You can perform this action on the whole alignment,
- or selected rows, columns, or regions.</em> <br></li>
- <li><strong>Get Cross-References</strong> (not applet)<br><em>This option is visible where sequences have cross-references to
- other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
- Select the database to view all cross-referenced sequences in a new <a href="../features/splitView.html">split frame</a> window.</em> <br></li>
- <li><strong>Autocalculate Consensus</strong><br> <em>For
- large alignments it can be useful to deselect "Autocalculate
- Consensus" when editing. This prevents the sometimes lengthy
- calculations performed after each sequence edit.</em> <br></li>
- <li><strong>Sort Alignment With New Tree</strong><br> <em>If
- this option is selected, the alignment will be automatically sorted
- whenever a new tree is calculated or loaded.</em> <br>
- </li>
+ Smith and Waterman algorithm to selected sequences. See <a
+ href="../calculations/pairwise.html"
+ >pairwise alignments</a>.
+ </em><br></li>
+ <li><strong>Principal Component Analysis</strong><br> <em>Shows
+ a spatial clustering of the sequences based on similarity scores
+ calculated over the alignment.. See <a
+ href="../calculations/pca.html"
+ >Principal Component Analysis</a>.
+ </em> <br></li>
+ <li><strong>Extract Scores ... (optional)</strong><br> <em>This
+ option is only visible if Jalview detects one or more
+ white-space separated values in the description line of the
+ alignment sequences.<br> When selected, these numbers are
+ parsed into sequence associated annotation which can then be
+ used to sort the alignment via the Sort by→Score menu.
+ </em> <br></li>
+ <li><strong>Translate as cDNA</strong> (not applet)<br>
+ <em>This option is visible for nucleotide alignments. Selecting
+ this option shows the DNA's calculated protein product in a new
+ <a href="../features/splitView.html">split frame</a> window.
+ Note that the translation is not frame- or intron-aware; it
+ simply translates all codons in each sequence, using the
+ standard <a href="../misc/geneticCode.html">genetic code</a>
+ (any incomplete final codon is discarded). You can perform this
+ action on the whole alignment, or selected rows, columns, or
+ regions.
+ </em> <br></li>
+ <li><strong>Get Cross-References</strong> (not applet)<br>
+ <em>This option is visible where sequences have
+ cross-references to other standard databases; for example, an
+ EMBL entry may have cross-references to one or more UNIPROT
+ entries. Select the database to view all cross-referenced
+ sequences in a new <a href="../features/splitView.html">split
+ frame</a> window.
+ </em> <br></li>
+ <li><strong>Autocalculate Consensus</strong><br> <em>For
+ large alignments it can be useful to deselect
+ "Autocalculate Consensus" when editing. This prevents
+ the sometimes lengthy calculations performed after each sequence
+ edit.</em> <br></li>
+ <li><strong>Sort Alignment With New Tree</strong><br> <em>If
+ this option is selected, the alignment will be automatically
+ sorted whenever a new tree is calculated or loaded.</em> <br></li>
<li><strong>Show Flanking Regions</strong><br> <em>Opens
a new alignment window showing any additional sequence data
either side of the current alignment. Useful in conjunction with
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Alignment Window Menus</title></head>
+<head>
+<title>Alignment Window Menus</title>
+</head>
<body>
-<p><strong>Alignment Window Colour Menu</strong></p>
+ <p>
+ <strong>Alignment Window Colour Menu</strong>
+ </p>
<ul>
<li><strong>Apply Colour To All Groups<br>
- </strong><em>If this is selected, any changes made to the background colour
- will be applied to all currently defined groups.<br>
- </em></li>
- <li><strong><a href="../colourSchemes/textcolour.html">Colour
- Text ...</a></strong><em><br>
- Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
- </em></li>
- <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
- Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
- Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br>
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
- a description of all colour schemes.</em><br>
+ </strong><em>If this is selected, any changes made to the background
+ colour will be applied to all currently defined groups.<br>
+ </em></li>
+ <li><strong><a href="../colourSchemes/textcolour.html">Colour
+ Text ...</a></strong><em><br> Opens the Colour Text dialog box to
+ set a different text colour for light and dark background, and
+ the intensity threshold for transition between them. </em></li>
+ <li>Colour Scheme options: <strong>None, ClustalX,
+ Blosum62 Score, Percentage Identity, Zappo, Taylor,
+ Hydrophobicity, Helix Propensity, Strand Propensity, Turn
+ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+ Defined<br>
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
+ a description of all colour schemes.
+ </em><br>
</li>
<li><strong>By Conservation<br>
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
- by Conservation</a>.</em><br>
- </li>
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+ by Conservation</a>.
+ </em><br></li>
<li><strong>Modify Conservation Threshold<br>
- </strong><em>Use this to display the conservation threshold slider window.
- Useful if the window has been closed, or if the 'by conservation' option
- appears to be doing nothing!</em><br>
- </li>
+ </strong><em>Use this to display the conservation threshold slider
+ window. Useful if the window has been closed, or if the 'by
+ conservation' option appears to be doing nothing!</em><br></li>
<li><strong>Above Identity Threshold<br>
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
- Identity</a></em><strong>.<br>
- </strong></li>
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above
+ Percentage Identity</a></em><strong>.<br>
+ </strong></li>
<li><strong>Modify Identity Threshold<br>
- </strong><em>Use this to set the threshold value for colouring above Identity.
- Useful if the window has been closed.<br>
- </em></li>
- <li><strong>By Annotation</strong><br>
- <em>Colours the alignment on a per-column value from a specified annotation.
- See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
- </li>
- <li><strong>By RNA Helices</strong><br>
- <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
- <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
- Colouring</a>.</em><br>
- </li>
+ </strong><em>Use this to set the threshold value for colouring above
+ Identity. Useful if the window has been closed.<br>
+ </em></li>
+ <li><strong>By Annotation</strong><br> <em>Colours
+ the alignment on a per-column value from a specified annotation.
+ See <a href="../colourSchemes/annotationColouring.html">Annotation
+ Colouring</a>.
+ </em><br></li>
+ <li><strong>By RNA Helices</strong><br> <em>Colours
+ the helices of an RNA alignment loaded from a Stockholm file.
+ See <a href="../colourSchemes/rnahelicesColouring.html">RNA
+ Helices Colouring</a>.
+ </em><br></li>
</ul>
</body>
</html>
</head>
<body>
-<p><strong>Alignment Window Edit Menu</strong></p>
-<ul>
- <li><strong>Undo (Control Z)</strong><em><br>
- This will undo any edits you make to the alignment. This applies to
- insertion or deletion of gaps, cutting residues or sequences from the
- alignment or pasting sequences to the current alignment or sorting the
- alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
- adjustments to group sizes, or changes to the annotation panel. </em></li>
- <li><strong>Redo (Control Y)<br>
- </strong><em>Any actions which you undo can be redone using redo. </em></li>
- <li><strong>Cut (Control X)<br>
- </strong><em>This will make a copy of the currently selected residues
- before removing them from your alignment. Click on a sequence name if
- you wish to select a whole sequence. <br>
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
- <li><strong>Copy (Control C)</strong><br>
- <em>Copies the currently selected residues to the system clipboard
- - you can also do this by pressing <CTRL> and C (<APPLE>
- and C on MacOSX). <br>
- If you try to paste the clipboard contents to a text editor, you will
- see the format of the copied residues FASTA.</em></li>
- <li><strong>Paste </strong>
- <ul>
- <li><strong>To New Alignment (Control Shift V)<br>
- </strong><em>A new alignment window will be created from sequences
- previously copied or cut to the system clipboard. <br>
- Use <CTRL> and <SHIFT> and V(<APPLE> and
- <SHIFT;> and and V on MacOSX) to paste.</em></li>
- <li><strong>Add To This Alignment (Control V)<br>
- </strong><em>Copied sequences from another alignment window can be added
- to the current Jalview alignment. </em></li>
- </ul>
- </li>
- <li><strong>Delete (Backspace)<br>
- </strong><em>This will delete the currently selected residues without
- copying them to the clipboard. Like the other edit operations, this can
- be undone with <strong>Undo</strong>.</em></li>
- <li><strong>Remove Left (Control L)<br>
- </strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the left of the leftmost marked column. To mark a column,
- mouse click the scale bar above the alignment. Click again to unmark a
- column, or select "Deselect All" to deselect all columns.</em></li>
- <li><strong>Remove Right (Control R)<br>
- </strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the left of the leftmost marked column. To mark a column,
- mouse click the scale bar above the alignment. Click again to unmark a
- column, or select "Deselect All" to deselect all columns.</em></li>
- <li><strong>Remove Empty Columns (Control E)<br>
- </strong><em>All columns which only contain gap characters ("-",
- ".") will be deleted.<br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>. </em></li>
- <li><strong>Remove All Gaps (Control Shift E)</strong><br>
- <em>Gap characters ("-", ".") will be deleted
- from the selected area of the alignment. If no selection is made, ALL
- the gaps in the alignment will be removed.<br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>. </em></li>
- <li><strong>Remove Redundancy (Control D)<br>
- </strong><em>Selecting this option brings up a window asking you to select
- a threshold. If the percentage identity between any two sequences
- (under the current alignment) exceeds this value then one of the
- sequences (the shorter) is discarded. Press the "Apply"
- button to remove redundant sequences. The "Undo" button will
- undo the last redundancy deletion.</em></li>
- <li><strong>Pad Gaps<br>
- </strong><em>When selected, the alignment will be kept at minimal width (so
- there are no empty columns before or after the first or last aligned
- residue) and all sequences will be padded with gap characters
- before and after their terminating residues.<br>
- This switch is useful when making a tree using unaligned sequences and
- when working with alignment analysis programs which require 'properly
- aligned sequences' to be all the same length.<br>
- You may set the default for <strong>Pad Gaps</strong> in the <a
- href="../features/preferences.html">preferences</a>. </em></li>
-</ul>
+ <p>
+ <strong>Alignment Window Edit Menu</strong>
+ </p>
+ <ul>
+ <li><strong>Undo (Control Z)</strong><em><br> This
+ will undo any edits you make to the alignment. This applies to
+ insertion or deletion of gaps, cutting residues or sequences
+ from the alignment or pasting sequences to the current alignment
+ or sorting the alignment. <strong>NOTE:</strong> It DOES NOT
+ undo colour changes, adjustments to group sizes, or changes to
+ the annotation panel. </em></li>
+ <li><strong>Redo (Control Y)<br>
+ </strong><em>Any actions which you undo can be redone using redo. </em></li>
+ <li><strong>Cut (Control X)<br>
+ </strong><em>This will make a copy of the currently selected residues
+ before removing them from your alignment. Click on a sequence
+ name if you wish to select a whole sequence. <br> Use
+ <CTRL> and X (<APPLE> and X on MacOSX) to cut.
+ </em></li>
+ <li><strong>Copy (Control C)</strong><br> <em>Copies
+ the currently selected residues to the system clipboard - you
+ can also do this by pressing <CTRL> and C (<APPLE>
+ and C on MacOSX). <br> If you try to paste the clipboard
+ contents to a text editor, you will see the format of the copied
+ residues FASTA.
+ </em></li>
+ <li><strong>Paste </strong>
+ <ul>
+ <li><strong>To New Alignment (Control Shift V)<br>
+ </strong><em>A new alignment window will be created from sequences
+ previously copied or cut to the system clipboard. <br>
+ Use <CTRL> and <SHIFT> and V(<APPLE> and
+ <SHIFT;> and and V on MacOSX) to paste.
+ </em></li>
+ <li><strong>Add To This Alignment (Control V)<br>
+ </strong><em>Copied sequences from another alignment window can be
+ added to the current Jalview alignment. </em></li>
+ </ul></li>
+ <li><strong>Delete (Backspace)<br>
+ </strong><em>This will delete the currently selected residues without
+ copying them to the clipboard. Like the other edit operations,
+ this can be undone with <strong>Undo</strong>.
+ </em></li>
+ <li><strong>Remove Left (Control L)<br>
+ </strong><em>If the alignment has marked columns, the alignment will be
+ trimmed to the left of the leftmost marked column. To mark a
+ column, mouse click the scale bar above the alignment. Click
+ again to unmark a column, or select "Deselect All" to
+ deselect all columns.</em></li>
+ <li><strong>Remove Right (Control R)<br>
+ </strong><em>If the alignment has marked columns, the alignment will be
+ trimmed to the left of the leftmost marked column. To mark a
+ column, mouse click the scale bar above the alignment. Click
+ again to unmark a column, or select "Deselect All" to
+ deselect all columns.</em></li>
+ <li><strong>Remove Empty Columns (Control E)<br>
+ </strong><em>All columns which only contain gap characters
+ ("-", ".") will be deleted.<br> You may
+ set the default gap character in <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ <li><strong>Remove All Gaps (Control Shift E)</strong><br>
+ <em>Gap characters ("-", ".") will be
+ deleted from the selected area of the alignment. If no selection
+ is made, ALL the gaps in the alignment will be removed.<br>
+ You may set the default gap character in <a
+ href="../features/preferences.html"
+ >preferences</a>.
+ </em></li>
+ <li><strong>Remove Redundancy (Control D)<br>
+ </strong><em>Selecting this option brings up a window asking you to
+ select a threshold. If the percentage identity between any two
+ sequences (under the current alignment) exceeds this value then
+ one of the sequences (the shorter) is discarded. Press the
+ "Apply" button to remove redundant sequences. The
+ "Undo" button will undo the last redundancy deletion.</em></li>
+ <li><strong>Pad Gaps<br>
+ </strong><em>When selected, the alignment will be kept at minimal width
+ (so there are no empty columns before or after the first or last
+ aligned residue) and all sequences will be padded with gap
+ characters before and after their terminating residues.<br>
+ This switch is useful when making a tree using unaligned
+ sequences and when working with alignment analysis programs
+ which require 'properly aligned sequences' to be all the same
+ length.<br> You may set the default for <strong>Pad
+ Gaps</strong> in the <a href="../features/preferences.html">preferences</a>.
+ </em></li>
+ </ul>
</body>
</html>
</head>
<body>
-<p><strong>Alignment Window File Menu</strong></p>
-<ul>
- <li><strong>Fetch Sequence</strong><br>
- <em>Shows a dialog window in which you can select known ids from
- Uniprot, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services provided by
- the European Bioinformatics Institute. See <a
- href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
- <li><strong>Add Sequences</strong><em><br>
- Add sequences to the visible alignment from file, URL, or cut &
- paste window </em></li>
- <li><strong>Reload</strong><em><br>
- Reloads the alignment from the original file, if available.<br>
- <strong>Warning: This will delete any edits, analyses and
- colourings applied since the alignment was last saved, and cannot be
- undone.</strong></em></li>
- <li><strong>Save (Control S)</strong><em><br>
- Saves the alignment to the file it was loaded from (if available), in
- the same format, updating the original in place. </em></li>
- <li><strong>Save As (Control Shift S)<br>
- </strong><em>Save the alignment to local file. A file selection window will
- open, use the "Files of type:" selection box to determine
- which <a href="../io/index.html">alignment format</a> to save as.</em></li>
- <li><strong>Output to Textbox<br>
- </strong><em>The alignment will be displayed in plain text in a new window,
- which you can "Copy and Paste" using the pull down menu, or
- your standard operating system copy and paste keys. The output window
- also has a <strong>"New Window"</strong> button to import the
- (possibly edited) text as a new alignment.<br>
- Select the format of the text by selecting one of the following menu
- items.</em>
- <ul>
- <li><strong>FASTA</strong> <em></em></li>
- <li><strong>MSF</strong></li>
- <li><strong>CLUSTAL</strong></li>
- <li><strong>BLC</strong></li>
- <li><strong>PIR</strong></li>
- <li><strong>PFAM</strong></li>
- <li><strong>PileUp</strong></li>
- <li><strong>AMSA</strong></li>
- <li><strong>STH</strong></li>
- <li><strong>PHYLIP</strong></li>
- <li><strong>JSON</strong></li>
- </ul>
- </li>
- <li><strong>Page Setup ...</strong><br>
- <em>Open the printing system's Page Setup dialog box, to
- control page size, layout and orientation.</em></li>
- <li><strong>Print (Control P)<br>
- </strong><em>Jalview will print the alignment using the current fonts and
- colours of your alignment. If the alignment has annotations visible,
- these will be printed below the alignment. If the alignment is wrapped
- the number of residues per line of your alignment will depend on the
- paper width or your alignment window width, whichever is the smaller. </em></li>
- <li><strong>Export Image</strong> <em><br>
- Creates an alignment graphic with the current view's annotation,
- alignment background colours and group colours. If the alignment is <a
- href="../features/wrap.html">wrapped</a>, the output will also be
- wrapped and will have the same visible residue width as the open
- alignment. </em>
- <ul>
- <li><strong>HTML<br>
- </strong><em>Create a <a href="../io/export.html">web page</a> from your
- alignment.</em></li>
- <li><strong>EPS<br>
- </strong><em>Create an <a href="../io/export.html">Encapsulated
- Postscript</a> file from your alignment.</em></li>
- <li><strong>PNG<br>
- </strong><em>Create a <a href="../io/export.html">Portable Network
- Graphics</a> file from your alignment.</em></li>
- <li><strong>SVG<br>
- </strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
- <li><strong>BioJS<br>
- </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
- </ul>
- </li>
- <li><strong>Export Features</strong><em><br>
- All features visible on the alignment can be saved to file or displayed
- in a textbox in either Jalview or GFF format</em></li>
- <li><strong>Export Annotations</strong><em><br>
- All annotations visible on the alignment can be saved to file or
- displayed in a textbox in Jalview annotations format. </em></li>
- <li><strong>Load Associated Tree<br>
- </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
- trees</a> stored in the Newick file format, and associate them with the
- alignment. Note: the ids of the tree file and your alignment MUST be
- the same.</em></li>
- <li><strong>Load Features / Annotations<br>
- </strong><em>Load files describing precalculated <a
- href="../features/featuresFormat.html">sequence features</a> or <a
- href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
- <li><strong>Close (Control W)</strong><br>
- <em>Close the alignment window. Make sure you have saved your
- alignment before you close - either as a Jalview project or by using
- the <strong>Save As</strong> menu.</em></li>
-</ul>
+ <p>
+ <strong>Alignment Window File Menu</strong>
+ </p>
+ <ul>
+ <li><strong>Fetch Sequence</strong><br> <em>Shows a
+ dialog window in which you can select known ids from Uniprot,
+ EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services
+ provided by the European Bioinformatics Institute. See <a
+ href="../features/seqfetch.html"
+ >Sequence Fetcher</a>
+ </em>.</li>
+ <li><strong>Add Sequences</strong><em><br> Add
+ sequences to the visible alignment from file, URL, or cut &
+ paste window </em></li>
+ <li><strong>Reload</strong><em><br> Reloads the
+ alignment from the original file, if available.<br> <strong>Warning:
+ This will delete any edits, analyses and colourings applied
+ since the alignment was last saved, and cannot be undone.</strong></em></li>
+ <li><strong>Save (Control S)</strong><em><br> Saves
+ the alignment to the file it was loaded from (if available), in
+ the same format, updating the original in place. </em></li>
+ <li><strong>Save As (Control Shift S)<br>
+ </strong><em>Save the alignment to local file. A file selection window
+ will open, use the "Files of type:" selection box to
+ determine which <a href="../io/index.html">alignment format</a>
+ to save as.
+ </em></li>
+ <li><strong>Output to Textbox<br>
+ </strong><em>The alignment will be displayed in plain text in a new
+ window, which you can "Copy and Paste" using the pull
+ down menu, or your standard operating system copy and paste
+ keys. The output window also has a <strong>"New
+ Window"</strong> button to import the (possibly edited) text as a
+ new alignment.<br> Select the format of the text by
+ selecting one of the following menu items.
+ </em>
+ <ul>
+ <li><strong>FASTA</strong> <em></em></li>
+ <li><strong>MSF</strong></li>
+ <li><strong>CLUSTAL</strong></li>
+ <li><strong>BLC</strong></li>
+ <li><strong>PIR</strong></li>
+ <li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>PHYLIP</strong></li>
+ <li><strong>JSON</strong></li>
+ </ul></li>
+ <li><strong>Page Setup ...</strong><br> <em>Open the
+ printing system's Page Setup dialog box, to control page size,
+ layout and orientation.</em></li>
+ <li><strong>Print (Control P)<br>
+ </strong><em>Jalview will print the alignment using the current fonts
+ and colours of your alignment. If the alignment has annotations
+ visible, these will be printed below the alignment. If the
+ alignment is wrapped the number of residues per line of your
+ alignment will depend on the paper width or your alignment
+ window width, whichever is the smaller. </em></li>
+ <li><strong>Export Image</strong> <em><br> Creates an
+ alignment graphic with the current view's annotation, alignment
+ background colours and group colours. If the alignment is <a
+ href="../features/wrap.html"
+ >wrapped</a>, the output will also be wrapped and will have the same
+ visible residue width as the open alignment. </em>
+ <ul>
+ <li><strong>HTML<br>
+ </strong><em>Create a <a href="../io/export.html">web page</a> from
+ your alignment.
+ </em></li>
+ <li><strong>EPS<br>
+ </strong><em>Create an <a href="../io/export.html">Encapsulated
+ Postscript</a> file from your alignment.
+ </em></li>
+ <li><strong>PNG<br>
+ </strong><em>Create a <a href="../io/export.html">Portable
+ Network Graphics</a> file from your alignment.
+ </em></li>
+ <li><strong>SVG<br>
+ </strong><em>Create a <a href="../io/export.html">Scalable
+ Vector Graphics</a> file from your alignment for embedding in
+ web pages.
+ </em></li>
+ <li><strong>BioJS<br>
+ </strong><em>Create a <a href="../io/export.html">BioJS MSA
+ Viewer HTML </a> file from your alignment.
+ </em></li>
+ </ul></li>
+ <li><strong>Export Features</strong><em><br> All
+ features visible on the alignment can be saved to file or
+ displayed in a textbox in either Jalview or GFF format</em></li>
+ <li><strong>Export Annotations</strong><em><br> All
+ annotations visible on the alignment can be saved to file or
+ displayed in a textbox in Jalview annotations format. </em></li>
+ <li><strong>Load Associated Tree<br>
+ </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
+ trees</a> stored in the Newick file format, and associate them
+ with the alignment. Note: the ids of the tree file and your
+ alignment MUST be the same.
+ </em></li>
+ <li><strong>Load Features / Annotations<br>
+ </strong><em>Load files describing precalculated <a
+ href="../features/featuresFormat.html"
+ >sequence features</a> or <a
+ href="../features/annotationsFormat.html"
+ >alignment annotations</a>.
+ </em></li>
+ <li><strong>Close (Control W)</strong><br> <em>Close
+ the alignment window. Make sure you have saved your alignment
+ before you close - either as a Jalview project or by using the <strong>Save
+ As</strong> menu.
