-<html>\r
-<head><title>Popup Menu</title></head>\r
-\r
-<body>\r
-<p><strong>Popup Menu</strong><br>\r
- <em>This menu is visible when right clicking either within a selected region \r
- on the alignment or on a selected sequence name.</em></p>\r
-<ul>\r
- <li><strong>Define </strong> \r
- <ul>\r
- <li><strong>Group<br>\r
- </strong><em>This will display a window asking for the name of the currently \r
- selected group. Click OK to set the name, cancel to use the default group \r
- name. </em><strong><br>\r
- </strong></li>\r
- <li><strong>Remove Group<br>\r
- </strong><em>This will undefine the selected group. </em><strong> <br>\r
- </strong></li>\r
- <li><strong>Group Colour<br>\r
- </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> \r
- of the group.</em><strong> <br>\r
- </strong></li>\r
- <li><strong>Boxes<br>\r
- </strong><em>If selected the background of a residue within the selected \r
- group will be coloured according to the assigned colour scheme.</em><strong> \r
- <br>\r
- </strong></li>\r
- <li><strong> Text<br>\r
- </strong><em>If selected the selected group will display text. </em><strong><br>\r
- </strong></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If selected the selected group will display text in a colour \r
- slightly darker than the background colour of that residue.</em><strong><br>\r
- </strong></li>\r
- <li><strong>Border Colour <br>\r
- </strong><em>Selecting this will display a "Colour Chooser" \r
- window. Select a colour than press OK to set the border colour of a group.</em><strong><br>\r
- </strong></li>\r
- </ul>\r
- </li>\r
- <li><strong>Sequence <br>\r
- </strong><em>This menu is only visible if you right-click on a sequence name. \r
- </em> \r
- <ul>\r
- <li><strong>Edit Name/Description<br>\r
- </strong><em>You may edit the name and description of each sequence. A \r
- window will be displayed asking for a new sequence name and sequence description \r
- to be entered. Press OK to accept your edit. To save sequence descriptions, \r
- you must save in Fasta, PIR or Jalview File format.</em><strong><br>\r
- </strong></li>\r
- <li><strong>View PDB Structure<br>\r
- </strong><em>\r
- If the sequence has a PDB file associated with it Jalview will display \r
- a 3D interactive viewer of the file.<br>\r
-This entry is only present if the sequence has an\r
- <a href="../features/viewingpdbs.html">associated PDB structure</a>.\r
- If you can't see this entry for your sequence, and the sequence name\r
- is a uniprot identifier, then try enabling the "View \r
- -> Sequence Features" and opening the popup menu again.</em>\r
- </li>\r
- </ul>\r
- </li>\r
- <li><strong><em>Link</em></strong><br>\r
- <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> \r
- Connections tab. It is only displayed when you right click (Apple click) on \r
- a sequence id. </em><strong><br>\r
- <br>\r
- </strong></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Popup Menu</title>
+</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>
+
+ </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>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>.
+ <br /> 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>
+<!--
+ <p>
+ <em>Other menu entries may also be shown if the current
+ selection includes sequences with associated structure data:</em><br>
+ <ul>
+ <li><strong>Associate Structure with Sequence</strong>
+ <ul>
+ <li><strong>From File<br>
+ </strong><em>Load a PDB file from local disk which will be associated
+ with this sequence. This file will be used if the user subsequently
+ clicks on "View Structure" menu item.</em></li>
+ <li><strong>Enter PDB id<br>
+ </strong><em>Enter the PDB id from an input window. This PDB id will
+ be used by the service WSDBFetch, provided by the EBI, to fetch the
+ PDB file if the user subsequently clicks on its "View Structure"
+ menu item. </em></li>
+ <li><strong>Discover PDB ids<br>
+ </strong><em>This will use the service WSDBFetch, provided by the
+ EBI, to retrieve all PDB ids associated with the sequences in the
+ alignment if the sequences have valid Uniprot names or accession ids.
+ </em></li>
+ </ul>
+ </li>
+
+ <ul>
+ <li><strong>Structure→View all <em>N</em>
+ structures<br />
+ </strong><em>Opens a new window containing all structures associated
+ with the current selection, superposed according to the currently
+ selected region of the alignment.<br />(This capability was
+ added in Jalview 2.7)
+ </em></li>
+ <li><strong>Structure→View all <em>N</em>
+ representative structures<br />
+ </strong><em>Open a new window containing exactly one structure per
+ currently selected sequence.<br /> (The View representative
+ structures option was introduced in Jalview 2.8.1)
+ </em></li>
+ </ul>
+ <br> -->
+
+ <li><strong>Hide Sequences</strong><br> <em>Hides the
+ currently selected sequences in this alignment view.</em><strong><br>
+ </strong></li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff