Changeset 4089

Timestamp:

Dec 22, 2010, 12:34:38 PM (12 years ago)

Author:

olle

Message:

Refs #668. Refs #287. Support for running msInspect feature detection from Proteios SE updated to allow user selected strategy option:

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated by adding a menu select box for selecting a strategy option. The option string parameter is coupled to new valid parameter VString RunMsInspect.VMSINSPECTSTRATEGY. The default option is marked "default", and corresponds to no strategy option being used.

2. Class/file action/msInspect/RunMsInspect.java in client/servlet/ updated to retrieve the string from new valid parameter VString VMSINSPECTSTRATEGY and transferring it as a job parameter to plug-in class RunMsInspectPlugin.

3. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to retrieve the strategy string from the job parameter. If the string is null or an empty string (corresponding to the default option), no changes are made to the msInspect command line. Otherwise, the retrieved string is used as value for an extra option --strategy=value in the msInspect command line.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

Location:

trunk

Files:

• client/servlet/src/locale/en/dictionary (modified) (1 diff)
• client/servlet/src/org/proteios/action/file/UseSpectrumFileForMsInspectSearchExtension.java (modified) (2 diffs)
• client/servlet/src/org/proteios/action/msInspect/RunMsInspect.java (modified) (4 diffs)
• plugin/src/org/proteios/plugins/RunMsInspectPlugin.java (modified) (6 diffs)

trunk/client/servlet/src/locale/en/dictionary

@@ -425 +425 @@
 MsInspect=msInspect
 MsInspectFeatureDetection=msInspect Feature Detection
+MsInspectStrategySelect=Strategy
 MwInDaltons=Molecular weight (Da)
 MyFiles=My Files

trunk/client/servlet/src/org/proteios/action/file/UseSpectrumFileForMsInspectSearchExtension.java

@@ -36 +36 @@
 import org.proteios.gui.form.Form;
 import org.proteios.gui.form.FormFactory;
+import org.proteios.gui.form.Option;
+import org.proteios.gui.form.Select;
 import org.proteios.gui.layout.RowLayout;
 
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
+import se.lu.thep.waf.constraints.VString;
 
 import java.util.ArrayList;
@@ -129 +132 @@
     Fieldset fs = new Fieldset("MsInspect");
     form.addFieldset(fs);
+    // Select box variables
+    VString validStringParam = null;
+    List<Option> optionList = null;
+    String selected = null;
+    // Add strategy menu
+    validStringParam = RunMsInspect.VMSINSPECTSTRATEGY;
+    optionList = new ArrayList<Option>();
+    optionList.add(new Option("", "default"));
+    optionList.add(new Option("BaseFeatureStrategy", "BaseFeatureStrategy"));
+    optionList.add(new Option("BaseFeatureStrategyModular", "BaseFeatureStrategyModular"));
+    optionList.add(new Option("FeatureStrategy", "FeatureStrategy"));
+    optionList.add(new Option("FeatureStrategyPeakClusters", "FeatureStrategyPeakClusters"));
+    optionList.add(new Option("FeatureStrategyPeakClustersNegCharge", "FeatureStrategyPeakClustersNegCharge"));
+    optionList.add(new Option("FeatureStrategySmallMolecule", "FeatureStrategySmallMolecule"));
+    optionList.add(new Option("FeatureStrategySmallMoleculeNeg", "FeatureStrategySmallMoleculeNeg"));
+    optionList.add(new Option("FeatureStrategyWindow", "FeatureStrategyWindow"));
+    selected = new String("");
+    Select<VString> strategySelectBox = new Select<VString>(validStringParam, optionList);
+    strategySelectBox.selectOption(selected);
+    strategySelectBox.setLabel("MsInspectStrategySelect");
+    strategySelectBox.setHelp("Note: The installed version of msInspect might not support all strategy options");
+    fs.add(strategySelectBox);
     /*
      * Add the tool bar with 'Next' button(s) to the form.