+ </em></li>
+ </ul>
</body>
</html>
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<p><strong>Alignment Window Format Menu</strong></p>
+<p>
+ <strong>Alignment Window Format Menu</strong>
+</p>
<ul>
- <li><strong>Font...</strong><br>
- <em>Opens the "Choose Font" dialog box, in order to change the font
- of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster
- alignment rendering. </em></em></li>
+ <li><strong>Font...</strong><br> <em>Opens the
+ "Choose Font" dialog box, in order to change the font of
+ the display and enable or disable 'smooth fonts' (anti-aliasing)
+ for faster alignment rendering. </em></em></li>
<li><strong>Wrap<br>
- </strong><em>When ticked, the alignment display is "<a
- href="../features/wrap.html">wrapped</a>" to the width of the alignment
- window. This is useful if your alignment has only a few sequences to view
- its full width at once.<br>
- Additional options for display of sequence numbering and scales are also visible
- in wrapped layout mode:</em>
+ </strong><em>When ticked, the alignment display is "<a
+ href="../features/wrap.html"
+ >wrapped</a>" to the width of the alignment window. This is
+ useful if your alignment has only a few sequences to view its full
+ width at once.<br> Additional options for display of sequence
+ numbering and scales are also visible in wrapped layout mode:
+ </em>
<ul>
- <li><strong>Scale Left</strong><br>
- <em>Show the sequence position for the first aligned residue in each row
- in the left column of the alignment.</em></li>
- <li><strong>Scale Right</strong><br>
- <em>Show the sequence position for the last aligned residue in each row
- in the right-most column of the alignment.</em></li>
- <li><strong>Scale Above</strong><br>
- <em>Show the alignment column position scale.</em></li>
+ <li><strong>Scale Left</strong><br> <em>Show the
+ sequence position for the first aligned residue in each row in
+ the left column of the alignment.</em></li>
+ <li><strong>Scale Right</strong><br> <em>Show the
+ sequence position for the last aligned residue in each row in
+ the right-most column of the alignment.</em></li>
+ <li><strong>Scale Above</strong><br> <em>Show the
+ alignment column position scale.</em></li>
</ul>
<li><strong>Show Sequence Limits<br>
- </strong><em>If this box is selected the sequence name will have the start
- and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
+ </strong><em>If this box is selected the sequence name will have the start
+ and end position of the sequence appended to the name, in the
+ format NAME/START-END</em></li>
<li><strong>Right Align Sequence ID<br>
- </strong> <em>If this box is selected then the sequence names displayed in
- the sequence label area will be aligned against the left-hand edge of the
- alignment display, rather than the left-hand edge of the alignment window.</em></li>
+ </strong> <em>If this box is selected then the sequence names displayed in
+ the sequence label area will be aligned against the left-hand edge
+ of the alignment display, rather than the left-hand edge of the
+ alignment window.</em></li>
<li><strong>Show Hidden Markers<br>
- </strong><em>When this box is selected, positions in the alignment where rows
- and columns are hidden will be marked by blue arrows.</em></li>
- <li><strong>Boxes</strong><em><br>
- If this is selected the background of a residue will be coloured using the
- selected background colour. Useful if used in conjunction with "Colour
- Text." </em></li>
+ </strong><em>When this box is selected, positions in the alignment where
+ rows and columns are hidden will be marked by blue arrows.</em></li>
+ <li><strong>Boxes</strong><em><br> If this is selected
+ the background of a residue will be coloured using the selected
+ background colour. Useful if used in conjunction with "Colour
+ Text." </em></li>
<li><strong>Text<br>
- </strong><em>If this is selected the residues will be displayed using the
- standard 1 character amino acid alphabet.</em></li>
+ </strong><em>If this is selected the residues will be displayed using the
+ standard 1 character amino acid alphabet.</em></li>
<li><strong>Colour Text<br>
- </strong><em>If this is selected the residues will be coloured according to
- the background colour associated with that residue. The colour is slightly
- darker than background so the amino acid symbol remains visible. </em></li>
+ </strong><em>If this is selected the residues will be coloured according
+ to the background colour associated with that residue. The colour
+ is slightly darker than background so the amino acid symbol
+ remains visible. </em></li>
<li><strong>Show Gaps<br>
- </strong><em>When this is selected, gap characters will be displayed as "."
- or "-". If unselected, then gap characters will appear as blank
- spaces. <br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>.</em></li>
- <li><strong>Centre Column Labels<br>
- </strong><em>When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
- </em></li>
- <li><strong>Show Unconserved<br>
- </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
- </em></li>
-
+ </strong><em>When this is selected, gap characters will be displayed as
+ "." or "-". If unselected, then gap characters
+ will appear as blank spaces. <br> You may set the default gap
+ character in <a href="../features/preferences.html">preferences</a>.
+ </em></li>
+ <li><strong>Centre Column Labels<br>
+ </strong><em>When this is selected, the text labels within each annotation
+ row will be centred on the column that they are associated with. </em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all consensus sequence symbols will be
+ rendered as a '.', highlighting mutations in highly conserved
+ alignments. </em></li>
+
</ul>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><body>
-<p><strong>Alignment Window Select Menu</strong></p>
-<ul>
-
- <li><a href="../features/search.html"><strong>Find... (Control F)</strong></a><br>
- <em>Opens the Find dialog box to search for residues, sequence name or residue
- position within the alignment and create new sequence features from the queries.
+<head>
+<body>
+ <p>
+ <strong>Alignment Window Select Menu</strong>
+ </p>
+ <ul>
+
+ <li><a href="../features/search.html"><strong>Find...
+ (Control F)</strong></a><br> <em>Opens the Find dialog box to
+ search for residues, sequence name or residue position within
+ the alignment and create new sequence features from the queries.
</em>
- <li><strong>Select All (Control A)</strong><strong><br>
+ <li><strong>Select All (Control A)</strong><strong><br>
</strong><em>Selects all the sequences and residues in the alignment. <br>
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></em></li>
- <li><strong>Deselect All (Escape)<br>
- </strong><em>Removes the current selection box (red dashed box) from the
- alignment window. All selected sequences, residues and marked columns
- will be deselected. </em><em> <br>
- Use <ESCAPE> to deselect all.</em></li>
- <li><strong>Invert Sequence Selection (Control I)<br>
- </strong><em>Any sequence ids currently not selected will replace the
- current selection. </em></li>
- <li><strong>Invert Column Selection (Control Alt I)<br>
- </strong><em>Any columns currently not selected will replace the current
- column selection. </em></li>
- <li><strong>Create Group (Control G)<br></strong>
- <em>Create a group containing the currently selected sequences.</em></li>
- <li><strong>Remove Group (Shift Control G)<br></strong>
- <em>Ungroup the currently selected sequence group.</em></li>
- <li><strong>Make Groups for selection<br /></strong> <em>The
- currently selected groups of the alignment will be subdivided
- according to the contents of the currently selected region. <br />Use
- this to subdivide an alignment based on the different combinations
- of residues at marked columns.
- </em></li>
- <li><strong>Undefine Groups (Control U)<br>
- </strong><em>The alignment will be reset with no defined groups.<br>
- <strong>WARNING</strong>: This cannot be undone.</em></li>
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to
+ select all.
+ </em></em></li>
+ <li><strong>Deselect All (Escape)<br>
+ </strong><em>Removes the current selection box (red dashed box) from the
+ alignment window. All selected sequences, residues and marked
+ columns will be deselected. </em><em> <br> Use
+ <ESCAPE> to deselect all.
+ </em></li>
+ <li><strong>Invert Sequence Selection (Control I)<br>
+ </strong><em>Any sequence ids currently not selected will replace the
+ current selection. </em></li>
+ <li><strong>Invert Column Selection (Control Alt I)<br>
+ </strong><em>Any columns currently not selected will replace the current
+ column selection. </em></li>
+ <li><strong>Create Group (Control G)<br></strong> <em>Create
+ a group containing the currently selected sequences.</em></li>
+ <li><strong>Remove Group (Shift Control G)<br></strong> <em>Ungroup
+ the currently selected sequence group.</em></li>
+ <li><strong>Make Groups for selection<br /></strong> <em>The
+ currently selected groups of the alignment will be subdivided
+ according to the contents of the currently selected region. <br />Use
+ this to subdivide an alignment based on the different
+ combinations of residues at marked columns.
+ </em></li>
+ <li><strong>Undefine Groups (Control U)<br>
+ </strong><em>The alignment will be reset with no defined groups.<br>
+ <strong>WARNING</strong>: This cannot be undone.
+ </em></li>
<li><strong><a
- href="../features/columnFilterByAnnotation.html">Select/Hide Columns by Annotation</a></strong> <br />
- <em>Select or Hide columns in the alignment according to
- secondary structure, labels and values shown in alignment
- annotation rows. </em></li>
+ href="../features/columnFilterByAnnotation.html"
+ >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select or
+ Hide columns in the alignment according to secondary structure,
+ labels and values shown in alignment annotation rows. </em></li>
</ul>
</body>
</html>
</head>
<body>
-<p><strong>Alignment Window View Menu</strong></p>
-<ul>
- <li><strong>New View (Control T)</strong><em><br>
- Creates a new view from the current alignment view. </em></li>
- <li><strong>Expand Views (X)</strong><em><br>
- Display each view associated with the alignment in its own alignment window,
- allowing several views to be displayed simultaneously. </em></li>
- <li><strong>Gather Views (G)</strong><em><br>
- Each view associated with the alignment will be displayed within its own tab
- on the current alignment window. </em></li>
- <li><strong>Show→(all Columns / Sequences / Sequences and Columns</strong>)</strong><em><br>
- All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
- <li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region)</strong><em><br>
- Hides the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
- <li><strong>Automatic Scrolling<br>
- </strong><em>When selected, the view will automatically scroll to display the
- highlighted sequence position corresponding to the position under the mouse
- pointer in a linked alignment or structure view.</em>
- </li>
- <li><strong>Show Sequence Features</strong><br>
- <em>Show or hide sequence features on this alignment.</em></li>
- <li><strong><a href="../features/featuresettings.html">Sequence Feature Settings...</a></strong><em><br>
- Opens the Sequence Feature Settings dialog box to control the colour and display
- of sequence features on the alignment, and configure and retrieve features
- from DAS annotation servers.</em></li>
- <li><strong>Sequence ID Tooltip</strong><em> (application only)
- <br>This submenu's options allow the inclusion or exclusion of
- non-positional sequence features or database cross references
- from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
- <li><strong>Alignment Properties...<br>
- </strong><em>Displays some simple statistics computed for the
- current alignment view and any named properties defined on the
- whole alignment.</em></li>
- <li><strong><a href="../features/overview.html">Overview Window</a><br>
- </strong><em>A scaled version of the alignment will be displayed in a small
- window. A red box will indicate the currently visible area of the alignment.
- Move the visible region using the mouse. </em></li>
-</ul>
-<p> </p>
+ <p>
+ <strong>Alignment Window View Menu</strong>
+ </p>
+ <ul>
+ <li><strong>New View (Control T)</strong><em><br>
+ Creates a new view from the current alignment view. </em></li>
+ <li><strong>Expand Views (X)</strong><em><br> Display
+ each view associated with the alignment in its own alignment
+ window, allowing several views to be displayed simultaneously. </em></li>
+ <li><strong>Gather Views (G)</strong><em><br> Each
+ view associated with the alignment will be displayed within its
+ own tab on the current alignment window. </em></li>
+ <li><strong>Show→(all Columns / Sequences /
+ Sequences and Columns</strong>)</strong><em><br> All hidden Columns /
+ Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences /
+ Selected Region / All but Selected Region)</strong><em><br>
+ Hides the currently selected Columns / Sequences / Region or
+ everything but the selected Region.</em></li>
+ <li><strong>Automatic Scrolling<br>
+ </strong><em>When selected, the view will automatically scroll to
+ display the highlighted sequence position corresponding to the
+ position under the mouse pointer in a linked alignment or
+ structure view.</em></li>
+ <li><strong>Show Sequence Features</strong><br> <em>Show
+ or hide sequence features on this alignment.</em></li>
+ <li><strong><a href="../features/featuresettings.html">Sequence
+ Feature Settings...</a></strong><em><br> Opens the Sequence
+ Feature Settings dialog box to control the colour and display of
+ sequence features on the alignment, and configure and retrieve
+ features from DAS annotation servers.</em></li>
+ <li><strong>Sequence ID Tooltip</strong><em> (application
+ only) <br>This submenu's options allow the inclusion or
+ exclusion of non-positional sequence features or database cross
+ references from the tooltip shown when the mouse hovers over the
+ sequence ID panel.
+ </em></li>
+ <li><strong>Alignment Properties...<br>
+ </strong><em>Displays some simple statistics computed for the current
+ alignment view and any named properties defined on the whole
+ alignment.</em></li>
+ <li><strong><a href="../features/overview.html">Overview
+ Window</a><br> </strong><em>A scaled version of the alignment
+ will be displayed in a small window. A red box will indicate the
+ currently visible area of the alignment. Move the visible region
+ using the mouse. </em></li>
+ </ul>
+ <p> </p>
</body>
</html>
</head>
<body>
-<p><strong>Desktop Menus</strong></p>
-<ul>
- <li><em> <strong>File</strong></em>
- <ul>
- <li><strong>Input Alignment from</strong><em> (See more on <a
- href="../io/index.html">file formats</a>) </em>
- <ul>
- <li><strong>File (Control O)</strong><br>
- <em>open file(s) on your local file system</em></li>
- <li><strong>URL</strong><br>
- <em>open a file from a website. The URL MUST start with http://</em></li>
- <li><strong>Textbox</strong><br>
- <em>copy and paste an alignment into a text window</em></li>
- </ul>
- </li>
- <li><strong>Fetch Sequence<br>
- </strong><em>Shows a dialog window in which you can select known ids from
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
- the European Bioinformatics Institute.</em></li>
- <li><strong>Save Project</strong><br>
- <em>Saves all currently open alignment windows with their current
- view settings and any associated trees, as a <a
- href="../features/jalarchive.html">Jalview Archive</a> (which has a
- .jar extension).</em></li>
- <li><strong>Load Project</strong><br>
- <em>Loads Jalview archives <strong>only</strong>.</em></li>
- <li><strong>Quit</strong><br>
- <em>Close Jalview. <br>
- <strong>Note - any annotation you have made on alignments will be lost
- unless you Save your work before quitting.</strong></em><br>
- </li>
- </ul>
- </li>
- <li><strong>Tools</strong>
- <ul>
- <li><strong><a href="../features/preferences.html">Preferences<br>
- </a></strong><em>Change the default visual settings for opening new alignment
- windows.</em></li>
- <li><strong>Show Memory Usage<br></strong>
- <em>When ticked, the currently available memory will be displayed in the
- bottom right of the desktop background area.<br>
- See the <a href="../memory.html">help on Jalview memory settings</a> for more information.</em></li>
- <li><strong>Collect Garbage<br></strong>
- <em>Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
- </em></li>
- <li><strong>Java Console<br/></strong>
- <em>Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.</em></li>
- <li><strong>Jalview News<br/></strong>
- <em>Opens the <a href="../webServices/newsreader.html">Jalview News</a> dialog box. </em></li>
- <li><strong>Groovy Console...<em> (only available if groovy is on the classpath)</em><br></strong>
- <em>Open's the <a href="../groovy.html">Groovy Console</a> for interactive scripting.</em><strong><br></strong></li>
-
- </ul>
- </li>
- <li><strong>Vamsas</strong>
- <em>For more details, read the <a href="../vamsas/index.html">Jalview VAMSAS documentation</a>.<br/>
- When no session is active, the menu provides options for initiating a new VAMSAS session:</em>
- <ul>
- <li><strong>Connect to<br/></strong>
- <em>Connect to one of the existing sessions available.</em></li>
- <li><strong>New VAMSAS session<br/></strong>
- <em>Initiates a new local VAMSAS session.</em></li>
- <li><strong>Load VAMSAS session...<br/></strong>
- <em>Opens a file browser allowing you to choose a VAMSAS document to import into a new local session.</em></li>
- </ul>
- <em>When Jalview is joined to a VAMSAS session, the menu contains the following:</em>
- <ul>
- <li><strong>Session Update<br/></strong>
- <em>Sends alignment data in the Jalview desktop to the VAMSAS session.</em></li>
- <li><strong>Save VAMSAS Session...<br/></strong>
- <em>Saves the current session to a VAMSAS document archive.</em></li>
- <li><strong>Stop VAMSAS Session<br/></strong>
- <em>Disconnects from the current session. You may be asked if you want to save the current session's data if no other VAMSAS clients are connected.</em></li>
- </ul>
- </li>
- <li><strong>Help </strong>
- <ul>
- <li><strong>About<br>
- </strong><em>Displays the version and creation date of the application, as
- well as acknowledgements and a citation reference. </em></li>
- <li><strong>Documentation<br>
- </strong><em>Displays help files as a browseable, searchable set of pages
- with a table of contents. </em><strong><br>
- </strong></li>
- </ul>
- </li>
- <li><strong>Window</strong><br>
- <em>Each time a new window is added to the Jalview Desktop a
- corresponding menu item will be added to the "Window" menu
- that will bring the window to the top of the pile when it is selected.
- <ul>
- <li><strong>Close All</strong><br>
- Close all alignment and analysis windows.<br><strong>Note: This will erase all alignments from memory, and cannot be undone!</strong></li>
- <li><strong>Raise Associated Windows</strong><br>
- Bring all windows associated with the current alignment to the top of the pile.
- </li>
- <li><strong>Minimise Associated Windows</strong><br>
- Hide all windows related to the current alignment behind icons on the Jalview Desktop.
- </ul>
- </em></li>
- </ul>
+ <p>
+ <strong>Desktop Menus</strong>
+ </p>
+ <ul>
+ <li><em> <strong>File</strong></em>
+ <ul>
+ <li><strong>Input Alignment from</strong><em> (See
+ more on <a href="../io/index.html">file formats</a>)
+ </em>
+ <ul>
+ <li><strong>File (Control O)</strong><br> <em>open
+ file(s) on your local file system</em></li>
+ <li><strong>URL</strong><br> <em>open a file
+ from a website. The URL MUST start with http://</em></li>
+ <li><strong>Textbox</strong><br> <em>copy and
+ paste an alignment into a text window</em></li>
+ </ul></li>
+ <li><strong>Fetch Sequence<br>
+ </strong><em>Shows a dialog window in which you can select known ids
+ from Uniprot, EMBL, EMBLCDS or PDB database using Web
+ Services provided by the European Bioinformatics Institute.</em></li>
+ <li><strong>Save Project</strong><br> <em>Saves
+ all currently open alignment windows with their current view
+ settings and any associated trees, as a <a
+ href="../features/jalarchive.html"
+ >Jalview Archive</a> (which has a .jar extension).
+ </em></li>
+ <li><strong>Load Project</strong><br> <em>Loads
+ Jalview archives <strong>only</strong>.
+ </em></li>
+ <li><strong>Quit</strong><br> <em>Close Jalview.
+ <br> <strong>Note - any annotation you have
+ made on alignments will be lost unless you Save your work
+ before quitting.</strong>
+ </em><br></li>
+ </ul></li>
+ <li><strong>Tools</strong>
+ <ul>
+ <li><strong><a href="../features/preferences.html">Preferences<br>
+ </a></strong><em>Change the default visual settings for opening new
+ alignment windows.</em></li>
+ <li><strong>Show Memory Usage<br></strong> <em>When
+ ticked, the currently available memory will be displayed in
+ the bottom right of the desktop background area.<br>
+ See the <a href="../memory.html">help on Jalview memory
+ settings</a> for more information.
+ </em></li>
+ <li><strong>Collect Garbage<br></strong> <em>Selecting
+ this will initiate the Java Virtual Machine garbage
+ collector, which might help free up some memory... perhaps.
+ </em></li>
+ <li><strong>Java Console<br /></strong> <em>Toggles
+ the display of a the Jalview Java Console window. This
+ setting will be remembered in your user preferences.</em></li>
+ <li><strong>Jalview News<br /></strong> <em>Opens the
+ <a href="../webServices/newsreader.html">Jalview News</a>
+ dialog box.
+ </em></li>
+ <li><strong>Groovy Console...<em> (only
+ available if groovy is on the classpath)</em><br></strong> <em>Open's
+ the <a href="../groovy.html">Groovy Console</a> for
+ interactive scripting.
+ </em><strong><br></strong></li>
+
+ </ul></li>
+ <li><strong>Vamsas</strong> <em>For more details, read the
+ <a href="../vamsas/index.html">Jalview VAMSAS documentation</a>.<br />
+ When no session is active, the menu provides options for
+ initiating a new VAMSAS session:
+ </em>
+ <ul>
+ <li><strong>Connect to<br /></strong> <em>Connect to
+ one of the existing sessions available.</em></li>
+ <li><strong>New VAMSAS session<br /></strong> <em>Initiates
+ a new local VAMSAS session.</em></li>
+ <li><strong>Load VAMSAS session...<br /></strong> <em>Opens
+ a file browser allowing you to choose a VAMSAS document to
+ import into a new local session.</em></li>
+ </ul> <em>When Jalview is joined to a VAMSAS session, the menu
+ contains the following:</em>
+ <ul>
+ <li><strong>Session Update<br /></strong> <em>Sends
+ alignment data in the Jalview desktop to the VAMSAS session.</em></li>
+ <li><strong>Save VAMSAS Session...<br /></strong> <em>Saves
+ the current session to a VAMSAS document archive.</em></li>
+ <li><strong>Stop VAMSAS Session<br /></strong> <em>Disconnects
+ from the current session. You may be asked if you want to
+ save the current session's data if no other VAMSAS clients
+ are connected.</em></li>
+ </ul></li>
+ <li><strong>Help </strong>
+ <ul>
+ <li><strong>About<br>
+ </strong><em>Displays the version and creation date of the
+ application, as well as acknowledgements and a citation
+ reference. </em></li>
+ <li><strong>Documentation<br>
+ </strong><em>Displays help files as a browseable, searchable set of
+ pages with a table of contents. </em><strong><br> </strong></li>
+ </ul></li>
+ <li><strong>Window</strong><br> <em>Each time a new
+ window is added to the Jalview Desktop a corresponding menu item
+ will be added to the "Window" menu that will bring the
+ window to the top of the pile when it is selected.
+ <ul>
+ <li><strong>Close All</strong><br> Close all
+ alignment and analysis windows.<br>
+ <strong>Note: This will erase all alignments from
+ memory, and cannot be undone!</strong></li>
+ <li><strong>Raise Associated Windows</strong><br>
+ Bring all windows associated with the current alignment to
+ the top of the pile.</li>
+ <li><strong>Minimise Associated Windows</strong><br>
+ Hide all windows related to the current alignment behind
+ icons on the Jalview Desktop.
+ </ul>
+ </em></li>
+ </ul>
</body>
</html>
</head>
<body>
-<p><strong>Jalview's Menus</strong></p>
-<p>Menus are used in 3 places in Jalview - the "Desktop
-Menu", the "Alignment Menu" and the "Popup
-Menu".</p>
-<p>The <a href="desktopMenu.html">Desktop Menu</a> is always visible
-and is the starting point for loading new alignments.</p>
-<p>The <a href="alignmentMenu.html">Alignment Window Menus</a> are
-accessible once an alignment has been opened.</p>
-<p>The <a href="popupMenu.html">Popup Menus</a> are opened by
-clicking with the right mouse button in the alignment display area or on
-a sequence label in the alignment window.</p>
-<p>The <a href="alwannotationpanel.html">Annotations Menu</a> is opened
-by right-clicking on an annotation row label or in an annotation row.</p>
+ <p>
+ <strong>Jalview's Menus</strong>
+ </p>
+ <p>Menus are used in 3 places in Jalview - the "Desktop
+ Menu", the "Alignment Menu" and the "Popup
+ Menu".</p>
+ <p>
+ The <a href="desktopMenu.html">Desktop Menu</a> is always visible
+ and is the starting point for loading new alignments.
+ </p>
+ <p>
+ The <a href="alignmentMenu.html">Alignment Window Menus</a> are
+ accessible once an alignment has been opened.
+ </p>
+ <p>
+ The <a href="popupMenu.html">Popup Menus</a> are opened by clicking
+ with the right mouse button in the alignment display area or on a
+ sequence label in the alignment window.
+ </p>
+ <p>
+ The <a href="alwannotationpanel.html">Annotations Menu</a> is opened
+ by right-clicking on an annotation row label or in an annotation
+ row.
+ </p>
</body>
</html>
</head>
<body>
- <p>
- <strong>Popup Menu</strong><br> <em>This menu is visible
- when right clicking either within a selected region on the alignment
- or on a selected sequence name. It may not be accessible when in
- 'Cursor Mode' (toggled with the F2 key).</em>
- </p>
- <ul>
- <li><strong>Selection</strong>
- <ul>
- <li><a name="sqreport"><strong>Sequence Details...<br>
- </strong></a><em>(Since Jalview 2.8)<br>Open an <a
- href="../io/exportseqreport.html">HTML report containing the
- annotation and database cross references</a> normally shown in
- the sequence's tooltip.
- </em></li>
- <li><strong>Show Annotations...<br>
- </strong><em>Choose to show (unhide) either All or a selected type of
- annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
- <li><strong>Hide Annotations...<br>
- </strong><em>Choose to hide either All or a selected type of annotation
- for the selected sequences. (Since Jalview 2.8.2)</em></li>
- <li><a name="addrefannot"><strong>Add Reference
- Annotations<br>
- </strong><em>Add to the alignment window any annotations on the
- selected sequences which have been read from reference sources or
- calculated (for example, secondary structure derived from 3D
- structure). (Since Jalview 2.8.2)</em></li>
- <li><strong>Edit </strong>
- <ul>
- <li><strong>Copy</strong><br> <em>Copies the
- selected region. In the applet version, the copied sequences are
- not available to the system clipboard.</em></li>
- <li><strong>Cut<br>
- </strong><em>Cuts the selected region from the alignment. In the
- applet version, the copied sequences are not available to the
- system clipboard.</em></li>
- <li><strong>Edit Sequence</strong><br> <em>Edit the
- selected sequence(s) directly. Spaces will be converted to the
- current gap character.</em></li>
- <li><strong>To Upper Case</strong><em><strong><br>
- </strong><em>Changes the case of selected region to lower case.</em> </em></li>
- <li><strong>To Lower Case<br>
- </strong><em>Changes the case of selected region to upper case.</em><strong>
- </strong></li>
- <li><strong>Toggle Case</strong><br> <em>Switches
- the case of all residues within the selected region.</em></li>
- </ul></li>
- <li><strong>Output to Textbox<br>
- </strong><em>The selection area will be output to a a text window in the
- selected alignment format. </em></li>
- <li><strong><a href="../features/creatinFeatures.html">Create
- Sequence Feature...</a></strong><br> <em>Opens the dialog box for
- creating sequence features over the currently selected region on
- each selected sequence.</em></li>
- <li><strong>Create Group<br>
- </strong><em>This will define a new group from the current selection.</em><strong>
- </strong></li>
- <li><strong>Remove Group<br>
- </strong><em>This will undefine the selected group. </em><strong> </strong></li>
- <li><strong>Edit (New) Group</strong><br> <em>Group
- Editing Menu</em> <br />Options in this menu modify the name and
- display properties of the currently selected group, or a new group
- defined using the current selection.
- <ul>
- <li><strong>Name: <Group></strong> or <strong>Edit
- name and description</strong><br> <em>The first entry in the
- menu displays the name for the currently selected group, if it
- has one. Selecting this option opens a window allowing the name
- and description for this group to be edited. Click OK to set the
- new name and decription, and cancel to leave the existing name
- and description unchanged.</em></li>
- <li><strong>Group Colour<br>
- </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
- of the group.
- </em><strong> </strong></li>
- <li><strong>Boxes<br>
- </strong><em>If selected the background of a residue within the
- selected group will be coloured according to the assigned colour
- scheme.</em><strong> </strong></li>
- <li><strong>Text<br>
- </strong><em>If selected the selected group will display text. </em></li>
- <li><strong>Colour Text<br>
- </strong><em>If selected the selected group will display text in a
- colour slightly darker than the background colour of that
- residue.</em></li>
- <li><strong>Border Colour <br>
- </strong><em>Selecting this will display a "Colour Chooser"
- window. Select a colour than press OK to set the border colour
- of a group.</em></li>
- <li><strong>Show Unconserved<br>
- </strong><em>When this is selected, all symbols in the group matching
- the consensus sequence at that column will be rendered as a '.',
- highlighting mutations in the group area. </em></li>
- </ul></li>
+ <p>
+ <strong>Popup Menu</strong><br> <em>This menu is visible
+ when right clicking either within a selected region on the
+ alignment or on a selected sequence name. It may not be accessible
+ when in 'Cursor Mode' (toggled with the F2 key).</em>
+ </p>
+ <ul>
+ <li><strong>Selection</strong>
+ <ul>
+ <li><a name="sqreport"><strong>Sequence
+ Details...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+ href="../io/exportseqreport.html"
+ >HTML report containing the annotation and database cross
+ references</a> normally shown in the sequence's tooltip.
+ </em></li>
+ <li><strong>Show Annotations...<br>
+ </strong><em>Choose to show (unhide) either All or a selected type
+ of annotation for the selected sequences. (Since Jalview
+ 2.8.2)</em></li>
+ <li><strong>Hide Annotations...<br>
+ </strong><em>Choose to hide either All or a selected type of
+ annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><a name="addrefannot"><strong>Add
+ Reference Annotations<br>
+ </strong><em>Add to the alignment window any annotations on the
+ selected sequences which have been read from reference
+ sources or calculated (for example, secondary structure
+ derived from 3D structure). (Since Jalview 2.8.2)</em></li>
+ <li><strong>Edit </strong>
+ <ul>
+ <li><strong>Copy</strong><br> <em>Copies the
+ selected region. In the applet version, the copied
+ sequences are not available to the system clipboard.</em></li>
+ <li><strong>Cut<br>
+ </strong><em>Cuts the selected region from the alignment. In the
+ applet version, the copied sequences are not available
+ to the system clipboard.</em></li>
+ <li><strong>Edit Sequence</strong><br> <em>Edit
+ the selected sequence(s) directly. Spaces will be
+ converted to the current gap character.</em></li>
+ <li><strong>To Upper Case</strong><em><strong><br>
+ </strong><em>Changes the case of selected region to lower
+ case.</em> </em></li>
+ <li><strong>To Lower Case<br>
+ </strong><em>Changes the case of selected region to upper case.</em><strong>
+ </strong></li>
+ <li><strong>Toggle Case</strong><br> <em>Switches
+ the case of all residues within the selected region.</em></li>
+ </ul></li>
+ <li><strong>Output to Textbox<br>
+ </strong><em>The selection area will be output to a a text window in
+ the selected alignment format. </em></li>
+ <li><strong><a
+ href="../features/creatinFeatures.html"
+ >Create Sequence Feature...</a></strong><br> <em>Opens the
+ dialog box for creating sequence features over the currently
+ selected region on each selected sequence.</em></li>
+ <li><strong>Create Group<br>
+ </strong><em>This will define a new group from the current
+ selection.</em><strong> </strong></li>
+ <li><strong>Remove Group<br>
+ </strong><em>This will undefine the selected group. </em><strong>
+ </strong></li>
+ <li><strong>Edit (New) Group</strong><br> <em>Group
+ Editing Menu</em> <br />Options in this menu modify the name and
+ display properties of the currently selected group, or a new
+ group defined using the current selection.
+ <ul>
+ <li><strong>Name: <Group></strong> or <strong>Edit
+ name and description</strong><br> <em>The first entry
+ in the menu displays the name for the currently selected
+ group, if it has one. Selecting this option opens a
+ window allowing the name and description for this group
+ to be edited. Click OK to set the new name and
+ decription, and cancel to leave the existing name and
+ description unchanged.</em></li>
+ <li><strong>Group Colour<br>
+ </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
+ of the group.
+ </em><strong> </strong></li>
+ <li><strong>Boxes<br>
+ </strong><em>If selected the background of a residue within the
+ selected group will be coloured according to the
+ assigned colour scheme.</em><strong> </strong></li>
+ <li><strong>Text<br>
+ </strong><em>If selected the selected group will display text. </em></li>
+ <li><strong>Colour Text<br>
+ </strong><em>If selected the selected group will display text in
+ a colour slightly darker than the background colour of
+ that residue.</em></li>
+ <li><strong>Border Colour <br>
+ </strong><em>Selecting this will display a "Colour
+ Chooser" window. Select a colour than press OK to
+ set the border colour of a group.</em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all symbols in the group
+ matching the consensus sequence at that column will be
+ rendered as a '.', highlighting mutations in the group
+ area. </em></li>
+ </ul></li>
- </ul></li>
- <li><strong>Sequence Id<br>
- </strong><em>This menu is only visible if you right-click on a sequence
- name. </em>
- <ul>
- <li><a name="sqreport"><strong>Sequence Details
- ...<br>
- </strong></a><em>(Since Jalview 2.8)<br>Open an <a
- href="../io/exportseqreport.html">HTML report containing the
- annotation and database cross references</a> normally shown in the
- sequence's tooltip.
- </em></li>
- <li><strong>Edit Name/Description<br>
- </strong><em>You may edit the name and description of each sequence. A
- window will be displayed asking for a new sequence name and
- sequence description to be entered. Press OK to accept your edit.
- To save sequence descriptions, you must save in Fasta, PIR or
- Jalview File format.</em></li>
- <li><a href="sqaddrefannot"><strong>Add Reference
- Annotations<br>
- </strong><em>When enabled, copies any available alignment annotation
- for this sequence to the current view.</em></li>
- <li><strong>Set as Reference</strong> or <strong>Unmark as Reference</strong><br/>
- Sets or unsets the reference sequence for the the alignment.
- </li>
-
- <li><strong>Represent Group With (Sequence Id)</strong><br>
- <em>All sequences in the current selection group will be
- hidden, apart from (Sequence Id). Any edits performed on the
- visible representative sequence will be propagated to the hidden
- sequences. </em></li>
- <li><a name="sqid.popup"><strong>Link</strong><br> <em>This
- menu item lists all links which have been set up in the <a
- href="../features/preferences.html">Preferences</a> Connections
- tab.<br> Since Jalview 2.4, links will also be made for
- database cross references (where the database name exactly
- matches the link name set up in <a
- href="../features/preferences.html">Preferences</a>). <br>Since
- Jalview 2.5, links are also shown for non-positional sequence
- features attached to the sequence, and any regular-expression
- based URL links that matched the description line.
- </em><strong><br> </strong></li>
- </ul></li>
- <li><strong>3D Structure Data...</strong> </strong><em>This menu is
- visible when you right-click on a sequence name. When this option is clicked, Jalview will open a <a href="../features/structurechooser.html">'Structure Chooser' </a>
- dialogue with options to select the structure which will eventually be opened in
- a 3D interactive view.<br> These entries will only be present if the sequence
- has <a href="../features/viewingpdbs.html">associated PDB structures</a>.</em></li><li><strong>VARNA 2D Structure</strong><br/><em>
- If the sequence or alignment has RNA structure,
- then <strong>VARNA 2D Structure</strong> entries will also be present enabling
- you to open a linked view of the RNA structure in <a
- href="../features/varna.html">VARNA</a>.
- </em>
- </li>
+ </ul></li>
+ <li><strong>Sequence Id<br>
+ </strong><em>This menu is only visible if you right-click on a sequence
+ name. </em>
+ <ul>
+ <li><a name="sqreport"><strong>Sequence
+ Details ...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+ href="../io/exportseqreport.html"
+ >HTML report containing the annotation and database cross
+ references</a> normally shown in the sequence's tooltip.
+ </em></li>
+ <li><strong>Edit Name/Description<br>
+ </strong><em>You may edit the name and description of each sequence.
+ A window will be displayed asking for a new sequence name
+ and sequence description to be entered. Press OK to accept
+ your edit. To save sequence descriptions, you must save in
+ Fasta, PIR or Jalview File format.</em></li>
+ <li><a href="sqaddrefannot"><strong>Add
+ Reference Annotations<br>
+ </strong><em>When enabled, copies any available alignment
+ annotation for this sequence to the current view.</em></li>
+ <li><strong>Set as Reference</strong> or <strong>Unmark
+ as Reference</strong><br /> Sets or unsets the reference sequence for
+ the the alignment.</li>
+
+ <li><strong>Represent Group With (Sequence Id)</strong><br>
+ <em>All sequences in the current selection group will be
+ hidden, apart from (Sequence Id). Any edits performed on the
+ visible representative sequence will be propagated to the
+ hidden sequences. </em></li>
+ <li><a name="sqid.popup"><strong>Link</strong><br>
+ <em>This menu item lists all links which have been set
+ up in the <a href="../features/preferences.html">Preferences</a>
+ Connections tab.<br> Since Jalview 2.4, links will
+ also be made for database cross references (where the
+ database name exactly matches the link name set up in <a
+ href="../features/preferences.html"
+ >Preferences</a>). <br>Since Jalview 2.5, links are also
+ shown for non-positional sequence features attached to the
+ sequence, and any regular-expression based URL links that
+ matched the description line.
+ </em><strong><br> </strong></li>
+ </ul></li>
+ <li><strong>3D Structure Data...</strong> </strong><em>This menu is
+ visible when you right-click on a sequence name. When this
+ option is clicked, Jalview will open a <a
+ href="../features/structurechooser.html"
+ >'Structure Chooser' </a> dialogue with options to select the
+ structure which will eventually be opened in a 3D interactive
+ view.<br> These entries will only be present if the
+ sequence has <a href="../features/viewingpdbs.html">associated
+ PDB structures</a>.
+ </em></li>
+ <li><strong>VARNA 2D Structure</strong><br />
+ <em> If the sequence or alignment has RNA structure, then <strong>VARNA
+ 2D Structure</strong> entries will also be present enabling you to open
+ a linked view of the RNA structure in <a
+ href="../features/varna.html"
+ >VARNA</a>.
+ </em></li>
<li><a name="hideinserts"><strong>Hide Insertions</strong></a><br />
- <em>Hides columns containing gaps in the current sequence or
+ <em>Hides columns containing gaps in the current sequence or
selected region, and reveals columns not including gaps.</em>
<li><strong>Hide Sequences</strong><br> <em>Hides the
- currently selected sequences in this alignment view.</em><strong><br>
- </strong></li>
- </ul>
+ currently selected sequences in this alignment view.</em><strong><br>
+ </strong></li>
+ </ul>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Web Service Menu</title></head>
+<head>
+<title>Web Service Menu</title>
+</head>
<body>
- <p><strong>Web Service Menu</strong><br /> <em>This menu
- is dynamic, and may contain user-defined web service entries in
- addition to any of the following ones:</em>
-
- <ul>
- <li><strong>Fetch DB References</strong><br> <em>This
- submenu contains options for accessing any of the database services
- that Jalview is aware of (e.g. DAS sequence servers and the
- WSDBFetch service provided by the EBI) to verify sequence start/end
- positions and retrieve all database cross references and PDB ids
- associated with all or just the selected sequences in the alignment.
- <ul>
- <li>'Retrieve full Sequence' - when checked, Jalview will
- retrieve the full sequence for any accessions associated with
- sequences in the alignment. <br> <strong>Note: This
- could cause out of memory errors when working with genomic
- sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
- </li>
- <li>'Standard Databases' will check sequences against the EBI
- databases plus any active DAS sequence sources<</li>
- </ul> Other submenus allow you to pick a specific source to query -
- sources are listed alphabetically according to their nickname.
- </em>
- </li>
- </ul>
- <p>Selecting items from the following submenus will start a
- remote service on compute facilities at the University of Dundee, or
- elsewhere. You need a continuous network connection in order to use
- these services through Jalview.
- </p>
- <ul>
- <li><strong>Alignment</strong><br /><em> Align the currently
- selected sequences or all sequences in the alignment, or re-align
- unaligned sequences to the aligned sequences. Entries in this menu
- provide access to the various alignment programs supported by <a
- href="../webServices/JABAWS.html">JABAWS</a>. See the <a
- href="../webServices/msaclient.html">Multiple Sequence
- Alignment webservice client</a> entry for more information.</em></li>
- <li><strong>Secondary Structure Prediction</strong>
- <ul>
- <li><strong>JPred Secondary Structure Prediction</strong><br>
- <em>Secondary structure prediction by network consensus. See
- the <a href="../webServices/jnet.html">Jpred3</a> client entry for
- more information. The behaviour of this calculation depends on
- the current selection:
- <ul>
- <li>If nothing is selected, and the displayed sequences
- appear to be aligned, then a JNet prediction will be run for
- the first sequence in the alignment, using the current
- alignment. Otherwise the first sequence will be submitted for
- prediction.</li>
- <li>If just one sequence (or a region on one sequence) has
- been selected, it will be submitted to the automatic JNet
- prediction server for homolog detection and prediction.</li>
- <li>If a set of sequences are selected, and they appear to
- be aligned, then the alignment will be used for a Jnet
- prediction on the <strong>first</strong> sequence in the set
- (that is, the one that appears first in the alignment window).
- </li>
- </ul> </em>
- </ul></li>
- <li><strong>Analysis</strong><br />
- <ul>
- <li><strong>Multi-Harmony</strong><br> <em>Performs
- functional residue analysis on a protein family alignment with
- sub-families defined on it. See the <a
- href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
- information.</em>
- </li>
- </ul></li>
- </ul>
+ <p>
+ <strong>Web Service Menu</strong><br /> <em>This menu is
+ dynamic, and may contain user-defined web service entries in
+ addition to any of the following ones:</em>
+ <ul>
+ <li><strong>Fetch DB References</strong><br> <em>This
+ submenu contains options for accessing any of the database
+ services that Jalview is aware of (e.g. DAS sequence servers and
+ the WSDBFetch service provided by the EBI) to verify sequence
+ start/end positions and retrieve all database cross references
+ and PDB ids associated with all or just the selected sequences
+ in the alignment.
+ <ul>
+ <li>'Retrieve full Sequence' - when checked, Jalview will
+ retrieve the full sequence for any accessions associated
+ with sequences in the alignment. <br> <strong>Note:
+ This could cause out of memory errors when working with
+ genomic sequence records !</strong><br> <strong>Added
+ in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the
+ EBI databases plus any active DAS sequence sources<</li>
+ </ul> Other submenus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em></li>
+ </ul>
+ <p>Selecting items from the following submenus will start a remote
+ service on compute facilities at the University of Dundee, or
+ elsewhere. You need a continuous network connection in order to use
+ these services through Jalview.</p>
+ <ul>
+ <li><strong>Alignment</strong><br />
+ <em> Align the currently selected sequences or all sequences in
+ the alignment, or re-align unaligned sequences to the aligned
+ sequences. Entries in this menu provide access to the various
+ alignment programs supported by <a
+ href="../webServices/JABAWS.html"
+ >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
+ Sequence Alignment webservice client</a> entry for more
+ information.
+ </em></li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <ul>
+ <li><strong>JPred Secondary Structure Prediction</strong><br>
+ <em>Secondary structure prediction by network consensus.
+ See the <a href="../webServices/jnet.html">Jpred3</a> client
+ entry for more information. The behaviour of this
+ calculation depends on the current selection:
+ <ul>
+ <li>If nothing is selected, and the displayed
+ sequences appear to be aligned, then a JNet prediction
+ will be run for the first sequence in the alignment,
+ using the current alignment. Otherwise the first
+ sequence will be submitted for prediction.</li>
+ <li>If just one sequence (or a region on one
+ sequence) has been selected, it will be submitted to the
+ automatic JNet prediction server for homolog detection
+ and prediction.</li>
+ <li>If a set of sequences are selected, and they
+ appear to be aligned, then the alignment will be used
+ for a Jnet prediction on the <strong>first</strong>
+ sequence in the set (that is, the one that appears first
+ in the alignment window).
+ </li>
+ </ul>
+ </em>
+ </ul></li>
+ <li><strong>Analysis</strong><br />
+ <ul>
+ <li><strong>Multi-Harmony</strong><br> <em>Performs
+ functional residue analysis on a protein family alignment
+ with sub-families defined on it. See the <a
+ href="../webServices/shmr.html"
+ >Multi-Harmony service</a> entry for more information.
+ </em></li>
+ </ul></li>
+ </ul>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Amino Acid Properties</title>
+<head>
+<title>Amino Acid Properties</title>
</head>
-<body><div align="center">
-<h1>Amino Acid Properties</h1>
- <img src="properties.gif">
- <br>
- <table width="295" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td width="291"><pre><font size="4" face="Courier New, Courier, mono"><strong>ILVCAGMFYWHKREQDNSTPBZX-</strong>
+<body>
+ <div align="center">
+ <h1>Amino Acid Properties</h1>
+ <img src="properties.gif"> <br>
+ <table width="295" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="291"><pre>
+ <font size="4" face="Courier New, Courier, mono"><strong>ILVCAGMFYWHKREQDNSTPBZX-</strong>
XXXXXXXXXXX·······X···XX Hydrophobic
········XXXXXXXXXX·XXXXX Polar
··XXXX·········XXXXX··XX Small
·······XXXX···········XX Aromatic
··········XXX·········XX Positive
·············X·X······XX Negative
-··········XXXX·X······XX Charged</font></pre></td>
- </tr>
- </table>
+··········XXXX·X······XX Charged</font>
+ </pre></td>
+ </tr>
+ </table>
</div>
-<p><br>
- From Livingstone, C. D. and Barton, G. J. (1993), <br>
- "Protein Sequence Alignments: A Strategy for the Hierarchical Analysis of Residue
- Conservation", Comp. Appl. Bio. Sci., 9, 745-756. </p>
+ <p>
+ <br> From Livingstone, C. D. and Barton, G. J. (1993), <br>
+ "Protein Sequence Alignments: A Strategy for the Hierarchical
+ Analysis of Residue Conservation", Comp. Appl. Bio. Sci., 9,
+ 745-756.
