Changeset 3934

Timestamp:

Nov 2, 2010, 9:29:39 AM (13 years ago)

Author:

Gregory Vincic

Message:

Refs #698. Moved getSpectrumFileContactInputForm to action SpectrumFileContactDataAdderExtension?.

Location:

trunk/client/servlet/src/org/proteios

Files:

• action/file/SpectrumFileContactDataAdderExtension.java (modified) (2 diffs, 1 prop)
• gui/form/FormFactory.java (modified) (119 diffs)

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

@@ -1 +1 @@
 /*
- $Id$
- 
- Copyright (C) 2009 Gregory Vincic
-
- This file is part of Proteios.
- Available at http://www.proteios.org/
-
- Proteios is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- Proteios is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
- 02111-1307, USA.
- */
+    $Id$
+     
+    Copyright (C) 2009 Olle Mansson
+    Copyright (C) 2010 Gregory Vincic
+    
+    This file is part of Proteios.
+    Available at http://www.proteios.org/
+    
+    Proteios is free software; you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+    
+    Proteios is distributed in the hope that it will be useful, but
+    WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    General Public License for more details.
+    
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+    02111-1307, USA.
+*/
 package org.proteios.action.file;
 
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.GregorianCalendar;
+import java.util.List;
 import org.proteios.ActionLink;
 import org.proteios.Context;
@@ -35 +40 @@
 import org.proteios.gui.TitledWindow;
 import org.proteios.gui.Toolbar;
-import org.proteios.gui.form.Form;
-import org.proteios.gui.form.FormFactory;
+import org.proteios.gui.form.*;
 import org.proteios.gui.layout.RowLayout;
-
 import se.lu.thep.waf.ActionException;
-import se.lu.thep.waf.constraints.InvalidParameterValue;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.GregorianCalendar;
-import java.util.List;
+import se.lu.thep.waf.constraints.*;
 
 /**
- * This action allows contact data to be added to spectrum files.
- * Contact data are selected after the spectrum files have been selected.
- * One edit job per spectrum file is created.
- * 
- * @author olle
- */
+    This action allows contact data to be added to spectrum files.
+    Contact data are selected after the spectrum files have been selected.
+    One edit job per spectrum file is created.
+    
+    @author olle
+*/
 public class SpectrumFileContactDataAdderExtension
-    extends ProteiosAction<SpectrumFileContactDataAdderExtension>
-    implements ContextEnabled
+extends ProteiosAction<SpectrumFileContactDataAdderExtension>
+implements ContextEnabled
 {
-
-  @Override
-  protected void runMe()
-      throws ActionException, InvalidParameterValue
-  {
-    /***********************************************************************
-     * Check input
-     */
-    /*
-     * Get the id's of all selected files. FormFactory.VID is the valid
-     * identifier used when rendering the list of files, thus we use it to
-     * get the valid list of item ids.
-     */
-    List<Integer> spectrumFileIds = getValidIntegerList(FormFactory.VID);
-    log.debug("spectrumFileIds = " + spectrumFileIds);
-    /*
-     * Make sure at least one file has been selected
-     */
-    if (spectrumFileIds == null || spectrumFileIds.size() == 0)
-    {
-      /*
-       * If we return to this action after an error in a forward action,
-       * the spectrum file id list is stored in SpectrumFileContactDataAdder.VSPECTRUMFILEID
-       * instead of FormFactory.VID. Check this to determine if the current
-       * action should set an error message, or continue to allow
-       * an error message from the forward action to be displayed.
-       */
-      spectrumFileIds = getValidIntegerList(SpectrumFileContactDataAdder.VSPECTRUMFILEID);
-      log.debug("spectrumFileIds from SpectrumFileContactDataAdder.VSPECTRUMFILEID = " + spectrumFileIds);
-      if (spectrumFileIds == null || spectrumFileIds.size() == 0)
-      {
-        setError("Please select at least one spectrum file");
-        return;
-      }
-    }
-    /*
-     * Create a form for selection of contact data parameters.
-     */
-    // Default filename prefix
-    DbControl dc = newDbControl();
-    Project project = isProjectActive(dc);
-    String outputDirPrefixDefault = new String("OutputDir_");
-    String outputDir;
-    /*
-     * Add time stamp to output directory prefix in this class,
-     * instead of in job plugin class, as we want output files
-     * for all jobs created in the same session to share the same
-     * time stamp, even if the jobs are not executed simultaneously.
-     */
-    // Append time stamp in YYYYMMDD_HHMM format to output directory default
-    outputDir = appendTimestampToString(outputDirPrefixDefault);
-    log.debug("outputDir = \"" + outputDir + "\"");
-    // Get logged-in user from whose profile default contact information should be taken.
-    User user = getOwner();
-    log.debug("user = \"" + user + "\"");
-    // Get form
-    Form form = getFormFactory().getSpectrumFileContactInputForm(
-      project, outputDir, user);
-    String contactDataTitle = new String("EnterContactData");
-    Title title = new Title(contactDataTitle);
-    // Instruction area
-    TitledWindow instructionArea = new TitledWindow();
-    String instruction = "Enter contact data to be added to spectrum file(s).";
-    instruction += " One spectrum file edit job is created for each peak list file in mzData or mzML format.";
-    instruction += " MzData uses name, institution, and contact info fields.";
-    instruction += " MzML uses name, address, URL, and email fields.";
-    instructionArea.setContent(instruction);
-    instructionArea.setTitle("Description");
-    // Toolbar
-    Toolbar tb = new Toolbar();
-    form.setToolbar(tb);
-    // Add 'Next' button to create edit jobs
-    ActionLink nextEdit = getActionFactory().getActionLink(
-      SpectrumFileContactDataAdder.class, "NextCreateSpectrumFileContactAdderJobs");
-    for (Integer spectrumFileId : spectrumFileIds)
-    {
-      getFormFactory().addHiddenField(form, SpectrumFileContactDataAdder.VSPECTRUMFILEID, spectrumFileId);
-    }
-    tb.add(nextEdit);
-    /***********************************************************************
-     * Layout
-     */
-    RowLayout layout = getLayoutFactory().getRowLayout();
-    layout.add(title);
-    layout.add(instructionArea);
-    layout.add(form);
-    setLayout(layout);
-  }
-
-
-  /**
-   * Append time stamp to string
-   * 
-   * @param origStr String Original string
-   * @return String Original string with appended "YYYYMMDD_HHMM" times tamp and underscore.
-   */
-  private String appendTimestampToString(String origStr)
-  {
-    // Append time stamp in YYYYMMDD_HHMM format to string
-    String outputStr = origStr;
-    Calendar cal = GregorianCalendar.getInstance();
-    boolean includeDatePart = true;
-    boolean includeTimePart = true;
-    boolean includeSeconds = false;
-    String dateElementSeparator = new String("");
-    String dateTimeSeparator = new String("_");
-    String timeElementSeparator = new String("");
-    String timestampStr = fetchTimestamp(cal, 0,
-      includeDatePart, includeTimePart, includeSeconds,
-      dateElementSeparator, dateTimeSeparator, timeElementSeparator);
-    log.debug("timestampStr = \"" + timestampStr + "\"");
-    if (timestampStr != null && !timestampStr.equals(""))
-    {
-      outputStr = outputStr + timestampStr;
-    }
-    //
-    return outputStr;
-  }
-
-
-  /**
-   * Fetches timestamp string.
-   * If Calendar instance is null, null will be returned.
-   * 
-   * @param inputCal Calendar Timestamp to use
-   * @param secondsToAdd int Number of seconds to add (subtract if negative) to
-   *        timestamp
-   * @param includeDatePart Boolean Flag indicating that date part should be included (default = true).
-   * @param includeTimePart Boolean Flag indicating that time part should be included (default = true).
-   * @param includeSeconds Boolean Flag indicating that seconds should be included in time part (default = true).
-   * @param dateElementSeparator String Separator between date elements  (default = "-").
-   * @param dateTimeSeparator String Separator between date and time parts  (default = " ").
-   * @param timeElementSeparator String Separator between time elements  (default = ":").
-   * @return String Constructed timestamp string.
-   */
-  public String fetchTimestamp(Calendar inputCal, int secondsToAdd,
-      Boolean includeDatePart, Boolean includeTimePart, Boolean includeSeconds,
-      String dateElementSeparator, String dateTimeSeparator, String timeElementSeparator)
-  {
-    if (inputCal == null)
-    {
-      return null;
-    }
-    // Set defaults if needed
-    if (includeDatePart == null)
-    {
-      includeDatePart = true;
-    }
-    if (includeTimePart == null)
-    {
-      includeTimePart = true;
-    }
-    if (includeSeconds == null)
-    {
-      includeSeconds = true;
-    }
-    if (dateElementSeparator == null)
-    {
-      dateElementSeparator = new String("-");
-    }
-    if (dateTimeSeparator == null)
-    {
-      dateTimeSeparator = new String(" ");
-    }
-    if (timeElementSeparator == null)
-    {
-      timeElementSeparator = new String(":");
-    }
-    //
-    StringBuilder sb = new StringBuilder();
-    //
-    // Make a copy of the input Calendar object, as we don't want to change
-    // the value of the latter
-    Calendar cal = (Calendar) inputCal.clone();
-    long timeInMilliSec = cal.getTimeInMillis();
-    timeInMilliSec += secondsToAdd * 1000;
-    cal.setTimeInMillis(timeInMilliSec);
-    int year = cal.get(Calendar.YEAR);
-    int month = cal.get(Calendar.MONTH) + 1;
-    int day = cal.get(Calendar.DAY_OF_MONTH);
-    int hour = cal.get(Calendar.HOUR_OF_DAY);
-    int min = cal.get(Calendar.MINUTE);
-    int sec = cal.get(Calendar.SECOND);
-    String monthStr = leftPaddedString(Integer.toString(month), 2, '0');
-    String dayStr = leftPaddedString(Integer.toString(day), 2, '0');
-    String hourStr = leftPaddedString(Integer.toString(hour), 2, '0');
-    String minStr = leftPaddedString(Integer.toString(min), 2, '0');
-    String secStr = leftPaddedString(Integer.toString(sec), 2, '0');
-    // Construct time stamp
-    if (includeDatePart)
-    {     
-      sb.append(year);
-      sb.append(dateElementSeparator);
-      sb.append(monthStr);
-      sb.append(dateElementSeparator);
-      sb.append(dayStr);
-    }
-    if (includeDatePart && includeTimePart)
-    {     
-      sb.append(dateTimeSeparator);
-    }
-    if (includeTimePart)
-    {
-      sb.append(hourStr);
-      sb.append(timeElementSeparator);
-      sb.append(minStr);
-      if (includeSeconds)
-      {
-        sb.append(timeElementSeparator);
-        sb.append(secStr);
-      }
-    }
-    String timestamp = sb.toString();
-    //
-    return timestamp;
-  }
-
-
-  /**
-   * Returns a string padded from the left with a given character to have at
-   * least a given length. If the input string length that is equal to or
-   * larger than the minimum length, the string will be returned unchanged. If
