<body>\r
<p><strong>Alignment Window View Menu</strong></p>\r
<ul>\r
- <li><strong>New View (Control T)</strong><em><br>\r
- Creates a new view from the current alignment view. </em></li>\r
- <li><strong>Expand Views (X)</strong><em><br>\r
- Display each view associated with the alignment in its own alignment\r
- window, allowing several views to be displayed simultaneously. </em></li>\r
- <li><strong>Gather Views (G)</strong><em><br>\r
- Each view associated with the alignment will be displayed within its\r
- own tab on the current alignment window. </em></li>\r
- <li><strong>Show→(all Columns / Sequences)</strong><em><br>\r
- All hidden Columns / Sequences will be revealed. </em></li>\r
- <li><strong>Hide→(all Columns / Sequences)</strong><em><br>\r
- Hides the all the currently selected Columns / Sequences</em></li>\r
- <li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will be\r
- displayed below the alignment. The default setting is to display the\r
- conservation calculation, quality calculation and consensus values as\r
- bar charts. </em></li>\r
- <li><strong>Show Sequence Features</strong><br>\r
- <em>Show or hide sequence features on this alignment.</em></li>\r
- <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>\r
- Opens the Sequence\r
- Feature Settings dialog box to control the colour and display of\r
- sequence features on the alignment, and configure and retrieve features\r
- from DAS annotation servers.</em></li>\r
- <li><strong><a href="../features/overview.html">Overview\r
- Window</a><br>\r
- </strong><em>A scaled version of the alignment will be displayed in a small\r
- window. A red box will indicate the currently visible area of the\r
- alignment. Move the visible region using the mouse. </em></li>\r
+ <li><strong>New View (Control T)</strong><em><br>\r
+ Creates a new view from the current alignment view. </em></li>\r
+ <li><strong>Expand Views (X)</strong><em><br>\r
+ Display each view associated with the alignment in its own alignment window, \r
+ allowing several views to be displayed simultaneously. </em></li>\r
+ <li><strong>Gather Views (G)</strong><em><br>\r
+ Each view associated with the alignment will be displayed within its own tab \r
+ on the current alignment window. </em></li>\r
+ <li><strong>Show→(all Columns / Sequences)</strong><em><br>\r
+ All hidden Columns / Sequences will be revealed. </em></li>\r
+ <li><strong>Hide→(all Columns / Sequences)</strong><em><br>\r
+ Hides the all the currently selected Columns / Sequences</em></li>\r
+ <li><strong>Show Annotations<br>\r
+ </strong><em>If this is selected the "Annotation Panel" will be \r
+ displayed below the alignment. The default setting is to display the conservation \r
+ calculation, quality calculation and consensus values as bar charts. </em></li>\r
+ <li><strong>Show Sequence Features</strong><br>\r
+ <em>Show or hide sequence features on this alignment.</em></li>\r
+ <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>\r
+ Opens the Sequence Feature Settings dialog box to control the colour and display \r
+ of sequence features on the alignment, and configure and retrieve features \r
+ from DAS annotation servers.</em></li>\r
+ <li><strong>Alignment Properties<br>\r
+ </strong><em>Displays simple properties of current alignment view with additional \r
+ global alignment properties</em></li>\r
+ <li><strong><a href="../features/overview.html">Overview Window</a><br>\r
+ </strong><em>A scaled version of the alignment will be displayed in a small \r
+ window. A red box will indicate the currently visible area of the alignment. \r
+ Move the visible region using the mouse. </em></li>\r
</ul>\r
<p> </p>\r
</body>\r
-<html>
-<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><strong>Edit </strong>
- <ul>
- <li><strong>Copy</strong><br>
- <em>Copys 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>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>Group</strong><br>
- <em>Group Operations</em>
- <ul>
- <li><strong>Group</strong><em>This will display a window
- asking for the name of the currently selected group. Click OK to set
- the name, cancel to use the default group name. </em></li>
- <li><strong>Remove Group<br>
- </strong><em>This will undefine the selected group. </em><strong> </strong></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>
- </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><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>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 PDB 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 "View PDB
- 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>
- <li><strong>View PDB Structure<br>
- </strong><em> If the sequence has an associated PDB file added by one of
- the methods described above, Jalview will display a 3D interactive
- viewer of the file.<br>
- This entry is only present if the sequence has an <a
