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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git] / help / html / features / wrap.html
diff --git a/help/html/features/wrap.html b/help/html/features/wrap.html
index e18e273..8f562eb 100755 (executable)
--- a/help/html/features/wrap.html
+++ b/help/html/features/wrap.html
@@ -1,18 +1,344 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- * 
+ * 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/>.
--->
+ * 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>Wrap Alignment</title>
+</head>
+
+<body>
+  <p>
+    <strong>View&#8594;Wrap alignment </strong>
+  </p>
+  <p>Use this feature to wrap an alignment to the screen width.</p>
+  <p>All output (HTML, Printing, JPG etc) will also be in this
+    wrapped format.</p>
+  <p>This is most useful when looking at alignments with less than
+    20 sequences.</p>
+  <table width="480" border="1">
+    <tr>
+      <td>
+
+        <table border="0" cellpadding="0" cellspacing="0">
+          <tr>
+            <td colspan="6">&nbsp;</td>
+            <td colspan="9">10<br> |
+            </td>
+            <td></td>
+            <td colspan="9">20<br> |
+            </td>
+            <td></td>
+          </tr>
+          <tr>
+            <td nowrap>ADHR_DROPS/7-107&nbsp;&nbsp;</td>
+            <td bgcolor="#e6331a">K</td>
+            <td bgcolor="#1ab3b3">H</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">C</td>
+            <td bgcolor="#1ab3b3">Y</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td>D</td>
+            <td bgcolor="#80b3e6">C</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td>A</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td>E</td>
+            <td bgcolor="#1acc1a">T</td>
+            <td bgcolor="#1acc1a">S</td>
+            <td bgcolor="#e6331a">K</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#80b3e6">M</td>
+            <td>T</td>
+            <td bgcolor="#e6331a">K</td>
+            <td>N</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">A</td>
+          </tr>
+          <tr>
+            <td nowrap>ADH_DROHE/5-105&nbsp;&nbsp;</td>
+            <td>S</td>
+            <td>N</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">F</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#cc4dcc">D</td>
+            <td bgcolor="#1acc1a">T</td>
+            <td bgcolor="#1acc1a">S</td>
+            <td bgcolor="#e6331a">R</td>
+            <td>E</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td>K</td>
+            <td>S</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#cccc00">P</td>
+            <td>K</td>
+          </tr>
+          <tr>
+            <td nowrap>PGDH_HUMAN/6-106&nbsp;&nbsp;</td>
+            <td bgcolor="#e6331a">K</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#1acc1a">T</td>
+            <td bgcolor="#e6994d">G</td>
+            <td>A</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td>Q</td>
+            <td bgcolor="#e6994d">G</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#e6994d">G</td>
+            <td>R</td>
+            <td>A</td>
+            <td>F</td>
+            <td>A</td>
+            <td bgcolor="#cc4dcc">E</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td>L</td>
+            <td bgcolor="#e6331a">K</td>
+            <td bgcolor="#e6994d">G</td>
+            <td>.</td>
+            <td bgcolor="#80b3e6">A</td>
+          </tr>
+          <tr>
+            <td height="5"></td>
+          </tr>
+          <tr>
+            <td colspan="6">&nbsp;</td>
+            <td colspan="9">36<br> |
+            </td>
+            <td></td>
+            <td colspan="9">46<br> |
+            </td>
+            <td></td>
+          </tr>
+          <tr>
+            <td nowrap>ADHR_DROPS/7-107&nbsp;&nbsp;</td>
+            <td bgcolor="#e6331a">K</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td>Q</td>
+            <td>S</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td>E</td>
+            <td bgcolor="#1acc1a">N</td>
+            <td bgcolor="#cccc00">P</td>
+            <td bgcolor="#cccc00">P</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>A</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#1acc1a">Q</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td>Q</td>
