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menus
authoramwaterhouse <Andrew Waterhouse>
Fri, 27 May 2005 14:28:34 +0000 (14:28 +0000)
committeramwaterhouse <Andrew Waterhouse>
Fri, 27 May 2005 14:28:34 +0000 (14:28 +0000)
help/html/menus/alignmentMenu.html [new file with mode: 0755] patch | blob
help/html/menus/desktopMenu.html [new file with mode: 0755] patch | blob
help/html/menus/index.html [new file with mode: 0755] patch | blob
help/html/menus/popupMenu.html [new file with mode: 0755] patch | blob

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
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+<html>\r
+<head><title>Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Menu</strong></p>\r
+<ul>\r
+  <li><strong>File</strong></li>\r
+  <ul>\r
+    <li><strong>Save As<br>\r
+      </strong><em>Save the alignment to local file. A file selection window will \r
+      open, use the &quot;Files of type:&quot; selection box to determine which \r
+      <a href="../io/index.html">alignment format</a> to save as.<br>\r
+      </em></li>\r
+    <li><strong>Export</strong> <em><br>\r
+      Creates an alignment output maintaining the alignment background colours \r
+      and group colours. If the alignment is wrapped, the output will also be \r
+      wrapped and will have the same visible residue width as the open alignment. \r
+      </em> \r
+      <ul>\r
+        <li><strong>HTML<br>\r
+          </strong><em>Create a <a href="../io/index.html#export">web page</a> \r
+          from your alignment.</em></li>\r
+        <li><strong>EPS<br>\r
+          </strong><em>Create an <a href="../io/index.html#export">Encapsulated \r
+          Postscript</a> file from your alignment.</em></li>\r
+        <li><strong>PNG<br>\r
+          </strong><em>Create a <a href="../io/index.html#export">Portable Network \r
+          Graphics</a> file from your alignment.</em></li>\r
+      </ul>\r
+    </li>\r
+    <li><strong>Output to Textbox<br>\r
+      </strong><em>The alignment will be displayed in plain text in a new window \r
+      which you can &quot;Copy and Paste&quot; using the pull down menu, or your \r
+      standard operating system copy and paste keys. <br>\r
+      Select the format of the text by selecting one of the following menu items.</em> \r
+      <ul>\r
+        <li><strong>FASTA</strong> <em></em></li>\r
+        <li><strong>MSF</strong></li>\r
+        <li><strong>CLUSTAL</strong></li>\r
+        <li><strong>BLC</strong></li>\r
+        <li><strong>PIR</strong></li>\r
+        <li><strong>PFAM<br>\r
+          </strong></li>\r
+      </ul>\r
+    </li>\r
+    <li><strong>Print<br>\r
+      </strong><em>Jalview will print the alignment using the current fonts and \r
+      coloursof your alignment. If the alignment has annotations visible, these \r
+      will be printed below the alignment. If the alignment is wrapped the number \r
+      of residues per line of your alignment will depend on the paper width or \r
+      your alignment window width, whichever is the smaller. </em></li>\r
+    <li><strong>Load Associated Tree<br>\r
+      </strong><em>Jalview can load in trees which are in the Newick file format \r
+      and associate them with a particular alignment. Note: the ids of the tree \r
+      file and your alignment MUST be the same.</em></li>\r
+    <li><strong>Close<br>\r
+      </strong><em>Close the alignment window. Be aware that changes to your alignment \r
+      will not be save unless specifically actioned from the &quot;Save As&quot; \r
+      menu.<br>\r
+      </em></li>\r
+  </ul>\r
+  <li><strong>Edit</strong></li>\r
+</ul>\r
+<blockquote> \r
+  <ul>\r
