remove system.out

[jalview.git] / help / html / features / preferences.html

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 5f88d62..0abce06 100755 (executable)
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -18,12 +18,17 @@
     files. </li>\r
   <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong> Preferences</a> \r
     tab contains settings affecting the export of sequence alignments and EPS \r
-    f</li>\r
+    files.</li>\r
+  <li>The <a href="#editing"><strong>&quot;DAS Settings&quot;</strong> Preferences</a> \r
+    tab allows you to select which DAS sources to use when fetching DAS Features.</li>\r
 </ul>\r
 </p>\r
 <p><strong><a name="visual">Visual</a> Preferences tab</strong></p>\r
 <p><em>Maximise Window</em> - If this is selected, a new alignment window will stretch \r
   to fit the available space.</p>\r
+<p><em>Show Overview Window</em> - When this is selected, the <a\r
+  href="overview.html">alignment overview</a> panel is opened by\r
+  default for a new alignment window.</p>\r
 <p><em>Show Annotations</em> - If this is selected the new window will display an annotation \r
   panel below the sequences. This annotation panel may have several rows describing \r
   the whole alignment. The 3 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em> \r
@@ -35,6 +40,8 @@
   alignment window. </p>\r
 <p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering \r
   of the alignment.</p>\r
+<p><em>Wrap Alignment</em> - Select whether to open new alignment windows in wrapped \r
+  mode or not.</p>\r
 <p><em>Gap Symbol</em> - The default gap symbol may be set to either &quot;-&quot; or &quot;.&quot;</p>\r
 <p><em>Colour</em> - The default colour scheme for a new alignment window. If \r
   the chosen option is &quot;User Defined&quot; then the last User Defined Colour \r
@@ -57,6 +64,9 @@
   <br>\r
   You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen \r
   sequence id when you click on it. </p>\r
+<p>eg.<br>\r
+  UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&amp;library=uniref100<br>\r
+  Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$</p>\r
 <p><em>Default Browser (Unix)</em><br>\r
   Its difficult in Java to detect the default web browser for Unix users. If Jalview \r
   can't find your default web browser, enter the name or full path to your web \r
@@ -94,15 +104,13 @@ the program reading the EPS file.
   will not be appended to the sequence id. </p>\r
 </p>\r
 <p><em>Use Modeller Output</em></p>\r
-<p>This option only applies to PIR format output. Jalview can now read and write \r
-  PIR files with sequence descriptions compatible with the program <a href="http://salilab.org/modeller/">Modeller</a>. \r
-  If this option is selected Jalview will write the sequence description in the \r
-  following format:</p>\r
-<pre>&gt;P1;O80429_MAIZE\r
-sequence:O80429_MAIZE:1:.:140:.:.</pre>\r
-If a sequence description existed before the file was saved, it will be appended \r
-to the new Modeller style desciption. The Jalview id/start-end option is ignored \r
-if Modeller output is selected. \r
+<p>This option only applies to PIR format output. Jalview\r
+  automatically reads PIR files with sequence descriptions compatible\r
+  with the program <a\r
+  href="http://salilab.org/modeller/">Modeller</a>.\r
+  If this option is selected <a href="../io/modellerpir.html">Jalview will write Modeller style PIR\r
+  files</a> with correct start/end numbering and PDB file association (if\r
+  available). The Jalview id/start-end option is ignored if Modeller output is selected.\r
 <p><a name="editing"><strong>Editing Preferences tab</strong></a></p>\r
 <p>There are currently 2 options available which can be selected / deselected. \r
 </p>\r
@@ -113,6 +121,8 @@ if Modeller output is selected.
   this setting. </p>\r
 <p><em>Pad gaps when editing</em> - New alignment windows will &quot;Pad Gaps&quot; \r
   according to this setting.</p>\r
+<p><a name="editing"><strong>DAS Settings </strong></a></p>\r
+<p>See <a href="dassettings.html">DAS Settings</a></p>\r
 <p>&nbsp;</p>\r
 <p>&nbsp;</p>\r
 </body>\r