trunk/client/servlet/src/org/proteios/action/msInspect/RunMsInspect.java

@@ -53 +53 @@
 import se.lu.thep.waf.constraints.VBoolean;
 import se.lu.thep.waf.constraints.VInteger;
+import se.lu.thep.waf.constraints.VString;
 
 
@@ -66 +67 @@
   public static final VBoolean VMSINSPECTUSEWEBINTERFACEFLAG = new VBoolean(
       "active.msinspectusewebinterfaceflag", false);
+  public static final VString VMSINSPECTSTRATEGY = new VString(
+      "active.msinspectstrategy", 0, 255, false);
   
   @Override
@@ -118 +121 @@
     log.debug("tmpDir = \"" + tmpDir + "\"");
     log.debug("uploadOutputFileFlag = " + uploadOutputFileFlag);
+    // Get the msInspect parameters to use for the feature detection
+    String strategy = getValidString(VMSINSPECTSTRATEGY);
+    log.debug("strategy = \"" + strategy + "\"");
     /***********************************************************************
      * Get MsInspect feature detection plugin definition
@@ -203 +209 @@
         Project.class, null);
       job.setParameterValue("project", projectParam, activeProject);
+      //
+      StringParameterType strategyParam = new StringParameterType();
+      job.setParameterValue("strategy", strategyParam, strategy);
       //
       dc.saveItem(job);

trunk/plugin/src/org/proteios/plugins/RunMsInspectPlugin.java

@@ -329 +329 @@
     Boolean uploadOutputFileFlag;
     String timeStampStr;
+    String strategy;
 
     msInspectInstallPath = (String) job.getValue("msInspectInstallPath");
@@ -338 +339 @@
     uploadOutputFileFlag = (Boolean) job.getValue("uploadOutputFileFlag");
     timeStampStr = (String) job.getValue("timeStampStr");
+    strategy = (String) job.getValue("strategy");
 
     // Perform msInspect feature detection using local search engine
     msInspectSearchLocal(request, response, progress, tmpDir,
       msInspectInstallPath, msInspectProgramName, msInspectMemoryInMegaBytes,
-      spectrumFileId, dirId, uploadOutputFileFlag, timeStampStr);
+      spectrumFileId, dirId, uploadOutputFileFlag, timeStampStr, strategy);
     done();
   }
@@ -384 +386 @@
    * @param uploadOutputFileFlag Boolean The upload output file flag
    * @param timeStampStr String Time stamp string in YYYY_MM_DD_hh_mm_ss format
+   * @param strategy String Strategy algorithm option for the feature detection
    */
   private void msInspectSearchLocal(Request request, Response response,
@@ -389 +392 @@
       String msInspectInstallPath, String msInspectProgramName, Integer msInspectMemoryInMegaBytes,
       Integer spectrumFileId, Integer dirId,
-      Boolean uploadOutputFileFlag, String timeStampStr)
+      Boolean uploadOutputFileFlag, String timeStampStr, String strategy)
   {
     log.debug("msInspectInstallPath = \"" + msInspectInstallPath + "\"");
@@ -399 +402 @@
     log.debug("uploadOutputFileFlag = " + uploadOutputFileFlag);
     log.debug("timeStampStr = \"" + timeStampStr + "\"");
+    log.debug("strategy = \"" + strategy + "\"");
     // Create msInspect program path
     String delimiter = "/";
@@ -485 +489 @@
       cmdList.add(msInspectProgramPath);
       cmdList.add("--findpeptides");
+      if (strategy != null && !strategy.equals(""))
+      {
+        // Add strategy algorithm option
+        String strategyOption = new String("--strategy=" + strategy);
+        cmdList.add(strategyOption);
+      }
       cmdList.add("--outdir=" + msInspectOutputDirPath);
       cmdList.add(spectrumFileTmp.getPath());