+          </tr>
+          <tr>
+            <td nowrap>ADH_DROHE/5-105&nbsp;&nbsp;</td>
+            <td>N</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#cc4dcc">D</td>
+            <td>R</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#cc4dcc">D</td>
+            <td bgcolor="#1acc1a">N</td>
+            <td bgcolor="#cccc00">P</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td>A</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#cc4dcc">E</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td>K</td>
+          </tr>
+          <tr>
+            <td nowrap>PGDH_HUMAN/6-106&nbsp;&nbsp;</td>
+            <td bgcolor="#e6331a">K</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#cc4dcc">D</td>
+            <td>W</td>
+            <td>N</td>
+            <td>L</td>
+            <td>E</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td bgcolor="#e6994d">G</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>V</td>
+            <td>Q</td>
+            <td bgcolor="#80b3e6">C</td>
+            <td>K</td>
+            <td>A</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td>L</td>
+          </tr>
+          <tr>
+            <td height="5"></td>
+          </tr>
+          <tr>
+            <td colspan="6">&nbsp;</td>
+            <td colspan="9">62<br> |
+            </td>
+            <td></td>
+            <td colspan="9">72<br> |
+            </td>
+            <td></td>
+          </tr>
+          <tr>
+            <td nowrap>ADHR_DROPS/7-107&nbsp;&nbsp;</td>
+            <td>S</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td>K</td>
+            <td bgcolor="#1ab3b3">H</td>
+            <td>S</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>T</td>
+            <td>Q</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#80b3e6">F</td>
+            <td bgcolor="#80b3e6">F</td>
+            <td bgcolor="#80b3e6">W</td>
+            <td>T</td>
+            <td bgcolor="#80b3e6">F</td>
+            <td bgcolor="#cc4dcc">D</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#1acc1a">T</td>
+            <td bgcolor="#80b3e6">M</td>
+            <td bgcolor="#80b3e6">A</td>
+            <td>R</td>
+            <td bgcolor="#cc4dcc">E</td>
+            <td bgcolor="#cc4dcc">E</td>
+            <td>M</td>
+          </tr>
+          <tr>
+            <td nowrap>ADH_DROHE/5-105&nbsp;&nbsp;</td>
+            <td>A</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td>N</td>
+            <td bgcolor="#cccc00">P</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>K</td>
+            <td>V</td>
+            <td>T</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td bgcolor="#1acc1a">T</td>
+            <td bgcolor="#80b3e6">F</td>
+            <td bgcolor="#1ab3b3">Y</td>
+            <td bgcolor="#cccc00">P</td>
+            <td bgcolor="#1ab3b3">Y</td>
+            <td bgcolor="#cc4dcc">D</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#1acc1a">T</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td bgcolor="#cccc00">P</td>
+            <td>L</td>
+            <td>A</td>
+            <td bgcolor="#cc4dcc">E</td>
+            <td>T</td>
+          </tr>
+          <tr>
+            <td nowrap>PGDH_HUMAN/6-106&nbsp;&nbsp;</td>
+            <td>D</td>
+            <td>E</td>
+            <td>Q</td>
+            <td bgcolor="#80b3e6">F</td>
+            <td>E</td>
+            <td bgcolor="#cccc00">P</td>
+            <td>.</td>
+            <td>.</td>
+            <td>.</td>
+            <td>Q</td>
+            <td>K</td>
+            <td bgcolor="#1acc1a">T</td>
+            <td bgcolor="#80b3e6">L</td>
+            <td bgcolor="#80b3e6">F</td>
+            <td bgcolor="#80b3e6">I</td>
+            <td>Q</td>
+            <td bgcolor="#80b3e6">C</td>
+            <td bgcolor="#cc4dcc">D</td>
+            <td bgcolor="#80b3e6">V</td>
+            <td>A</td>
+            <td>D</td>
+            <td>Q</td>
+            <td>Q</td>
+            <td bgcolor="#1acc1a">Q</td>
+            <td>L</td>
+            <td>.</td>
+          </tr>
+          <tr>
+            <td height="5"></td>
+          </tr>
+
+
+        </table>
+  </table>
+
+
+</body>
+</html>