- href="../features/viewingpdbs.html">associated PDB structure</a>. </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><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.</em><strong><br>
- </strong></li>
- </ul>
- </li>
- <li><strong>Hide Sequences</strong><br>
- <em>Hides the currently selected seuqences in this alignment view.</em><strong><br>
- <br>
- </strong></li>
-</ul>
-</body>
-</html>
+<html>\r
+<head>\r
+<title>Popup Menu</title>\r
+</head>\r
+\r
+<body>\r
+<p><strong>Popup Menu</strong><br>\r
+<em>This menu is visible when right clicking either within a\r
+selected region on the alignment or on a selected sequence name. It may\r
+not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>\r
+<ul>\r
+ <li><strong>Selection</strong> \r
+ <ul>\r
+ <li><strong>Edit </strong> \r
+ <ul>\r
+ <li><strong>Copy</strong><br>\r
+ <em>Copys the selected region. In the applet version, the copied sequences \r
+ are not available to the system clipboard.</em></li>\r
+ <li><strong>Cut<br>\r
+ </strong><em>Cuts the selected region from the alignment. In the applet \r
+ version, the copied sequences are not available to the system clipboard.</em></li>\r
+ <li><strong>Edit Sequence</strong><br>\r
+ <em>Edit the selected sequence(s) directly. Spaces will be converted \r
+ to current gap character.</em></li>\r
+ <li><strong>To Upper Case</strong><em><strong><br>\r
+ </strong><em>Changes the case of selected region to lower case.</em> \r
+ </em></li>\r
+ <li><strong>To Lower Case<br>\r
+ </strong><em>Changes the case of selected region to upper case.</em><strong> \r
+ </strong></li>\r
+ <li><strong>Toggle Case</strong><br>\r
+ <em>Switches the case of all residues within the selected region.</em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Output to Textbox<br>\r
+ </strong><em>The selection area will be output to a a text window in the \r
+ selected alignment format. </em></li>\r
+ <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>\r
+ <em>Opens the dialog box for creating sequence features over the currently \r
+ selected region on each selected sequence.</em></li>\r
+ <li><strong>Group</strong><br>\r
+ <em>Group Operations</em> \r
+ <ul>\r
+ <li><strong>Group</strong><em>This will display a window asking for \r
+ the name of the currently selected group. Click OK to set the name, \r
+ cancel to use the default group name. </em></li>\r
+ <li><strong>Remove Group<br>\r
+ </strong><em>This will undefine the selected group. </em><strong> \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> </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
+ </strong></li>\r
+ <li><strong>Text<br>\r
+ </strong><em>If selected the selected group will display text. </em></li>\r
+ <li><strong>Colour Text<br>\r
+ </strong><em>If selected the selected group will display text in a \r
+ colour slightly darker than the background colour of that residue.</em></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 \r
+ a group.</em></li>\r
+ </ul>\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Sequence Id<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></li>\r
+ <li><em> </em></li>\r
+ <li><strong>Represent Group With (Sequence Id)</strong><br>\r
+ <em>All sequences in the current selection group will be hidden, apart \r
+ from (Sequence Id). Any edits performed on the visible representative \r
+ sequence will be propagated to the hidden sequences. </em></li>\r
+ <li><strong>Link</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.</em><strong><br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Structure</strong> \r
+ <ul>\r
+ <li><strong>Associate Structure with Sequence</strong> \r
+ <ul>\r
+ <li><strong>From File<br>\r
+ </strong><em>Load a PDB file from local disk which will be associated \r
+ with this sequence. This file will be used if the user subsequently \r
+ clicks on "View PDB Structure" menu item.</em></li>\r
+ <li><strong>Enter PDB id<br>\r
+ </strong><em>Enter the PDB id from an input window. This PDB id will \r
+ be used by the service WSDBFetch, provided by the EBI, to fetch the \r
+ PDB file if the user subsequently clicks on "View PDB Structure" \r
+ menu item. </em></li>\r
+ <li><strong>Discover PDB ids<br>\r
+ </strong><em>This will use the service WSDBFetch, provided by the \r
+ EBI, to retrieve all PDB ids associated with the sequences in the \r
+ alignment if the sequences have valid Uniprot names or accession ids. \r
+ </em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>View Structure<br>\r
+ </strong><em> If the sequence has an associated PDB file added by one \r
+ of the methods described above, Jalview will display a 3D interactive \r
+ viewer of the file.<br>\r
+ This entry is only present if the sequence has an <a\r
+ href="../features/viewingpdbs.html">associated PDB structure</a>.</em><br>\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Hide Sequences</strong><br>\r
+ <em>Hides the currently selected seuqences in this alignment view.</em><strong><br>\r
+ <br>\r
+ </strong></li>\r
+</ul>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff