Changeset 4082

Timestamp:

Dec 17, 2010, 10:15:37 AM (12 years ago)

Author:

olle

Message:

Refs #668. Refs #287. the following classes/files were updated to refer to processing with msInspect program as "feature detection" in displayed text:

1. action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/.

2. action/msInspect/RunMsInspect.java in client/servlet/.

3. plugins/RunMsInspectPlugin.java in plugin/.

4. locale/en/dictionary in client/servlet/.

Location:

trunk

Files:

• client/servlet/src/locale/en/dictionary (modified) (2 diffs)
• client/servlet/src/org/proteios/action/file/UseSpectrumFileForMsInspectSearchExtension.java (modified) (4 diffs)
• client/servlet/src/org/proteios/action/msInspect/RunMsInspect.java (modified) (5 diffs)
• plugin/src/org/proteios/plugins/RunMsInspectPlugin.java (modified) (11 diffs)

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

@@ -424 +424 @@
 MsFile=MS File
 MsInspect=msInspect
-MsInspectFeatureFinding=msInspect Feature Finding
-MsInspectSearch=msInspect Search
+MsInspectFeatureDetection=msInspect Feature Detection
 MwInDaltons=Molecular weight (Da)
 MyFiles=My Files
@@ -464 +463 @@
 NextMascotEditParametersBeforeCreatingSearchJobs=Next - Edit parameters before search
 Next=Next
-NextMsInspectCreateSearchJobs=Next - Create search job[s]
+NextMsInspectCreateFeatureDetectionJobs=Next - Create feature detection job[s]
 NextOMSSACreateSearchJobs=Next - Create search job[s]
 NextOMSSAEditParametersBeforeCreatingSearchJobs=Next - Edit parameters before search

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

@@ -93 +93 @@
      * Create a form for selection of plugin.
      */
-    String pageTitle = new String("MsInspectSearch");
+    String pageTitle = new String("MsInspectFeatureDetection");
     Title title = new Title(pageTitle);
     // Instruction area
     TitledWindow instructionArea = new TitledWindow();
-    String instruction = "msInspect feature finding will be performed on";
+    String instruction = "msInspect feature detection will be performed on";
     instruction += " selected spectrum files (only mzML and mzXML supported).<BR>";
     instruction += "<BR>";
@@ -135 +135 @@
     // Add 'Next' button to create search jobs
     ActionLink nextSearch = getActionFactory().getActionLink(
-      RunMsInspect.class, "NextMsInspectCreateSearchJobs");
+      RunMsInspect.class, "NextMsInspectCreateFeatureDetectionJobs");
     for (Integer spectrumFileId : spectrumFileIds)
     {
@@ -148 +148 @@
      */
     RowLayout layout = getLayoutFactory().getRowLayout();
-    layout.add(new Title("MsInspectFeatureFinding"));
+    layout.add(new Title("MsInspectFeatureDetection"));
     layout.add(instructionArea);
     layout.add(form);
@@ -165 +165 @@
      * this by adding a FileContext to the list of contexts.
      */
-    FileContext files = new FileContext("UseSpectrumFileForMsInspectSearch", "Use spectrum file(s) for msInspect feature finding",
+    FileContext files = new FileContext("UseSpectrumFileForMsInspectSearch", "Use spectrum file(s) for msInspect feature detection",
       UseSpectrumFileForMsInspectSearchExtension.class);
     contexts.add(files);

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

@@ -74 +74 @@
      * Check input
      */
-    // Get the spectrum file items to use for the search
+    // Get the spectrum file items to use for the feature detection
     List<Integer> spectrumFileIds = getValidIntegerList(VSPECTRUMFILEID);
     log.debug("spectrumFileIds from RunMsInspect.VSPECTRUMFILEID = " + spectrumFileIds);
@@ -85 +85 @@
     }
     /***********************************************************************
-     * Get MsInspect search constants from Properties file
+     * Get MsInspect feature detection constants from Properties file
      */
     MsInspectPropertiesFile pf = new MsInspectPropertiesFile();
@@ -119 +119 @@
     log.debug("uploadOutputFileFlag = " + uploadOutputFileFlag);
     /***********************************************************************
-     * Get MsInspect search plugin definition
+     * Get MsInspect feature detection plugin definition
      */
     DbControl dc = newDbControl();
@@ -152 +152 @@
      * Create job
      */
-    // Get MsInspect search plugin definition
+    // Get MsInspect feature detection plugin definition
     PluginDefinition pluginDef = PluginDefinition.getByClassName(
       dc, "org.proteios.plugins.RunMsInspectPlugin");
@@ -173 +173 @@
       // Set estimated execution time to next fastest, SHORT
       job.setEstimatedExecutionTime(Job.ExecutionTime.SHORT);
-      job.setName("MsInspect Search Spectrum File: " + spectrumFile.getName());
-      job.setDescription("MsInspect Search Spectrum File: " + spectrumFile.getName() + "[" + spectrumFile.getId() + "]");
+      job.setName("MsInspect Feature Detection Spectrum File: " + spectrumFile.getName());
+      job.setDescription("MsInspect Feature Detection Spectrum File: " + spectrumFile.getName() + "[" + spectrumFile.getId() + "]");
       //
       StringParameterType msInspectInstallPathParam = new StringParameterType();

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

@@ -313 +313 @@
     timeStampStr = (String) job.getValue("timeStampStr");
 
-    // Perform msInspect search using local search engine
+    // Perform msInspect feature detection using local search engine
     msInspectSearchLocal(request, response, progress, tmpDir,
       msInspectInstallPath, msInspectProgramName, msInspectMemoryInMegaBytes,
@@ -344 +344 @@
 
   /**
-   * Start a job that performs an msInspect search using a locally installed
-   * msInspect search engine.
+   * Start a job that performs an msInspect feature detection using a locally installed
+   * msInspect feature detection engine.
    * 
    * @param request Request
@@ -392 +392 @@
     File spectrumFile = factory.getById(File.class, spectrumFileId);
     log.debug("spectrumFile (original) = " + spectrumFile);
-    // Always use original spectrum filename, even if a converted file is used for msInspect search
+    // Always use original spectrum filename, even if a converted file is used for msInspect feature detection
     String originalSpectrumFilename = spectrumFile.getName();
     String spectrumBaseFilename = new String(originalSpectrumFilename);
@@ -416 +416 @@
     String msInspectInputFilePath = new String(tmpDir + "/" + msInspectInputFilename);
     String spectrumPath = new String(msInspectInputFilePath);
-    log.debug("spectrumPath for temporary file used for local msInspect search = " + spectrumPath);
+    log.debug("spectrumPath for temporary file used for local msInspect feature detection = " + spectrumPath);
     java.io.File spectrumFileTmp = new java.io.File(spectrumPath);
     try
@@ -435 +435 @@
     String msInspectOutputPath = msInspectOutputDirPath + delimiter + msInspectOutputFilename;
     log.debug("msInspectOutputPath = \"" + msInspectOutputPath + "\""); 
-    // Prepare msInspect search command for use with local installation
+    // Prepare msInspect feature detection command for use with local installation
     boolean imported = false;
     try
@@ -457 +457 @@
       cmd = cmd + " " + spectrumFileTmp;
       //
-      // Execute msInspect search using local installation
+      // Execute msInspect feature detection using local installation
       //
       if (isJobAborted())
@@ -488 +488 @@
       catch (InterruptedException se)
       {
-        log.warn("InterruptedException when performing msInspect search via locally installed search engine: " + se);
+        log.warn("InterruptedException when performing msInspect feature detection via locally installed search engine: " + se);
         abort();
         proc.destroy();
@@ -551 +551 @@
       log.debug("msInspectOutputFilename = \"" + msInspectOutputFilename + "\""); 
       log.debug("msInspectOutputPath = \"" + msInspectOutputPath + "\""); 
-      String doneMessage = new String("msInspect search finished");
+      String doneMessage = new String("msInspect feature detection finished");
       //
       doneMessage = doneMessage + "\n" + "msInspect input file: " + originalSpectrumFilename;
@@ -565 +565 @@
         {
           String description = new String(
-            "msInspect search for " + spectrumFile.getName() + "[" + spectrumFile
+            "msInspect feature detection for " + spectrumFile.getName() + "[" + spectrumFile
               .getId() + "] using option " + "\"--findpeptides\"");
           try
@@ -613 +613 @@
       else
       {
-        err.add(new BaseException("No msInspect search could be performed"));
+        err.add(new BaseException("No msInspect feature detection could be performed"));
         response.setError(errorMessage, err);
       }
@@ -817 +817 @@
 
   /**
-   * Uploads output file from locally installed msInspect search engine into
+   * Uploads output file from locally installed msInspect feature detection engine into
    * Proteios.
    *