+ </p>
<br>
-</div>
+ </div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Amino Acids</title>
+<head>
+<title>Amino Acids</title>
<style type="text/css">
<!--
td {
<body>
-<div align="center">
- <table width="450" BORDER ="1" cellpadding="3" BGCOLOR="#FFFFFF">
- <tr>
- <td width="15">A</td>
- <td width="25">Ala</td>
- <td width="90">Alanine</td>
- <td width="80">aliphatic<br>
- hydrophobic<br>
- neutral </td>
- <td width="43" valign="middle">GCT<br>
- GCC<br>
- GCA<br>
- GCG</td>
- <td width="125"><img src="ala.jpg" width="94" height="81"></td>
- </tr>
- <tr>
- <td>B</td>
- <td> </td>
- <td>either aspartic acid or asparagine</td>
- <td> </td>
- <td> </td>
- <td> </td>
- </tr>
- <tr>
- <td>C</td>
- <td>Cys</td>
- <td>Cysteine</td>
- <td>polar<br>
- hydrophobic<br>
- neutral </td>
- <td>TGT<br>
- TGC</td>
- <td><img src="cys.jpg" width="82" height="95"></td>
- </tr>
- <tr>
- <td>D</td>
- <td>Asp</td>
- <td>Aspartic Acid</td>
- <td>polar<br>
- hydrophilic<br>
- charged (-) </td>
- <td>GAT<br>
- GAC</td>
- <td><img src="aspartate.jpg" width="95" height="103"></td>
- </tr>
- <tr>
- <td>E</td>
- <td>Glu</td>
- <td>Glutamic Acid</td>
- <td>polar<br>
- hydrophilic<br>
- charged (-) </td>
- <td>GAA<br>
- GAG</td>
- <td><img src="glutamate.jpg" width="93" height="128"></td>
- </tr>
- <tr>
- <td>F</td>
- <td>Phe</td>
- <td>Phenylalanine</td>
- <td>aromatic<br>
- hydrophobic<br>
- neutral</td>
- <td>TTT<br>
- TTC</td>
- <td><img src="phe.jpg" width="87" height="134"></td>
- </tr>
- <tr>
- <td>G</td>
- <td>Gly</td>
- <td>Glycine</td>
- <td> </td>
- <td>GGT<br>
- GGC<br>
- GGA<br>
- GGG</td>
- <td><img src="gly.jpg" width="97" height="79"></td>
- </tr>
- <tr>
- <td>H</td>
- <td>His</td>
- <td>Histidine</td>
- <td>aromatic<br>
- polar<br>
- hydrophilic<br>
- charged (+) </td>
- <td>CAT<br>
- CAC</td>
- <td><img src="his.jpg" width="97" height="142"></td>
- </tr>
- <tr>
- <td>I</td>
- <td>Ile</td>
- <td>Isoleucine</td>
- <td>aliphatic<br>
- hydrophobic<br>
- neutral </td>
- <td>ATT<br>
- ATC<br>
- ATA</td>
- <td><img src="iso.jpg" width="101" height="125"></td>
- </tr>
- <tr>
- <td>K</td>
- <td>Lys</td>
- <td>Lysine</td>
- <td> </td>
- <td>AAA<br>
- AAG</td>
- <td><img src="lys.jpg" width="79" height="167"></td>
- </tr>
- <tr>
- <td>L</td>
- <td>Leu</td>
- <td>Leucine</td>
- <td>aliphatic<br>
- hydrophobic<br>
- neutral </td>
- <td>TTG<br>
- TTA<br>
- CTT<br>
- CTC<br>
- CTA<br>
- CTG</td>
- <td><img src="leu.jpg" width="97" height="120"></td>
- </tr>
- <tr>
- <td>M</td>
- <td>Met</td>
- <td>Methionine</td>
- <td>hydrophobic<br>
- neutral </td>
- <td>ATG</td>
- <td><img src="met.jpg" width="86" height="151"></td>
- </tr>
- <tr>
- <td>N</td>
- <td>Asn</td>
- <td>Asparagine</td>
- <td>polar<br>
- hydrophilic<br>
- neutral </td>
- <td>AAT<br>
- AAC</td>
- <td><img src="asparagine.jpg" width="84" height="116"></td>
- </tr>
- <tr>
- <td>P</td>
- <td>Pro</td>
- <td>Proline</td>
- <td>hydrophobic<br>
- neutral</td>
- <td>CCT<br>
- CCC<br>
- CCA<br>
- CCG</td>
- <td><img src="pro.jpg" width="101" height="90"></td>
- </tr>
- <tr>
- <td>Q</td>
- <td>Gln</td>
- <td>Glutamine</td>
- <td>polar<br>
- hydrophilic<br>
- neutral</td>
- <td>CAA<br>
- CAG</td>
- <td><img src="glutamine.jpg" width="81" height="137"></td>
- </tr>
- <tr>
- <td>R</td>
- <td>Arg</td>
- <td>Arginine</td>
- <td>polar<br>
- hydrophilic<br>
- charged (+) </td>
- <td>CGT<br>
- CGC<br>
- CGA<br>
- CGG<br>
- AGA<br>
- AGG</td>
- <td><img src="arg.jpg" width="95" height="187"></td>
- </tr>
- <tr>
- <td>S</td>
- <td>Ser</td>
- <td>Serine</td>
- <td>polar<br>
- hydrophilic<br>
- neutral </td>
- <td>TCT<br>
- TCC<br>
- TCA<br>
- TCG<br>
- AGT<br>
- AGC</td>
- <td><img src="ser.jpg" width="96" height="74"></td>
- </tr>
- <tr>
- <td>T</td>
- <td>Thr</td>
- <td>Threonine</td>
- <td>polar<br>
- hydrophilic<br>
- neutral </td>
- <td>ACT<br>
- ACC<br>
- ACA<br>
- ACG</td>
- <td><img src="thr.jpg" width="94" height="96"></td>
- </tr>
- <tr>
- <td>V</td>
- <td>Val</td>
- <td>Valine</td>
- <td>aliphatic<br>
- hydrophobic<br>
- neutral </td>
- <td>GTT<br>
- GTC<br>
- GTA<br>
- GTG</td>
- <td><img src="val.jpg" width="99" height="98"></td>
- </tr>
- <tr>
- <td>W</td>
- <td>Trp</td>
- <td>Tryptophan</td>
- <td>aromatic<br>
- hydrophobic<br>
- neutral</td>
- <td>TGG</td>
- <td><img src="tryp.jpg" width="106" height="173"></td>
- </tr>
- <tr>
- <td>X</td>
- <td> </td>
- <td>UNKNOWN</td>
- <td> </td>
- <td> </td>
- <td> </td>
- </tr>
- <tr>
- <td>Y</td>
- <td>Tyr</td>
- <td>Tyrosine</td>
- <td>aromatic<br>
- polar<br>
- hydrophobic </td>
- <td>TAT<br>
- TAC</td>
- <td><img src="tyr.jpg" width="85" height="152"></td>
- </tr>
- <tr>
- <td>Z</td>
- <td> </td>
- <td>either glutamic acid or glutamine</td>
- <td> </td>
- <td> </td>
- <td> </td>
- </tr>
- <tr>
- <td> </td>
- <td>End</td>
- <td>Terminator</td>
- <td> </td>
- <td>TAA<br>
- TAG<br>
- TGA</td>
- <td> </td>
- </tr>
- </table>
+ <div align="center">
+ <table width="450" BORDER="1" cellpadding="3" BGCOLOR="#FFFFFF">
+ <tr>
+ <td width="15">A</td>
+ <td width="25">Ala</td>
+ <td width="90">Alanine</td>
+ <td width="80">aliphatic<br> hydrophobic<br>
+ neutral
+ </td>
+ <td width="43" valign="middle">GCT<br> GCC<br>
+ GCA<br> GCG
+ </td>
+ <td width="125"><img src="ala.jpg" width="94" height="81"></td>
+ </tr>
+ <tr>
+ <td>B</td>
+ <td> </td>
+ <td>either aspartic acid or asparagine</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td>Cys</td>
+ <td>Cysteine</td>
+ <td>polar<br> hydrophobic<br> neutral
+ </td>
+ <td>TGT<br> TGC
+ </td>
+ <td><img src="cys.jpg" width="82" height="95"></td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td>Asp</td>
+ <td>Aspartic Acid</td>
+ <td>polar<br> hydrophilic<br> charged (-)
+ </td>
+ <td>GAT<br> GAC
+ </td>
+ <td><img src="aspartate.jpg" width="95" height="103"></td>
+ </tr>
+ <tr>
+ <td>E</td>
+ <td>Glu</td>
+ <td>Glutamic Acid</td>
+ <td>polar<br> hydrophilic<br> charged (-)
+ </td>
+ <td>GAA<br> GAG
+ </td>
+ <td><img src="glutamate.jpg" width="93" height="128"></td>
+ </tr>
+ <tr>
+ <td>F</td>
+ <td>Phe</td>
+ <td>Phenylalanine</td>
+ <td>aromatic<br> hydrophobic<br> neutral
+ </td>
+ <td>TTT<br> TTC
+ </td>
+ <td><img src="phe.jpg" width="87" height="134"></td>
+ </tr>
+ <tr>
+ <td>G</td>
+ <td>Gly</td>
+ <td>Glycine</td>
+ <td> </td>
+ <td>GGT<br> GGC<br> GGA<br> GGG
+ </td>
+ <td><img src="gly.jpg" width="97" height="79"></td>
+ </tr>
+ <tr>
+ <td>H</td>
+ <td>His</td>
+ <td>Histidine</td>
+ <td>aromatic<br> polar<br> hydrophilic<br>
+ charged (+)
+ </td>
+ <td>CAT<br> CAC
+ </td>
+ <td><img src="his.jpg" width="97" height="142"></td>
+ </tr>
+ <tr>
+ <td>I</td>
+ <td>Ile</td>
+ <td>Isoleucine</td>
+ <td>aliphatic<br> hydrophobic<br> neutral
+ </td>
+ <td>ATT<br> ATC<br> ATA
+ </td>
+ <td><img src="iso.jpg" width="101" height="125"></td>
+ </tr>
+ <tr>
+ <td>K</td>
+ <td>Lys</td>
+ <td>Lysine</td>
+ <td> </td>
+ <td>AAA<br> AAG
+ </td>
+ <td><img src="lys.jpg" width="79" height="167"></td>
+ </tr>
+ <tr>
+ <td>L</td>
+ <td>Leu</td>
+ <td>Leucine</td>
+ <td>aliphatic<br> hydrophobic<br> neutral
+ </td>
+ <td>TTG<br> TTA<br> CTT<br> CTC<br> CTA<br>
+ CTG
+ </td>
+ <td><img src="leu.jpg" width="97" height="120"></td>
+ </tr>
+ <tr>
+ <td>M</td>
+ <td>Met</td>
+ <td>Methionine</td>
+ <td>hydrophobic<br> neutral
+ </td>
+ <td>ATG</td>
+ <td><img src="met.jpg" width="86" height="151"></td>
+ </tr>
+ <tr>
+ <td>N</td>
+ <td>Asn</td>
+ <td>Asparagine</td>
+ <td>polar<br> hydrophilic<br> neutral
+ </td>
+ <td>AAT<br> AAC
+ </td>
+ <td><img src="asparagine.jpg" width="84" height="116"></td>
+ </tr>
+ <tr>
+ <td>P</td>
+ <td>Pro</td>
+ <td>Proline</td>
+ <td>hydrophobic<br> neutral
+ </td>
+ <td>CCT<br> CCC<br> CCA<br> CCG
+ </td>
+ <td><img src="pro.jpg" width="101" height="90"></td>
+ </tr>
+ <tr>
+ <td>Q</td>
+ <td>Gln</td>
+ <td>Glutamine</td>
+ <td>polar<br> hydrophilic<br> neutral
+ </td>
+ <td>CAA<br> CAG
+ </td>
+ <td><img src="glutamine.jpg" width="81" height="137"></td>
+ </tr>
+ <tr>
+ <td>R</td>
+ <td>Arg</td>
+ <td>Arginine</td>
+ <td>polar<br> hydrophilic<br> charged (+)
+ </td>
+ <td>CGT<br> CGC<br> CGA<br> CGG<br> AGA<br>
+ AGG
+ </td>
+ <td><img src="arg.jpg" width="95" height="187"></td>
+ </tr>
+ <tr>
+ <td>S</td>
+ <td>Ser</td>
+ <td>Serine</td>
+ <td>polar<br> hydrophilic<br> neutral
+ </td>
+ <td>TCT<br> TCC<br> TCA<br> TCG<br> AGT<br>
+ AGC
+ </td>
+ <td><img src="ser.jpg" width="96" height="74"></td>
+ </tr>
+ <tr>
+ <td>T</td>
+ <td>Thr</td>
+ <td>Threonine</td>
+ <td>polar<br> hydrophilic<br> neutral
+ </td>
+ <td>ACT<br> ACC<br> ACA<br> ACG
+ </td>
+ <td><img src="thr.jpg" width="94" height="96"></td>
+ </tr>
+ <tr>
+ <td>V</td>
+ <td>Val</td>
+ <td>Valine</td>
+ <td>aliphatic<br> hydrophobic<br> neutral
+ </td>
+ <td>GTT<br> GTC<br> GTA<br> GTG
+ </td>
+ <td><img src="val.jpg" width="99" height="98"></td>
+ </tr>
+ <tr>
+ <td>W</td>
+ <td>Trp</td>
+ <td>Tryptophan</td>
+ <td>aromatic<br> hydrophobic<br> neutral
+ </td>
+ <td>TGG</td>
+ <td><img src="tryp.jpg" width="106" height="173"></td>
+ </tr>
+ <tr>
+ <td>X</td>
+ <td> </td>
+ <td>UNKNOWN</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <td>Y</td>
+ <td>Tyr</td>
+ <td>Tyrosine</td>
+ <td>aromatic<br> polar<br> hydrophobic
+ </td>
+ <td>TAT<br> TAC
+ </td>
+ <td><img src="tyr.jpg" width="85" height="152"></td>
+ </tr>
+ <tr>
+ <td>Z</td>
+ <td> </td>
+ <td>either glutamic acid or glutamine</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <td> </td>
+ <td>End</td>
+ <td>Terminator</td>
+ <td> </td>
+ <td>TAA<br> TAG<br> TGA
+ </td>
+ <td> </td>
+ </tr>
+ </table>
</div>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Genetic Code</title>
+<head>
+<title>Genetic Code</title>
<style type="text/css">
<!--
td {
<body>
-<div align="center">
- <h2>The Genetic Code </h2>
- <table width="474" border="0">
- <tr>
- <td width="16%"> </td>
- <td width="70%">2nd Position</td>
- <td width="14%"> </td>
- </tr>
- <tr>
- <td><p>1st Position</p>
- <p>(5' end)</p></td>
- <td><table border=1 cellpadding=3>
- <tr align=center bgcolor="#FFFFEE">
- <td width="24"></td>
- <td width="55"><h2>U</h2></td>
- <td width="70"><h2>C</h2></td>
- <td width="55"><h2>A</h2></td>
- <td width="55"><h2>G</h2></td>
- <td width="22"></td>
- </tr>
- <tr align=center bgcolor="#FFFFEE">
- <td><h1>U</h1></td>
- <td>Phe<br>Phe<br>Leu<br>Leu</td>
- <td>Ser<br>Ser<br>Ser<br>Ser</td>
- <td>Tyr<br>Tyr<br>STOP</i><br>STOP</i></td>
- <td>Cys<br>Cys<br>STOP</i><br>Trp</td>
+ <div align="center">
+ <h2>The Genetic Code</h2>
+ <table width="474" border="0">
+ <tr>
+ <td width="16%"> </td>
+ <td width="70%">2nd Position</td>
+ <td width="14%"> </td>
+ </tr>
+ <tr>
+ <td><p>1st Position</p>
+ <p>(5' end)</p></td>
+ <td><table border=1 cellpadding=3>
+ <tr align=center bgcolor="#FFFFEE">
+ <td width="24"></td>
+ <td width="55"><h2>U</h2></td>
+ <td width="70"><h2>C</h2></td>
+ <td width="55"><h2>A</h2></td>
+ <td width="55"><h2>G</h2></td>
+ <td width="22"></td>
+ </tr>
+ <tr align=center bgcolor="#FFFFEE">
+ <td><h1>U</h1></td>
+ <td>Phe<br>Phe<br>Leu<br>Leu
+ </td>
+ <td>Ser<br>Ser<br>Ser<br>Ser
+ </td>
+ <td>Tyr<br>Tyr<br>STOP</i><br>STOP</i></td>
+ <td>Cys<br>Cys<br>STOP</i><br>Trp
+ </td>
- <td>U<br>C<br>A<br>G</td>
- </tr>
- <tr bgcolor="#FFFFEE">
- <td><h1>C</h1></td>
- <td>Leu<br>Leu<br>Leu<br>Leu</td>
- <td>Pro<br>Pro<br>Pro<br>Pro</td>
- <td>His<br>His<br>Gln<br>Gln</td>
- <td>Arg<br>Arg<br>Arg<br>Arg</td>
- <td>U<br>C<br>A<br>G</td>
- </tr>
- <tr bgcolor="#FFFFEE">
- <td><h1>A</h1></td>
- <td>Ile<br>Ile<br>Ile<br>Met</td>
- <td>Thr<br>Thr<br>Thr<br>Thr</td>
- <td>Asn<br>Asn<br>Lys<br>Lys</td>
- <td>Ser<br>Ser<br>Arg<br>Arg</td>
- <td>U<br>C<br>A<br>G</td>
- </tr>
- <tr bgcolor="#FFFFEE">
- <td><h1>G</h1></td>
- <td>Val<br>Val<br>Val<br>Val</td>
- <td>Ala<br>Ala<br>Ala<br>Ala</td>
- <td>Asp<br>Asp<br>Glu<br>Glu</td>
- <td>Gly<br>Gly<br>Gly<br>Gly</td>
- <td>U<br>C<br>A<br>G</td>
- </tr>
- </table></td>
- <td><p>3rd Position</p>
- <p>(3'end)</p></td>
- </tr>
- </table>
-</div>
+ <td>U<br>C<br>A<br>G
+ </td>
+ </tr>
+ <tr bgcolor="#FFFFEE">
+ <td><h1>C</h1></td>
+ <td>Leu<br>Leu<br>Leu<br>Leu
+ </td>
+ <td>Pro<br>Pro<br>Pro<br>Pro
+ </td>
+ <td>His<br>His<br>Gln<br>Gln
+ </td>
+ <td>Arg<br>Arg<br>Arg<br>Arg
+ </td>
+ <td>U<br>C<br>A<br>G
+ </td>
+ </tr>
+ <tr bgcolor="#FFFFEE">
+ <td><h1>A</h1></td>
+ <td>Ile<br>Ile<br>Ile<br>Met
+ </td>
+ <td>Thr<br>Thr<br>Thr<br>Thr
+ </td>
+ <td>Asn<br>Asn<br>Lys<br>Lys
+ </td>
+ <td>Ser<br>Ser<br>Arg<br>Arg
+ </td>
+ <td>U<br>C<br>A<br>G
+ </td>
+ </tr>
+ <tr bgcolor="#FFFFEE">
+ <td><h1>G</h1></td>
+ <td>Val<br>Val<br>Val<br>Val
+ </td>
+ <td>Ala<br>Ala<br>Ala<br>Ala
+ </td>
+ <td>Asp<br>Asp<br>Glu<br>Glu
+ </td>
+ <td>Gly<br>Gly<br>Gly<br>Gly
+ </td>
+ <td>U<br>C<br>A<br>G
+ </td>
+ </tr>
+ </table></td>
+ <td><p>3rd Position</p>
+ <p>(3'end)</p></td>
+ </tr>
+ </table>
+ </div>
</body>
</html>
</style>
</head>
<body>
- <p>
- <strong>Nucleic Acid Support</strong>
- </p>
- <p>
- <em>Colour Schemes</em>
- </p>
- <p>Jalview has color schemes for nucleic acid based sequences,
- ability to fetch sequences from RFAM and RNA secondary structure
- coloring</p>
- <p>
- Information on the <a href="../colourSchemes/nucleotide.html">Nucleotide
- colour scheme</a> and <a href="../colourSchemes/purinepyrimidine.html">
- Purine/Pyrimidine colour scheme</a> are available under the Colour Menu.
- See <a href="../colourSchemes/index.html">Colour Schemes</a>.
- </p>
- <p>
- <em>RNA Support</em>
- </p>
- Jalview supports annotation of RNA sequences with secondary structure
- information. You can interactively
- <a href="../features/annotation.html#rna">create and edit RNA
- secondary structure annotation rows</a>, or import data in the following
- way:
- <ul>
- <li><em>RFAM</em> - Sequences can be <a
- href="../features/seqfetch.html">fetched</a> from the RFAM database
- by accession number or ID.</li>
- <li><em>Stockholm files</em> - WUSS (or VIENNA) dot-bracket
- notation found in the secondary structure annotation line will be
- imported as sequence or alignment associated secondary structure
- annotation.</li>
- <li><em>Clustal files</em> - certain RNA alignment programs, such
- as <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocaRNA</a>
- output consensus RNA secondary structure lines in the line normally
- reserved for the Clustal consensus line in a clustal file.</li>
- <li><em>RNAML</em> Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li>
- </ul>
- <p>
- <strong>RNA Secondary Structure Visualization and Analysis</strong><br />
- If a sequence or RNA alignment has secondary structure information,
- the alignment will have a secondary structure line shown below it, and
- a number of additional options become available:
- <ul>
- <li><a href="../colourschemes/rnaHelicesColouring.html">RNA
- Helix colouring</a> - highlights columns of alignment involved in
- particular RNA helices, Uses the first displayed secondary structure annotation.</li>
- <li><a href="../calculations/structureconsensus.html">Base Pair
- Conservation Analysis</a> - shown as a histogram and base-pair logo
- below the alignment. Uses the first displayed secondary structure annotation row.</li>
- <li><a href="../features/varna.html">2D Structure
- Visualization in VARNA</a> - allows linked viewing of the consensus or
- an individual sequence's structure. Accessed via the Sequence ID popup menu.</li>
+ <p>
+ <strong>Nucleic Acid Support</strong>
+ </p>
+ <p>
+ <em>Colour Schemes</em>
+ </p>
+ <p>Jalview has color schemes for nucleic acid based sequences,
+ ability to fetch sequences from RFAM and RNA secondary structure
+ coloring</p>
+ <p>
+ Information on the <a href="../colourSchemes/nucleotide.html">Nucleotide
+ colour scheme</a> and <a href="../colourSchemes/purinepyrimidine.html">
+ Purine/Pyrimidine colour scheme</a> are available under the Colour
+ Menu. See <a href="../colourSchemes/index.html">Colour Schemes</a>.
+ </p>
+ <p>
+ <em>RNA Support</em>
+ </p>
+ Jalview supports annotation of RNA sequences with secondary structure
+ information. You can interactively
+ <a href="../features/annotation.html#rna">create and edit RNA
+ secondary structure annotation rows</a>, or import data in the following
+ way:
+ <ul>
+ <li><em>RFAM</em> - Sequences can be <a
+ href="../features/seqfetch.html"
+ >fetched</a> from the RFAM database by accession number or ID.</li>
+ <li><em>Stockholm files</em> - WUSS (or VIENNA) dot-bracket
+ notation found in the secondary structure annotation line will be
+ imported as sequence or alignment associated secondary structure
+ annotation.</li>
+ <li><em>Clustal files</em> - certain RNA alignment programs,
+ such as <a
+ href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp"
+ >LocaRNA</a> output consensus RNA secondary structure lines in the
+ line normally reserved for the Clustal consensus line in a clustal
+ file.</li>
+ <li><em>RNAML</em> Jalview can import RNAML files containing
+ sequences and extended secondary structure annotation derived from
+ RNA 3D structure</li>
+ </ul>
+ <p>
+ <strong>RNA Secondary Structure Visualization and Analysis</strong><br />
+ If a sequence or RNA alignment has secondary structure information,
+ the alignment will have a secondary structure line shown below it,
+ and a number of additional options become available:
+ <ul>
+ <li><a href="../colourschemes/rnaHelicesColouring.html">RNA
+ Helix colouring</a> - highlights columns of alignment involved in
+ particular RNA helices, Uses the first displayed secondary
+ structure annotation.</li>
+ <li><a href="../calculations/structureconsensus.html">Base
+ Pair Conservation Analysis</a> - shown as a histogram and base-pair
+ logo below the alignment. Uses the first displayed secondary
+ structure annotation row.</li>
+ <li><a href="../features/varna.html">2D Structure
+ Visualization in VARNA</a> - allows linked viewing of the consensus
+ or an individual sequence's structure. Accessed via the Sequence
+ ID popup menu.</li>
<li><strong>per sequence secondary structure
annotation</strong><br /> Sequence associated secondary structure
annotation imported via stockholm, PDB files, or other sources can
Annotation→Secondary Structure</strong> option (only present when
per-sequence secondary structure is available).</li>
</ul>
- <p><strong>Pseudo-knots</strong><br/>
- Jalview 2.8.2 introduced limited support for working with structures including pseudoknots. Where possible, extended WUSS symbols (e.g. different types of parentheses, or upper and lower case letters) are preserved when parsing RNA structure annotation and will be shaded differently when displayed in the structure.<br/>
- Extended WUSS annotation is also employed to distinguish different base pair interactions obtained from RNAML files.</p>
-
- <p><strong>Limitations when working with RNA in Jalview</strong><br/>
- Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation
- </br>
- <em>Jalview's RNA handling capabilities were introduced in v2.8</em>
- </p>
- <p align="center"> </p>
+ <p>
+ <strong>Pseudo-knots</strong><br /> Jalview 2.8.2 introduced limited
+ support for working with structures including pseudoknots. Where
+ possible, extended WUSS symbols (e.g. different types of
+ parentheses, or upper and lower case letters) are preserved when
+ parsing RNA structure annotation and will be shaded differently when
+ displayed in the structure.<br /> Extended WUSS annotation is also
+ employed to distinguish different base pair interactions obtained
+ from RNAML files.