-   * the input string length is smaller than the minimum length, the string
-   * will be padded from the left with the given character until the length is
-   * exactly the given minimum length.
-   * 
-   * @param inStr String Input string
-   * @param minChars int The minimum number of characters in the resulting
-   *        string
-   * @param padChar char Character to use for optional padding
-   * @return String A string optionally padded from the left to have at least
-   *         'minChars' characters.
-   */
-  private String leftPaddedString(String inStr, int minChars, char padChar)
-  {
-    String startStr = null;
-    if (inStr != null)
-    {
-      startStr = new String(inStr);
-    }
-    else
-    {
-      startStr = new String("");
-    }
-    int startLen = startStr.length();
-    String resultStr = null;
-    if (startLen >= minChars)
-    {
-      resultStr = startStr;
-    }
-    else
-    {
-      resultStr = startStr;
-      for (int i = startLen; i < minChars; i++)
-      {
-        resultStr = padChar + resultStr;
-      }
-    }
-    return resultStr;
-  }
-
-
-  /**
-   * Tell the application in which context this action should be available
-   */
-  public List<Context> listContexts()
-  {
-    List<Context> contexts = new ArrayList<Context>(1);
-    /*
-     * We want our action to appear as an extension when viewing files. Do
-     * this by adding a FileContext to the list of contexts.
-     */
-    FileContext files = new FileContext("SpectrumFileContactDataAdder", "Add contact data to spectrum file(s)",
-      SpectrumFileContactDataAdderExtension.class);
-    files.setDescription("First select spectrum files, then contact data");
-    contexts.add(files);
-    return contexts;
-  }
+    
+    public static final VString VNONREQUIRED_FILENAME = new VString("fileName",0, 255, false); 
+    public static final VString VNONREQUIRED_NAME = new VString("name", 0, 255,false);
+    public static final VString VNONREQUIRED_INSTITUTION = new VString("institution", 0, 255, false);
+    public static final VString VNONREQUIRED_ADDRESS = new VString("address",0, 255, false);
+    public static final VString VNONREQUIRED_URL = new VString("url", 0, 255,false);
+    public static final VString VNONREQUIRED_EMAIL = new VString("email", 0,255, false);
+    public static final VString VNONREQUIRED_CONTACT_INFO = new VString("contactInfo", 0, 255, false);
+    
+    @Override
+    protected void runMe()
+    throws ActionException, InvalidParameterValue
+    {
+        /*
+            Get the id's of all selected files. FormFactory.VID is the valid
+            identifier used when rendering the list of files, thus we use it to
+            get the valid list of item ids.
+        */
+        List<Integer> spectrumFileIds = getValidIntegerList(FormFactory.VID);
+        log.debug("spectrumFileIds = " + spectrumFileIds);
+        /*
+            Make sure at least one file has been selected
+        */
+        if (spectrumFileIds == null || spectrumFileIds.size() == 0)
+        {
+            /*
+                If we return to this action after an error in a forward action,
+                the spectrum file id list is stored in SpectrumFileContactDataAdder.VSPECTRUMFILEID
+                instead of FormFactory.VID. Check this to determine if the current
+                action should set an error message, or continue to allow
+                an error message from the forward action to be displayed.
+            */
+            spectrumFileIds = getValidIntegerList(SpectrumFileContactDataAdder.VSPECTRUMFILEID);
+            log.debug("spectrumFileIds from SpectrumFileContactDataAdder.VSPECTRUMFILEID = " + spectrumFileIds);
+            if (spectrumFileIds == null || spectrumFileIds.size() == 0)
+            {
+                setError("Please select at least one spectrum file");
+                return;
+            }
+        }
+        /*
+            Create a form for selection of contact data parameters.
+        */
+        // Default filename prefix
+        DbControl dc = newDbControl();
+        Project project = isProjectActive(dc);
+        String outputDirPrefixDefault = new String("OutputDir_");
+        String outputDir;
+        /*
+            Add time stamp to output directory prefix in this class,
+            instead of in job plugin class, as we want output files
+            for all jobs created in the same session to share the same
+            time stamp, even if the jobs are not executed simultaneously.
+        */
+        // Append time stamp in YYYYMMDD_HHMM format to output directory default
+        outputDir = appendTimestampToString(outputDirPrefixDefault);
+        log.debug("outputDir = \"" + outputDir + "\"");
+        // Get logged-in user from whose profile default contact information should be taken.
+        User user = getOwner();
+        log.debug("user = \"" + user + "\"");
+        // Get form
+        Form form = getSpectrumFileContactInputForm(project, outputDir, user);
+        String contactDataTitle = new String("EnterContactData");
+        Title title = new Title(contactDataTitle);
+        // Instruction area
+        TitledWindow instructionArea = new TitledWindow();
+        String instruction = "Enter contact data to be added to spectrum file(s).";
+        instruction += " One spectrum file edit job is created for each peak list file in mzData or mzML format.";
+        instruction += " MzData uses name, institution, and contact info fields.";
+        instruction += " MzML uses name, address, URL, and email fields.";
+        instructionArea.setContent(instruction);
+        instructionArea.setTitle("Description");
+        // Toolbar
+        Toolbar tb = new Toolbar();
+        form.setToolbar(tb);
+        // Add 'Next' button to create edit jobs
+        ActionLink nextEdit = getActionFactory().getActionLink(
+        SpectrumFileContactDataAdder.class, "NextCreateSpectrumFileContactAdderJobs");
+        for (Integer spectrumFileId : spectrumFileIds)
+        {
+            getFormFactory().addHiddenField(form, SpectrumFileContactDataAdder.VSPECTRUMFILEID, spectrumFileId);
+        }
+        tb.add(nextEdit);
+        // Layout
+        RowLayout layout = getLayoutFactory().getRowLayout();
+        layout.add(title);
+        layout.add(instructionArea);
+        layout.add(form);
+        setLayout(layout);
+    }
+    
+    /**
+        Append time stamp to string
+        
+        @param origStr String Original string
+        @return String Original string with appended "YYYYMMDD_HHMM" times tamp and underscore.
+    */
+    private String appendTimestampToString(String origStr)
+    {
+        // Append time stamp in YYYYMMDD_HHMM format to string
+        String outputStr = origStr;
+        Calendar cal = GregorianCalendar.getInstance();
+        boolean includeDatePart = true;
+        boolean includeTimePart = true;
+        boolean includeSeconds = false;
+        String dateElementSeparator = new String("");
+        String dateTimeSeparator = new String("_");
+        String timeElementSeparator = new String("");
+        String timestampStr = fetchTimestamp(cal, 0,
+        includeDatePart, includeTimePart, includeSeconds,
+        dateElementSeparator, dateTimeSeparator, timeElementSeparator);
+        log.debug("timestampStr = \"" + timestampStr + "\"");
+        if (timestampStr != null && !timestampStr.equals(""))
+        {
+            outputStr = outputStr + timestampStr;
+        }
+        //
+        return outputStr;
+    }
+    
+    /**
+        Fetches timestamp string.
+        If Calendar instance is null, null will be returned.
+        
+        @param inputCal Calendar Timestamp to use
+        @param secondsToAdd int Number of seconds to add (subtract if negative) to
+               timestamp
+        @param includeDatePart Boolean Flag indicating that date part should be included (default = true).
+        @param includeTimePart Boolean Flag indicating that time part should be included (default = true).
+        @param includeSeconds Boolean Flag indicating that seconds should be included in time part (default = true).
+        @param dateElementSeparator String Separator between date elements  (default = "-").
+        @param dateTimeSeparator String Separator between date and time parts  (default = " ").
+        @param timeElementSeparator String Separator between time elements  (default = ":").
+        @return String Constructed timestamp string.
+    */
+    public String fetchTimestamp(Calendar inputCal, int secondsToAdd,
+    Boolean includeDatePart, Boolean includeTimePart, Boolean includeSeconds,
+    String dateElementSeparator, String dateTimeSeparator, String timeElementSeparator)
+    {
+        if (inputCal == null)
+        {
+            return null;
+        }
+        // Set defaults if needed
+        if (includeDatePart == null)
+        {
+            includeDatePart = true;
+        }
+        if (includeTimePart == null)
+        {
+            includeTimePart = true;
+        }
+        if (includeSeconds == null)
+        {
+            includeSeconds = true;
+        }
+        if (dateElementSeparator == null)
+        {
+            dateElementSeparator = new String("-");
+        }
+        if (dateTimeSeparator == null)