+    <li><strong>Undo</strong><em><br>\r
+      This will undo any edits you make to the alignment. This applies to insertion \r
+      or deletion of gaps, cutting residues or sequences from the alignment, pasting \r
+      </em></li>\r
+    <li><strong>Redo<br>\r
+      </strong></li>\r
+    <li><strong>Cut</strong></li>\r
+    <li><strong>Copy</strong></li>\r
+    <li><strong>Paste </strong> \r
+      <ul>\r
+        <li><strong>To New Alignment</strong></li>\r
+        <li><strong>Add To This Alignment</strong></li>\r
+      </ul>\r
+    </li>\r
+    <li><strong>Delete</strong></li>\r
+    <li><strong>Select All</strong></li>\r
+    <li><strong>Deselect All</strong></li>\r
+    <li><strong>Invert Selection</strong></li>\r
+    <li><strong>Undefine Groups</strong></li>\r
+    <li><strong>Remove Left</strong></li>\r
+    <li><strong>Remove Right</strong></li>\r
+    <li><strong>Remove Empty Columns</strong></li>\r
+    <li><strong>Remove All Gaps</strong></li>\r
+    <li><strong>Remove Redundancy</strong></li>\r
+    <li><strong>Pad Gaps</strong></li>\r
+  </ul>\r
+</blockquote>\r
+<ul>\r
+  <li><strong>Search</strong></li>\r
+</ul>\r
+<blockquote>\r
+  <ul>\r
+    <li><strong>Find</strong></li>\r
+  </ul>\r
+</blockquote>\r
+<ul>\r
+  <li><strong>View</strong></li>\r
+</ul>\r
+<blockquote> \r
+  <ul>\r
+    <li><strong>Font</strong></li>\r
+    <li><strong>Wrap</strong></li>\r
+    <li><strong>Show Full Sequence ID</strong></li>\r
+    <li><strong>Boxes</strong></li>\r
+    <li><strong>Text</strong></li>\r
+    <li><strong>Colour Text</strong></li>\r
+    <li><strong>Show Gaps</strong></li>\r
+    <li><strong>Show Annotations</strong></li>\r
+    <li><strong>Sequence Features</strong></li>\r
+    <li><strong>Overview Window</strong></li>\r
+  </ul>\r
+</blockquote>\r
+<ul>\r
+  <li><strong>Colour</strong></li>\r
+</ul>\r
+<blockquote> \r
+  <ul>\r
+    <li><strong>Apply Colour To All Groups</strong></li>\r
+    <li><strong>None</strong></li>\r
+    <li><strong>ClustalX</strong></li>\r
+    <li><strong>Blosum62 Score</strong></li>\r
+    <li><strong>Percentage Identity</strong></li>\r
+    <li><strong>Zappo</strong></li>\r
+    <li><strong>Taylor</strong></li>\r
+    <li><strong>Hydrophobicity</strong></li>\r
+    <li><strong>Helix Propensity</strong></li>\r
+    <li><strong>Strand Propensity</strong></li>\r
+    <li><strong>Turn Propensity</strong></li>\r
+    <li><strong>Buried Index</strong></li>\r
+    <li><strong>Nucleotide</strong></li>\r
+    <li><strong>User Defined</strong></li>\r
+    <li><strong>By Conservation</strong></li>\r
+    <li><strong>Modify Conservation Threshold</strong></li>\r
+    <li><strong>Above Identity Threshold</strong></li>\r
+    <li><strong>Modify Identity Threshold</strong></li>\r
+  </ul>\r
+</blockquote>\r
+<ul>\r
+  <li><strong>Calculate</strong></li>\r
+</ul>\r
+<blockquote> \r
+  <ul>\r
+    <li><strong>Sort </strong> \r
+      <ul>\r
+        <li><strong>by ID</strong></li>\r
+        <li><strong>by Group</strong></li>\r
+        <li><strong>by Pairwise Identity</strong></li>\r
+      </ul>\r
+    </li>\r
+    <li><strong>Calculate Tree </strong> \r
+      <ul>\r
+        <li><strong>Average Distance Using % Identity</strong></li>\r
+        <li><strong>Neighbour Joining Using % Identity</strong></li>\r
+        <li><strong>Average Distance Using Blosum62</strong></li>\r
+        <li><strong>Neighbour Joining Using Blosum62</strong></li>\r
+      </ul>\r
+    </li>\r
+    <li><strong>Paiwise Alignments</strong></li>\r
+    <li><strong>Principal Component Analysis</strong></li>\r
+    <li><strong>Web Service </strong> \r
+      <ul>\r