+ </p>
+
+ <p>
+ <strong>Limitations when working with RNA in Jalview</strong><br />
+ Currently, Jalview is not able to export RNA secondary structure
+ annotation in any format other than Jalview annotation </br> <em>Jalview's
+ RNA handling capabilities were introduced in v2.8</em>
+ </p>
+ <p align="center"> </p>
</body>
</html>
<title>Jalview Privacy Statement</title>
</head>
<body>
-<p><strong>Privacy for Jalview Users</strong><br>
-<p>The Jalview Desktop application which is available from the
-www.jalview.org site does not contain code designed to collect personal or
-private information without your consent. However, we do collect usage
-statistics to work out who is using Jalview, so we can apply for funding
-to support Jalview development, and make it better for our users.</p>
-<p>Usage data is collected from the logs of various web services that the Jalview Desktop contacts through its normal operation.
-These are described below:</p>
-<ul>
- <li><em>HTTP logs on the Jalview website</em><br>
- We record IP addresses of machines which access the web site, either
- via the browser when downloading the application, or when the Jalview
- Desktop user interface is launched.<br><br>
- <ul>
- <li><i>The JNLP file at www.jalview.org/webstart/jalview.jnlp
- is retrieved to determine if you are running the latest version of
- Jalview.</i></li>
- <li><i>The questionnaire web service at
- www.jalview.org/cgi-bin/questionnaire.pl is checked and a unique
- cookie for the current questionnaire is stored in the Jalview
- properties file.</i></li>
- <li><i>The Jalview web services stack is contacted to
- retrieve the currently available web services. All interactions with
- the public Jalview web services are logged, but we delete all job data
- (input data and results) after about two weeks.</i></li>
- </ul><br>
- </li>
- <li><em>Google Analytics</em><br>
- Since Jalview 2.4.0b2, the Jalview Desktop records usage data with
- Google Analytics via the <a
- href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
- class.<br>
- The Google Analytics logs for Jalview version 2.4 only record the fact
- that the application was started, but in the future, we will use this
- mechanism to improve the Desktop user interface, by tracking which
- parts of the user interface are being used most often.</li>
-</ul>
-</p>
-<p><strong>Stopping Jalview from calling home</strong><br>
-If you run Jalview in 'headless mode' via the command line, then the
-program shouldn't try to contact any of the web servers mentioned above
-(if it does, then it's a bug!). You can also specify some <a
- href="features/commandline.html">command line options</a> to disable
-the questionnaire and usage statistics check. Finally, the <a
- href="features/preferences.html#connections">Connections Tab</a> of the
-Jalview preferences contains options for controlling the submission of
-usage statistics.
-<p><strong>Other Web Clients in Jalview</strong><br>
-The Jalview desktop is intended to make it easier to interact with
-web-based bioinformatics resources. However, we can't take any
-responsibility for the integrity of any external services you might
-access via the program. Sorry!</p>
+ <p>
+ <strong>Privacy for Jalview Users</strong><br>
+ <p>The Jalview Desktop application which is available from the
+ www.jalview.org site does not contain code designed to collect
+ personal or private information without your consent. However, we do
+ collect usage statistics to work out who is using Jalview, so we can
+ apply for funding to support Jalview development, and make it better
+ for our users.</p>
+ <p>Usage data is collected from the logs of various web services
+ that the Jalview Desktop contacts through its normal operation.
+ These are described below:</p>
+ <ul>
+ <li><em>HTTP logs on the Jalview website</em><br> We
+ record IP addresses of machines which access the web site, either
+ via the browser when downloading the application, or when the
+ Jalview Desktop user interface is launched.<br>
+ <br>
+ <ul>
+ <li><i>The JNLP file at
+ www.jalview.org/webstart/jalview.jnlp is retrieved to
+ determine if you are running the latest version of Jalview.</i></li>
+ <li><i>The questionnaire web service at
+ www.jalview.org/cgi-bin/questionnaire.pl is checked and a
+ unique cookie for the current questionnaire is stored in the
+ Jalview properties file.</i></li>
+ <li><i>The Jalview web services stack is contacted to
+ retrieve the currently available web services. All
+ interactions with the public Jalview web services are
+ logged, but we delete all job data (input data and results)
+ after about two weeks.</i></li>
+ </ul>
+ <br></li>
+ <li><em>Google Analytics</em><br> Since Jalview 2.4.0b2,
+ the Jalview Desktop records usage data with Google Analytics via
+ the <a href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
+ class.<br> The Google Analytics logs for Jalview version 2.4
+ only record the fact that the application was started, but in the
+ future, we will use this mechanism to improve the Desktop user
+ interface, by tracking which parts of the user interface are being
+ used most often.</li>
+ </ul>
+ </p>
+ <p>
+ <strong>Stopping Jalview from calling home</strong><br> If you
+ run Jalview in 'headless mode' via the command line, then the
+ program shouldn't try to contact any of the web servers mentioned
+ above (if it does, then it's a bug!). You can also specify some <a
+ href="features/commandline.html"
+ >command line options</a> to disable the questionnaire and usage
+ statistics check. Finally, the <a
+ href="features/preferences.html#connections"
+ >Connections Tab</a> of the Jalview preferences contains options for
+ controlling the submission of usage statistics.
+ <p>
+ <strong>Other Web Clients in Jalview</strong><br> The Jalview
+ desktop is intended to make it easier to interact with web-based
+ bioinformatics resources. However, we can't take any responsibility
+ for the integrity of any external services you might access via the
+ program. Sorry!
+ </p>
</body>
</html>
<title>VAMSAS Interoperation</title>
</head>
<body>
-<p><strong>VAMSAS Interoperation</strong></p>
-<p>Jalview can interact with other applications using "the <strong>VAMSAS
-Interoperation framework</strong>" which is an experimental model for
-interoperation between bioinformatics applications (<strong>V</strong>isualization
-and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,
-<strong>Alignements</strong> and <strong>S</strong>tructures).
-Currently, the only other VAMSAS enabled application is <a
- href="http://www.topali.org">TOPALi</a> - a user friendly program for
-phylogenetics and evolutionary analysis.
-<p>VAMSAS enabled applications access a shared bioinformatics
-dataset containing sequences, alignments, annotation and trees, which
-can be represented by an XML document analogous to a <a
- href="../features/jalarchive.html">Jalview Project Archive</a>.</p>
-<br>
-<strong>Connecting to a VAMSAS session</strong><br>
-The VAMSAS functionality in Jalview is accessed through the Desktop's <strong>Vamsas</strong>
-menu. The options available in this menu depend on whether the
-application is currently interacting with a VAMSAS dataset in a <strong>VAMSAS
-session</strong>. When the application is not connected to a session is active,
-the menu options are as follows:<br>
-<ul>
- <li><em>Connect to an existing session</em><br>
- If visible, this submenu contains a list of existing sessions that the
- VAMSAS framework has discovered on your computer. <br>
- Choose one to connect to it.</li>
- <li><em>New VAMSAS Session</em><br>
- This option will create a new session on your computer.</li>
- <li><em>Load VAMSAS Session...</em><br>
- This option will open a file browser window allowing you to select a
- VAMSAS session archive from which a new session will be created.<br/>
- <em>New in 2.5:</em>Sessions created from an imported document inherit
- the file or URL for the document.</li>
+ <p>
+ <strong>VAMSAS Interoperation</strong>
+ </p>
+ <p>
+ Jalview can interact with other applications using "the <strong>VAMSAS
+ Interoperation framework</strong>" which is an experimental model for
+ interoperation between bioinformatics applications (<strong>V</strong>isualization
+ and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,
+ <strong>Alignements</strong> and <strong>S</strong>tructures).
+ Currently, the only other VAMSAS enabled application is <a
+ href="http://www.topali.org"
+ >TOPALi</a> - a user friendly program for phylogenetics and
+ evolutionary analysis.
+ <p>
+ VAMSAS enabled applications access a shared bioinformatics dataset
+ containing sequences, alignments, annotation and trees, which can be
+ represented by an XML document analogous to a <a
+ href="../features/jalarchive.html"
+ >Jalview Project Archive</a>.
+ </p>
+ <br>
+ <strong>Connecting to a VAMSAS session</strong>
+ <br> The VAMSAS functionality in Jalview is accessed through the
+ Desktop's
+ <strong>Vamsas</strong> menu. The options available in this menu
+ depend on whether the application is currently interacting with a
+ VAMSAS dataset in a
+ <strong>VAMSAS session</strong>. When the application is not connected
+ to a session is active, the menu options are as follows:
+ <br>
+ <ul>
+ <li><em>Connect to an existing session</em><br> If
+ visible, this submenu contains a list of existing sessions that
+ the VAMSAS framework has discovered on your computer. <br>
+ Choose one to connect to it.</li>
+ <li><em>New VAMSAS Session</em><br> This option will
+ create a new session on your computer.</li>
+ <li><em>Load VAMSAS Session...</em><br> This option will
+ open a file browser window allowing you to select a VAMSAS session
+ archive from which a new session will be created.<br /> <em>New
+ in 2.5:</em>Sessions created from an imported document inherit the
+ file or URL for the document.</li>
-</ul>
-<br>
-<strong>VAMSAS and Firewalls</strong>: VAMSAS uses sockets to
-communicate between different programs. This means that after starting a
-session, your firewall software may ask you whether to allow the java
-executable access to the internet (port 53782). If you do not allow
-this, messages will not be exchanged with other VAMSAS applications.</br>
-<br>
-Once you have successfully connected to a VAMSAS session, any data made
-available by other VAMSAS applications will be automatically imported
-into Jalview. However, in order to share the data in Jalview with other
-VAMSAS applications, you must manually select the <strong>Vamsas→"Session
-Update"</strong> entry that is visible when a session is active. Selecting
-this option will update the VAMSAS session document, with the data
-loaded into Jalview. Any new alignments, trees and annotation will be
-written to the session, in addition to any edits you have made to data
-originally stored in the document. <br>
-<strong>Saving the current session</strong><br>
-You can save the current session as a VAMSAS Session archive using the <strong>Vamsas→"Session
-Update"</strong>. The file contains a snapshot of the current VAMSAS
-session, including data from any other applications connected to the
-session. <strong>Leaving a VAMSAS session</strong><br>
-A session can be disconnected from at any time using the <strong>Vamsas→"Stop
-Session"</strong> option. Selecting this option will only disconnect Jalview
-from the session - any other applications will remain connected to the
-session. If Jalview is the only application connected to the session and
-you have not yet saved the VAMSAS session then you will be prompted with
-an optional 'Save VAMSAS session...' dialog box, allowing the session to
-be saved and returned to at a later date. <br>
-<strong>VAMSAS Session Persistence</strong><br>
-VAMSAS sessions are persistent - this means that they exist
-independently of any VAMSAS applications that are connected to them.
-This means that if something goes wrong with a VAMSAS application and it
-crashes or otherwise fails, the VAMSAS session it is connected to will
-(hopefully) be unaffected. For instance, if Jalview is killed or crashes
-whilst it is still connected to a session, that session can be recovered
-in a new Jalview instance using the <strong>Vamsas→"Existing
-session"</strong> sub menu.</p>
-<p><strong>A quick Demo</strong>
-<br>
-Jalview can talk to itself through VAMSAS. Simply start two copies of
-the application, create a new vamsas session in one, and connect to the
-new session in the other. Then load your data into one of the
-applications, and use the
-<strong>Vamsas→"Session Update"</strong>
-menu entry to try to propagate the data to the other application.
-<br>
-<table>
- <tr>
- <td>Data Sharing Capability</td>
- <td>Jalview Version</td>
- </tr>
- <tr>
- <td>Alignments, sequences and annotation, trees, database
- references, cDNA/protein mappings.</td>
- <td>2.4</td>
- </tr>
- <tr>
- <td>Mouseover location across linked DNA, protein and structure
- positions.</td>
- <td>2.4</td>
- </tr>
- <tr>
- <td>Jalview project settings (Multiple views, groups, tree
- partitions, colouring, window positions)</td>
- <td>2.5</td>
- </tr>
- <tr>
- <td>Sequence region and column selections</td>
- <td>2.5</td>
- </tr>
-</table>
-<br />
-<p>Version 0.2 of the VAMSAS client library is used in <em>Jalview
-2.5</em>. For further details about the VAMSAS framework, please check the
-<a href="http://www.vamsas.ac.uk">VAMSAS website</a>. The VAMSAS
-framework is implemented as a Java 1.4 Library and depends on a number
-of other open source projects. Its source is released under the
-LGPL license. </p>
+ </ul>
+ <br>
+ <strong>VAMSAS and Firewalls</strong>: VAMSAS uses sockets to
+ communicate between different programs. This means that after starting
+ a session, your firewall software may ask you whether to allow the
+ java executable access to the internet (port 53782). If you do not
+ allow this, messages will not be exchanged with other VAMSAS
+ applications.
+ </br>
+ <br> Once you have successfully connected to a VAMSAS session,
+ any data made available by other VAMSAS applications will be
+ automatically imported into Jalview. However, in order to share the
+ data in Jalview with other VAMSAS applications, you must manually
+ select the
+ <strong>Vamsas→"Session Update"</strong> entry that is
+ visible when a session is active. Selecting this option will update
+ the VAMSAS session document, with the data loaded into Jalview. Any
+ new alignments, trees and annotation will be written to the session,
+ in addition to any edits you have made to data originally stored in
+ the document.
+ <br>
+ <strong>Saving the current session</strong>
+ <br> You can save the current session as a VAMSAS Session archive
+ using the
+ <strong>Vamsas→"Session Update"</strong>. The file
+ contains a snapshot of the current VAMSAS session, including data from
+ any other applications connected to the session.
+ <strong>Leaving a VAMSAS session</strong>
+ <br> A session can be disconnected from at any time using the
+ <strong>Vamsas→"Stop Session"</strong> option.
+ Selecting this option will only disconnect Jalview from the session -
+ any other applications will remain connected to the session. If
+ Jalview is the only application connected to the session and you have
+ not yet saved the VAMSAS session then you will be prompted with an
+ optional 'Save VAMSAS session...' dialog box, allowing the session to
+ be saved and returned to at a later date.
+ <br>
+ <strong>VAMSAS Session Persistence</strong>
+ <br> VAMSAS sessions are persistent - this means that they exist
+ independently of any VAMSAS applications that are connected to them.
+ This means that if something goes wrong with a VAMSAS application and
+ it crashes or otherwise fails, the VAMSAS session it is connected to
+ will (hopefully) be unaffected. For instance, if Jalview is killed or
+ crashes whilst it is still connected to a session, that session can be
+ recovered in a new Jalview instance using the
+ <strong>Vamsas→"Existing session"</strong> sub menu.
+ </p>
+ <p>
+ <strong>A quick Demo</strong> <br> Jalview can talk to itself
+ through VAMSAS. Simply start two copies of the application, create a
+ new vamsas session in one, and connect to the new session in the
+ other. Then load your data into one of the applications, and use the
+ <strong>Vamsas→"Session Update"</strong> menu entry
+ to try to propagate the data to the other application. <br>
+ <table>
+ <tr>
+ <td>Data Sharing Capability</td>
+ <td>Jalview Version</td>
+ </tr>
+ <tr>
+ <td>Alignments, sequences and annotation, trees, database
+ references, cDNA/protein mappings.</td>
+ <td>2.4</td>
+ </tr>
+ <tr>
+ <td>Mouseover location across linked DNA, protein and
+ structure positions.</td>
+ <td>2.4</td>
+ </tr>
+ <tr>
+ <td>Jalview project settings (Multiple views, groups, tree
+ partitions, colouring, window positions)</td>
+ <td>2.5</td>
+ </tr>
+ <tr>
+ <td>Sequence region and column selections</td>
+ <td>2.5</td>
+ </tr>
+ </table>
+ <br />
+ <p>
+ Version 0.2 of the VAMSAS client library is used in <em>Jalview
+ 2.5</em>. For further details about the VAMSAS framework, please check
+ the <a href="http://www.vamsas.ac.uk">VAMSAS website</a>. The VAMSAS
+ framework is implemented as a Java 1.4 Library and depends on a
+ number of other open source projects. Its source is released under
+ the LGPL license.
+ </p>
</body>
</html>
<title>AACon Web Service</title>
</head>
<body>
- <strong>AACon Alignment Conservation Calculation Service</strong>
- <p>The JABAWS AACon service implements 17 different conservation
- scores for protein sequence alignments.</p>
- <p>
- The majority of these scores were described by Valdar in 2002 (Scoring
- residue conservation. <em>Proteins: Structure, Function, and
- Genetics</em> 43(2): 227-241. <a
- href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a> or
- available on the <a
- href="http://www.well.ox.ac.uk/~valdar/publications.html">Valdar
- Group publications page</a>), but the SMERFs score was developed later
- and described by Manning et al. in 2008 (<a
- href="http://www.biomedcentral.com/1471-2105/9/51">BMC
- Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
- </p>
- <p>
- <strong>Enabling and disabling AACon calculations</strong><br /> When
- the <strong>AACon Calculation</strong> entry in the <strong>Web
- Services→Conservation</strong> is ticked, AACon calculations will be
- performed every time the alignment is modified. Selecting the menu
- item will enable or disable automatic recalculation.
- </p>
- <p>
- <strong>Configuring which AACon calculations are performed</strong><br />
- The <strong>Web Services→Conservation→Change AACon
- Settings ...</strong> menu entry will open a <a href="webServicesParams.html">web
- services parameter dialog</a> for the currently configured AACon server.
- Standard presets are provided for quick and more expensive
- conservation calculations, and parameters are also provided to change
- the way that SMERFS calculations are performed.<br /> <em>AACon
- settings for an alignment are saved in <a
- href="../features/jalarchive.html">Jalview projects</a> along with
- the latest calculation results.
- </em>
- </p>
- <p>
- <strong>Changing the server used for AACon calculations</strong><br />
- If you are working with alignments too large to analyse with the
- public JABAWS server, then you will most likely have already
- configured <a href="webServicesPrefs.html">additional JABAWS
- servers</a>. By default, Jalview will chose the first AACon service
- available from the list of JABAWS servers available. If available, you can switch to
- use another AACon service by selecting it from the <strong>Web
- Services→Conservation→Switch Server</strong> submenu.
- </p>
+ <strong>AACon Alignment Conservation Calculation Service</strong>
+ <p>The JABAWS AACon service implements 17 different conservation
+ scores for protein sequence alignments.</p>
+ <p>
+ The majority of these scores were described by Valdar in 2002
+ (Scoring residue conservation. <em>Proteins: Structure,
+ Function, and Genetics</em> 43(2): 227-241. <a
+ href="http://www.ncbi.nlm.nih.gov/pubmed/12112692"
+ >PubMed</a> or available on the <a
+ href="http://www.well.ox.ac.uk/~valdar/publications.html"
+ >Valdar Group publications page</a>), but the SMERFs score was
+ developed later and described by Manning et al. in 2008 (<a
+ href="http://www.biomedcentral.com/1471-2105/9/51"
+ >BMC Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
+ </p>
+ <p>
+ <strong>Enabling and disabling AACon calculations</strong><br />
+ When the <strong>AACon Calculation</strong> entry in the <strong>Web
+ Services→Conservation</strong> is ticked, AACon calculations will be
+ performed every time the alignment is modified. Selecting the menu
+ item will enable or disable automatic recalculation.
+ </p>
+ <p>
+ <strong>Configuring which AACon calculations are performed</strong><br />
+ The <strong>Web Services→Conservation→Change
+ AACon Settings ...</strong> menu entry will open a <a
+ href="webServicesParams.html"
+ >web services parameter dialog</a> for the currently configured AACon
+ server. Standard presets are provided for quick and more expensive
+ conservation calculations, and parameters are also provided to
+ change the way that SMERFS calculations are performed.<br /> <em>AACon
+ settings for an alignment are saved in <a
+ href="../features/jalarchive.html"
+ >Jalview projects</a> along with the latest calculation results.
+ </em>
+ </p>
+ <p>
+ <strong>Changing the server used for AACon calculations</strong><br />
+ If you are working with alignments too large to analyse with the
+ public JABAWS server, then you will most likely have already
+ configured <a href="webServicesPrefs.html">additional JABAWS
+ servers</a>. By default, Jalview will chose the first AACon service
+ available from the list of JABAWS servers available. If available,
+ you can switch to use another AACon service by selecting it from the
+ <strong>Web Services→Conservation→Switch Server</strong>
+ submenu.
+ </p>
</body>
</html>
<title>The JABAWS system</title>
</head>
<body>
-<p><strong>The</strong> <strong><em>JA</em></strong>va <strong><em>B</em></strong>ioinformatics
-<strong><em>A</em></strong>nalysis <strong><em>W</em></strong>eb <strong><em>S</em></strong>ervices
-<strong>system</strong> (<strong>JABAWS</strong>)<br>
-Jalview includes a client for interacting with programmatic (SOAP) web
-services for the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
-service model, developed at the University of Dundee by Peter Troshin
-and Geoff Barton. This is an open source system that provides a
-framework for wrapping command line bioinformatics analysis programs
-that enables them to be executed locally or on a cluster using data and
-analysis parameters provided by a program linked with the JABA engine directly or
-accessing it remotely <em>via</em> its web services interface.</p>
-<p>The list of JABAWS servers known to the Jalview desktop is shown
-in the <a href="webServicesPrefs.html">Web Services Preferences
-Panel</a>, and detailed information about a particular service is available
-from the help text and web pages accessible from its <a
- href="webServicesParams.html">job parameters dialog box</a>.</p>
-<p><strong>Obtaining JABAWS</strong><br>
-One of the aims of JABAWS is to enable you to easily perform
-computationally intensive bioinformatics analysis tasks using your own
-computational facilities. It can be installed on a workstation to
-provide stand-alone execution of analysis programs, or as a job
-submission engine - enabling larger numbers of jobs to be handled. If
-you would like to download and install JABAWS for your own use, please
-go to <a href="http://www.compbio.dundee.ac.uk/jabaws">http://www.compbio.dundee.ac.uk/jabaws</a>
-for more information.</p>
-<p><strong>Configuring your own JABAWS services for use by
-Jalview</strong><br>
-Once you have downloaded and installed JABAWS, and verified it is
-working, all that is needed is to add the URL for your JABAWS server(s) to
-the list in the <a href="webServicesPrefs.html">Web Services
-Preferences Panel</a>. After adding your service and saving your preferences
-or hitting the 'refresh web services' button, you should be able to
-submit jobs to the server via the alignment window's web services menu.
-Your JABAWS servers list is stored in your Jalview preferences, so you
-will only have to configure Jalview once for each new server.</p>
-<p><em>Support for accessing JABAWS servers was introduced in
-Jalview 2.6.</em></p>
-<p><em>Option for adding JABAWS servers which fails validation
-was introduced from version 2.8.2 </em></p>
+ <p>
+ <strong>The</strong> <strong><em>JA</em></strong>va <strong><em>B</em></strong>ioinformatics
+ <strong><em>A</em></strong>nalysis <strong><em>W</em></strong>eb <strong><em>S</em></strong>ervices
+ <strong>system</strong> (<strong>JABAWS</strong>)<br> Jalview
+ includes a client for interacting with programmatic (SOAP) web
+ services for the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
+ service model, developed at the University of Dundee by Peter
+ Troshin and Geoff Barton. This is an open source system that
+ provides a framework for wrapping command line bioinformatics
+ analysis programs that enables them to be executed locally or on a
+ cluster using data and analysis parameters provided by a program
+ linked with the JABA engine directly or accessing it remotely <em>via</em>
+ its web services interface.
+ </p>
+ <p>
+ The list of JABAWS servers known to the Jalview desktop is shown in
+ the <a href="webServicesPrefs.html">Web Services Preferences
+ Panel</a>, and detailed information about a particular service is
+ available from the help text and web pages accessible from its <a
+ href="webServicesParams.html"
+ >job parameters dialog box</a>.
+ </p>
+ <p>
+ <strong>Obtaining JABAWS</strong><br> One of the aims of JABAWS
+ is to enable you to easily perform computationally intensive
+ bioinformatics analysis tasks using your own computational
+ facilities. It can be installed on a workstation to provide
+ stand-alone execution of analysis programs, or as a job submission
+ engine - enabling larger numbers of jobs to be handled. If you would
+ like to download and install JABAWS for your own use, please go to <a
+ href="http://www.compbio.dundee.ac.uk/jabaws"
+ >http://www.compbio.dundee.ac.uk/jabaws</a> for more information.
+ </p>
+ <p>
+ <strong>Configuring your own JABAWS services for use by
+ Jalview</strong><br> Once you have downloaded and installed JABAWS,
+ and verified it is working, all that is needed is to add the URL for
+ your JABAWS server(s) to the list in the <a
+ href="webServicesPrefs.html"
+ >Web Services Preferences Panel</a>. After adding your service and
+ saving your preferences or hitting the 'refresh web services'
+ button, you should be able to submit jobs to the server via the
+ alignment window's web services menu. Your JABAWS servers list is
+ stored in your Jalview preferences, so you will only have to
+ configure Jalview once for each new server.
+ </p>
+ <p>
+ <em>Support for accessing JABAWS servers was introduced in
+ Jalview 2.6.</em>
+ </p>
+ <p>
+ <em>Option for adding JABAWS servers which fails validation was
+ introduced from version 2.8.2 </em>
+ </p>
</body>
</html>
<title>RNAalifold Web Service</title>
</head>
<body>
- <strong>RNAalifold RNA Alignment Secondary Structure
- Prediction Service</strong>
- <p>
- RNAalifold analyses the pattern of base pair conservation in an RNA
- alignment in order to predict a consensus secondary structure.<br>It
- is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
- RNA</a> Secondary Structure Prediction and Comparison Package. It was
- described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
- Gruber, and Peter F. Stadler, <em>RNAalifold: Improved consensus
- structure prediction for RNA alignments</em> (BMC Bioinformatics, 9:474,
- 2008). Download the paper at <a
- href="http://www.biomedcentral.com/1471-2105/9/474">http://www.biomedcentral.com/1471-2105/9/474</a>.
- </p>
- <p>
- <strong>Running RNAalifold from Jalview</strong><br />
- <p>
- Jalview supports access to RNAalifold services provided by JABA 2.1
- servers. To enable RNAalifold predictions for an RNA alignment, go to
- <strong>Webservices→Secondary Structure Prediction</strong> and
- select <strong>RNAalifold prediction</strong> to run with current
- defaults, and <strong>Change settings ...</strong> to adjust
- prediction parameters. The RNA secondary structure prediction for the
- alignment will be shown as alignment annotation, and any edits will
- trigger the prediction to be recalculated.
- <p>
- <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
- Jalview only provide access to a selection of the RNAalifold
- arguments. For a full description, see the documentation at <a
- href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
- </p>
- <p>
- <strong>Supported Arguments which give alternate structures</strong>
- </p>
- <p>
- <em>Partition Function (-p)</em><br /> Calculate the Partition
- Function and base pairing probability matrix in addition to the mfe
- structure. A coarse representation of the pair probabilities in the
- form of a pseudo bracket notation, as well as the centroid structure
- derived from the pair probabilities are displayed. The most likely
- base pairings are stored in a separate file by RNAalifold and
- represented in Jalview by a bar graph annotation line labeled
- 'Contact Probabilities'.
- </p>
- <p>
- <em>Maximum Expected Accuracy Structure (--MEA)</em><br /> Calculate
- an MEA structure where the expected Accuracy is computed from the base
- pair probabilities. A more detailed description can be found in the <strong>RNAfold</strong>
- program documentation at <a
- href="http://www.tbi.univie.ac.at/RNA/RNAfold.html">http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
- </p>
- <p>
- <strong>Example RNAalifold Structure Annotation rows</strong>
- <p>
- <div align="center">
- <img src="RNAalifoldAnnotationRows.png" width="500" height="216">
- </div>
- <p>
+ <strong>RNAalifold RNA Alignment Secondary Structure
+ Prediction Service</strong>
+ <p>
+ RNAalifold analyses the pattern of base pair conservation in an RNA
+ alignment in order to predict a consensus secondary structure.<br>It
+ is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
+ RNA</a> Secondary Structure Prediction and Comparison Package. It was
+ described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
+ Gruber, and Peter F. Stadler, <em>RNAalifold: Improved
+ consensus structure prediction for RNA alignments</em> (BMC
+ Bioinformatics, 9:474, 2008). Download the paper at <a
+ href="http://www.biomedcentral.com/1471-2105/9/474"
+ >http://www.biomedcentral.com/1471-2105/9/474</a>.
+ </p>
+ <p>
+ <strong>Running RNAalifold from Jalview</strong><br />
+ <p>
+ Jalview supports access to RNAalifold services provided by JABA 2.1
+ servers. To enable RNAalifold predictions for an RNA alignment, go
+ to <strong>Webservices→Secondary Structure Prediction</strong>
+ and select <strong>RNAalifold prediction</strong> to run with
+ current defaults, and <strong>Change settings ...</strong> to adjust
+ prediction parameters. The RNA secondary structure prediction for
+ the alignment will be shown as alignment annotation, and any edits
+ will trigger the prediction to be recalculated.
+ <p>
+ <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
+ Jalview only provide access to a selection of the RNAalifold
+ arguments. For a full description, see the documentation at <a
+ href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html"
+ >http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
+ </p>
+ <p>
+ <strong>Supported Arguments which give alternate structures</strong>
+ </p>
+ <p>
+ <em>Partition Function (-p)</em><br /> Calculate the Partition
+ Function and base pairing probability matrix in addition to the mfe
+ structure. A coarse representation of the pair probabilities in the
+ form of a pseudo bracket notation, as well as the centroid structure
+ derived from the pair probabilities are displayed. The most likely
+ base pairings are stored in a separate file by RNAalifold and
+ represented in Jalview by a bar graph annotation line labeled
+ 'Contact Probabilities'.
+ </p>
+ <p>
+ <em>Maximum Expected Accuracy Structure (--MEA)</em><br />
+ Calculate an MEA structure where the expected Accuracy is computed
+ from the base pair probabilities. A more detailed description can be
+ found in the <strong>RNAfold</strong> program documentation at <a
+ href="http://www.tbi.univie.ac.at/RNA/RNAfold.html"
+ >http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
+ </p>
+ <p>
+ <strong>Example RNAalifold Structure Annotation rows</strong>
+ <p>
+ <div align="center">
+ <img src="RNAalifoldAnnotationRows.png" width="500" height="216">
+ </div>
+ <p>
</body>
</html>
-->
<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-Database Reference Fetching
+<head>Database Reference Fetching
</head>
<p>
-<p><strong>Discovering Database References for Sequences</strong><br>
-Database references are associated with a sequence are displayed as a
-list in the tooltip shown when mousing over its sequence ID. Jalview
-uses references for the retrieval of <a
- href="../features/viewingpdbs.html">PDB structures</a> and <a
- href="../features/dasfeatures.html">DAS features</a>, and for
-retrieving sequence cross-references such as the protein products of a
-DNA sequence.</p>
-<p><strong>Initiating reference retrieval</strong><br>
-The application provides three ways to access the retrieval function. Either:
-<ul><li>select the <strong>Discover PDB IDs</strong> option from the structure submenu of the sequence's popup menu</li>
-<li>Choose one of the options from the 'Fetch DB Refs' submenu in the alignment window's <strong>Web Services</strong> menu:<ul>
-<li><em>Standard Databases</em> will fetch references from the EBI databases plus currently selected DAS sources</li>
-<li>The other entries submenus leading to lists of individual database sources that Jalview can access.</li></ul></li>
-<li>Answer 'Yes' when asked if you wish to retrieve database references for your sequences after initiating a DAS Sequence Feature fetch.</li>
-</ul>
+<p>
+ <strong>Discovering Database References for Sequences</strong><br>
+ Database references are associated with a sequence are displayed as a
+ list in the tooltip shown when mousing over its sequence ID. Jalview
+ uses references for the retrieval of <a
+ href="../features/viewingpdbs.html"
+ >PDB structures</a> and <a href="../features/dasfeatures.html">DAS
+ features</a>, and for retrieving sequence cross-references such as the
+ protein products of a DNA sequence.
+</p>
+<p>
+ <strong>Initiating reference retrieval</strong><br> The
+ application provides three ways to access the retrieval function.
+ Either:
+<ul>
+ <li>select the <strong>Discover PDB IDs</strong> option from the
+ structure submenu of the sequence's popup menu
+ </li>
+ <li>Choose one of the options from the 'Fetch DB Refs' submenu in
+ the alignment window's <strong>Web Services</strong> menu:
+ <ul>
+ <li><em>Standard Databases</em> will fetch references from
+ the EBI databases plus currently selected DAS sources</li>
+ <li>The other entries submenus leading to lists of individual
+ database sources that Jalview can access.</li>
+ </ul>
+ </li>
+ <li>Answer 'Yes' when asked if you wish to retrieve database
+ references for your sequences after initiating a DAS Sequence
+ Feature fetch.</li>
+</ul>
<p>Jalview discovers references for a sequence by generating a set
-of ID queries from the ID string of each sequence in the alignment. It
-then tries to query a subset of all the databases it can access in order to match
-the alignment sequence to any records retrieved from the database. If a
-match is found, then the sequence is annotated with that database's
-reference, and any cross-references that its records contain.</p>
-<p><strong>The Sequence Identification Process</strong><br>
-The method of accession id discovery is derived from the method which
-earlier Jalview versions used for Uniprot sequence feature retrieval,
-and was originally restricted to the identification of valid Uniprot
-accessions.<br>
-Essentially, Jalview will try to retrieve records from a subset of the databases
-accessible by the <a href="../features/seqfetch.html">sequence
-fetcher</a> using each sequence's ID string (or each string in the ID
-separated by the '∣' symbol).</p>
+ of ID queries from the ID string of each sequence in the alignment. It
+ then tries to query a subset of all the databases it can access in
+ order to match the alignment sequence to any records retrieved from
+ the database. If a match is found, then the sequence is annotated with
+ that database's reference, and any cross-references that its records
+ contain.</p>
+<p>
+ <strong>The Sequence Identification Process</strong><br> The
+ method of accession id discovery is derived from the method which
+ earlier Jalview versions used for Uniprot sequence feature retrieval,
+ and was originally restricted to the identification of valid Uniprot
+ accessions.<br> Essentially, Jalview will try to retrieve records
+ from a subset of the databases accessible by the <a
+ href="../features/seqfetch.html"
+ >sequence fetcher</a> using each sequence's ID string (or each string in
+ the ID separated by the '∣' symbol).
+</p>
<p>If a record (or set of records) is retrieved by any query derived
-from the ID string of a sequence, then the sequence is aligned to the
-ones retrieved to determine the correct start and end residue positions
-(which are displayed when the 'Show Full Sequence ID' option). This is
-important for the correct display of the location of any features
-associated with that database.</p>
+ from the ID string of a sequence, then the sequence is aligned to the
+ ones retrieved to determine the correct start and end residue
+ positions (which are displayed when the 'Show Full Sequence ID'
+ option). This is important for the correct display of the location of
+ any features associated with that database.</p>
<p>If the alignment reveals differences between the sequence in the
-alignment and the one in the record, then Jalview will assume that the
-aligned sequence is not the one in the retrieved record.</p>
-<p>In some cases, the ID used to retrieve records may be out
-of date and a dialog box will be opened indicating that a 100% match
-between the sequence and the record was identified, but the
-sequence name is different. In this case, the can be manually
-changed (by right clicking on the sequence ID and selecting <strong>Sequence→Edit
-Name</strong>).
+ alignment and the one in the record, then Jalview will assume that the
+ aligned sequence is not the one in the retrieved record.</p>
+<p>
+ In some cases, the ID used to retrieve records may be out of date and
+ a dialog box will be opened indicating that a 100% match between the
+ sequence and the record was identified, but the sequence name is
+ different. In this case, the can be manually changed (by right
+ clicking on the sequence ID and selecting <strong>Sequence→Edit
+ Name</strong>).
<ul>
- <li><em>Note</em><br>
- Please remember to save your alignment if either the start/end
- numbering, or the sequence IDs were updated during the ID
- retrieval process.</li>
+ <li><em>Note</em><br> Please remember to save your alignment
+ if either the start/end numbering, or the sequence IDs were updated
+ during the ID retrieval process.</li>
</ul>
<body></body>
</html>
<title>Web Services</title>
</head>
<body>
- <p>
- <strong>Web services</strong>
- </p>
+ <p>
+ <strong>Web services</strong>
+ </p>
- <p>Jalview includes clients for a variety of web services for both
- bioinformatic data retrieval and analysis.
- <ul>
- <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
- utilises web services for sequence, alignment and structure retrieval
- provided by the European Bioinformatics Institute (EBI) and
- Distributed Annotation System servers that are capable of serving
- sequences.</li>
- <li>The <a href="../features/dasfeatures.html">DAS Feature
- Fetcher</a> enables the retrieval and visualization of features from DAS
- annotation sources</li>
- <li>The <a href="dbreffetcher.html">Database Reference
- Fetcher</a> transfers database references from records available from
- DAS or the public sequence databases.</li>
- <li>The <strong>Web Services</strong> menu in each alignment
- window also provides access to the following:
- <ul>
- <li>Programs for <a href="msaclient.html">multiple sequence
- alignment</a>, made available <em>via</em> <a href="JABAWS.html">Java
- Bioinformatic Analysis Web Service (JABAWS)</a> servers.</li>
- <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
- structure prediction</a> based at the University of Dundee.</li>
- <li>Services for alignment analysis, such as <a
- href="shmr.html">Multi-Harmony</a>.
- </ul>
- <p>
- <strong>Web Service Dialog Box</strong>
- </p> <img src="clwqueued.gif">
- <p>This dialog box is displayed when a web service job is
- submitted. It gives the name of the service and any method citation
- information, and monitors the progress of the calculation. The
- cancel button will permanently cancel the job, but this is only
- possible for some services.</p> The <a href="webServicesPrefs.html">Web
- Services Preference panel</a> controls the display and appearance of the
- submission and analysis services in the <strong>Web Services</strong>
- menu.</li>
- <li>If Jalview encounters problems accessing any services, it may
- display a <a href="webServicesPrefs.html#wswarnings">warning
- dialog box</a> (this can be turned off using the web services
- preferences tab).</li>
- </ul>
- </p>
- <p>
- <strong>More about Jalview's Web Services</strong> <br> Jalview's
- distributed computations utilise <a
- href="http://en.wikipedia.org/wiki/SOAP">SOAP</a> and <a
- href="http://en.wikipedia.org/wiki/Representational_State_Transfer">REST</a>
- web services exposing sequence alignment, analysis, and secondary
- structure prediction programs. Originally, Jalview 2's services were
- maintained by the Barton group at the University of Dundee, and ran
- programs on the Life Sciences High-performace Computing Cluster. With
- the advent of <a href="http://www.compbio.dundee.ac.uk/JABAWS">JABAWS</a>,
- however, it is possible for anyone to host Jalview web services.
- </p>
+ <p>Jalview includes clients for a variety of web services for both
+ bioinformatic data retrieval and analysis.
+ <ul>
+ <li>The <a href="../features/seqfetch.html">Sequence
+ Fetcher</a> utilises web services for sequence, alignment and
+ structure retrieval provided by the European Bioinformatics
+ Institute (EBI) and Distributed Annotation System servers that are
+ capable of serving sequences.
+ </li>
+ <li>The <a href="../features/dasfeatures.html">DAS Feature
+ Fetcher</a> enables the retrieval and visualization of features from
+ DAS annotation sources
+ </li>
+ <li>The <a href="dbreffetcher.html">Database Reference
+ Fetcher</a> transfers database references from records available
+ from DAS or the public sequence databases.
+ </li>
+ <li>The <strong>Web Services</strong> menu in each alignment
+ window also provides access to the following:
+ <ul>
+ <li>Programs for <a href="msaclient.html">multiple
+ sequence alignment</a>, made available <em>via</em> <a
+ href="JABAWS.html"
+ >Java Bioinformatic Analysis Web Service (JABAWS)</a> servers.
+ </li>
+ <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
+ structure prediction</a> based at the University of Dundee.
+ </li>
+ <li>Services for alignment analysis, such as <a
+ href="shmr.html"
+ >Multi-Harmony</a>.
+ </ul>
+ <p>
+ <strong>Web Service Dialog Box</strong>
+ </p> <img src="clwqueued.gif">
+ <p>This dialog box is displayed when a web service job is
+ submitted. It gives the name of the service and any method
+ citation information, and monitors the progress of the
+ calculation. The cancel button will permanently cancel the job,
+ but this is only possible for some services.</p> The <a
+ href="webServicesPrefs.html"
+ >Web Services Preference panel</a> controls the display and appearance
+ of the submission and analysis services in the <strong>Web
+ Services</strong> menu.
+ </li>
+ <li>If Jalview encounters problems accessing any services, it
+ may display a <a href="webServicesPrefs.html#wswarnings">warning
+ dialog box</a> (this can be turned off using the web services
+ preferences tab).
+ </li>
+ </ul>
+ </p>
+ <p>
+ <strong>More about Jalview's Web Services</strong> <br>
+ Jalview's distributed computations utilise <a
+ href="http://en.wikipedia.org/wiki/SOAP"
+ >SOAP</a> and <a
+ href="http://en.wikipedia.org/wiki/Representational_State_Transfer"
+ >REST</a> web services exposing sequence alignment, analysis, and
+ secondary structure prediction programs. Originally, Jalview 2's
+ services were maintained by the Barton group at the University of
+ Dundee, and ran programs on the Life Sciences High-performace
+ Computing Cluster. With the advent of <a
+ href="http://www.compbio.dundee.ac.uk/JABAWS"
+ >JABAWS</a>, however, it is possible for anyone to host Jalview web
+ services.
+ </p>
</body>
</html>
<title>JNet Secondary Structure Prediction</title>
</head>
<body>
-<strong>JNet Secondary Structure Prediction</strong>
-<p>
+ <strong>JNet Secondary Structure Prediction</strong>
+ <p>
Secondary structure prediction methods attempts to infer the likely
secondary structure for a protein based on its amino acid
composition and similarity to sequences with known secondary
series of neural networks trained to predict different secondary
structure types from a sequence profile, and when necessary, employs
a jury network to identify the most likely secondary structure
- prediction.<br><ul><li>Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)<br/>
-JPred4: a protein secondary structure prediction server<br/>
-<em>Nucleic Acids Research</em>, <strong>Web Server issue</strong> (first published 15th April 2015)<br/>
-<a href="http://dx.doi.org/10.1093/nar/gkv332">http://dx.doi.org/10.1093/nar/gkv332</a>
- </li>
- <li>Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
- secondary structure prediction server <em>Nucleic Acids Research</em> <strong>36</strong>
- W197-W201</li>
- <li>Cuff J. A and Barton G.J (1999) Application of enhanced
- multiple sequence alignment profiles to improve protein secondary
- structure prediction <em>Proteins</em> <strong>40</strong> 502-511</li>
-</ul>
-</p>
-The function available from the
-<strong>Web Service→Secondary Structure
-Prediction→JNet Secondary Structure Prediction</strong>
-menu does two different kinds of prediction, dependent upon the
-currently selected region:
-</p>
-<ul>
- <li>If nothing is selected, and the displayed sequences appear to
- be aligned, then a JNet prediction will be run for the first sequence
- in the alignment, using the current alignment. Otherwise the first
- sequence will be submitted for prediction.</li>
- <li>If just one sequence (or a region on one sequence) has been
- selected, it will be submitted to the automatic JNet prediction server
- for homolog detection and prediction.</li>
- <li>If a set of sequences are selected, and they appear to be
- aligned, then the alignment will be used for a Jnet prediction on the <strong>first</strong>
- sequence selected in the set (that is, the one nearest the top of the
- alignment window).</li>
-</ul>
-<p><strong>Note</strong>: JNet secondary structure prediction is a
-'non-column-separable' service - predictions are based on the sequence
-profile of contiguous stretches of amino-acid sequence. A prediction
-will only be made on the visible parts of a sequence (see <a
- href="../features/hiddenRegions.html">hiding columns</a>) as if it were
-a contiguous polypeptide chain. Prediction accuracy at the hidden column
-boundaries may therefore be less than indicated by JNet's own
-reliability score (see below).</p>
-<p>The result of a JNet prediction for a sequence is a new annotated
-alignment window:</p>
-<img src="jnetprediction.gif">
-<p>The sequence for which the prediction was made is the first one
-in the alignment. If a sequence based prediction was made then the
-remaining sequences in the alignment are the aligned parts of homologs
-which were used to construct a sequence profile for the prediction. If
-the prediction was made using a multiple alignment, then the original
-multiple alignment will be returned, annotated with the prediction.</p>
-The annotation bars below the alignment are as follows:
-</p>
-<ul>
- <li>Lupas_21, Lupas_14, Lupas_28<br>
- <em>Coiled-coil predictions for the sequence. These are binary
- predictions for each location.</em></li>
- <li>JNETSOL25,JNETSOL5,JNETSOL0<br>
- <em>Solvent accessibility predictions - binary predictions of 25%,
- 5% or 0% solvent accessibility.</em></li>
- <li>JNetPRED<br>
- <em>The consensus prediction - helices are marked as red tubes,
- and sheets as dark green arrows.</em></li>
- <li>JNetCONF<br>
- <em>The confidence estimate for the prediction. High values mean
- high confidence. prediction - helices are marked as red tubes, and
- sheets as dark green arrows.</em></li>
- <li>JNetALIGN<br>
- <em>Alignment based prediction - helices are marked as red tubes,
- and sheets as dark green arrows.</em></li>
- <li>JNetHMM<br>
- <em>HMM profile based prediction - helices are marked as red
- tubes, and sheets as dark green arrows.</em></li>
- <li>jpred<br>
- <em>Jpred prediction - helices are marked as red tubes, and sheets
- as dark green arrows.</em></li>
- <li>JNETPSSM<br>
- <em>PSSM based prediction - helices are marked as red tubes, and
- sheets as dark green arrows.</em></li>
- <li>JNETFREQ<br>
- <em>Amino Acid frequency based prediction - helices are marked as
- red tubes, and sheets as dark green arrows.</em></li>
- <li>JNETJURY<br>
- <em>A '*' in this annotation indicates that the JNETJURY was
- invoked to rationalise significantly different primary predictions.</em></li>
-</ul>
-</p>
- <em>JNet annotation created in Jalview 2.8.2 and later versions
- can be displayed on other alignments via the <a
- href="../features/annotation.html#seqannots">Add reference
- annotation</a> Sequence ID popup menu option.
- </em>
- <em>As of Jalview 2.6, the Jnet service accessed accessed via the
-'Secondary structure prediction' submenu should be considered a legacy
-Jalview SOAP service, and will be replaced in the near future by a
-JPred4 Rest service.</em>
+ prediction.<br>
+ <ul>
+ <li>Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)<br />
+ JPred4: a protein secondary structure prediction server<br /> <em>Nucleic
+ Acids Research</em>, <strong>Web Server issue</strong> (first
+ published 15th April 2015)<br /> <a
+ href="http://dx.doi.org/10.1093/nar/gkv332"
+ >http://dx.doi.org/10.1093/nar/gkv332</a>
+ </li>
+ <li>Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
+ secondary structure prediction server <em>Nucleic Acids
+ Research</em> <strong>36</strong> W197-W201
+ </li>
+ <li>Cuff J. A and Barton G.J (1999) Application of enhanced
+ multiple sequence alignment profiles to improve protein secondary
+ structure prediction <em>Proteins</em> <strong>40</strong> 502-511
+ </li>
+ </ul>
+ </p>
+ The function available from the
+ <strong>Web Service→Secondary Structure
+ Prediction→JNet Secondary Structure Prediction</strong> menu does two
+ different kinds of prediction, dependent upon the currently selected
+ region:
+ </p>
+ <ul>
+ <li>If nothing is selected, and the displayed sequences appear
+ to be aligned, then a JNet prediction will be run for the first
+ sequence in the alignment, using the current alignment. Otherwise
+ the first sequence will be submitted for prediction.</li>
+ <li>If just one sequence (or a region on one sequence) has been
+ selected, it will be submitted to the automatic JNet prediction
+ server for homolog detection and prediction.</li>
+ <li>If a set of sequences are selected, and they appear to be
+ aligned, then the alignment will be used for a Jnet prediction on
+ the <strong>first</strong> sequence selected in the set (that is,
+ the one nearest the top of the alignment window).
