Changeset 4311

Timestamp:

Mar 26, 2012, 4:52:31 PM (11 years ago)

Author:

Fredrik Levander

Message:

 

Location:

trunk

Files:

• FeatureHitMatcher.java (added)
• HitsComparisonReportPlugin.java (added)
• api/core/src/org/proteios/core/File.java (modified) (9 diffs)
• api/core/src/org/proteios/core/data/FeatureData.java (modified) (1 diff)
• client/servlet/src/content/openms_featurefinder_centroided_ini_file_template.ini (modified) (1 diff)
• client/servlet/src/org/proteios/action/file/UseSpectrumFileForOpenMsSearchExtension.java (modified) (3 diffs)
• contrib/SpectrumLibraryExport/src/satoshi/.directory (added)
• plugin/src/org/proteios/plugins/RunOpenMsPlugin.java (modified) (68 diffs)
• proteios_ftp_server.bat (added)

trunk/api/core/src/org/proteios/core/File.java

@@ -48 +48 @@
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.net.URLConnection;
 import java.security.MessageDigest;
 import java.text.SimpleDateFormat;
@@ -279 +280 @@
         "https://srm.swegrid.se/snic/bils");
     }
+    if (uri != null && uri
+      .startsWith("https://srm.swegrid.se/snic/bils/lu_proteomics/qtof/mzml/201102/K-M_Andersson"))
+    {
+      uri = uri
+        .replace(
+          "https://srm.swegrid.se/snic/bils/lu_proteomics/qtof/mzml/201102",
+          "http://fileserver.immunoprot.lth.se/tmp");
+    }
+    if (uri != null && uri
+      .startsWith("https://srm.swegrid.se/snic/bils/lu_proteomics/qtof/mzml/201101/K-M_Andersson"))
+    {
+      uri = uri
+        .replace(
+          "https://srm.swegrid.se/snic/bils/lu_proteomics/qtof/mzml/201101",
+          "http://fileserver.immunoprot.lth.se/tmp");
+    }
     return uri;
   }
@@ -298 +315 @@
       if (uniformResourceIdentifier != null)
       {
-        if (!(uniformResourceIdentifier.startsWith("http://") || uniformResourceIdentifier
-          .startsWith("https://")))
-        {
-          throw new InvalidDataException(
-            "Protocol must be http:// or https://");
-        }
+        /*
+         * if (!(uniformResourceIdentifier.startsWith("http://") ||
+         * uniformResourceIdentifier .startsWith("https://"))) { throw
+         * new InvalidDataException(
+         * "Protocol must be http:// or https://"); }
+         */
         new URI(uniformResourceIdentifier);
       }
@@ -770 +787 @@
 
   /**
-   * Set the mime type for this <code>File</code> item. It can be any
-   * mimetype or one avalible in the mimetype table.
+   * Set the mime type for this <code>File</code> item. It can be any mimetype
+   * or one avalible in the mimetype table.
    * 
    * @param mimeType The new mime type for this item
@@ -1082 +1099 @@
 
   /**
-   * Get an <code>InputStream</code> that can be used to download the
-   * physical file for this file item. The client application should call
-   * <code>close()</code> method to finish the download. If the physical
-   * file isn't at the primary location there is an attempt at downloading the
-   * file from the URI. If no URI is given an empty stream is returned.
+   * Get an <code>InputStream</code> that can be used to download the physical
+   * file for this file item. The client application should call
+   * <code>close()</code> method to finish the download. If the physical file
+   * isn't at the primary location there is an attempt at downloading the file
+   * from the URI. If no URI is given an empty stream is returned.
    * 
    * @param offset Start reading the physical at the specified offset, use 0
@@ -1099 +1116 @@
     if (getInternalName() == null)
     {
-      if (getUniformResourceIdentifier() != null)
+      if (getUniformResourceIdentifier() != null && !getUniformResourceIdentifier()
+        .startsWith("file://"))
       {
         try
         {
-          HttpURLConnection connection = getConnection(getUniformResourceIdentifier());
+          URLConnection connection = getConnection(getUniformResourceIdentifier());
           InputStream fis = connection.getInputStream();
           if (isCompressed())
@@ -1120 +1138 @@
         }
       }
+      else if (getUniformResourceIdentifier() != null && getUniformResourceIdentifier()
+        .startsWith("file://"))
+      {
+        try
+        {
+          InputStream fis = new BufferedInputStream(
+            new FileInputStream(getUniformResourceIdentifier()
+              .substring(7)));
+          if (isCompressed())
+          {
+            fis = new GZIPInputStream(fis);
+          }
+          if (offset > 0)
+          {
+            fis.skip(offset);
+          }
+          return fis;
+        }
+        catch (Exception e)
+        {
+          throw new BaseException(e);
+        }
+
+      }
       else
       {
@@ -1154 +1196 @@
 
   /**
-   * Get an <code>InputStream</code> that can be used to download the
-   * physical file for this file item. The client application should call
-   * <code>close()</code> method to finish the download. If the physical
-   * file isn't at the primary location there is an attempt at downloading the
-   * file from the URI. If no URI is given an empty stream is returned. Does
-   * not attempt to decompress contents of a file stored compressed
-   * internally.
+   * Get an <code>InputStream</code> that can be used to download the physical
+   * file for this file item. The client application should call
+   * <code>close()</code> method to finish the download. If the physical file
+   * isn't at the primary location there is an attempt at downloading the file
+   * from the URI. If no URI is given an empty stream is returned. Does not
+   * attempt to decompress contents of a file stored compressed internally.
    * 
    * @param offset Start reading the physical at the specified offset, use 0
@@ -1177 +1218 @@
         try
         {
-          HttpURLConnection connection = getConnection(getUniformResourceIdentifier());
+          URLConnection connection = getConnection(getUniformResourceIdentifier());
           InputStream fis = connection.getInputStream();
           if (offset > 0)

trunk/api/core/src/org/proteios/core/data/FeatureData.java

@@ -66 +66 @@
    * Project origin reference.
    * 
-   * @hibernate.many-to-one column="`project`" not-null="true" update="false"
+   * @hibernate.many-to-one column="`project`" index=`project_idx` not-null="true" update="false"
    */
   public ProjectData getProject()

trunk/client/servlet/src/content/openms_featurefinder_centroided_ini_file_template.ini

@@ -1 +1 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-  <NODE name="FeatureFinder" description="Detects two-dimensional features in LC-MS data.">
-    <ITEM name="version" value="1.7.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
-    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureFinder&apos;">
+  <NODE name="FeatureFinderCentroided" description="Detects two-dimensional features in LC-MS data.">
+    <ITEM name="version" value="1.9.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
+    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureFinderCentroided&apos;">
       <ITEM name="in" value="" type="string" description="input file (valid formats: &apos;mzML&apos;)" tags="input file" />
       <ITEM name="out" value="" type="string" description="output file (valid formats: &apos;featureXML&apos;)" tags="output file" />
       <ITEM name="seeds" value="" type="string" description="User-specified seed list. This feature is not supported by all algorithms! (valid formats: &apos;featureXML&apos;)" tags="input file" />
-      <ITEM name="type" value="centroided" type="string" description="FeatureFinder algorithm type" restrictions="centroided,isotope_wavelet,mrm" />
       <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
       <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />

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

@@ -47 +47 @@
 import se.lu.thep.waf.constraints.InvalidParameterValue;
 import se.lu.thep.waf.constraints.VBoolean;
-import se.lu.thep.waf.constraints.VFloat;
-import se.lu.thep.waf.constraints.VInteger;
 import se.lu.thep.waf.constraints.VString;
 
@@ -174 +172 @@
     validStringParam = RunOpenMs.VOPENMS_PEAKPICKER_ALGORITHM;
     optionList = new ArrayList<Option>();
-    optionList.add(new Option("high_res", "High resolution"));
-    optionList.add(new Option("wavelet", "Wavelet"));
-    selected = new String("high_res");
+    optionList.add(new Option("HiRes", "High resolution"));
+    optionList.add(new Option("Wavelet", "Wavelet"));
+    selected = new String("HighRes");
     Select<VString> peakPickerAlgorithmSelectBox = new Select<VString>(validStringParam, optionList);
     peakPickerAlgorithmSelectBox.selectOption(selected);
@@ -200 +198 @@
     validStringParam = RunOpenMs.VOPENMS_FEATUREFINDER_ALGORITHM;
     optionList = new ArrayList<Option>();
-    optionList.add(new Option("centroided", "Centroided"));
-    optionList.add(new Option("isotope_wavelet", "Isotope wavelet"));
-    selected = new String("centroided");
+    optionList.add(new Option("Centroided", "Centroided"));
+    optionList.add(new Option("IsotopeWavelet", "Isotope wavelet"));
+    selected = new String("Centroided");
     Select<VString> featureFinderAlgorithmSelectBox = new Select<VString>(validStringParam, optionList);
     featureFinderAlgorithmSelectBox.selectOption(selected);

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

@@ -28 +28 @@
 package org.proteios.plugins;
 
-import org.apache.commons.httpclient.methods.multipart.Part;
-import org.apache.commons.httpclient.methods.multipart.PartSource;
-import org.apache.commons.httpclient.methods.multipart.StringPart;
 import org.proteios.core.AbortablePluginInterface;
 import org.proteios.core.BaseException;
@@ -40 +37 @@
 import org.proteios.core.ProgressReporter;
 import org.proteios.core.SessionControl;
-import org.proteios.core.User;
 import org.proteios.core.plugin.About;
 import org.proteios.core.plugin.AboutImpl;
@@ -93 +89 @@
 
 
-    StreamGobbler(InputStream is, String type, OutputStream redirect, ProgressReporter progress)
+    StreamGobbler(InputStream is, String type, OutputStream redirect,
+        ProgressReporter progress)
     {
       this.is = is;
@@ -157 +154 @@
   }
 
-
   /**
    * Logger used. Used to log specific events.
@@ -190 +186 @@
    * Constants for input data
    */
-  private final String OPENMS_PROGRAM_PEAKPICKER = "peakpicker";
-  private final String OPENMS_PROGRAM_FEATUREFINDER = "featurefinder";
-  private final String FEATUREFINDER_ALGORITHM_CENTROIDED = "centroided";
+  private final String OPENMS_PROGRAM_PEAKPICKER = "PeakPicker";
+  private final String OPENMS_PROGRAM_FEATUREFINDER = "FeatureFinder";
+  private final String FEATUREFINDER_ALGORITHM_CENTROIDED = "Centroided";
   /*
    * OpenMS program specifier.
@@ -214 +210 @@
   private String lineSeparator;
 
+
   /**
    * Get size of byte buffer for writing a String to an OutputStream.
@@ -349 +346 @@
 
   /**
-   * Set OpenMS INI file path.
-   * Note that this method is private, as the value is assumed
-   * to be set by the constructor.
+   * Set OpenMS INI file path. Note that this method is private, as the value
+   * is assumed to be set by the constructor.
    * 
    * @param openMsIniFilePath String The OpenMS INI file path to set.
@@ -373 +369 @@
 
   /**
-   * Set line separator string to use (Internal use only).
-   * Setter method made private to ensure that this
-   * configuration is obtained from this class.
+   * Set line separator string to use (Internal use only). Setter method made
+   * private to ensure that this configuration is obtained from this class.
    * 
    * @param lineSeparator String The line separator string to use.
@@ -430 +425 @@
     String openMsPeakPickerProgramName;
     String openMsFeatureFinderProgramName;
-    //Integer openMsMemoryInMegaBytes;
+    // Integer openMsMemoryInMegaBytes;
     Boolean useExistingTemporaryInputFileFlag;
     String originalSpectrumFilename;
@@ -447 +442 @@
 
     openMsInstallPath = (String) job.getValue("openMsInstallPath");
-    openMsPeakPickerProgramName = (String) job.getValue("openMsPeakPickerProgramName");
-    openMsFeatureFinderProgramName = (String) job.getValue("openMsFeatureFinderProgramName");
-    //openMsMemoryInMegaBytes = (Integer) job.getValue("openMsMemoryInMegaBytes");
+    openMsPeakPickerProgramName = (String) job
+      .getValue("openMsPeakPickerProgramName");
+    openMsFeatureFinderProgramName = (String) job
+      .getValue("openMsFeatureFinderProgramName");
+    // openMsMemoryInMegaBytes = (Integer)
+    // job.getValue("openMsMemoryInMegaBytes");
     tmpDir = (String) job.getValue("tmpDir");
     iniFilenamePrefix = (String) job.getValue("iniFilenamePrefix");
-    useExistingTemporaryInputFileFlag = (Boolean) job.getValue("useExistingTemporaryInputFileFlag");
-    originalSpectrumFilename = (String) job.getValue("originalSpectrumFilename");
-    temporaryInputFilename = (String) job.getValue("temporaryInputFilename");
+    useExistingTemporaryInputFileFlag = (Boolean) job
+      .getValue("useExistingTemporaryInputFileFlag");
+    originalSpectrumFilename = (String) job
+      .getValue("originalSpectrumFilename");
+    temporaryInputFilename = (String) job
+      .getValue("temporaryInputFilename");
     spectrumFileId = (Integer) job.getValue("spectrumFileId");
     dirId = (Integer) job.getValue("dirId");
@@ -462 +463 @@
     openMsProgram = (String) job.getValue("openMsProgram");
     peakPickerAlgorithm = (String) job.getValue("peakPickerAlgorithm");
-    featureFinderAlgorithm = (String) job.getValue("featureFinderAlgorithm");
-    featureFinderIsotopicPatternChargeHigh = (Integer) job.getValue("featureFinderIsotopicPatternChargeHigh");
-    featureFinderIsotopicPatternMzTolerance = (Float) job.getValue("featureFinderIsotopicPatternMzTolerance");
-    featureFinderFeatureMinRtSpan = (Float) job.getValue("featureFinderFeatureMinRtSpan");
+    featureFinderAlgorithm = (String) job
+      .getValue("featureFinderAlgorithm");
+    featureFinderIsotopicPatternChargeHigh = (Integer) job
+      .getValue("featureFinderIsotopicPatternChargeHigh");
+    featureFinderIsotopicPatternMzTolerance = (Float) job
+      .getValue("featureFinderIsotopicPatternMzTolerance");
+    featureFinderFeatureMinRtSpan = (Float) job
+      .getValue("featureFinderFeatureMinRtSpan");
     log.debug("openMsInstallPath = \"" + openMsInstallPath + "\"");
-    log.debug("openMsPeakPickerProgramName = \"" + openMsPeakPickerProgramName + "\"");
-    log.debug("openMsFeatureFinderProgramName = \"" + openMsFeatureFinderProgramName + "\"");
+    log
+      .debug("openMsPeakPickerProgramName = \"" + openMsPeakPickerProgramName + "\"");
+    log
+      .debug("openMsFeatureFinderProgramName = \"" + openMsFeatureFinderProgramName + "\"");
     log.debug("tmpDir = \"" + tmpDir + "\"");
     log.debug("iniFilenamePrefix = \"" + iniFilenamePrefix + "\"");
-    log.debug("useExistingTemporaryInputFileFlag = " + useExistingTemporaryInputFileFlag);
-    log.debug("originalSpectrumFilename = \"" + originalSpectrumFilename + "\"");
-    log.debug("temporaryInputFilename = \"" + temporaryInputFilename + "\"");
+    log
+      .debug("useExistingTemporaryInputFileFlag = " + useExistingTemporaryInputFileFlag);
+    log
+      .debug("originalSpectrumFilename = \"" + originalSpectrumFilename + "\"");
+    log
+      .debug("temporaryInputFilename = \"" + temporaryInputFilename + "\"");
     log.debug("spectrumFileId = " + spectrumFileId);
     log.debug("dirId = " + dirId);
@@ -481 +491 @@
     log.debug("openMsProgram = \"" + openMsProgram + "\"");
     log.debug("peakPickerAlgorithm = \"" + peakPickerAlgorithm + "\"");
-    log.debug("featureFinderAlgorithm = \"" + featureFinderAlgorithm + "\"");
-    log.debug("featureFinderIsotopicPatternChargeHigh = " + featureFinderIsotopicPatternChargeHigh);
-    log.debug("featureFinderIsotopicPatternMzTolerance = " + featureFinderIsotopicPatternMzTolerance);
-    log.debug("featureFinderFeatureMinRtSpan = " + featureFinderFeatureMinRtSpan);
+    log
+      .debug("featureFinderAlgorithm = \"" + featureFinderAlgorithm + "\"");
+    log
+      .debug("featureFinderIsotopicPatternChargeHigh = " + featureFinderIsotopicPatternChargeHigh);
+    log
+      .debug("featureFinderIsotopicPatternMzTolerance = " + featureFinderIsotopicPatternMzTolerance);
+    log
+      .debug("featureFinderFeatureMinRtSpan = " + featureFinderFeatureMinRtSpan);
     // Save OpenMS program specifier for use when processing progress info
     setOpenMsProgramSpecifier(openMsProgram);
@@ -491 +505 @@
     String programAlgorithm = new String("");
     String outputFileExtension = new String(".txt");
-    if (openMsProgram != null && openMsProgram.equals(OPENMS_PROGRAM_PEAKPICKER))
+    if (openMsProgram != null && openMsProgram
+      .equalsIgnoreCase(OPENMS_PROGRAM_PEAKPICKER))
     {
       openMsProgramName = new String(openMsPeakPickerProgramName);
@@ -497 +512 @@
       outputFileExtension = "." + openMsProgram + ".mzML";
     }
-    else if (openMsProgram != null && openMsProgram.equals(OPENMS_PROGRAM_FEATUREFINDER))
+    else if (openMsProgram != null && openMsProgram
+      .equalsIgnoreCase(OPENMS_PROGRAM_FEATUREFINDER))
     {
       openMsProgramName = new String(openMsFeatureFinderProgramName);
@@ -507 +523 @@
     log.debug("outputFileExtension = " + outputFileExtension);
     // Perform OpenMS feature detection using local search engine
-    openMsSearchLocal(request, response, progress,
-      tmpDir,
-      iniFilenamePrefix,
-      openMsInstallPath, openMsProgramName, programAlgorithm,
-      featureFinderIsotopicPatternChargeHigh,
+    openMsSearchLocal(request, response, progress, tmpDir,
+      iniFilenamePrefix, openMsInstallPath, openMsProgramName,
+      programAlgorithm, featureFinderIsotopicPatternChargeHigh,
       featureFinderIsotopicPatternMzTolerance,
-      featureFinderFeatureMinRtSpan,
-      useExistingTemporaryInputFileFlag, originalSpectrumFilename,
-      temporaryInputFilename,
-      spectrumFileId, dirId, uploadOutputFileFlag, deleteOutputFileFlag,
+      featureFinderFeatureMinRtSpan, useExistingTemporaryInputFileFlag,
+      originalSpectrumFilename, temporaryInputFilename, spectrumFileId,
+      dirId, uploadOutputFileFlag, deleteOutputFileFlag,
       outputFileExtension, timeStampStr, openMsProgram);
     done();
@@ -538 +551 @@
 
   /**
-   * Start a job that performs an OpenMS feature detection using a locally installed
-   * OpenMS feature detection engine.
+   * Start a job that performs an OpenMS feature detection using a locally
+   * installed OpenMS feature detection engine.
    * 
    * @param request Request
@@ -545 +558 @@
    * @param progress ProgressReporter
    * @param tmpDir String Directory for temporary files
-   * @param iniFilenamePrefix String Prefix for filename of temporary OpenMS program INI file
+   * @param iniFilenamePrefix String Prefix for filename of temporary OpenMS
+   *        program INI file
    * @param openMsInstallPath String The openMs install path
    * @param openMsProgramName String The openMS program name
    * @param programAlgorithm String The program algorithm.
-   * @param featureFinderIsotopicPatternChargeHigh Integer FeatureFinder isotopic_pattern:charge_high
-   * @param featureFinderIsotopicPatternMzTolerance Float FeatureFinder isotopic_pattern:mz_tolerance
-   * @param featureFinderFeatureMinRtSpan Float FeatureFinder feature:min_rt_span
-   * @param useExistingTemporaryInputFileFlag Boolean Flag indicating that existing temporary input file should be used.
+   * @param featureFinderIsotopicPatternChargeHigh Integer FeatureFinder
+   *        isotopic_pattern:charge_high
+   * @param featureFinderIsotopicPatternMzTolerance Float FeatureFinder
+   *        isotopic_pattern:mz_tolerance
+   * @param featureFinderFeatureMinRtSpan Float FeatureFinder
+   *        feature:min_rt_span
+   * @param useExistingTemporaryInputFileFlag Boolean Flag indicating that
+   *        existing temporary input file should be used.
    * @param originalSpectrumFilename String The original spectrum filename.
    * @param temporaryInputFilename String Optional temporary input filename.
@@ -560 +578 @@
    * @param deleteOutputFileFlag Boolean The delete output file flag
    * @param outputFileExtension String File extension for the output file.
-   * @param timeStampStr String Time stamp string in YYYY_MM_DD_hh_mm_ss format
+   * @param timeStampStr String Time stamp string in YYYY_MM_DD_hh_mm_ss
+   *        format
    * @param openMsProgram String The openMS program specifier
    */
   private void openMsSearchLocal(Request request, Response response,
-      ProgressReporter progress,
-      String tmpDir,
-      String iniFilenamePrefix,
-      String openMsInstallPath,
-      String openMsProgramName,
+      ProgressReporter progress, String tmpDir, String iniFilenamePrefix,
+      String openMsInstallPath, String openMsProgramName,
       String programAlgorithm,
       Integer featureFinderIsotopicPatternChargeHigh,
@@ -574 +590 @@
       Float featureFinderFeatureMinRtSpan,
       Boolean useExistingTemporaryInputFileFlag,
-      String originalSpectrumFilename,
-      String temporaryInputFilename,
-      Integer spectrumFileId,
-      Integer dirId,
-      Boolean uploadOutputFileFlag,
-      Boolean deleteOutputFileFlag,
-      String outputFileExtension,
-      String timeStampStr, String openMsProgram)
+      String originalSpectrumFilename, String temporaryInputFilename,
+      Integer spectrumFileId, Integer dirId,
+      Boolean uploadOutputFileFlag, Boolean deleteOutputFileFlag,
+      String outputFileExtension, String timeStampStr,
+      String openMsProgram)
   {
     log.debug("openMsInstallPath = \"" + openMsInstallPath + "\"");
     log.debug("openMsProgramName = \"" + openMsProgramName + "\"");
     log.debug("programAlgorithm = " + programAlgorithm);
-    log.debug("featureFinderIsotopicPatternChargeHigh = " + featureFinderIsotopicPatternChargeHigh);
-    log.debug("featureFinderIsotopicPatternMzTolerance = " + featureFinderIsotopicPatternMzTolerance);
-    log.debug("featureFinderFeatureMinRtSpan = " + featureFinderFeatureMinRtSpan);
+    log
+      .debug("featureFinderIsotopicPatternChargeHigh = " + featureFinderIsotopicPatternChargeHigh);
+    log
+      .debug("featureFinderIsotopicPatternMzTolerance = " + featureFinderIsotopicPatternMzTolerance);
+    log
+      .debug("featureFinderFeatureMinRtSpan = " + featureFinderFeatureMinRtSpan);
     log.debug("tmpDir = \"" + tmpDir + "\"");
     log.debug("iniFilenamePrefix = \"" + iniFilenamePrefix + "\"");
-    log.debug("useExistingTemporaryInputFileFlag = " + useExistingTemporaryInputFileFlag);
-    log.debug("originalSpectrumFilename = \"" + originalSpectrumFilename + "\"");
-    log.debug("temporaryInputFilename = \"" + temporaryInputFilename + "\"");
+    log
+      .debug("useExistingTemporaryInputFileFlag = " + useExistingTemporaryInputFileFlag);
+    log
+      .debug("originalSpectrumFilename = \"" + originalSpectrumFilename + "\"");
+    log
+      .debug("temporaryInputFilename = \"" + temporaryInputFilename + "\"");
     log.debug("spectrumFileId = " + spectrumFileId);
     log.debug("dirId = " + dirId);
     log.debug("uploadOutputFileFlag = " + uploadOutputFileFlag);
     log.debug("deleteOutputFileFlag = " + deleteOutputFileFlag);
-    log.debug("outputFileExtension = \"" + outputFileExtension + "\""); 
+    log.debug("outputFileExtension = \"" + outputFileExtension + "\"");
     log.debug("timeStampStr = \"" + timeStampStr + "\"");
     log.debug("openMsProgram = \"" + openMsProgram + "\"");
@@ -613 +632 @@
     log.debug("openMsOutputDirPath = \"" + openMsOutputDirPath + "\"");
     openMsOutputDirPath = tmpDir + "/" + openMsOutputDirPath;
-    log.debug("openMsOutputDirPath (modified) = \"" + openMsOutputDirPath + "\"");
+    log
+      .debug("openMsOutputDirPath (modified) = \"" + openMsOutputDirPath + "\"");
     //
     DbControl dc = sc.newDbControl();
@@ -619 +639 @@
     // Create output file type
     FileType outputFileType = null;
-    if (openMsProgram != null && openMsProgram.equals(OPENMS_PROGRAM_PEAKPICKER))
+    if (openMsProgram != null && openMsProgram
+      .equalsIgnoreCase(OPENMS_PROGRAM_PEAKPICKER))
     {
       outputFileType = factory.getBySystemId(FileType.class,
         FileType.MZML);
     }
-    else if (openMsProgram != null && openMsProgram.equals(OPENMS_PROGRAM_FEATUREFINDER))
+    else if (openMsProgram != null && openMsProgram
+      .equalsIgnoreCase(OPENMS_PROGRAM_FEATUREFINDER))
     {
       outputFileType = factory.getBySystemId(FileType.class,
         FileType.OPENMS_FEATURES);
     }
+    if (programAlgorithm != null && !programAlgorithm.equals(""))
+    {
+      openMsProgramPath += programAlgorithm;
+    }
+
     /*
-    // Get spectrum file
-    File spectrumFile = factory.getById(File.class, spectrumFileId);
-    log.debug("spectrumFile (original) = " + spectrumFile);
-    // Get spectrum file size in bytes for progress calculation
-    long fileSizeInBytes = spectrumFile.getSizeInBytes();
-    setInputFileSizeInBytes(fileSizeInBytes);
-    */
-    // Always use original spectrum filename, even if a converted file is used for OpenMS feature detection
-    //String originalSpectrumFilename = spectrumFile.getName();
+     * // Get spectrum file File spectrumFile = factory.getById(File.class,
+     * spectrumFileId); log.debug("spectrumFile (original) = " +
+     * spectrumFile); // Get spectrum file size in bytes for progress
+     * calculation long fileSizeInBytes = spectrumFile.getSizeInBytes();
+     * setInputFileSizeInBytes(fileSizeInBytes);
+     */
+    // Always use original spectrum filename, even if a converted file is
+    // used for OpenMS feature detection
+    // String originalSpectrumFilename = spectrumFile.getName();
     String spectrumBaseFilename = new String(originalSpectrumFilename);
     String fileExtension = new String("");
@@ -644 +671 @@
     if (dotIndex > 0)
     {
-      fileExtension = originalSpectrumFilename.substring(dotIndex+1);
-      spectrumBaseFilename = originalSpectrumFilename.substring(0, dotIndex);
+      fileExtension = originalSpectrumFilename.substring(dotIndex + 1);
+      spectrumBaseFilename = originalSpectrumFilename.substring(0,
+        dotIndex);
     }
     // Copy spectrum file item to local file used for OpenMS input
     progress.display(0, "Making local file copy");
-    String openMsInputBaseFilename = new String(spectrumBaseFilename + "_" + timeStampStr);
+    String openMsInputBaseFilename = new String(
+      spectrumBaseFilename + "_" + timeStampStr);
     String openMsInputFilename = new String(openMsInputBaseFilename);
     if (!fileExtension.equals(""))
@@ -655 +684 @@
       openMsInputFilename = openMsInputFilename + "." + fileExtension;
     }
-    //log.debug("originalSpectrumFilename = \"" + originalSpectrumFilename + "\"");
+    // log.debug("originalSpectrumFilename = \"" + originalSpectrumFilename
+    // + "\"");
     log.debug("spectrumBaseFilename = \"" + spectrumBaseFilename + "\"");
     log.debug("fileExtension = \"" + fileExtension + "\"");
-    log.debug("openMsInputBaseFilename = \"" + openMsInputBaseFilename + "\"");
+    log
+      .debug("openMsInputBaseFilename = \"" + openMsInputBaseFilename + "\"");
     log.debug("openMsInputFilename = \"" + openMsInputFilename + "\"");
     // Get temporary local input file name to use
@@ -674 +705 @@
     log.debug("temporaryInputFilename used = " + temporaryInputFilename);
     // Get input file path
-    String openMsInputFilePath = new String(tmpDir + "/" + temporaryInputFilename);
+    String openMsInputFilePath = new String(
+      tmpDir + "/" + temporaryInputFilename);
     log.debug("openMsInputFilePath = \"" + openMsInputFilePath + "\"");
     // Get temporary local input file
@@ -686 +718 @@
       setInputFileSizeInBytes(fileSizeInBytes);
