jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
\r
\r
-### Disembl configuration - NOT DISTRIBUTED ### \r
+### Disembl configuration Tisean - Disembl dependancy cannot be redistributed (!) ### \r
#local.disembl.bin.windows= \r
local.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py\r
cluster.disembl.bin=/homes/pvtroshin/soft/DisEMBL-1.4raw/DisEMBL.py\r
-#disembl.parameters.file=conf/settings/JronnParameters.xml\r
+disembl.parameters.file=conf/settings/DisemblParameters.xml\r
disembl.limits.file=conf/settings/DisemblLimits.xml\r
disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
\r
+### AACon configuration ###\r
local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe \r
local.aacon.bin=/sw/java/latest/bin/java\r
cluster.aacon.bin=/sw/java/latest/bin/java\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
+ These can be supported but not recommended to change so what's the point?\r
\r
-
\ No newline at end of file
+ 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
import org.apache.log4j.Logger;\r
\r
import compbio.data.sequence.Score;\r
+import compbio.engine.client.CommandBuilder;\r
import compbio.engine.client.Executable;\r
import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
* 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 < fasta_file'\r
* print 'Mode: "default"(nothing) or "scores" which will give scores per\r
* residue in TAB separated format'\r
+ * \r
+ * Internal parameters names are: sj\r
+ * \r
+ * //TODO? pw jd ct rt lt\r
+ * \r
+ * the order is preserved\r
*/\r
public class Disembl extends SkeletalExecutable<Disembl>\r
implements\r
// Cache for Limits information\r
private static LimitsManager<Disembl> limits;\r
\r
+ // CHECK THIS !!!\r
public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
\r
public Disembl() {\r
return this.getClass();\r
}\r
\r
+ @Override\r
+ public CommandBuilder<Disembl> getParameters(ExecProvider provider) {\r
+ // If Savitzky-Golay smoothing parameter is specified then set it\r
+ String val = cbuilder.getParamValue("sg");\r
+ log.info("DisEMBL sav-gol value: " + val);\r
+ if (val != null) {\r
+ cbuilder.removeParam("sg");\r
+ cbuilder.setFirst(val);\r
+ }\r
+ return super.getParameters(provider);\r
+ }\r
}\r
Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
assertNotNull(aseqs);\r
assertEquals(aseqs.size(), 3);\r
- Score aseq = aseqs.get(0);\r
+ Score aseq = aseqs.get("Foobar");\r
assertNotNull(aseq);\r
assertNotNull(aseq.getScores());\r
// System.out.println(aseq);\r
assertNotNull(al1.getResults());\r
HashSet<Score> annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.size(), 1);\r
+ assertEquals(annotations.size(), 18);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
git://source.jalview.org / jabaws.git / commitdiff