+ </li>
+ </ul>
+ <p>
+ <strong>Note</strong>: JNet secondary structure prediction is a
+ 'non-column-separable' service - predictions are based on the
+ sequence profile of contiguous stretches of amino-acid sequence. A
+ prediction will only be made on the visible parts of a sequence (see
+ <a href="../features/hiddenRegions.html">hiding columns</a>) as if
+ it were a contiguous polypeptide chain. Prediction accuracy at the
+ hidden column boundaries may therefore be less than indicated by
+ JNet's own reliability score (see below).
+ </p>
+ <p>The result of a JNet prediction for a sequence is a new
+ annotated alignment window:</p>
+ <img src="jnetprediction.gif">
+ <p>The sequence for which the prediction was made is the first one
+ in the alignment. If a sequence based prediction was made then the
+ remaining sequences in the alignment are the aligned parts of
+ homologs which were used to construct a sequence profile for the
+ prediction. If the prediction was made using a multiple alignment,
+ then the original multiple alignment will be returned, annotated
+ with the prediction.</p>
+ The annotation bars below the alignment are as follows:
+ </p>
+ <ul>
+ <li>Lupas_21, Lupas_14, Lupas_28<br> <em>Coiled-coil
+ predictions for the sequence. These are binary predictions for
+ each location.</em></li>
+ <li>JNETSOL25,JNETSOL5,JNETSOL0<br> <em>Solvent
+ accessibility predictions - binary predictions of 25%, 5% or 0%
+ solvent accessibility.</em></li>
+ <li>JNetPRED<br> <em>The consensus prediction -
+ helices are marked as red tubes, and sheets as dark green
+ arrows.</em></li>
+ <li>JNetCONF<br> <em>The confidence estimate for the
+ prediction. High values mean high confidence. prediction -
+ helices are marked as red tubes, and sheets as dark green
+ arrows.</em></li>
+ <li>JNetALIGN<br> <em>Alignment based prediction -
+ helices are marked as red tubes, and sheets as dark green
+ arrows.</em></li>
+ <li>JNetHMM<br> <em>HMM profile based prediction -
+ helices are marked as red tubes, and sheets as dark green
+ arrows.</em></li>
+ <li>jpred<br> <em>Jpred prediction - helices are
+ marked as red tubes, and sheets as dark green arrows.</em></li>
+ <li>JNETPSSM<br> <em>PSSM based prediction - helices
+ are marked as red tubes, and sheets as dark green arrows.</em></li>
+ <li>JNETFREQ<br> <em>Amino Acid frequency based
+ prediction - helices are marked as red tubes, and sheets as dark
+ green arrows.</em></li>
+ <li>JNETJURY<br> <em>A '*' in this annotation
+ indicates that the JNETJURY was invoked to rationalise
+ significantly different primary predictions.</em></li>
+ </ul>
+ </p>
+ <em>JNet annotation created in Jalview 2.8.2 and later versions
+ can be displayed on other alignments via the <a
+ href="../features/annotation.html#seqannots"
+ >Add reference annotation</a> Sequence ID popup menu option.
+ </em>
+ <em>As of Jalview 2.6, the Jnet service accessed accessed via the
+ 'Secondary structure prediction' submenu should be considered a
+ legacy Jalview SOAP service, and will be replaced in the near future
+ by a JPred4 Rest service.</em>
</body>
</html>
<title>Multiple Sequence Alignment Web Service</title>
</head>
<body>
-<strong>Multiple Sequence Alignment Web Services</strong>
- <p>
- Multiple sequence alignment services are accessed from the <strong>Alignment</strong>
- submenu of the Alignment Window's <strong>Web Service</strong> menu.
- When an entry from one of these menus is selected, either the
- currently selected residues, or the whole sequence set (if there is no
- selection or only one sequence is selected) will be submitted for
- multiple sequence alignment.
- </p>
- <p>There are two kinds of multiple sequence alignment operations
-available:
-<ul>
- <li><em>alignment</em> - where a new alignment is constructed from
- the input</li>
- <li><em>realignment</em> - where any aligned sequences will be
- used by the service to construct a profile based alignment of the
- remaining unaligned sequences.</li>
-</ul>
- <strong>JABAWS Alignment services</strong><br> Most alignment services are
- provided by the
- <a href="JABAWS.html">JABAWS framework</a>, which allows you to
- customise the precise parameters used when running each alignment
- prgoram. In addition to the 'Default settings', you may choose from a
- range of alignment preset settings, or create your own using the
- <a href="webServicesParams.html">'Edit Settings And Run ..' dialog
- box</a>.
- </p>
- <p><strong>Alignment programs supported by JABAWS</strong>. <br/>Versions shown are those bundled with JABAWS 2.01 - if you are using a different server, check its home page to find out which versions are provided.<ul>
- <li><a href="http://www.clustal.org/">Clustal Omega and Clustal W</a> (version 2.0.12)</li>
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.8.57b)</li>
- <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>
- <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
- </ul>
-</p>
+ <strong>Multiple Sequence Alignment Web Services</strong>
+ <p>
+ Multiple sequence alignment services are accessed from the <strong>Alignment</strong>
+ submenu of the Alignment Window's <strong>Web Service</strong> menu.
+ When an entry from one of these menus is selected, either the
+ currently selected residues, or the whole sequence set (if there is
+ no selection or only one sequence is selected) will be submitted for
+ multiple sequence alignment.
+ </p>
+ <p>There are two kinds of multiple sequence alignment operations
+ available:
+ <ul>
+ <li><em>alignment</em> - where a new alignment is constructed
+ from the input</li>
+ <li><em>realignment</em> - where any aligned sequences will be
+ used by the service to construct a profile based alignment of the
+ remaining unaligned sequences.</li>
+ </ul>
+ <strong>JABAWS Alignment services</strong>
+ <br> Most alignment services are provided by the
+ <a href="JABAWS.html">JABAWS framework</a>, which allows you to
+ customise the precise parameters used when running each alignment
+ prgoram. In addition to the 'Default settings', you may choose from a
+ range of alignment preset settings, or create your own using the
+ <a href="webServicesParams.html">'Edit Settings And Run ..' dialog
+ box</a>.
+ </p>
+ <p>
+ <strong>Alignment programs supported by JABAWS</strong>. <br />Versions
+ shown are those bundled with JABAWS 2.01 - if you are using a
+ different server, check its home page to find out which versions are
+ provided.
+ <ul>
+ <li><a href="http://www.clustal.org/">Clustal Omega and
+ Clustal W</a> (version 2.0.12)</li>
+ <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a>
+ (version 6.8.57b)</li>
+ <li><a href="http://www.drive5.com/muscle">Muscle</a> (version
+ 3.8.31)</li>
+ <li><a
+ href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+ >Tcoffee</a> (version 8.99)</li>
+ <li><a href="http://probcons.stanford.edu/">Probcons</a>
+ (version 1.12)</li>
+ </ul>
+ </p>
-<p><strong>Multiple Alignments of Sequences with hidden
-columns</strong><br>
-Multiple alignment services are 'column separable' analysis operations.
-If the input contains <a href="../features/hiddenRegions.html">hidden
-columns</a> then each visible segment of the input sequence set will be
-submitted for alignment separately, and the results concatenated (with
-the hidden regions preserved) once all alignment functions have
-completed. Each sub-job's state is reported in its own tab:
-<p>
-<center><strong>Multiple Multiple Sequence Alignment
-sub jobs running at once</strong>
-<center>
-</p>
-<center><img src="multimafftjbs.gif" align="centre"></center>
-</p>
+ <p>
+ <strong>Multiple Alignments of Sequences with hidden
+ columns</strong><br> Multiple alignment services are 'column
+ separable' analysis operations. If the input contains <a
+ href="../features/hiddenRegions.html"
+ >hidden columns</a> then each visible segment of the input sequence
+ set will be submitted for alignment separately, and the results
+ concatenated (with the hidden regions preserved) once all alignment
+ functions have completed. Each sub-job's state is reported in its
+ own tab:
+ <p>
+ <center>
+ <strong>Multiple Multiple Sequence Alignment sub jobs
+ running at once</strong>
+ <center>
+ </p>
+ <center>
+ <img src="multimafftjbs.gif" align="centre">
+ </center>
+ </p>
</body>
</html>
<head>Jalview Desktop RSS News Reader
</head>
<body>
- <p>
- <strong>The Jalview Desktop RSS News Reader</strong><br /> The
- Jalview Desktop includes a built in news reader for the <a
- href="http://www.jalview.org/feeds/desktop/rss">Jalview Desktop
- News Channel</a>.
- </p>
+ <p>
+ <strong>The Jalview Desktop RSS News Reader</strong><br /> The
+ Jalview Desktop includes a built in news reader for the <a
+ href="http://www.jalview.org/feeds/desktop/rss"
+ >Jalview Desktop News Channel</a>.
+ </p>
- <p>We will use the desktop news channel to keep you informed of
- important updates relevant to users of the Jalview desktop, such as
- web service outages and user community events.</p>
- <p>The news reader will be launched automatically when you start
- the Desktop if new items are available. Should you want to browse
- older items, however, you can open it manually from the 'Jalview news
- reader' option in the Desktop's 'Tools' menu.</p>
- <img src="jalviewrssreader.gif" align="center" width="513" height="337"
- alt="Snapshot of the Jalview Desktop's RSS reader" />
- <p>
- The <em>Jalview news reader</em> was introduced in <a
- href="http://www.jalview.org/releaseHistory.html#Jalview2.7">Jalview
- version 2.7</a>. Its implementation is based on <a
- href="http://jswingreader.sourceforge.net/">JSwingReader</a>.
- </p>
+ <p>We will use the desktop news channel to keep you informed of
+ important updates relevant to users of the Jalview desktop, such as
+ web service outages and user community events.</p>
+ <p>The news reader will be launched automatically when you start
+ the Desktop if new items are available. Should you want to browse
+ older items, however, you can open it manually from the 'Jalview
+ news reader' option in the Desktop's 'Tools' menu.</p>
+ <img src="jalviewrssreader.gif" align="center" width="513"
+ height="337" alt="Snapshot of the Jalview Desktop's RSS reader"
+ />
+ <p>
+ The <em>Jalview news reader</em> was introduced in <a
+ href="http://www.jalview.org/releaseHistory.html#Jalview2.7"
+ >Jalview version 2.7</a>. Its implementation is based on <a
+ href="http://jswingreader.sourceforge.net/"
+ >JSwingReader</a>.
+ </p>
</body>
</html>
<title>JABAWS Protein Disorder Prediction Services</title>
</head>
<body>
- <p>
- <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
- The <strong>Web Services→Disorder</strong> menu in the alignment
- window allows access to protein disorder prediction services provided
- by the configured <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
- servers</a>. Each service operates on sequences in the alignment or
- currently selected region (<em>since Jalview 2.8.0b1</em>) to identify
- regions likely to be unstructured or flexible, or alternately, fold to
- form globular domains.
- </p>
- <p>
- Predictor results include both <a href="../features/seqfeatures.html">sequence
- features</a> and sequence associated <a
- href="../features/annotation.html">alignment annotation</a> rows.
- Features display is controlled from the <a
- href="../features/featureSettings.html">Feature Settings</a> dialog
- box. Clicking on the ID for a disorder prediction annotation row will
- highlight or select (if double clicked) the associated sequence for
- that row. You can also use the <em>Sequence Associated</em> option in
- the <a href="../colourSchemes/annotationColouring.html">Colour By
- Annotation</a> dialog box to colour sequences according to the results of
- predictors shown as annotation rows.
- </p>
- <p>JABAWS 2.0 provides four disorder predictors which are described
- below:</p>
- <ul>
- <li><a href="#disembl">DisEMBL</a></li>
- <li><a href="#iupred">IUPred</a></li>
- <li><a href="#ronn">RONN</a></li>
- <li><a href="#globplot">GlobPlot</a></li>
- </ul>
- <p>
- <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
- (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of machine-learning
- based predictors trained to recognise disorder-related annotation
- found on PDB structures.
- </p>
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>COILS</strong></td>
- <td>Sequence Feature &<br />Annotation Row
- </td>
- <td>Predicts loops/coils according to DSSP definition<a
- href="#dsspstates">[1]</a>.<br />Features mark range(s) of residues
- predicted as loops/coils, and annotation row gives raw value for
- each residue. Value over 0.516 indicates loop/coil.
- </td>
- </tr>
- <tr>
- <td><strong>HOTLOOPS</strong></td>
- <td>Sequence Feature &<br />Annotation Row
- </td>
- <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
- namely those loops with a high degree of mobility as determined from
- Cα temperature factors (B factors). It follows that highly
- dynamic loops should be considered protein disorder."<br />
- Features mark range(s) of residues predicted to be hot loops and
- annotation row gives raw value for each residue. Values over 0.6
- indicates hot loop.
- </td>
- </tr>
- <tr>
- <td><strong>REMARK465</strong></td>
- <td>Sequence Feature &<br />Annotation Row
- </td>
- <td>"Missing coordinates in X-ray structure as defined by
- remark465 entries in PDB. Nonassigned electron densities most often
- reflect intrinsic disorder, and have been used early on in disorder
- prediction."<br /> Features gives range(s) of residues
- predicted as disordered, and annotation row gives raw value for each
- residue. Value over 0.1204 indicates disorder.
- </td>
- </tr>
- </table>
+ <p>
+ <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
+ The <strong>Web Services→Disorder</strong> menu in the
+ alignment window allows access to protein disorder prediction
+ services provided by the configured <a
+ href="http://www.compbio.dundee.ac.uk/jabaws"
+ >JABAWS servers</a>. Each service operates on sequences in the
+ alignment or currently selected region (<em>since Jalview
+ 2.8.0b1</em>) to identify regions likely to be unstructured or
+ flexible, or alternately, fold to form globular domains.
+ </p>
+ <p>
+ Predictor results include both <a
+ href="../features/seqfeatures.html"
+ >sequence features</a> and sequence associated <a
+ href="../features/annotation.html"
+ >alignment annotation</a> rows. Features display is controlled from
+ the <a href="../features/featureSettings.html">Feature Settings</a>
+ dialog box. Clicking on the ID for a disorder prediction annotation
+ row will highlight or select (if double clicked) the associated
+ sequence for that row. You can also use the <em>Sequence
+ Associated</em> option in the <a
+ href="../colourSchemes/annotationColouring.html"
+ >Colour By Annotation</a> dialog box to colour sequences according to
+ the results of predictors shown as annotation rows.
+ </p>
+ <p>JABAWS 2.0 provides four disorder predictors which are
+ described below:</p>
+ <ul>
+ <li><a href="#disembl">DisEMBL</a></li>
+ <li><a href="#iupred">IUPred</a></li>
+ <li><a href="#ronn">RONN</a></li>
+ <li><a href="#globplot">GlobPlot</a></li>
+ </ul>
+ <p>
+ <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
+ (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of
+ machine-learning based predictors trained to recognise
+ disorder-related annotation found on PDB structures.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>COILS</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>Predicts loops/coils according to DSSP definition<a
+ href="#dsspstates"
+ >[1]</a>.<br />Features mark range(s) of residues predicted as
+ loops/coils, and annotation row gives raw value for each
+ residue. Value over 0.516 indicates loop/coil.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>HOTLOOPS</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
+ namely those loops with a high degree of mobility as determined
+ from Cα temperature factors (B factors). It follows that
+ highly dynamic loops should be considered protein
+ disorder."<br /> Features mark range(s) of residues
+ predicted to be hot loops and annotation row gives raw value for
+ each residue. Values over 0.6 indicates hot loop.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>REMARK465</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>"Missing coordinates in X-ray structure as defined
+ by remark465 entries in PDB. Nonassigned electron densities most
+ often reflect intrinsic disorder, and have been used early on in
+ disorder prediction."<br /> Features gives range(s) of
+ residues predicted as disordered, and annotation row gives raw
+ value for each residue. Value over 0.1204 indicates disorder.
+ </td>
+ </tr>
+ </table>
- <p>
- <a name="dsspstates"></a>[1]. DSSP Classification: α-helix (H),
- 310-helix (G), β-strand (E) are ordered, and all other states
- (β-bridge (B), β-turn (T), bend (S), π-helix (I), and
- coil (C)) considered loops or coils.
- </p>
+ <p>
+ <a name="dsspstates"></a>[1]. DSSP Classification: α-helix
+ (H), 310-helix (G), β-strand (E) are ordered, and all other
+ states (β-bridge (B), β-turn (T), bend (S), π-helix
+ (I), and coil (C)) considered loops or coils.
+ </p>
- <p>
- <strong><a name="ronn"></a><a
- href="http://www.strubi.ox.ac.uk/RONN">RONN</a></strong> <em>a.k.a.</em>
- Regional Order Neural Network<br />This predictor employs an approach
- known as the 'bio-basis' method to predict regions of disorder in
- sequences based on their local similarity with a gold-standard set of
- disordered protein sequences. It yields a set of disorder prediction
- scores, which are shown as sequence annotation below the alignment.
- </p>
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>JRonn</strong>[2]</td>
- <td>Annotation Row</td>
- <td>RONN score for each residue in the sequence. Scores above
- 0.5 identify regions of the protein likely to be disordered.</td>
- </tr>
- </table>
- <p>
- <em>[2]. JRonn denotes the score for this server because JABAWS
- runs a Java port of RONN developed by Peter Troshin and distributed
- as part of <a href="http://www.biojava.org/">Biojava 3</a>
- </em>
- </p>
- <p>
- <strong><a name="iupred"></a><a
- href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br /> IUPred
- employs an empirical model to estimate likely regions of disorder.
- There are three different prediction types offered, each using
- different parameters optimized for slightly different applications. It
- provides raw scores based on two models for predicting regions of
- 'long disorder' and 'short disorder'. A third predictor identifies
- regions likely to form structured domains.
- </p>
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>Long disorder</strong></td>
- <td>Annotation Row</td>
- <td>Prediction of context-independent global disorder that
- encompasses at least 30 consecutive residues of predicted disorder.
- Employs a 100 residue window for calculation.<br />Values above 0.5
- indicates the residue is intrinsically disordered.
- </td>
- </tr>
- <tr>
- <td><strong>Short disorder</strong></td>
- <td>Annotation Row</td>
- <td>Predictor for short, (and probably) context-dependent,
- disordered regions, such as missing residues in the X-ray structure
- of an otherwise globular protein. Employs a 25 residue window for
- calculation, and includes adjustment parameter for chain termini
- which favors disorder prediction at the ends.<br />Values above 0.5
- indicate short-range disorder.
- </td>
- </tr>
- <tr>
- <td><strong>Structured domains</strong></td>
- <td>Sequence Feature</td>
- <td>Features highlighting likely globular domains useful for
- structure genomics investigation. <br />Post-analysis of disordered
- region profile to find continuous regions confidently predicted to
- be ordered. Neighbouring regions close to each other are merged,
- while regions shorter than the minimal domain size of at least 30
- residues are ignored.
- </td>
- </tr>
- </table>
- <p>
- <strong><a name="globplot"></a><a
- href="http://globplot.embl.de/">GLOBPLOT</a></strong><br /> Defines regions
- of globularity or natively unstructured regions based on a running sum
- of the propensity of residues to be structured or unstructured. The
- propensity is calculated based on the probability of each amino acid
- being observed within well defined regions of secondary structure or
- within regions of random coil. The initial signal is smoothed with a
- Savitzky-Golay filter, and its first order derivative computed.
- Residues for which the first order derivative is positive are
- designated as natively unstructured, whereas those with negative
- values are structured.<br />
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>Disordered Region</strong></td>
- <td>Sequence Feature</td>
- <td><br />Sequence features marking range(s) of residues with
- positive dydx values (correspond to the #Disorder column from JABAWS
- results)</td>
- </tr>
- <tr>
- <td><strong>Globular Domain</strong>
- <td>Sequence Feature</td>
- <td>Putative globular domains</td>
- </tr>
- <tr>
- <td><strong>Dydx</strong></td>
- <td>Annotation row</td>
- <td>First order derivative of smoothed score. Values above 0
- indicates residue is disordered.</td>
- </tr>
- <tr>
- <td><strong>Smoothed Score<br />Raw Score
- </strong></td>
- <td>Annotation Row</td>
- <td>The smoothed and raw scores used to create the differential
- signal that indicates the presence of unstructured regions.<br /> <em>These
- are hidden by default, but can be shown by right-clicking on the
- alignment annotation panel and selecting <strong>Show
- hidden annotation</strong>
- </em>
- </td>
- </tr>
- </table>
- <p>
- <em>Documentation and thresholds for the JABAWS Disorder
- predictors adapted from a personal communication by Nancy Giang,
- 2012.</em>
- </p>
+ <p>
+ <strong><a name="ronn"></a><a
+ href="http://www.strubi.ox.ac.uk/RONN"
+ >RONN</a></strong> <em>a.k.a.</em> Regional Order Neural Network<br />This
+ predictor employs an approach known as the 'bio-basis' method to
+ predict regions of disorder in sequences based on their local
+ similarity with a gold-standard set of disordered protein sequences.
+ It yields a set of disorder prediction scores, which are shown as
+ sequence annotation below the alignment.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>JRonn</strong>[2]</td>
+ <td>Annotation Row</td>
+ <td>RONN score for each residue in the sequence. Scores above
+ 0.5 identify regions of the protein likely to be disordered.</td>
+ </tr>
+ </table>
+ <p>
+ <em>[2]. JRonn denotes the score for this server because JABAWS
+ runs a Java port of RONN developed by Peter Troshin and
+ distributed as part of <a href="http://www.biojava.org/">Biojava
+ 3</a>
+ </em>
+ </p>
+ <p>
+ <strong><a name="iupred"></a><a
+ href="http://iupred.enzim.hu/Help.php"
+ >IUPred</a></strong><br /> IUPred employs an empirical model to estimate
+ likely regions of disorder. There are three different prediction
+ types offered, each using different parameters optimized for
+ slightly different applications. It provides raw scores based on two
+ models for predicting regions of 'long disorder' and 'short
+ disorder'. A third predictor identifies regions likely to form
+ structured domains.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>Long disorder</strong></td>
+ <td>Annotation Row</td>
+ <td>Prediction of context-independent global disorder that
+ encompasses at least 30 consecutive residues of predicted
+ disorder. Employs a 100 residue window for calculation.<br />Values
+ above 0.5 indicates the residue is intrinsically disordered.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Short disorder</strong></td>
+ <td>Annotation Row</td>
+ <td>Predictor for short, (and probably) context-dependent,
+ disordered regions, such as missing residues in the X-ray
+ structure of an otherwise globular protein. Employs a 25 residue
+ window for calculation, and includes adjustment parameter for
+ chain termini which favors disorder prediction at the ends.<br />Values
+ above 0.5 indicate short-range disorder.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Structured domains</strong></td>
+ <td>Sequence Feature</td>
+ <td>Features highlighting likely globular domains useful for
+ structure genomics investigation. <br />Post-analysis of
+ disordered region profile to find continuous regions confidently
+ predicted to be ordered. Neighbouring regions close to each
+ other are merged, while regions shorter than the minimal domain
+ size of at least 30 residues are ignored.