+        <li><strong>Clustal Alignment</strong></li>\r
+        <li><strong>JPred</strong></li>\r
+        <li><strong>Muscle Alignment</strong></li>\r
+      </ul>\r
+    </li>\r
+  </ul>\r
+  <p>&nbsp;</p>\r
+</blockquote>\r
+</body>\r
+</html>\r
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
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+<html>\r
+<head><title>Desktop Menu</title></head>\r
+\r
+<body>\r
+<p><strong>Desktop Menu</strong></p>\r
+<ul>\r
+  <li><strong>File</strong><em> </em> \r
+    <ul>\r
+      <li><strong>Input Alignment from</strong><em> (See more on <a href="../io/index.html">file \r
+        formats</a>) </em> \r
+        <ul>\r
+          <li><strong>File</strong><br>\r
+            <em>open file(s) on your local file system</em></li>\r
+          <li><strong>URL</strong><br>\r
+            <em>open a file from a website. The URL MUST start with http://</em></li>\r
+          <li><strong>Textbox</strong><br>\r
+            <em>copy and paste an alignment into a text window</em></li>\r
+        </ul>\r
+      </li>\r
+      <li><strong>Save Project</strong><br>\r
+        <em>Saves all currently open alignment windows with their current visible \r
+        settings as a Jalview File, with the .jar extension. Each alignment will \r
+        also save the currently active tree associated with the window, if one \r
+        exists. </em></li>\r
+      <li><strong>Load Project</strong><br>\r
+        <em>Loads Jalview file formatted alignments only. </em></li>\r
+      <li><strong>Quit</strong><br>\r
+        <em>Close Jalview. Warning - any annotations you have made on alignments \r
+        will be lost unless you Save your work before quitting.</em><br>\r
+      </li>\r
+    </ul>\r
+  </li>\r
+  <li><strong>Tools </strong> \r
+    <ul>\r
+      <li><strong><a href="../features/preferences.html">Preferences<br>\r
+        </a></strong><em>Change the default visual settings for opening new alignment \r
+        windows.</em><strong><br>\r
+        </strong></li>\r
+    </ul>\r
+  </li>\r
+  <li><strong>Help </strong> \r
+    <ul>\r
+      <li><strong>About, </strong></li>\r
+      <li><strong>Documentation<br>\r
+        </strong></li>\r
+    </ul>\r
+  </li>\r
+  <li><strong>Window</strong></li>\r
+</ul>\r
+</body>\r
+</html>\r
diff --git a/help/html/menus/index.html b/help/html/menus/index.html
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+<html>\r
+<head><title>Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Menus</strong></p>\r
+<p>Menus are used in 3 places in Jalview - the &quot;Desktop Menu&quot;, the &quot;Alignment \r
+  Menu&quot; and the &quot;Popup Menu&quot;.</p>\r
+<p>The <a href="desktopMenu.html">Desktop Menu</a> is always visible and is the \r
+  starting point for loading new alignments.</p>\r
+<p>The <a href="alignmentMenu.html">Alignment Menu</a> is visible once and alignment \r
+  has been opened.</p>\r
+<p>The <a href="popupMenu.html">Popup Menu</a> is made visible by clicking with \r
+  the right mouse button on a sequence or the name of a sequence in an alignment \r
+  window. </p>\r
+\r
+</body>\r
+</html>\r
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
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+<html>\r
+<head><title>Popup Menu</title></head>\r
+\r
+<body>\r
+<p><strong>Popup Menu</strong></p>\r
+<p><em>Define </em></p>\r
+<ul>\r
+  <li>Group, </li>\r
+  <li>Remove Group</li>\r
+  <li>Group Colour</li>\r
+  <li>Boxes</li>\r
+  <li> Text</li>\r
+  <li>Colour Text</li>\r
+  <li>Border Colour </li>\r
+</ul>\r
+<p><em>Sequence</em> </p>\r
+<ul>\r
+  <li>Edit Name</li>\r
+  <li>View PDB Structure</li>\r
+</ul>\r
+</body>\r
+</html>\r