       // Perform a number of attempts to create local file copy
-      temporaryInputFileExists = makeTemporaryLocalFileCopy(spectrumFile, openMsInputFilePath);
-    }
-    log.debug("temporaryInputFileExists = " + temporaryInputFileExists);      
+      temporaryInputFileExists = makeTemporaryLocalFileCopy(spectrumFile,
+        openMsInputFilePath);
+    }
+    log.debug("temporaryInputFileExists = " + temporaryInputFileExists);
     String spectrumPath = new String(openMsInputFilePath);
-    log.debug("spectrumPath for temporary file used for local OpenMS feature detection = " + spectrumPath);
+    log
+      .debug("spectrumPath for temporary file used for local OpenMS feature detection = " + spectrumPath);
     // Create OpenMS output file name
     String openMsOutputFilename = openMsInputBaseFilename + outputFileExtension;
@@ -699 +733 @@
     }
     String openMsOutputPath = openMsOutputDirPath + delimiter + openMsOutputFilename;
-    log.debug("openMsOutputFilename = \"" + openMsOutputFilename + "\""); 
+    log.debug("openMsOutputFilename = \"" + openMsOutputFilename + "\"");
     log.debug("openMsOutputPath = \"" + openMsOutputPath + "\"");
     // Create OpenMS INI file if needed
     String openMsIniFilePath = null;
-    log.debug("openMsProgram = \"" + openMsProgram + "\" programAlgorithm = \"" + programAlgorithm + "\"");
-    openMsIniFilePath = createOpenMsIniFile(
-      tmpDir,
-      iniFilenamePrefix,
-      timeStampStr,
-      openMsProgram,
-      programAlgorithm,
+    log
+      .debug("openMsProgram = \"" + openMsProgram + "\" programAlgorithm = \"" + programAlgorithm + "\"");
+    openMsIniFilePath = createOpenMsIniFile(tmpDir, iniFilenamePrefix,
+      timeStampStr, openMsProgram, programAlgorithm,
       featureFinderIsotopicPatternChargeHigh,
       featureFinderIsotopicPatternMzTolerance,
       featureFinderFeatureMinRtSpan);
     log.debug("openMsIniFilePath = " + openMsIniFilePath);
-    // Prepare OpenMS feature detection command for use with local installation
+    // Prepare OpenMS feature detection command for use with local
+    // installation
     boolean imported = false;
     try
@@ -721 +753 @@
       if (!temporaryInputFileExists)
       {
-        throw new IOException("Temporary spectrum file \"" + spectrumPath + "\" could no be saved. Closing down.");
+        throw new IOException(
+          "Temporary spectrum file \"" + spectrumPath + "\" could no be saved. Closing down.");
       }
       List<String> cmdList = new ArrayList<String>();
@@ -729 +762 @@
       cmdList.add("-out");
       cmdList.add(openMsOutputPath);
-      if (programAlgorithm != null && !programAlgorithm.equals(""))
-      {
-        // Add algorithm option
-        cmdList.add("-type");
-        cmdList.add(programAlgorithm);
-      }
       if (openMsIniFilePath != null && !openMsIniFilePath.equals(""))
       {
@@ -749 +776 @@
         deleteFile(tmpDir, temporaryInputFilename);
         // Delete other temporary files
-        cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename, true, outputFileExtension);
+        cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename,
+          true, outputFileExtension);
         throw new IOException("Job command is aborted. Closing down.");
       }
@@ -759 +787 @@
       Process proc = rt.exec(cmdArr);
       /*
-      // any error message?
-      StreamGobbler errorGobbler = new StreamGobbler(proc
-        .getErrorStream(), "ERR");
-      */
+       * // any error message? StreamGobbler errorGobbler = new
+       * StreamGobbler(proc .getErrorStream(), "ERR");
+       */
       // Parse out stream for progress info
       // any error message?
@@ -779 +806 @@
       catch (InterruptedException se)
       {
-        log.warn("InterruptedException when performing OpenMS feature detection via locally installed search engine: " + se);
+        log
+          .warn("InterruptedException when performing OpenMS feature detection via locally installed search engine: " + se);
         abort();
         proc.destroy();
@@ -792 +820 @@
         deleteFile(tmpDir, temporaryInputFilename);
         // Delete other temporary files
-        cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename, true, outputFileExtension);        
+        cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename,
+          true, outputFileExtension);
         throw new IOException("Job command is aborted. Closing down.");
       }
@@ -817 +846 @@
       String testOutputFilename = openMsInputBaseFilename + outputFileExtension;
       // Construct filename to use for uploaded result file
-      // Example: Spectrum file sample.mzML gets result file sample.peakpicker.mzML
+      // Example: Spectrum file sample.mzML gets result file
+      // sample.peakpicker.mzML
       String filenameOfUploadedFile = spectrumBaseFilename + outputFileExtension;
       if (localFileCanBeRead(tmpDir, testOutputFilename))
@@ -825 +855 @@
       else
       {
-        // Test output filename including original file extension in name
+        // Test output filename including original file extension in
+        // name
         testOutputFilename = openMsInputFilename + outputFileExtension;
         // Construct filename to use for uploaded result file
-        // Example: Spectrum file sample.mzml gets result file sample.peakpicker.mzml
+        // Example: Spectrum file sample.mzml gets result file
+        // sample.peakpicker.mzml
         filenameOfUploadedFile = originalSpectrumFilename + outputFileExtension;
         if (localFileCanBeRead(tmpDir, testOutputFilename))
@@ -843 +875 @@
         }
       }
-      log.debug("openMsOutputFilename = \"" + openMsOutputFilename + "\""); 
-      log.debug("openMsOutputPath = \"" + openMsOutputPath + "\""); 
+      log
+        .debug("openMsOutputFilename = \"" + openMsOutputFilename + "\"");
+      log.debug("openMsOutputPath = \"" + openMsOutputPath + "\"");
       //
       String programNameStr = "unknown program";
-      if (openMsProgram.equals(OPENMS_PROGRAM_PEAKPICKER))
+      if (openMsProgram.equalsIgnoreCase(OPENMS_PROGRAM_PEAKPICKER))
       {
         programNameStr = "PeakPicker";
       }
-      else if (openMsProgram.equals(OPENMS_PROGRAM_FEATUREFINDER))
+      else if (openMsProgram
+        .equalsIgnoreCase(OPENMS_PROGRAM_FEATUREFINDER))
       {
         programNameStr = "FeatureFinder";
       }
-      String doneMessage = new String("OpenMS feature detection with " + programNameStr + " finished");
+      String doneMessage = new String(
+        "OpenMS feature detection with " + programNameStr + " finished");
       //
       doneMessage = doneMessage + "\n" + "OpenMS input file: " + originalSpectrumFilename;
       //
-      log
-        .debug("openMsOutputPath = \"" + openMsOutputPath + "\"");
+      log.debug("openMsOutputPath = \"" + openMsOutputPath + "\"");
       doneMessage = doneMessage + "\n" + "OpenMS output file: " + openMsOutputPath;
       // Optional upload of OpenMS output file
@@ -872 +906 @@
           try
           {
-            log.debug("filenameOfUploadedFile = \"" + filenameOfUploadedFile + "\"");
-            uploadOpenMsOutputFile(tmpDir,
-              openMsOutputFilename, filenameOfUploadedFile, dirId, description, outputFileType);
+            log
+              .debug("filenameOfUploadedFile = \"" + filenameOfUploadedFile + "\"");
+            uploadOpenMsOutputFile(tmpDir, openMsOutputFilename,
+              filenameOfUploadedFile, dirId, description,
+              outputFileType);
             outputFileUploaded = true;
             doneMessage = doneMessage + "\n" + "Output file uploaded: " + filenameOfUploadedFile;
@@ -891 +927 @@
       // Delete temporary input file
       deleteFile(tmpDir, temporaryInputFilename);
-      // Clean up temporary files (result file only deleted if it could be uploaded)
+      // Clean up temporary files (result file only deleted if it could be
+      // uploaded)
       boolean deleteResultFile = deleteOutputFileFlag;
       if (uploadOutputFileFlag != null && uploadOutputFileFlag)
@@ -902 +939 @@
       }
       log.debug("deleteResultFile = " + deleteResultFile);
-      cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename, deleteResultFile, outputFileExtension);
+      cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename,
+        deleteResultFile, outputFileExtension);
       // Delete temporary OpenMS INI file
       deleteOptionalFile(openMsIniFilePath);
@@ -921 +959 @@
         programNameStr = "FeatureFinder";
       }
-      String errorMessage = new String("Nothing searched using OpenMS feature detection with " + programNameStr);
+      String errorMessage = new String(
+        "Nothing searched using OpenMS feature detection with " + programNameStr);
       //
       errorMessage = errorMessage + "\n" + "OpenMS input file: " + openMsInputFilename;
@@ -935 +974 @@
       else
       {
-        err.add(new BaseException("No OpenMS feature detection could be performed"));
+        err.add(new BaseException(
+          "No OpenMS feature detection could be performed"));
         response.setError(errorMessage, err);
       }
@@ -941 +981 @@
       deleteFile(tmpDir, temporaryInputFilename);
       // Clean up temporary files
-      cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename, true, outputFileExtension);
+      cleanUpTemporaryOpenMsFiles(tmpDir, openMsInputBaseFilename, true,
+        outputFileExtension);
       // Delete temporary OpenMS INI file
-      deleteOptionalFile(openMsIniFilePath);
+      // deleteOptionalFile(openMsIniFilePath);
     }
   }
@@ -955 +996 @@
    * @return boolean Returns 'true' if copying was successful, else 'false'.
    */
-  private boolean makeTemporaryLocalFileCopy(File sourceFile, String localFilePath)
+  private boolean makeTemporaryLocalFileCopy(File sourceFile,
+      String localFilePath)
   {
     // Perform a number of tries to copy file
@@ -975 +1017 @@
         if (numFileCopyAttempts >= MAX_NUMBER_OF_FILE_COPY_ATTEMPTS)
         {
-          errorInfo = new String("IOException when trying to save temporary file \"" + localFileTmp + "\": " + e);
-        }
-      }
-    }
-    log.debug("fileCopied = " + fileCopied + " numFileCopyAttempts = " + numFileCopyAttempts);
+          errorInfo = new String(
+            "IOException when trying to save temporary file \"" + localFileTmp + "\": " + e);
+        }
+      }
+    }
+    log
+      .debug("fileCopied = " + fileCopied + " numFileCopyAttempts = " + numFileCopyAttempts);
     return fileCopied;
   }
@@ -1096 +1140 @@
    * 
    * @param progress ProgressReporter The progress reporter instance to use.
-   * @param line String The information string to parse for progress information
-   */
-  private void updateProgressInformation(ProgressReporter progress, String line)
+   * @param line String The information string to parse for progress
+   *        information
+   */
+  private void updateProgressInformation(ProgressReporter progress,
+      String line)
   {
     // Parse output for progress report
     if (progress != null)
     {
-      if (getOpenMsProgramSpecifier().equals(OPENMS_PROGRAM_PEAKPICKER))
+      if (getOpenMsProgramSpecifier().equalsIgnoreCase(
+        OPENMS_PROGRAM_PEAKPICKER))
       {
         if (line.contains("Progress of 'loading mzML file':"))
@@ -1109 +1156 @@
           setCurrentPhase(1);
           setCurrentPhaseStr("Loading mzML file");
-        } 
+        }
         else if (line.contains("Progress of 'loading chromatograms':"))
         {
           setCurrentPhase(2);
           setCurrentPhaseStr("Loading chromatograms");
-        } 
+        }
         else if (line.contains("Progress of 'picking peaks':"))
         {
           setCurrentPhase(3);
           setCurrentPhaseStr("Picking peaks");
-        } 
+        }
         else if (line.contains("Progress of 'storing mzML file':"))
         {
           setCurrentPhase(4);
           setCurrentPhaseStr("Storing mzML file");
-        } 
-      }
-      else if (getOpenMsProgramSpecifier().equals(OPENMS_PROGRAM_FEATUREFINDER))
+        }
+      }
+      else if (getOpenMsProgramSpecifier().equalsIgnoreCase(
+        OPENMS_PROGRAM_FEATUREFINDER))
       {
         if (line.contains("Progress of 'loading mzML file':"))
@@ -1132 +1180 @@
           setCurrentPhase(1);
           setCurrentPhaseStr("Loading mzML file");
-        } 
-        else if (line.contains("Progress of 'Precalculating intensity scores':"))
+        }
+        else if (line
+          .contains("Progress of 'Precalculating intensity scores':"))
         {
           setCurrentPhase(2);
           setCurrentPhaseStr("Precalculating intensity scores");
-        } 
-        else if (line.contains("Progress of 'Precalculating mass trace scores':"))
+        }
+        else if (line
+          .contains("Progress of 'Precalculating mass trace scores':"))
         {
           setCurrentPhase(3);
           setCurrentPhaseStr("Precalculating mass trace scores");
-        } 
-        else if (line.contains("Progress of 'Precalculating isotope distributions':"))
+        }
+        else if (line
+          .contains("Progress of 'Precalculating isotope distributions':"))
         {
           setCurrentPhase(4);
           setCurrentPhaseStr("Precalculating isotope distributions");
-        } 
-        else if (line.contains("Progress of 'Calculating isotope pattern scores for charge 1':"))
+        }
+        else if (line
+          .contains("Progress of 'Calculating isotope pattern scores for charge 1':"))
         {
           setCurrentPhase(5);
           setCurrentPhaseStr("Calculating isotope pattern scores for charge 1");
-        } 
-        else if (line.contains(">Progress of 'Finding seeds for charge 1':"))
+        }
+        else if (line
+          .contains(">Progress of 'Finding seeds for charge 1':"))
         {
           setCurrentPhase(6);
           setCurrentPhaseStr("Finding seeds for charge 1");
-        } 
-        else if (line.contains("Progress of 'Extending seeds for charge 1':"))
+        }
+        else if (line
+          .contains("Progress of 'Extending seeds for charge 1':"))
         {
           setCurrentPhase(7);
           setCurrentPhaseStr("Extending seeds for charge 1");
-        } 
-        else if (line.contains("Progress of 'Calculating isotope pattern scores for charge 2':"))
+        }
+        else if (line
+          .contains("Progress of 'Calculating isotope pattern scores for charge 2':"))
         {
           setCurrentPhase(8);
           setCurrentPhaseStr("Calculating isotope pattern scores for charge 2");
-        } 
-        else if (line.contains(">Progress of 'Finding seeds for charge 2':"))
+        }
+        else if (line
+          .contains(">Progress of 'Finding seeds for charge 2':"))
         {
           setCurrentPhase(9);
           setCurrentPhaseStr("Finding seeds for charge 2");
-        } 
-        else if (line.contains("Progress of 'Extending seeds for charge 2':"))
+        }
+        else if (line
+          .contains("Progress of 'Extending seeds for charge 2':"))
         {
           setCurrentPhase(10);
           setCurrentPhaseStr("Extending seeds for charge 2");
-        } 
-        else if (line.contains("Progress of 'Calculating isotope pattern scores for charge 3':"))
+        }
+        else if (line
+          .contains("Progress of 'Calculating isotope pattern scores for charge 3':"))
         {
           setCurrentPhase(11);
           setCurrentPhaseStr("Calculating isotope pattern scores for charge 3");
-        } 
-        else if (line.contains(">Progress of 'Finding seeds for charge 3':"))
+        }
+        else if (line
+          .contains(">Progress of 'Finding seeds for charge 3':"))
         {
           setCurrentPhase(12);
           setCurrentPhaseStr("Finding seeds for charge 3");
-        } 
-        else if (line.contains("Progress of 'Extending seeds for charge 3':"))
+        }
+        else if (line
+          .contains("Progress of 'Extending seeds for charge 3':"))
         {
           setCurrentPhase(13);
           setCurrentPhaseStr("Extending seeds for charge 3");
-        } 
-        else if (line.contains("Progress of 'Calculating isotope pattern scores for charge 4':"))
+        }
+        else if (line
+          .contains("Progress of 'Calculating isotope pattern scores for charge 4':"))
         {
           setCurrentPhase(14);
           setCurrentPhaseStr("Calculating isotope pattern scores for charge 4");
-        } 
-        else if (line.contains(">Progress of 'Finding seeds for charge 4':"))
+        }
+        else if (line
+          .contains(">Progress of 'Finding seeds for charge 4':"))
         {
           setCurrentPhase(15);
           setCurrentPhaseStr("Finding seeds for charge 4");
-        } 
-        else if (line.contains("Progress of 'Extending seeds for charge 4':"))
+        }
+        else if (line
+          .contains("Progress of 'Extending seeds for charge 4':"))
         {
           setCurrentPhase(16);
           setCurrentPhaseStr("Extending seeds for charge 4");
-        } 
-        else if (line.contains("Progress of 'Resolving overlapping features':"))
+        }
+        else if (line
+          .contains("Progress of 'Resolving overlapping features':"))
         {
           setCurrentPhase(17);
           setCurrentPhaseStr("Resolving overlapping features");
-        } 
+        }
       }
       if (line.contains(" %"))
       {
-        // OpenMS programs typically outputs a percentage phase progress line like "18.15 %", with an optional message after the % sign.
+        // OpenMS programs typically outputs a percentage phase progress
+        // line like "18.15 %", with an optional message after the %
+        // sign.
         String testStr = new String(" %");
         int index = line.indexOf(testStr);
@@ -1224 +1290 @@
           String percentStr = line.substring(0, index);
           /*
-          System.out
-            .println(this.getClass().getSimpleName() + ": percentStr (1) = \"" + percentStr + "\"");
-          */
+           * System.out .println(this.getClass().getSimpleName() +
+           * ": percentStr (1) = \"" + percentStr + "\"");
+           */
           // Convert percent string to double
           double phasePercentCompleted = 0.0;
@@ -1237 +1303 @@
           // Construct progress message
           // Example; progressMessage = "Loading mzML file: 18.15%""
-          String progressMessage = new String(getCurrentPhaseStr() + ": " + percentStr + "%");
+          String progressMessage = new String(
+            getCurrentPhaseStr() + ": " + percentStr + "%");
           // Total progress includes more than OpenMS analysis
-          int percentCompleted = EstimatedTotalPercentage(phasePercentCompleted, getCurrentPhase());
+          int percentCompleted = EstimatedTotalPercentage(
+            phasePercentCompleted, getCurrentPhase());
           if (percentCompleted > 99)
           {
@@ -1252 +1320 @@
 
   /**
-   * Estimates total percentage of time to completion.
-   * Assumes a fixed number of phases for each application.
+   * Estimates total percentage of time to completion. Assumes a fixed number
+   * of phases for each application.
    * 
    * @param percentage double Percentage in current phase.
@@ -1262 +1330 @@
   {
     int numberOfPhases = 17;
-    if (getOpenMsProgramSpecifier().equals(OPENMS_PROGRAM_PEAKPICKER))
+    if (getOpenMsProgramSpecifier().equalsIgnoreCase(
+      OPENMS_PROGRAM_PEAKPICKER))
     {
       numberOfPhases = 4;
     }
-    else if (getOpenMsProgramSpecifier().equals(OPENMS_PROGRAM_FEATUREFINDER))
+    else if (getOpenMsProgramSpecifier().equalsIgnoreCase(
+      OPENMS_PROGRAM_FEATUREFINDER))
     {
       numberOfPhases = 17;
@@ -1274 +1344 @@
       phase = 1;
     }
-    // Simple estimate of total progress based on all phases taking equally long time
-    double phaseFraction = percentage/100.0;
-    // Total fraction is calculated from (phase - 1) finished phases and phaseFraction of current phase
-    double totalFraction = ((double)(phase - 1) + phaseFraction)/((double) numberOfPhases);
+    // Simple estimate of total progress based on all phases taking equally
+    // long time
+    double phaseFraction = percentage / 100.0;
+    // Total fraction is calculated from (phase - 1) finished phases and
+    // phaseFraction of current phase
+    double totalFraction = ((double) (phase - 1) + phaseFraction) / ((double) numberOfPhases);
     if (totalFraction > 1.0)
     {
       totalFraction = 1.0;
     }
-    double totalPercentage = 100.0*totalFraction;
+    double totalPercentage = 100.0 * totalFraction;
     int totalIntegerPercentage = (int) totalPercentage;
-    // System.out.println(this.getClass().getSimpleName() + ": percentage = " + percentage + " isAnalysisPhase = " + isAnalysisPhase + " fileSizeInBytes = " + fileSizeInBytes + " analysisIndexingRatio = " + analysisIndexingRatio + " totalPercentage = " + totalPercentage + " totalIntegerPercentage = " + totalIntegerPercentage);
+    // System.out.println(this.getClass().getSimpleName() +
+    // ": percentage = " + percentage + " isAnalysisPhase = " +
+    // isAnalysisPhase + " fileSizeInBytes = " + fileSizeInBytes +
+    // " analysisIndexingRatio = " + analysisIndexingRatio +
+    // " totalPercentage = " + totalPercentage +
+    // " totalIntegerPercentage = " + totalIntegerPercentage);
     return totalIntegerPercentage;
   }
@@ -1290 +1367 @@
 
   /**
-   * Uploads output file from locally installed OpenMS feature detection engine into
-   * Proteios.
-   * 
-   * @param directoryPath String Path to directory where output file is created
+   * Uploads output file from locally installed OpenMS feature detection
+   * engine into Proteios.
+   * 
+   * @param directoryPath String Path to directory where output file is
+   *        created
    * @param outputFileName String Filename of OpenMS result file
    * @param filenameOfUploadedFile String Filename to use for uploaded file
@@ -1308 +1386 @@
     log.debug("directoryPath = \"" + directoryPath + "\"");
     log.debug("outputFileName = \"" + outputFileName + "\"");
-    log.debug("filenameOfUploadedFile = \"" + filenameOfUploadedFile + "\"");
+    log
+      .debug("filenameOfUploadedFile = \"" + filenameOfUploadedFile + "\"");
     log.debug("dirId = " + dirId);
     log.debug("descr = \"" + descr + "\"");
@@ -1370 +1449 @@
    * 
    * @param dirPath String Path to directory with files to delete.
-   * @param commonFilenameStart String Common start of filename for files to delete.
-   * @param deleteResultFile boolean Flag to indicate if OpenMS result file should be deleted.
+   * @param commonFilenameStart String Common start of filename for files to
+   *        delete.
+   * @param deleteResultFile boolean Flag to indicate if OpenMS result file
+   *        should be deleted.
    * @param resultFileFileExtension String File extension for result file.
    */
-  private void cleanUpTemporaryOpenMsFiles(String dirPath, String commonFilenameStart, boolean deleteResultFile, String resultFileFileExtension)
-  {
-    log.debug("dirPath = " + dirPath + " commonFilenameStart = " + commonFilenameStart + " deleteResultFile = " + deleteResultFile + " resultFileFileExtension = " + resultFileFileExtension);
+  private void cleanUpTemporaryOpenMsFiles(String dirPath,
+      String commonFilenameStart, boolean deleteResultFile,
+      String resultFileFileExtension)
+  {
+    log
+      .debug("dirPath = " + dirPath + " commonFilenameStart = " + commonFilenameStart + " deleteResultFile = " + deleteResultFile + " resultFileFileExtension = " + resultFileFileExtension);
     if (dirPath == null || dirPath.equals(""))
     {
@@ -1413 +1497 @@
    * @param filenameEnd String End of names of files to delete.
    */
-  private void deleteFiles(String dirPath, String filenameStart, String filenameEnd)
-  {
-    log.debug("dirPath = " + dirPath + " filenameStart = " + filenameStart + " filenameEnd = " + filenameEnd);
+  private void deleteFiles(String dirPath, String filenameStart,
+      String filenameEnd)
+  {
+    log
+      .debug("dirPath = " + dirPath + " filenameStart = " + filenameStart + " filenameEnd = " + filenameEnd);
     if (filenameStart == null)
     {
@@ -1433 +1519 @@
         log.debug("filename = " + filename);
         // Check if file is selected for deletion
-        if (filename.startsWith(filenameStart) &&
-          filename.endsWith(filenameEnd))
+        if (filename.startsWith(filenameStart) && filename
+          .endsWith(filenameEnd))
         {
           String filePath = dirPath + "/" + filename;
@@ -1475 +1561 @@
    * Delete optional file.
    * 
-   * @param filePath String Path of the optional file. 
+   * @param filePath String Path of the optional file.
    */
   private void deleteOptionalFile(String filePath)
-  {   
+  {
     log.debug("filePath = " + filePath);
     if (filePath != null && !filePath.equals(""))
@@ -1493 +1579 @@
   /*
    * Creates a temporary OpenMS INI file with given parameter values.
-   * 
    * @param tmpDir String Path to directory for temporary files.
    * @param iniFilenamePrefix String Prefix for temporary OpenMS INI file
-   * @param timeStampStr String Time stamp string in YYYY_MM_DD_hh_mm_ss format
+   * @param timeStampStr String Time stamp string in YYYY_MM_DD_hh_mm_ss
+   * format
    * @param openMsProgram String The openMS program specifier
    * @param programAlgorithm String The program algorithm.
-   * @param featureFinderIsotopicPatternChargeHigh Integer FeatureFinder isotopic_pattern:charge_high
-   * @param featureFinderIsotopicPatternMzTolerance Float FeatureFinder isotopic_pattern:mz_tolerance
-   * @param featureFinderFeatureMinRtSpan Float FeatureFinder feature:min_rt_span
+   * @param featureFinderIsotopicPatternChargeHigh Integer FeatureFinder
+   * isotopic_pattern:charge_high
+   * @param featureFinderIsotopicPatternMzTolerance Float FeatureFinder
+   * isotopic_pattern:mz_tolerance
+   * @param featureFinderFeatureMinRtSpan Float FeatureFinder
+   * feature:min_rt_span
    * @return String The file path for the created temporary OpenMS INI file.
    */
-  private String createOpenMsIniFile(
-      String tmpDir,
-      String iniFilenamePrefix,
-      String timeStampStr,
-      String openMsProgram,
-      String programAlgorithm,
+  private String createOpenMsIniFile(String tmpDir, String iniFilenamePrefix,
+      String timeStampStr, String openMsProgram, String programAlgorithm,
       Integer featureFinderIsotopicPatternChargeHigh,
       Float featureFinderIsotopicPatternMzTolerance,
@@ -1516 +1601 @@
     String openMsIniFilePath = null;
     // Create OpenMS INI file if needed
-    if (openMsProgram != null && openMsProgram.equals(OPENMS_PROGRAM_FEATUREFINDER)
-        && programAlgorithm != null && programAlgorithm.equals(FEATUREFINDER_ALGORITHM_CENTROIDED))
+    if (openMsProgram != null && openMsProgram
+      .equalsIgnoreCase(OPENMS_PROGRAM_FEATUREFINDER) && programAlgorithm != null && programAlgorithm
+      .equalsIgnoreCase(FEATUREFINDER_ALGORITHM_CENTROIDED))
     {
       log.debug("timeStampStr = \"" + timeStampStr + "\"");
@@ -1532 +1618 @@
       String featureFinderIsotopicPatternMzToleranceStr = "" + featureFinderIsotopicPatternMzTolerance;
       String featureFinderFeatureMinRtSpanStr = "" + featureFinderFeatureMinRtSpan;
-      URL srcOpenMsIniFileUrl = RunOpenMsPlugin.class.getResource("/content/openms_featurefinder_centroided_ini_file_template.ini");
+      URL srcOpenMsIniFileUrl = RunOpenMsPlugin.class
+        .getResource("/content/openms_featurefinder_centroided_ini_file_template.ini");
       List<String> stringReplaceList = new ArrayList<String>(0);
-      // Add FeatureFinder isotopic_pattern:charge_high value to replacement list
+      // Add FeatureFinder isotopic_pattern:charge_high value to
+      // replacement list
       stringReplaceList.add(new String("__ISOTOPICPATTERN_CHARGEHIGH__"));
-      stringReplaceList.add(new String(featureFinderIsotopicPatternChargeHighStr));
-      // Add FeatureFinder isotopic_pattern:mz_tolerance value to replacement list
-      stringReplaceList.add(new String("__ISOTOPICPATTERN_MZTOLERANCE__"));
-      stringReplaceList.add(new String(featureFinderIsotopicPatternMzToleranceStr));
+      stringReplaceList.add(new String(
+        featureFinderIsotopicPatternChargeHighStr));
+      // Add FeatureFinder isotopic_pattern:mz_tolerance value to
+      // replacement list
+      stringReplaceList
+        .add(new String("__ISOTOPICPATTERN_MZTOLERANCE__"));
+      stringReplaceList.add(new String(
+        featureFinderIsotopicPatternMzToleranceStr));
       // Add FeatureFinder feature:min_rt_span value to replacement list
       stringReplaceList.add(new String("__FEATURE_MINRTSPAN__"));
       stringReplaceList.add(new String(featureFinderFeatureMinRtSpanStr));
       // Update file with new text data
-      updateTextFile(srcOpenMsIniFileUrl.toString(), targetIniDir, targetIniFile, stringReplaceList);
+      updateTextFile(srcOpenMsIniFileUrl, targetIniDir,
+        targetIniFile, stringReplaceList);
       openMsIniFilePath = tmpDir + "/" + targetIniFile;
     }
@@ -1552 +1645 @@
 
   /**
-   * Updates a copy of a file on the server file system by
-   * replacing key strings with new text.
+   * Updates a copy of a file on the server file system by replacing key
+   * strings with new text.
    * 
    * @param sourceFileURLStr String URL of file to update.
    * @param targetDir String Target directory path for updated file
    * @param targetFile String Target filename for updated file
-   * @param stringReplaceList List<String> List with pairs of key String and replacement String.
+   * @param stringReplaceList List<String> List with pairs of key String and
+   *        replacement String.
    * @throws BaseException
    */
-  private void updateTextFile(String sourceFileURLStr, String targetDir, String targetFile, List<String> stringReplaceList)
-    throws BaseException
+  private void updateTextFile(URL sourceFileURLStr, String targetDir,
+      String targetFile, List<String> stringReplaceList)
+      throws BaseException
   {
     log.debug("sourceFileURLStr = \"" + sourceFileURLStr + "\"");
     // Get source file path
-    String sourceFilePath = sourceFileURLStr.replace("file:", "");
-    log.debug("sourceFilePath = \"" + sourceFilePath + "\"");
+    //String sourceFilePath = sourceFileURLStr.replace("file:/", "");
+    //log.debug("sourceFilePath = \"" + sourceFilePath + "\"");
     // Get file path
     String filePath = targetDir + "/" + targetFile;
@@ -1574 +1669 @@
     // Check for optional string replacement
     int nStringPairs = 0;
-    if (stringReplaceList != null && stringReplaceList.size() > 0 && stringReplaceList.size()%2 == 0)
-    {
-      nStringPairs = stringReplaceList.size()/2;
+    if (stringReplaceList != null && stringReplaceList.size() > 0 && stringReplaceList
+      .size() % 2 == 0)
+    {
+      nStringPairs = stringReplaceList.size() / 2;
     }
     log.debug("nStringPairs = " + nStringPairs);
@@ -1591 +1687 @@
     catch (IOException e)
     {
-      log.debug("IOException when creating FileWriter for file \"" + textFile + "\": " + e);
+      log
+        .debug("IOException when creating FileWriter for file \"" + textFile + "\": " + e);
     }
     try
     {
-      //BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));
-      BufferedReader reader = new BufferedReader(new FileReader(sourceFilePath));
+      // BufferedReader reader = new BufferedReader(new
+      // InputStreamReader(inStream));
+      BufferedReader reader = new BufferedReader(new FileReader(
+        new java.io.File(sourceFileURLStr.toURI())));
       int lineNumber = 0;
       int linesCopied = 0;
-      for (String line = reader.readLine(); line != null; line = reader.readLine())
+      log.debug("Reading ini file");
+      for (String line = reader.readLine(); line != null; line = reader
+        .readLine())
       {
         lineNumber++;
-        // Check for optional string replacement
+        log.debug("Ini file line:" + lineNumber);
+        // Check for optional string replacement
         for (int i = 0; i < nStringPairs; i++)
         {
-          String stringToReplace = stringReplaceList.get(2*i);
-          String replaceString = stringReplaceList.get(2*i+1);
-          if (stringToReplace != null && replaceString != null && line.contains(stringToReplace))
-          {
-            log.debug("(1) stringToReplace = \"" + stringToReplace + "\" replaceString = \"" + replaceString + "\" line = \"" + line + "\"");
-            line = line.replace(stringToReplace, replaceString);
-            log.debug("(2) stringToReplace = \"" + stringToReplace + "\" replaceString = \"" + replaceString + "\" line = \"" + line + "\"");
-          }
-        }
-          // Store line in file
-        writeLine(fw, line);
-        linesCopied++;
+          String stringToReplace = stringReplaceList.get(2 * i);
+          String replaceString = stringReplaceList.get(2 * i + 1);
+          if (stringToReplace != null && replaceString != null && line
+            .contains(stringToReplace))
+          {
+            log
+              .debug("(1) stringToReplace = \"" + stringToReplace + "\" replaceString = \"" + replaceString + "\" line = \"" + line + "\"");
+            line = line.replace(stringToReplace, replaceString);
+            log
+              .debug("(2) stringToReplace = \"" + stringToReplace + "\" replaceString = \"" + replaceString + "\" line = \"" + line + "\"");
+          }
+        }
+        // Store line in file
+        writeLine(fw, line);
+        linesCopied++;
       }
     }
@@ -1622 +1727 @@
     {
       log.error(e.getMessage(), e);
-      //throw new BaseException(e);
+      // throw new BaseException(e);
     }
     finally
@@ -1634 +1739 @@
       catch (IOException e)
       {
-        log.debug("IOException when flushing FileWriter for file \"" + textFile + "\": " + e);
+        log
+          .debug("IOException when flushing FileWriter for file \"" + textFile + "\": " + e);
         fileSaveOk = false;
-      }   
+      }
       try
       {
@@ -1643 +1749 @@
       catch (IOException e)
       {
-        log.debug("IOException when closing FileWriter for file \"" + textFile + "\": " + e);
+        log
+          .debug("IOException when closing FileWriter for file \"" + textFile + "\": " + e);
         fileSaveOk = false;
       }
@@ -1664 +1771 @@
     if (fw == null)
     {
-      log.error("No FileWriter instance when trying to write string \"" + string + "\"");
+      log
+        .error("No FileWriter instance when trying to write string \"" + string + "\"");
       return;
     }
@@ -1673 +1781 @@
     catch (IOException e)
     {
-      log.debug("IOException when writing to FileWriter for file \"" + getOpenMsIniFilePath() + "\": " + e);
+      log
+        .debug("IOException when writing to FileWriter for file \"" + getOpenMsIniFilePath() + "\": " + e);
     }
   }