+        {
+            dateTimeSeparator = new String(" ");
+        }
+        if (timeElementSeparator == null)
+        {
+            timeElementSeparator = new String(":");
+        }
+        //
+        StringBuilder sb = new StringBuilder();
+        //
+        // Make a copy of the input Calendar object, as we don't want to change
+        // the value of the latter
+        Calendar cal = (Calendar) inputCal.clone();
+        long timeInMilliSec = cal.getTimeInMillis();
+        timeInMilliSec += secondsToAdd * 1000;
+        cal.setTimeInMillis(timeInMilliSec);
+        int year = cal.get(Calendar.YEAR);
+        int month = cal.get(Calendar.MONTH) + 1;
+        int day = cal.get(Calendar.DAY_OF_MONTH);
+        int hour = cal.get(Calendar.HOUR_OF_DAY);
+        int min = cal.get(Calendar.MINUTE);
+        int sec = cal.get(Calendar.SECOND);
+        String monthStr = leftPaddedString(Integer.toString(month), 2, '0');
+        String dayStr = leftPaddedString(Integer.toString(day), 2, '0');
+        String hourStr = leftPaddedString(Integer.toString(hour), 2, '0');
+        String minStr = leftPaddedString(Integer.toString(min), 2, '0');
+        String secStr = leftPaddedString(Integer.toString(sec), 2, '0');
+        // Construct time stamp
+        if (includeDatePart)
+        {
+            sb.append(year);
+            sb.append(dateElementSeparator);
+            sb.append(monthStr);
+            sb.append(dateElementSeparator);
+            sb.append(dayStr);
+        }
+        if (includeDatePart && includeTimePart)
+        {
+            sb.append(dateTimeSeparator);
+        }
+        if (includeTimePart)
+        {
+            sb.append(hourStr);
+            sb.append(timeElementSeparator);
+            sb.append(minStr);
+            if (includeSeconds)
+            {
+                sb.append(timeElementSeparator);
+                sb.append(secStr);
+            }
+        }
+        String timestamp = sb.toString();
+        //
+        return timestamp;
+    }
+    
+    /**
+        Returns a string padded from the left with a given character to have at
+        least a given length. If the input string length that is equal to or
+        larger than the minimum length, the string will be returned unchanged. If
+        the input string length is smaller than the minimum length, the string
+        will be padded from the left with the given character until the length is
+        exactly the given minimum length.
+        
+        @param inStr String Input string
+        @param minChars int The minimum number of characters in the resulting
+               string
+        @param padChar char Character to use for optional padding
+        @return String A string optionally padded from the left to have at least
+                'minChars' characters.
+    */
+    private String leftPaddedString(String inStr, int minChars, char padChar)
+    {
+        String startStr = null;
+        if (inStr != null)
+        {
+            startStr = new String(inStr);
+        }
+        else
+        {
+            startStr = new String("");
+        }
+        int startLen = startStr.length();
+        String resultStr = null;
+        if (startLen >= minChars)
+        {
+            resultStr = startStr;
+        }
+        else
+        {
+            resultStr = startStr;
+            for (int i = startLen; i < minChars; i++)
+            {
+                resultStr = padChar + resultStr;
+            }
+        }
+        return resultStr;
+    }
+    
+    /**
+        Returns a form for adding spectrum file contact data for a spectrum file.
+        
+        @param project Project The project in whose directory a new output
+               directory is created.
+        @param outputDirNameDefault String The default name of the output
+               directory.
+        @param user User The user from whose profile default contact information
+               should be taken.
+        @return Form for displaying spectrum file contact data.
+    */
+    public Form getSpectrumFileContactInputForm(Project project,
+    String outputDirNameDefault, User user)
+    {
+        Form form = new Form("spectrumFileContactInputForm");
+        // Get potential default contact information from user profile
+        String defaultName = new String("");
+        String defaultInstitution = new String("");
+        String defaultAddress = new String("");
+        String defaultEmail = new String("");
+        String defaultContactInfo = new String("");
+        if (user != null)
+        {
+            // Default name
+            if (user.getName() != null)
+            {
+                defaultName = user.getName();
+            }
+            // Default institution
+            if (user.getOrganisation() != null)
+            {
+                defaultInstitution = user.getOrganisation();
+            }
+            // Default address
+            if (user.getAddress() != null)
+            {
+                defaultAddress = user.getAddress();
+            }
+            // Default e-mail
+            if (user.getEmail() != null)
+            {
+                defaultEmail = user.getEmail();
+            }
+            // Default contact info
+            defaultContactInfo = addContactInfoElement(defaultContactInfo, "Name", defaultName);
+            defaultContactInfo = addContactInfoElement(defaultContactInfo, "Institution", defaultInstitution);
+            defaultContactInfo = addContactInfoElement(defaultContactInfo, "Address", defaultAddress);
+            defaultContactInfo = addContactInfoElement(defaultContactInfo, "Phone", user.getPhone());
+            defaultContactInfo = addContactInfoElement(defaultContactInfo, "Fax", user.getFax());
+            defaultContactInfo = addContactInfoElement(defaultContactInfo, "e-mail", defaultEmail);
+        }
+        //
+        Fieldset contactInputFS = new Fieldset();
+        contactInputFS.setTitle("SpectrumFileContactInput");
+        form.addFieldset(contactInputFS);
+        //
+        TextField<String> nameF = new TextField<String>(VNONREQUIRED_NAME);
+        nameF.setValue(defaultName);
+        nameF.setLabel("Name");
+        contactInputFS.add(nameF);
+        //
+        TextField<String> institutionF = new TextField<String>(VNONREQUIRED_INSTITUTION);
+        institutionF.setValue(defaultInstitution);
+        institutionF.setLabel("Institution");
+        contactInputFS.add(institutionF);
+        //
+        TextField<String> contactInfoF = new TextField<String>(VNONREQUIRED_CONTACT_INFO);
+        contactInfoF.setValue(defaultContactInfo);
+        contactInfoF.setLabel("ContactInfo");
+        contactInputFS.add(contactInfoF);
+        //
+        TextField<String> addressF = new TextField<String>(VNONREQUIRED_ADDRESS);
+        addressF.setValue(defaultAddress);
+        addressF.setLabel("Address");
+        contactInputFS.add(addressF);
+        //
+        TextField<String> urlF = new TextField<String>(VNONREQUIRED_URL);
+        urlF.setValue("");
+        urlF.setLabel("URL");
+        contactInputFS.add(urlF);
+        //
+        TextField<String> emailF = new TextField<String>(VNONREQUIRED_EMAIL);
+        emailF.setValue(defaultEmail);
+        emailF.setLabel("email");
+        contactInputFS.add(emailF);
+        //
+        Fieldset contactOutputFS = new Fieldset();
+        contactOutputFS.setTitle("SpectrumFileContactOutput");
+        form.addFieldset(contactOutputFS);
+        //
+        TextField<String> outputDirNameF = new TextField<String>(VNONREQUIRED_FILENAME);
+        outputDirNameF.setValue(outputDirNameDefault);
+        outputDirNameF.setLabel("OutputDirectoryName");
+        contactOutputFS.add(outputDirNameF);
+        //
+        return form;
+    }
+        
+    /**
+        Adds an element of data to contact info string.
+        
+        @param contactInfo String Current contact info string.
+        @param elementName String Name of contact info element.
+        @param elementValue String Contents of contact info element.
+        @return String Contact info string with the added info data.
+    */
+    private String addContactInfoElement(String contactInfo, String elementName, String elementValue)
+    {
+        if (elementValue != null && !elementValue.equals(""))
+        {
+            if (!contactInfo.equals(""))
+            {
+                contactInfo += ", ";
+            }
+            contactInfo += elementName + ": " + elementValue;
+        }
+        return contactInfo;
+    }
+    
+    /**
+        Tell the application in which context this action should be available
+    */
+    public List<Context> listContexts()
+    {
+        List<Context> contexts = new ArrayList<Context>(1);
+        /*
+            We want our action to appear as an extension when viewing files. Do
+            this by adding a FileContext to the list of contexts.
+        */
+        FileContext files = new FileContext("SpectrumFileContactDataAdder", "Add contact data to spectrum file(s)",
+        SpectrumFileContactDataAdderExtension.class);
+        files.setDescription("First select spectrum files, then contact data");
+        contexts.add(files);
+        return contexts;
+    }
 }