+ </td>
+ </tr>
+ </table>
+ <p>
+ <strong><a name="globplot"></a><a
+ href="http://globplot.embl.de/"
+ >GLOBPLOT</a></strong><br /> Defines regions of globularity or natively
+ unstructured regions based on a running sum of the propensity of
+ residues to be structured or unstructured. The propensity is
+ calculated based on the probability of each amino acid being
+ observed within well defined regions of secondary structure or
+ within regions of random coil. The initial signal is smoothed with a
+ Savitzky-Golay filter, and its first order derivative computed.
+ Residues for which the first order derivative is positive are
+ designated as natively unstructured, whereas those with negative
+ values are structured.<br />
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>Disordered Region</strong></td>
+ <td>Sequence Feature</td>
+ <td><br />Sequence features marking range(s) of residues
+ with positive dydx values (correspond to the #Disorder column
+ from JABAWS results)</td>
+ </tr>
+ <tr>
+ <td><strong>Globular Domain</strong>
+ <td>Sequence Feature</td>
+ <td>Putative globular domains</td>
+ </tr>
+ <tr>
+ <td><strong>Dydx</strong></td>
+ <td>Annotation row</td>
+ <td>First order derivative of smoothed score. Values above 0
+ indicates residue is disordered.</td>
+ </tr>
+ <tr>
+ <td><strong>Smoothed Score<br />Raw Score
+ </strong></td>
+ <td>Annotation Row</td>
+ <td>The smoothed and raw scores used to create the
+ differential signal that indicates the presence of unstructured
+ regions.<br /> <em>These are hidden by default, but can be
+ shown by right-clicking on the alignment annotation panel and
+ selecting <strong>Show hidden annotation</strong>
+ </em>
+ </td>
+ </tr>
+ </table>
+ <p>
+ <em>Documentation and thresholds for the JABAWS Disorder
+ predictors adapted from a personal communication by Nancy Giang,
+ 2012.</em>
+ </p>
</body>
</html>
<title>Multi-Group Sequence Harmony and Multi-Relief</title>
</head>
<body>
- <strong>Functional residue analysis with Sequence Harmony and
- Multi-Relief</strong>
- <p>
- The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or SHMR) service (<a
- href="#shmrref">Brandt, Feenstra and Heringa, 2010</a>) available
- from the <em>Analysis</em> sub-menu of the alignment window's web
- services menu provides a method for the identification of significant
- patterns of <em>sub-family variation</em> amongst the columns of an
- alignment.
- </p>
- <p>
- <strong>Instructions for use</strong><br> The service requires a
- protein sequence multiple alignment that has been sub-divided into
- groups containing at least two non-identical protein sequences. An
- easy way to create groups is to use the built-in <a
- href="../calculations/tree.html">neighbour-joining or UPGMA tree</a>
- routines to calculate a tree for the alignment, and then click on the
- tree to subdivide the alignment.
- </p>
- <p>
- The SHMR service operates on the currently selected visible region(s)
- of the alignment. Once submitted, a job progress window will display
- status information about your job, including a URL which allows you to
- visit the status page on the
- <a href="http://zeus.few.vu.nl/programs/shmrwww/">IBIVU SHMR server</a>.
- </p>
- <p>When the job is complete, Jalview will automatically open a new
- window containing the alignment and groups that were submitted for
- analysis, with additional histograms added portraying the SHMR scores
- for each column of the sub-grouped alignment.</p>
- <p>
- If you use this service in your work, please cite :<br /><a name="shmrref"/> Brandt,
- B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting
- functional specificity from sequence alignment. <a
- href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415">Nucleic
- Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
- <p>
- <strong><em>Note:</em></strong> The Multi-Harmony service is implemented with a prototype of Jalview's RESTful
- web service client introduced in Jalview 2.7. A few bugs remain in this prototype, which we intend to fixed in version 2.7.1.
- </ul>
- </p>
+ <strong>Functional residue analysis with Sequence Harmony and
+ Multi-Relief</strong>
+ <p>
+ The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or
+ SHMR) service (<a href="#shmrref">Brandt, Feenstra and Heringa,
+ 2010</a>) available from the <em>Analysis</em> sub-menu of the
+ alignment window's web services menu provides a method for the
+ identification of significant patterns of <em>sub-family
+ variation</em> amongst the columns of an alignment.
+ </p>
+ <p>
+ <strong>Instructions for use</strong><br> The service requires
+ a protein sequence multiple alignment that has been sub-divided into
+ groups containing at least two non-identical protein sequences. An
+ easy way to create groups is to use the built-in <a
+ href="../calculations/tree.html"
+ >neighbour-joining or UPGMA tree</a> routines to calculate a tree for
+ the alignment, and then click on the tree to subdivide the
+ alignment.
+ </p>
+ <p>
+ The SHMR service operates on the currently selected visible
+ region(s) of the alignment. Once submitted, a job progress window
+ will display status information about your job, including a URL
+ which allows you to visit the status page on the <a
+ href="http://zeus.few.vu.nl/programs/shmrwww/"
+ >IBIVU SHMR server</a>.
+ </p>
+ <p>When the job is complete, Jalview will automatically open a new
+ window containing the alignment and groups that were submitted for
+ analysis, with additional histograms added portraying the SHMR
+ scores for each column of the sub-grouped alignment.</p>
+ <p>
+ If you use this service in your work, please cite :<br />
+ <a name="shmrref" /> Brandt, B.W.*, Feenstra, K.A*. and Heringa, J.
+ (2010) Multi-Harmony: detecting functional specificity from sequence
+ alignment. <a
+ href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415"
+ >Nucleic Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
+
+ <p>
+ <strong><em>Note:</em></strong> The Multi-Harmony service is
+ implemented with a prototype of Jalview's RESTful web service client
+ introduced in Jalview 2.7. A few bugs remain in this prototype,
+ which we intend to fixed in version 2.7.1.
+ </ul>
+ </p>
</body>
</html>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head>
-Opening URLs from Jalview
+<head>Opening URLs from Jalview
</head>
<body>
-<p>
-<p><strong>Opening URLs from Jalview</strong><br>
-Both the applet and the desktop application are able to open URLs as
-'popups' in your web browser. <br>
-Double-clicking on the ID of a sequence will open the first URL that can
-be generated from its sequence ID. This is often the SRS site, but you
-can easily configure your own <a href="#urllinks">sequence URL links</a>.</p>
-<p>Other links for a sequence either derived from any other
-configured URL links, or imported from the sequence's annotation, are
-accessed by right clicking to open the sequence pop-up menu, and
-selecting from the <em>Links</em> submenu.</p>
-<p><strong><a name="urllinks">Configuring URL Links</a></strong>
-<br>URL links are defined in the "Connections" tab of the <a
- href="../features/preferences.html">Jalview desktop preferences</a>, or
-specified as <a
- href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
-parameters</a>. <br>
-By default the item "SRS" is added to this link menu. This
-link will show a web page in your default browser with the selected
-sequence id as part of the URL.<br>
-In the preferences dialog box, click <strong>new</strong> to add a new
-link, and <strong>edit</strong> to modify an existing link, or <strong>delete</strong>
-to remove it.<br>
-You can name the link, this will be displayed on a new menu item under
-the "Link" menu when you right click on a sequence id. <br>
-The URL string must contain a token that can be replaced with a sequence
-ID. The simplest token is "$SEQUENCE_ID$", which will be
-replaced by the chosen sequence id when you click on it.</p>
-<p>eg.<br>
-UniRef100 =
-http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br>
-Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br>
-<br>
-Links will also be made for any database cross references associated
-with the sequence where the database name exactly matches a URL link
-name. In this case, the $SEQUENCE_ID$ string will be replaced with the
-accession string for the database cross-reference, rather than the
-sequence ID for the sequence (<em>since Jalview 2.4</em>).</p>
-<p><strong>Regular Expression Substitution</strong><br>
-A url may contain a string of the form $SEQUENCE_ID=/<em>regular
-expression</em>/=$. In this case, the regular expression will be applied to
-the full sequence ID string and the resulting match will be inserted
-into the URL. Groups of parentheses can be used to specify which regions
-of the regular expression will be used to generate the URL:
-<ul>
- <li>Each top level parenthesis will yield a URL containing the
- text matched within that parenthesis.</li>
- <li>Regions matching sub-parentheses within a top-level
- parenthesis will be concatenated to form the text inserted into the URL
- for the top-level parenthesis.</li>
- <em>Please Note:
- <ul>
- <li>The regular expressions supported by Jalview are those
- provided by the <a href="www.javaregex.com">Stevesoft javaregex
- package</a>.</li>
- <li>Some characters must be escaped when specifying them as a
- match within a regular expression.</li>
- </ul>
- <br>
- Many Thanks to Bernd Brandt of the Free University of Amsterdam for
- testing this new regular-expression expansion feature! </em>
- <em>
-</ul>
-</p>
-</p>
+ <p>
+ <p>
+ <strong>Opening URLs from Jalview</strong><br> Both the applet
+ and the desktop application are able to open URLs as 'popups' in
+ your web browser. <br> Double-clicking on the ID of a sequence
+ will open the first URL that can be generated from its sequence ID.
+ This is often the SRS site, but you can easily configure your own <a
+ href="#urllinks"
+ >sequence URL links</a>.
+ </p>
+ <p>
+ Other links for a sequence either derived from any other configured
+ URL links, or imported from the sequence's annotation, are accessed
+ by right clicking to open the sequence pop-up menu, and selecting
+ from the <em>Links</em> submenu.
+ </p>
+ <p>
+ <strong><a name="urllinks">Configuring URL Links</a></strong> <br>URL
+ links are defined in the "Connections" tab of the <a
+ href="../features/preferences.html"
+ >Jalview desktop preferences</a>, or specified as <a
+ href="http://www.jalview.org/examples/appletParameters.html#parameters"
+ >applet parameters</a>. <br> By default the item "SRS"
+ is added to this link menu. This link will show a web page in your
+ default browser with the selected sequence id as part of the URL.<br>
+ In the preferences dialog box, click <strong>new</strong> to add a
+ new link, and <strong>edit</strong> to modify an existing link, or <strong>delete</strong>
+ to remove it.<br> You can name the link, this will be displayed
+ on a new menu item under the "Link" menu when you right
+ click on a sequence id. <br> The URL string must contain a
+ token that can be replaced with a sequence ID. The simplest token is
+ "$SEQUENCE_ID$", which will be replaced by the chosen
+ sequence id when you click on it.
+ </p>
+ <p>
+ eg.<br> UniRef100 =
+ http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br>
+ Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br> <br>
+ Links will also be made for any database cross references associated
+ with the sequence where the database name exactly matches a URL link
+ name. In this case, the $SEQUENCE_ID$ string will be replaced with
+ the accession string for the database cross-reference, rather than
+ the sequence ID for the sequence (<em>since Jalview 2.4</em>).
+ </p>
+ <p>
+ <strong>Regular Expression Substitution</strong><br> A url may
+ contain a string of the form $SEQUENCE_ID=/<em>regular
+ expression</em>/=$. In this case, the regular expression will be
+ applied to the full sequence ID string and the resulting match will
+ be inserted into the URL. Groups of parentheses can be used to
+ specify which regions of the regular expression will be used to
+ generate the URL:
+ <ul>
+ <li>Each top level parenthesis will yield a URL containing the
+ text matched within that parenthesis.</li>
+ <li>Regions matching sub-parentheses within a top-level
+ parenthesis will be concatenated to form the text inserted into
+ the URL for the top-level parenthesis.</li>
+ <em>Please Note:
+ <ul>
+ <li>The regular expressions supported by Jalview are those
+ provided by the <a href="www.javaregex.com">Stevesoft
+ javaregex package</a>.
+ </li>
+ <li>Some characters must be escaped when specifying them as
+ a match within a regular expression.</li>
+ </ul> <br> Many Thanks to Bernd Brandt of the Free University of
+ Amsterdam for testing this new regular-expression expansion
+ feature!
+ </em>
+ <em>
+ </ul>
+ </p>
+ </p>
</body>
</html>
<title>Web Service Job Parameter Dialog Box</title>
</head>
<body>
-<p><strong>Web service Job Parameter Dialog box</strong></p>
+ <p>
+ <strong>Web service Job Parameter Dialog box</strong>
+ </p>
-<p>Some Jalview services, including those provided by <a
- href="JABAWS.html">JABAWS</a>, support a range of parameters and
-options, enabling you to employ the most appropriate settings for the
-input data. In addition to any preset combinations provided by
-services themselves, the Web services parameters dialog box also allows
-you to create and store your own parameter sets, so they can be accessed
-quickly from the presets menu.</p>
-<p><Strong>Accessing the parameter dialog box</Strong><br>
-The parameters dialog box is opened by selecting the 'Edit and Run' menu
-entries within the JABAWS analysis submenu of the alignment window's web
-services menu. Once opened, it presents the parameters and options
-available for the chosen analysis for you to modify, and and also
-enables you to browse any available service presets and select, create
-or modify your own user defined parameter sets. Once you are satisfied
-with the analysis parameters, press the <strong>Start Job</strong>
-button to initiate the analysis.</p>
-<p><Strong>Getting help on the analysis parameters</Strong><br>
-Each option or parameter shown in the dialog is accompanied by a brief
-description, which is shown as a tooltip when the mouse is moved over
-it. For some, a link symbol will also be shown (as in the example
-below), indicating that further information is available online. In this
-case, right-clicking (or command-click) will open a pop-up menu allowing
-you to select a URL to open in your web browser.</p>
-<p>
-<center><img src="wsparams.gif" align="center" width="480"
- height="499" alt="Analysis Parameters Dialog Box for JABAWS Services">
-<br>
-Parameter settings dialog box for JABAWS MAFFT Service</center>
-</p>
-<p>The menu and text box at the top of the dialog box displays the
-name of the current parameter set. The name can be edited, should you
-wish to change or create a new user defined set, or clicked to present a
-menu enabling other sets to be browsed. The description shown below may
-also be edited (and the box resized to facilitate this), allowing you to
-provide notes to accompany the parameter set. The modification of these
-or any of the option or parameter settings will enable one or more of
-the following buttons, that allow you to:
-<ul>
- <li><em>Revert</em> the changes you have made. This will undo any
- changes you have made to the parameters and options with respect to the
- currently selected parameter set, reverting each setting to its default
- or last saved value.</li>
- <li><em>Create</em> a new parameter set. Selecting this option
- will create a new parameter set with the given name. New parameter sets
- will be saved for the current session, but a file chooser will also
- open which gives you the option to save the set for use in future
- sessions.</li>
- <li><em>Update</em> an existing user defined parameter set. This
- button will save any modifications you have made to the current
- parameter set.</li>
- <li><em>Rename</em> the current user defined parameter set. This
- will update the name recorded for the current parameter set.</li>
- <li><em>Delete</em> the current parameter set. Selecting this will
- erase the current user defined parameter set from memory, and delete
- its associated parameter file (if it exists).</li>
-</ul>
-</p>
-<p><em>Support for adjusting and saving web service parameter
-sets was added in Jalview 2.6</em></p>
+ <p>
+ Some Jalview services, including those provided by <a
+ href="JABAWS.html"
+ >JABAWS</a>, support a range of parameters and options, enabling you
+ to employ the most appropriate settings for the input data. In
+ addition to any preset combinations provided by services themselves,
+ the Web services parameters dialog box also allows you to create and
+ store your own parameter sets, so they can be accessed quickly from
+ the presets menu.
+ </p>
+ <p>
+ <Strong>Accessing the parameter dialog box</Strong><br> The
+ parameters dialog box is opened by selecting the 'Edit and Run' menu
+ entries within the JABAWS analysis submenu of the alignment window's
+ web services menu. Once opened, it presents the parameters and
+ options available for the chosen analysis for you to modify, and and
+ also enables you to browse any available service presets and select,
+ create or modify your own user defined parameter sets. Once you are
+ satisfied with the analysis parameters, press the <strong>Start
+ Job</strong> button to initiate the analysis.
+ </p>
+ <p>
+ <Strong>Getting help on the analysis parameters</Strong><br>
+ Each option or parameter shown in the dialog is accompanied by a
+ brief description, which is shown as a tooltip when the mouse is
+ moved over it. For some, a link symbol will also be shown (as in the
+ example below), indicating that further information is available
+ online. In this case, right-clicking (or command-click) will open a
+ pop-up menu allowing you to select a URL to open in your web
+ browser.
+ </p>
+ <p>
+ <center>
+ <img src="wsparams.gif" align="center" width="480" height="499"
+ alt="Analysis Parameters Dialog Box for JABAWS Services"
+ > <br> Parameter settings dialog box for JABAWS MAFFT Service
+ </center>
+ </p>
+ <p>The menu and text box at the top of the dialog box displays the
+ name of the current parameter set. The name can be edited, should
+ you wish to change or create a new user defined set, or clicked to
+ present a menu enabling other sets to be browsed. The description
+ shown below may also be edited (and the box resized to facilitate
+ this), allowing you to provide notes to accompany the parameter set.
+ The modification of these or any of the option or parameter settings
+ will enable one or more of the following buttons, that allow you to:
+
+ <ul>
+ <li><em>Revert</em> the changes you have made. This will undo
+ any changes you have made to the parameters and options with
+ respect to the currently selected parameter set, reverting each
+ setting to its default or last saved value.</li>
+ <li><em>Create</em> a new parameter set. Selecting this option
+ will create a new parameter set with the given name. New parameter
+ sets will be saved for the current session, but a file chooser
+ will also open which gives you the option to save the set for use
+ in future sessions.</li>
+ <li><em>Update</em> an existing user defined parameter set.
+ This button will save any modifications you have made to the
+ current parameter set.</li>
+ <li><em>Rename</em> the current user defined parameter set.
+ This will update the name recorded for the current parameter set.</li>
+ <li><em>Delete</em> the current parameter set. Selecting this
+ will erase the current user defined parameter set from memory, and
+ delete its associated parameter file (if it exists).</li>
+ </ul>
+ </p>
+ <p>
+ <em>Support for adjusting and saving web service parameter sets
+ was added in Jalview 2.6</em>
+ </p>
</body>
</html>
<title>The Web Services Preferences Dialog Box</title>
</head>
<body>
-<p><strong>The Web Services Preferences Dialog Box</strong></p>
+ <p>
+ <strong>The Web Services Preferences Dialog Box</strong>
+ </p>
-<p>Jalview includes a range of web services clients for data
-retrieval and analysis. The <em>Web Services</em> menu found in each
-alignment window provides access to some of these services, and is
-configured <em>via</em> the web services preference dialog box,
-available from the <em>Preferences</em> panel from the <strong>Tools→Preferences...</strong>
-menu from the Jalview Desktop window's menu bar.</p>
-<p>
-<center><img src="wsprefs.gif" align="center"
- alt="Web Services Preferences Panel" width="571" height="461"><br>
-Web Services Preference Panel</center>
-</p>
- <p>
- <strong>Configuring the list of JABAWS servers</strong><br> The
- main area of the panel shows the list of <a href="JABAWS.html">JABAWS</a>
- servers that Jalview is currently aware of. The list includes a colour coded status:
- green indicates that all services are available for a given server,
- amber signifies that one or more services on the server are not fully
- functional, and red highlights servers that could not be contacted or
- are not functional for some other reason.
- </p>
- <p>A server's URL may be added,
-edited by double clicking on it, or deleted by selecting it and using
-the buttons below. After adding or editing a server's URL, you will be
-asked if you wish to test the server. If you wish to do so, then first
-ensure you can view the new server's test report, which will be output
-on Jalview's standard console output (you can open Jalview's built in
-console viewer via the <strong>Tools→Java Console</strong> menu
-option).</p>
-<p><strong>Controlling the layout of the Web Services Menu</strong><br>
-The range of services that Jalview is able to access depends upon your
-requirements, and local computational resources. However, when a large
-number of resources are available, then the entries and sub menus in the
-<strong>web services</strong> menu can quickly become unwieldly. The
-options in the lower part of the dialog box enable you to control the
-display of each type of analysis service client in the web services
-menu. In addition, indexing options are provided that enable you to
-define the layout of the menus provided for JABAWS services by sorting
-them into submenus according to analysis type and/or host server.</p>
-<p><em>The web services preferences panel was added in Jalview
-2.6, and server status indications added in Jalview 2.8.</em></p>
-<p><strong><a name="wswarnings">Web Services Invalid
-URL warnings</a></strong><br>
-Jalview may inform you of any problems contacting the web services by
-showing a dialog box like the one below:<br>
-<center><img src="invalidurldialog.gif" align="center"
- alt="Web Services Invalid URL Warning dialog box" width="389"
- height="258"><br>
-Web Services Invalid URL Warning dialog box</center>
-<br>
-<strong><em>Note:</em></strong> this warning will be shown if you are running the Jalview desktop
-without any network connection, or if you have configured
-<a href="JABAWS.html">JABA services</a>
-which cannot be accessed from your location. Should you wish to disable
-these warnings, then uncheck the
-<em>Display warnings</em>
-check box in the web services preferences.
-</p>
-<p><em>The web services warnings dialog box was added in
-Jalview 2.6.1</em></p>
+ <p>
+ Jalview includes a range of web services clients for data retrieval
+ and analysis. The <em>Web Services</em> menu found in each alignment
+ window provides access to some of these services, and is configured
+ <em>via</em> the web services preference dialog box, available from
+ the <em>Preferences</em> panel from the <strong>Tools→Preferences...</strong>
+ menu from the Jalview Desktop window's menu bar.
+ </p>
+ <p>
+ <center>
+ <img src="wsprefs.gif" align="center"
+ alt="Web Services Preferences Panel" width="571" height="461"
+ ><br> Web Services Preference Panel
+ </center>
+ </p>
+ <p>
+ <strong>Configuring the list of JABAWS servers</strong><br> The
+ main area of the panel shows the list of <a href="JABAWS.html">JABAWS</a>
+ servers that Jalview is currently aware of. The list includes a
+ colour coded status: green indicates that all services are available
+ for a given server, amber signifies that one or more services on the
+ server are not fully functional, and red highlights servers that
+ could not be contacted or are not functional for some other reason.
+ </p>
+ <p>
+ A server's URL may be added, edited by double clicking on it, or
+ deleted by selecting it and using the buttons below. After adding or
+ editing a server's URL, you will be asked if you wish to test the
+ server. If you wish to do so, then first ensure you can view the new
+ server's test report, which will be output on Jalview's standard
+ console output (you can open Jalview's built in console viewer via
+ the <strong>Tools→Java Console</strong> menu option).
+ </p>
+ <p>
+ <strong>Controlling the layout of the Web Services Menu</strong><br>
+ The range of services that Jalview is able to access depends upon
+ your requirements, and local computational resources. However, when
+ a large number of resources are available, then the entries and sub
+ menus in the <strong>web services</strong> menu can quickly become
+ unwieldly. The options in the lower part of the dialog box enable
+ you to control the display of each type of analysis service client
+ in the web services menu. In addition, indexing options are provided
+ that enable you to define the layout of the menus provided for
+ JABAWS services by sorting them into submenus according to analysis
+ type and/or host server.
+ </p>
+ <p>
+ <em>The web services preferences panel was added in Jalview
+ 2.6, and server status indications added in Jalview 2.8.</em>
+ </p>
+ <p>
+ <strong><a name="wswarnings">Web Services Invalid URL
+ warnings</a></strong><br> Jalview may inform you of any problems
+ contacting the web services by showing a dialog box like the one
+ below:<br>
+ <center>
+ <img src="invalidurldialog.gif" align="center"
+ alt="Web Services Invalid URL Warning dialog box" width="389"
+ height="258"
+ ><br> Web Services Invalid URL Warning dialog box
+ </center>
+ <br>
+ <strong><em>Note:</em></strong> this warning will be shown if you are
+ running the Jalview desktop without any network connection, or if you
+ have configured
+ <a href="JABAWS.html">JABA services</a> which cannot be accessed from
+ your location. Should you wish to disable these warnings, then uncheck
+ the
+ <em>Display warnings</em> check box in the web services preferences.
+ </p>
+ <p>
+ <em>The web services warnings dialog box was added in Jalview
+ 2.6.1</em>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff