help/html/menus/popupMenu.html

   1 <html>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  -->
  22 <head>
  23 <title>Popup Menu</title>
  24 </head>
  25
  26 <body>
  27         <p>
  28                 <strong>Popup Menu</strong><br> <em>This menu is visible
  29                         when right clicking either within a selected region on the alignment
  30                         or on a selected sequence name. It may not be accessible when in
  31                         'Cursor Mode' (toggled with the F2 key).</em>
  32         </p>
  33         <ul>
  34                 <li><strong>Selection</strong>
  35                         <ul>
  36                                 <li><a name="sqreport"><strong>Sequence Details...<br>
  37                                         </strong></a><em>(Since Jalview 2.8)<br>Open an <a
  38                                                 href="../io/exportseqreport.html">HTML report containing the
  39                                                         annotation and database cross references</a>&nbsp;normally shown in
  40                                                 the sequence's tooltip.
  41                                 </em></li>
  42                                 <li><strong>Show Annotations...<br>
  43                                 </strong><em>Choose to show (unhide) either All or a selected type of
  44                                                 annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
  45                                 <li><strong>Hide Annotations...<br>
  46                                 </strong><em>Choose to hide either All or a selected type of annotation
  47                                                 for the selected sequences. (Since Jalview 2.8.2)</em></li>
  48                                 <li><a name="addrefannot"><strong>Add Reference
  49                                                         Annotations<br>
  50                                         </strong><em>Add to the alignment window any annotations on the
  51                                                         selected sequences which have been read from reference sources or
  52                                                         calculated (for example, secondary structure derived from 3D
  53                                                         structure). (Since Jalview 2.8.2)</em></li>
  54                                 <li><strong>Edit </strong>
  55                                         <ul>
  56                                                 <li><strong>Copy</strong><br> <em>Copies the
  57                                                                 selected region. In the applet version, the copied sequences are
  58                                                                 not available to the system clipboard.</em></li>
  59                                                 <li><strong>Cut<br>
  60                                                 </strong><em>Cuts the selected region from the alignment. In the
  61                                                                 applet version, the copied sequences are not available to the
  62                                                                 system clipboard.</em></li>
  63                                                 <li><strong>Edit Sequence</strong><br> <em>Edit the
  64                                                                 selected sequence(s) directly. Spaces will be converted to the
  65                                                                 current gap character.</em></li>
  66                                                 <li><strong>To Upper Case</strong><em><strong><br>
  67                                                         </strong><em>Changes the case of selected region to lower case.</em> </em></li>
  68                                                 <li><strong>To Lower Case<br>
  69                                                 </strong><em>Changes the case of selected region to upper case.</em><strong>
  70                                                 </strong></li>
  71                                                 <li><strong>Toggle Case</strong><br> <em>Switches
  72                                                                 the case of all residues within the selected region.</em></li>
  73                                         </ul></li>
  74                                 <li><strong>Output to Textbox<br>
  75                                 </strong><em>The selection area will be output to a a text window in the
  76                                                 selected alignment format. </em></li>
  77                                 <li><strong><a href="../features/creatinFeatures.html">Create
  78                                                         Sequence Feature...</a></strong><br> <em>Opens the dialog box for
  79                                                 creating sequence features over the currently selected region on
  80                                                 each selected sequence.</em></li>
  81                                 <li><strong>Create Group<br>
  82                                 </strong><em>This will define a new group from the current selection.</em><strong>
  83                                 </strong></li>
  84                                 <li><strong>Remove Group<br>
  85                                 </strong><em>This will undefine the selected group. </em><strong> </strong></li>
  86                                 <li><strong>Edit (New) Group</strong><br> <em>Group
  87                                                 Editing Menu</em> <br />Options in this menu modify the name and
  88                                         display properties of the currently selected group, or a new group
  89                                         defined using the current selection.
  90                                         <ul>
  91                                                 <li><strong>Name: &lt;Group&gt;</strong> or <strong>Edit
  92                                                                 name and description</strong><br> <em>The first entry in the
  93                                                                 menu displays the name for the currently selected group, if it
  94                                                                 has one. Selecting this option opens a window allowing the name
  95                                                                 and description for this group to be edited. Click OK to set the
  96                                                                 new name and decription, and cancel to leave the existing name
  97                                                                 and description unchanged.</em></li>
  98                                                 <li><strong>Group Colour<br>
  99                                                 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
 100                                                                 of the group.
