X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2Fsettings%2FDisemblParameters.xml;h=676395e7c5b53cb6df3cc116c0fc40acc1709f37;hb=550d715f5af9271247b20363d1212e7e0279f9ee;hp=9e50d5dd3ad740e703db5c6e7ddaf276bd26ead0;hpb=0b1c6520810e954fab65058df5931a06f5c43e5d;p=jabaws.git

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