</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><strong>Add <a href="../features/annotation.html#seqannots">Reference Annotations</a></strong><br>
+ <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 the <a
+ href="../features/structurechooser.html">'Structure
+ Chooser' </a>, which allows you to discover and view 3D structures
+ for the current selection. For more info, see <a
+ href="../features/viewingpdbs.html">viewing 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>
git://source.jalview.org / jalview.git / blobdiff