 101                                                 </em><strong> </strong></li>
 102                                                 <li><strong>Boxes<br>
 103                                                 </strong><em>If selected the background of a residue within the
 104                                                                 selected group will be coloured according to the assigned colour
 105                                                                 scheme.</em><strong> </strong></li>
 106                                                 <li><strong>Text<br>
 107                                                 </strong><em>If selected the selected group will display text. </em></li>
 108                                                 <li><strong>Colour Text<br>
 109                                                 </strong><em>If selected the selected group will display text in a
 110                                                                 colour slightly darker than the background colour of that
 111                                                                 residue.</em></li>
 112                                                 <li><strong>Border Colour <br>
 113                                                 </strong><em>Selecting this will display a &quot;Colour Chooser&quot;
 114                                                                 window. Select a colour than press OK to set the border colour
 115                                                                 of a group.</em></li>
 116                                                 <li><strong>Show Unconserved<br>
 117                                                 </strong><em>When this is selected, all symbols in the group matching
 118                                                                 the consensus sequence at that column will be rendered as a '.',
 119                                                                 highlighting mutations in the group area. </em></li>
 120                                         </ul></li>
 121
 122                         </ul></li>
 123                 <li><strong>Sequence Id<br>
 124                 </strong><em>This menu is only visible if you right-click on a sequence
 125                                 name. </em>
 126                         <ul>
 127                                 <li><a name="sqreport"><strong>Sequence Details
 128                                                         ...<br>
 129                                         </strong></a><em>(Since Jalview 2.8)<br>Open an <a
 130                                                 href="../io/exportseqreport.html">HTML report containing the
 131                                                         annotation and database cross references</a> normally shown in the
 132                                                 sequence's tooltip.
 133                                 </em></li>
 134                                 <li><strong>Edit Name/Description<br>
 135                                 </strong><em>You may edit the name and description of each sequence. A
 136                                                 window will be displayed asking for a new sequence name and
 137                                                 sequence description to be entered. Press OK to accept your edit.
 138                                                 To save sequence descriptions, you must save in Fasta, PIR or
 139                                                 Jalview File format.</em></li>
 140                                 <li><a href="sqaddrefannot"><strong>Add Reference
 141                                                         Annotations<br>
 142                                         </strong><em>When enabled, copies any available alignment annotation
 143                                                         for this sequence to the current view.</em></li>
 144               <li><strong>Set as Reference</strong> or <strong>Unmark as Reference</strong><br/>
 145               Sets or unsets the reference sequence for the the alignment.
 146               </li>
 147
 148                                 <li><strong>Represent Group With (Sequence Id)</strong><br>
 149                                         <em>All sequences in the current selection group will be
 150                                                 hidden, apart from (Sequence Id). Any edits performed on the
 151                                                 visible representative sequence will be propagated to the hidden
 152                                                 sequences. </em></li>
 153                                 <li><a name="sqid.popup"><strong>Link</strong><br> <em>This
 154                                                         menu item lists all links which have been set up in the <a
 155                                                         href="../features/preferences.html">Preferences</a> Connections
 156                                                         tab.<br> Since Jalview 2.4, links will also be made for
 157                                                         database cross references (where the database name exactly
 158                                                         matches the link name set up in <a
 159                                                         href="../features/preferences.html">Preferences</a>). <br>Since
 160                                                         Jalview 2.5, links are also shown for non-positional sequence
 161                                                         features attached to the sequence, and any regular-expression
 162                                                         based URL links that matched the description line.
 163                                         </em><strong><br> </strong></li>
 164                         </ul></li>
 165                 <li><strong>3D Structure Data...</strong> </strong><em>This menu is
 166                                 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>
 167                                  dialogue with options to select the structure which will eventually be opened in
 168                                 a 3D interactive view.<br> These entries will only be present if the sequence
 169                                 has <a href="../features/viewingpdbs.html">associated PDB structures</a>.
 170                                 <br /> If the sequence or alignment has RNA structure,
 171                                 then <strong>VARNA 2D Structure</strong> entries will also be present enabling
 172                                 you to open a linked view of the RNA structure in <a
 173                                 href="../features/varna.html">VARNA</a>.
 174                 </em>
 175                 </li>
 176     <li><a name="hideinserts"/><strong>Hide Insertions</strong><br />
 177     <em>Hides columns containing gaps in the current sequence or
 178         selected region, and reveals columns not including gaps.</em>
 179     <li><strong>Hide Sequences</strong><br> <em>Hides the
 180                                 currently selected sequences in this alignment view.</em><strong><br>
 181                                 </strong></li>
 182         </ul>
 183 </body>
 184 </html>