Merge branch 'JWS-29' into JABAWS_Release_2_0

[jabaws.git] / conf / settings / DisemblParameters.xml

diff --git a/conf/settings/DisemblParameters.xml b/conf/settings/DisemblParameters.xml
index 9e50d5d..676395e 100644 (file)
--- a/conf/settings/DisemblParameters.xml
+++ b/conf/settings/DisemblParameters.xml
@@ -1,19 +1,88 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <runnerConfig>\r
+<!-- \r
+    Extreme variation of this parameter does not have any impact on the output\r
+    so irrelevant. \r
+\r
        <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
        <prmSeparator>=</prmSeparator>\r
        <parameters>\r
-               <name>Default parameters should not be changed!</name>\r
-               <description>Normally the default parameters should not be changed. \r
-               If the query protein sequence is very long, >1000 residues, you can download the predictions and \r
-               use a local graph/plotting tool such as Grace or OpenOffice.org to plot and zoom the data. \r
-               Having identified the potential disordered regions, you should now have a good basis for setting \r
-               up expression vectors and/or comparing the data with obtained structural data. \r
-               </description>\r
-               <optionNames>-sg</optionNames>\r
+               <name>Savitzky-Golay smoothing frame</name>\r
+               <description>Algorithm Parameter: Savitzky-Golay smoothing frame</description>\r
+               <optionNames>sg</optionNames>\r
                <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
-               <defaultValue>1</defaultValue>\r
+               <defaultValue>8</defaultValue>\r
+               <validValue>\r
+                       <type>Integer</type>\r
+                       <min>1</min>\r
+                       <max>30</max>\r
+               </validValue>\r
        </parameters>\r
-</runnerConfig>\r
  \r
- 
\ No newline at end of file
+ These can be supported but not recommended to change so what's the point?\r
+ \r
+ Manual: Normally the default parameters should not be changed.\r
+\r
+       <parameters>\r
+               <name>Minimum peak width</name>\r
+               <description>Algorithm Parameter: Minimum peak width.</description>\r
+               <optionNames>pw</optionNames>\r
+               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+               <defaultValue>8</defaultValue>\r
+               <validValue>\r
+                       <type>Integer</type>\r
+                       <min>1</min>\r
+                       <max>30</max>\r
+               </validValue>\r
+       </parameters>\r
+       <parameters>\r
+               <name>Maximum join distance</name>\r
+               <description>Algorithm Parameter: Maximum join distance</description>\r
+               <optionNames>jd</optionNames>\r
+               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+               <defaultValue>4</defaultValue>\r
+               <validValue>\r
+                       <type>Integer</type>\r
+                       <min>1</min>\r
+                       <max>30</max>\r
+               </validValue>\r
+       </parameters>\r
+       <parameters>\r
+               <name>Coils threshold</name>\r
+               <description>Stringency values for different predictor: Coils threshold</description>\r
+               <optionNames>ct</optionNames>\r
+               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+               <defaultValue>1.2</defaultValue>\r
+               <validValue>\r
+                       <type>Float</type>\r
+                       <min>0.1</min>\r
+                       <max>10</max>\r
+               </validValue>\r
+       </parameters>\r
+       <parameters>\r
+               <name>Remark465 threshold</name>\r
+               <description>Stringency values for different predictor: Remark465 threshold</description>\r
+               <optionNames>rt</optionNames>\r
+               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+               <defaultValue>1.4</defaultValue>\r
+               <validValue>\r
+                       <type>Float</type>\r
+                       <min>0.1</min>\r
+                       <max>10</max>\r
+               </validValue>\r
+       </parameters>\r
+       <parameters>\r
+               <name>Hot loops threshold</name>\r
+               <description>Stringency values for different predictor: Hot loops threshold.</description>\r
+               <optionNames>lt</optionNames>\r
+               <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+               <defaultValue>1.2</defaultValue>\r
+               <validValue>\r
+                       <type>Float</type>\r
+                       <min>0.1</min>\r
+                       <max>10</max>\r
+               </validValue>\r
+       </parameters>\r
+       -->\r
+\r
+</runnerConfig>\r