trunk/client/servlet/src/org/proteios/gui/form/FormFactory.java

@@ -144 +144 @@
     public static final VDate VSTARTDATE = new VDate("startDate", true,Format.DATETIME, Format.DATE);
     public static final VDate VENDDATE = new VDate("endDate", true,Format.DATETIME, Format.DATE);
-    
     public static final VInteger VBIOMATERIALID = new VInteger("bioMaterialId",1, false);
-    // TODO what are valid values for the pistart parameter
-    
     public static final VString VSTAIN = new VString("stain", 0, 255, false);
     public static final VInteger VLABELID = new VInteger("labelId", 0, true);
@@ -172 +169 @@
     public static final VString VNONREQUIRED_SAMPLE_COMMENT = new VString("sampleComment", 0, 255, false);
     /**
-        * logger to use
+        logger to use
     */
     private static final org.apache.log4j.Logger log = org.apache.log4j.LogManager
@@ -178 +175 @@
     
     /**
-        * Default constructor. Initializes list excludedDeclMethods.
+        Default constructor. Initializes list excludedDeclMethods.
     */
     public FormFactory()
     {
         /*
-            * Initialize list excludedDeclMethods.
+            Initialize list excludedDeclMethods.
         */
         initExcludedDeclMethods();
@@ -189 +186 @@
     
     /**
-        * Get list of excluded getter methods declared in current class.
-        * 
-        * @return List<String> of excluded getter methods.
+        Get list of excluded getter methods declared in current class.
+        
+        @return List<String> of excluded getter methods.
     */
     public List<String> getExcludedDeclMethods()
@@ -199 +196 @@
     
     /**
-        * Set list of excluded getter methods declared in current class.
-        * 
-        * @param excludedDeclMethods List<String> of excluded getter methods to
-        *        set.
+        Set list of excluded getter methods declared in current class.
+        
+        @param excludedDeclMethods List<String> of excluded getter methods to
+               set.
     */
     public void setExcludedDeclMethods(List<String> excludedDeclMethods)
@@ -210 +207 @@
     
     /**
-        * Add list of excluded getter methods declared in current class.
-        * 
-        * @param excludedDeclMethods List<String> of excluded getter methods to to
-        *        add.
+        Add list of excluded getter methods declared in current class.
+        
+        @param excludedDeclMethods List<String> of excluded getter methods to to
+               add.
     */
     public void addExcludedDeclMethods(List<String> excludedDeclMethods)
@@ -220 +217 @@
         {
             /*
-                * Add excluded method if not already in list.
+                Add excluded method if not already in list.
             */
             if (!getExcludedDeclMethods().contains(exclMethod))
@@ -308 +305 @@
     
     /**
-        * Initializes list of excluded getter methods declared in current class.
+        Initializes list of excluded getter methods declared in current class.
     */
     public void initExcludedDeclMethods()
     {
         /*
-            * Initialize list of excluded declared methods.
+            Initialize list of excluded declared methods.
         */
         getExcludedDeclMethods().add("getType");
@@ -361 +358 @@
         {
             /*
-                * Set valid parameter name to signature of single-argument setter
-                * method, if existing, in order to separate between arguments of
-                * primitive types like boolean, int, float, and double, from those
-                * of wrapper class types like Boolean, Integer, Float, and Double.
+                Set valid parameter name to signature of single-argument setter
+                method, if existing, in order to separate between arguments of
+                primitive types like boolean, int, float, and double, from those
+                of wrapper class types like Boolean, Integer, Float, and Double.
             */
             setValueMethodSignature = setValueMethodName + ":" + valueClass
@@ -396 +393 @@
         {
             /*
-                * Set valid parameter name to signature of single-argument setter
-                * method, if existing, in order to separate between arguments of
-                * primitive types like boolean, int, float, and double, from those
-                * of wrapper class types like Boolean, Integer, Float, and Double.
+                Set valid parameter name to signature of single-argument setter
+                method, if existing, in order to separate between arguments of
+                primitive types like boolean, int, float, and double, from those
+                of wrapper class types like Boolean, Integer, Float, and Double.
             */
             setValueMethodSignature = setValueMethodName + ":" + valueClass
@@ -570 +567 @@
     
     /**
-        * @return Hidden
-        *         <code>TextField<String> using the valid parameter {@link #VTYPE}.
+        @return Hidden
+                <code>TextField<String> using the valid parameter {@link #VTYPE}.
     */
     private TextField<String> newTypeField()
@@ -585 +582 @@
     
     /**
-        * Form for user preferences configuration settings. Arguments
-        * NotificationConfiguration and TablePreferencesConfiguration are place
-        * holders for current values for the notification configuration and table
-        * preferences configuration form fields.
-        * 
-        * @param nc NotificationConfiguration object (need not be stored in
-        *        database) with default field values.
-        * @return Form A form for setting user preferences configuration values.
+        Form for user preferences configuration settings. Arguments
+        NotificationConfiguration and TablePreferencesConfiguration are place
+        holders for current values for the notification configuration and table
+        preferences configuration form fields.
+        
+        @param nc NotificationConfiguration object (need not be stored in
+               database) with default field values.
+        @return Form A form for setting user preferences configuration values.
     */
     public Form getUserPreferencesConfigurationForm(
@@ -609 +606 @@
     
     /**
-        * Fieldset for notification configuration settings. Argument
-        * NotificationConfiguration is place holder for current values for the
-        * notification configuration form fields.
-        * 
-        * @param nc NotificationConfiguration object (need not be stored in
-        *        database) with default field values.
-        * @return Fieldset A fieldset for setting NotificationConfiguration values.
+        Fieldset for notification configuration settings. Argument
+        NotificationConfiguration is place holder for current values for the
+        notification configuration form fields.
+        
+        @param nc NotificationConfiguration object (need not be stored in
+               database) with default field values.
+        @return Fieldset A fieldset for setting NotificationConfiguration values.
     */
     public Fieldset getNotificationConfigurationFieldset(
@@ -666 +663 @@
     
     /**
-        * Creates a select box for notification mode.
-        * 
-        * @param modeValue int Mode value for default selection.
-        * @return Select<VInteger> Select box for notification mode selection
+        Creates a select box for notification mode.
+        
+        @param modeValue int Mode value for default selection.
+        @return Select<VInteger> Select box for notification mode selection
     */
     private Select<VInteger> getNotificationModeSelectBox(int modeValue)
@@ -694 +691 @@
     
     /**
-        * Fieldset for table preferences configuration settings. Argument
-        * TablePreferencesConfiguration is place holder for current values for the
-        * table preferences configuration form fields.
-        * 
-        * @param tpc TablePreferencesConfiguration object (need not be stored in
-        *        database) with default field values.
-        * @return Fieldset A field set for setting TablePreferencesConfiguration
-        *         values.
+        Fieldset for table preferences configuration settings. Argument
+        TablePreferencesConfiguration is place holder for current values for the
+        table preferences configuration form fields.
+        
+        @param tpc TablePreferencesConfiguration object (need not be stored in
+               database) with default field values.
+        @return Fieldset A field set for setting TablePreferencesConfiguration
+                values.
     */
     public Fieldset getTablePreferencesConfigurationFieldset(
@@ -729 +726 @@
     
     /**
-        * Creates a select box for table preferences mode.
-        * 
-        * @param modeValue int Mode value for default selection.
-        * @return Select<VInteger> Select box for table preferences mode selection
+        Creates a select box for table preferences mode.
+        
+        @param modeValue int Mode value for default selection.
+        @return Select<VInteger> Select box for table preferences mode selection
     */
     private Select<VInteger> getTablePreferencesModeSelectBox(int modeValue)
@@ -757 +754 @@
     
     /**
-        * This will probably be removed when fixint #691
-        * @param peaklist to edit, or null if an empty form is needed
-        * @return Form for editing a peaklist
+        This will probably be removed when fixint #691
+        @param peaklist to edit, or null if an empty form is needed
+        @return Form for editing a peaklist
     */
     public Form getPeakListForm(PeakList peaklist)
@@ -767 +764 @@
         Annotator anna = new Annotator(factory);
         /***********************************************************************
-            * Properties fieldset
+            Properties fieldset
         */
         Fieldset propertiesFS = new Fieldset();
@@ -776 +773 @@
         propertiesFS.add(spectrumIdF);
         /***********************************************************************
-            * Precursor
+            Precursor
         */
         Fieldset precursorFS = new Fieldset();
         precursorFS.setTitle("Precursor");
         /***********************************************************************
-            * Peaklistset fieldset
+            Peaklistset fieldset
         */
         Fieldset peaklistsetFS = new Fieldset();
@@ -800 +797 @@
         }
         /***********************************************************************
-            * Init fields
+            Init fields
         */
         if (peaklist != null)
@@ -811 +808 @@
             }
             /*******************************************************************
-                * Precursors
+                Precursors
             */
             for (Precursor pc : peaklist.getPrecursorsQuery().list(
@@ -846 +843 @@
         }
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("Peaklist");
@@ -856 +853 @@
     
     /**
-        * @param hit Current Hit
-        * @param peakListFile Core file with peakList, or null
-        * @param peaklist to display, or null
-        * @return Form for displaying peaklist for hit
+        @param hit Current Hit
+        @param peakListFile Core file with peakList, or null
+        @param peaklist to display, or null
+        @return Form for displaying peaklist for hit
     */
     public Form getHitPeakListForm(Hit hit, File peakListFile,
@@ -868 +865 @@
         Annotator anna = new Annotator(factory);
         /***********************************************************************
-            * Properties fieldset
+            Properties fieldset
         */
         Fieldset propertiesFS = new Fieldset();
         propertiesFS.setTitle("Properties");
         /*
-            * Hit id field.
+            Hit id field.
         */
         TextField<String> hitDescription = new TextField<String>(new VString(
@@ -895 +892 @@
         propertiesFS.add(hitId);
         /*
-            * If there is a SpectrumSearch in the DB we can find modifications etc.
+            If there is a SpectrumSearch in the DB we can find modifications etc.
         */
         if (spectrumSearch != null)
@@ -916 +913 @@
         }
         /*
-            * File name field.
+            File name field.
         */
         TextField<String> fileNameF = new TextField<String>(new VString(
@@ -930 +927 @@
         propertiesFS.add(fileNameF);
         /*
-            * SpectrumId field.
+            SpectrumId field.
         */
         // TextField<Integer> spectrumIdF = new TextField<Integer>(new VInteger(
@@ -947 +944 @@
         propertiesFS.add(spectrumIdF);
         /*
-            * Retention time in minutes
+            Retention time in minutes
         */
         TextField<String> timeInMinutesF = new TextField<String>(new VString(
@@ -967 +964 @@
         propertiesFS.add(timeInMinutesF);
         /***********************************************************************
-            * Optional PeakList fieldsets
+            Optional PeakList fieldsets
         */
         Fieldset precursorFS = null;
@@ -974 +971 @@
         {
             /*******************************************************************
-                * Precursor
+                Precursor
             */
             precursorFS = new Fieldset();
             precursorFS.setTitle("Precursor");
             /*******************************************************************
-                * Peaklistset fieldset
+                Peaklistset fieldset
             */
             peaklistsetFS = new Fieldset();
@@ -988 +985 @@
             peaklistsetFS.add(plsNameF);
             /*******************************************************************
-                * Init fields
+                Init fields
             */
             // spectrumIdF.setValue(peaklist.getSpectrumId());
@@ -1009 +1006 @@
             {
                 /*
-                    * Do not display empty PeakListSet field set.
+                    Do not display empty PeakListSet field set.
                 */
                 peaklistsetFS = null;
             }
             /*******************************************************************
-                * Precursors
+                Precursors
             */
             for (Precursor pc : peaklist.getPrecursorList())
@@ -1050 +1047 @@
             {
                 /*
-                    * Do not display empty Precursor field set.
+                    Do not display empty Precursor field set.
                 */
                 precursorFS = null;
@@ -1056 +1053 @@
         }
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("HitPeaklist");
@@ -1072 +1069 @@
     
     /**
-        * @param a annotation
-        * @return String
+        @param a annotation
+        @return String
     */
     private String joinAnnotationValues(Annotation a)
@@ -1085 +1082 @@
     
     /**
-        * Returns a form for selecting spectrum mass range limits.
-        * 
-        * @param massCutoffLow String The lower cutoff mass value.
-        * @param massCutoffHigh String The upper cutoff mass value.
-        * @param spectrumId String The spectrum Id string.
-        * @return Form for selecting mass range limits.
+        Returns a form for selecting spectrum mass range limits.
+        
+        @param massCutoffLow String The lower cutoff mass value.
+        @param massCutoffHigh String The upper cutoff mass value.
+        @param spectrumId String The spectrum Id string.
+        @return Form for selecting mass range limits.
     */
     public Form getSpectrumMassRangeSelectionForm(String massCutoffLow,
@@ -1096 +1093 @@
     {
         /***********************************************************************
-            * Mass range fieldset
+            Mass range fieldset
         */
         Fieldset massRangeFS = new Fieldset();
@@ -1125 +1122 @@
         massRangeFS.add(spectrumIdF);
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("MassRangeSelectionForm");
@@ -1134 +1131 @@
     
     /**
-        * Returns a form with spectrum properties for a spectrum obtained from a
-        * spectrum file.
-        * 
-        * @param spectrumFile File Core file with spectrum.
-        * @param spectrumId String Spectrum id string.
-        * @param spectrum SpectrumInterface spectrum data.
-        * @return Form for displaying spectrum properties
+        Returns a form with spectrum properties for a spectrum obtained from a
+        spectrum file.
+        
+        @param spectrumFile File Core file with spectrum.
+        @param spectrumId String Spectrum id string.
+        @param spectrum SpectrumInterface spectrum data.
+        @return Form for displaying spectrum properties
     */
     public Form getSpectrumPropertiesForm(File spectrumFile, String spectrumId,
@@ -1146 +1143 @@
     {
         /***********************************************************************
-            * Properties fieldset
+            Properties fieldset
         */
         Fieldset propertiesFS = new Fieldset();
@@ -1156 +1153 @@
         propertiesFS.add(propertiesTable);
         /*
-            * File name
+            File name
         */
         String peakListFileName = null;
@@ -1165 +1162 @@
         addTableRow(propertiesTable, "Filename", peakListFileName, null, 0);
         /*
-            * File type
+            File type
         */
         String spectrumFileType = null;
@@ -1177 +1174 @@
         addTableRow(propertiesTable, "FileType", spectrumFileType, null, 0);
         /*
-            * SpectrumId
+            SpectrumId
         */
         String spectrumIdStr = null;
@@ -1186 +1183 @@
         addTableRow(propertiesTable, "SpectrumId", spectrumIdStr, null, 0);
         /*
-            * Retention time in minutes
+            Retention time in minutes
         */
         String timeInMinutesStr = null;
@@ -1205 +1202 @@
         timeInMinutesStr, null, 0);
         /***********************************************************************
-            * Optional spectrum fieldset
+            Optional spectrum fieldset
         */
         Table precursorTable = null;
@@ -1213 +1210 @@
             {
                 /***************************************************************
-                    * Precursors
+                    Precursors
                 */
                 int precursorNo = 0;
@@ -1273 +1270 @@
                     }
                     /*
-                        * Precursor extra data
+                        Precursor extra data
                     */
                     List<StringPairInterface> dataList = pc.getExtraDataList();
@@ -1294 +1291 @@
                     }
                     /*
-                        * Precursor fragmentation type
+                        Precursor fragmentation type
                     */
                     SpectrumPrecursor.FragmentationType fragmentationType = pc
@@ -1310 +1307 @@
             {
                 /*
-                    * Extra data.
+                    Extra data.
                 */
                 Table extraDataTable = new Table("AdditionalInformation");
@@ -1339 +1336 @@
         }
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("SpectrumProperties");
@@ -1347 +1344 @@
     
     /**
-        * Returns a form with spectrum file instrument data for a spectrum file.
-        * 
-        * @param spectrumFileInstrumentList List<SpectrumFileInstrumentInterface>
-        *        Spectrum file instrument list.
-        * @return Form for displaying spectrum file instrument data.
+        Returns a form with spectrum file instrument data for a spectrum file.
+        
+        @param spectrumFileInstrumentList List<SpectrumFileInstrumentInterface>
+               Spectrum file instrument list.
+        @return Form for displaying spectrum file instrument data.
     */
     public Form getSpectrumFileInstrumentForm(
@@ -1362 +1359 @@
         }
         /***********************************************************************
-            * Instrument fieldset
+            Instrument fieldset
         */
         Fieldset instrumentFS = new Fieldset();
@@ -1371 +1368 @@
             List<StringPairInterface> dataList;
             /*
-                * Name field.
+                Name field.
             */
             Table instrumentGeneralTable = new Table(
@@ -1392 +1389 @@
             // instrumentFS.add(instrumentGeneralTable);
             /*
-                * Serial No field.
+                Serial No field.
             */
             String instrumentSerialNo = null;
@@ -1404 +1401 @@
             instrumentFS.add(instrumentGeneralTable);
             /*
-                * Source field.
+                Source field.
             */
             Table sourceTable = new Table("SourceInformation");
@@ -1430 +1427 @@
             instrumentFS.add(sourceTable);
             /*
-                * AnalyzerList field.
+                AnalyzerList field.
             */
             List<SpectrumFileAnalyzerInterface> analyzerList = spectrumFileInstrument
@@ -1440 +1437 @@
                     Table analyzerTable = new Table("AnalyzerListInformation");
                     /*
-                        * // Only add table title header for first table if (j ==
-                        * 0) { analyzerTable.setTitle("AnalyzerListInformation"); }
+                        // Only add table title header for first table if (j ==
+                        0) { analyzerTable.setTitle("AnalyzerListInformation"); }
                     */
                     // analyzerTable.add(new Column<String>("Property"));
@@ -1474 +1471 @@
             }
             /*
-                * Detector field.
+                Detector field.
             */
             Table detectorTable = new Table("DetectorInformation");
@@ -1500 +1497 @@
             instrumentFS.add(detectorTable);
             /*
-                * Additional field.
+                Additional field.
             */
             Table additionalTable = new Table("AdditionalInformation");
@@ -1527 +1524 @@
         }
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("InstrumentInformation");
@@ -1535 +1532 @@
     
     /**
-        * Adds a table row to a table. A "value" argument that is null will be
-        * represented as an empty string, otherwise by its toString() value.
-        * 
-        * @param table Table The table to add a row to.
-        * @param nameKey String Property key string.
-        * @param value Object Property value object.
-        * @param actionClass Class<E extends ProteiosAction> Optional value cell
-        *        action.
-        * @param itemId int The item id to use for an optional action.
+        Adds a table row to a table. A "value" argument that is null will be
+        represented as an empty string, otherwise by its toString() value.
+        
+        @param table Table The table to add a row to.
+        @param nameKey String Property key string.
+        @param value Object Property value object.
+        @param actionClass Class<E extends ProteiosAction> Optional value cell
+               action.
+        @param itemId int The item id to use for an optional action.
     */
     private void addTableRow(Table table, String nameKey, Object value,
@@ -1576 +1573 @@
     
     /**
-        * Returns a form with spectrum file contact data for a spectrum file.
-        * 
-        * @param spectrumContact Spectrum file contact
-        *        data.
-        * @return Form for displaying spectrum file contact data.
+        Returns a form with spectrum file contact data for a spectrum file.
+        
+        @param spectrumContact Spectrum file contact
+               data.
+        @return Form for displaying spectrum file contact data.
     */
     public Form getSpectrumFileContactForm(
@@ -1590 +1587 @@
         }
         /***********************************************************************
-            * Contact fieldset
+            Contact fieldset
         */
         Fieldset contactFS = new Fieldset();
@@ -1600 +1597 @@
         contactFS.add(contactTable);
         /*
-            * Name
+            Name
         */
         String name = null;
@@ -1609 +1606 @@
         addTableRow(contactTable, "Name", name, null, 0);
         /*
-            * Institution
+            Institution
         */
         String institution = null;
@@ -1618 +1615 @@
         addTableRow(contactTable, "Institution", institution, null, 0);
         /*
-            * ContactInfo
+            ContactInfo
         */
         String contactInfo = null;
@@ -1627 +1624 @@
         addTableRow(contactTable, "ContactInfo", contactInfo, null, 0);
         /*
-            * Address
+            Address
         */
         String address = null;
@@ -1636 +1633 @@
         addTableRow(contactTable, "Address", address, null, 0);
         /*
-            * URL
+            URL
         */
         String url = null;
@@ -1645 +1642 @@
         addTableRow(contactTable, "URL", url, null, 0);
         /*
-            * Email
+            Email
         */
         String email = null;
@@ -1654 +1651 @@
         addTableRow(contactTable, "Email", email, null, 0);
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("ContactInformation");
@@ -1660 +1657 @@
         return form;
     }
-    
+        
     /**
-        * Returns a form for adding spectrum file contact data for a spectrum file.
-        * 
-        * @param project Project The project in whose directory a new output
-        *        directory is created.
-        * @param outputDirNameDefault String The default name of the output
-        *        directory.
-        * @param user User The user from whose profile default contact information
-        *        should be taken.
-        * @return Form for displaying spectrum file contact data.
-    */
-    public Form getSpectrumFileContactInputForm(Project project,
-    String outputDirNameDefault, User user)
-    {
-        Form form = new Form("spectrumFileContactInputForm");
-        // Get potential default contact information from user profile
-        String defaultName = new String("");
-        String defaultInstitution = new String("");
-        String defaultAddress = new String("");
-        String defaultEmail = new String("");
-        String defaultContactInfo = new String("");
-        if (user != null)
-        {
-            // Default name
-            if (user.getName() != null)
-            {
-                defaultName = user.getName();
-            }
-            // Default institution
-            if (user.getOrganisation() != null)
-            {
-                defaultInstitution = user.getOrganisation();
-            }
-            // Default address
-            if (user.getAddress() != null)
-            {
-                defaultAddress = user.getAddress();
-            }
-            // Default e-mail
-            if (user.getEmail() != null)
-            {
-                defaultEmail = user.getEmail();
-            }
-            // Default contact info
-            defaultContactInfo = addContactInfoElement(defaultContactInfo,
-            "Name", defaultName);
-            defaultContactInfo = addContactInfoElement(defaultContactInfo,
-            "Institution", defaultInstitution);
-            defaultContactInfo = addContactInfoElement(defaultContactInfo,
-            "Address", defaultAddress);
-            defaultContactInfo = addContactInfoElement(defaultContactInfo,
-            "Phone", user.getPhone());
-            defaultContactInfo = addContactInfoElement(defaultContactInfo,
-            "Fax", user.getFax());
-            defaultContactInfo = addContactInfoElement(defaultContactInfo,
-            "e-mail", defaultEmail);
-        }
-        //
-        Fieldset contactInputFS = new Fieldset();
-        contactInputFS.setTitle("SpectrumFileContactInput");
-        form.addFieldset(contactInputFS);
-        //
-        TextField<String> nameF = new TextField<String>(VNONREQUIRED_NAME);
-        nameF.setValue(defaultName);
-        nameF.setLabel("Name");
-        contactInputFS.add(nameF);
-        //
-        TextField<String> institutionF = new TextField<String>(
-        VNONREQUIRED_INSTITUTION);
-        institutionF.setValue(defaultInstitution);
-        institutionF.setLabel("Institution");
-        contactInputFS.add(institutionF);
-        //
-        TextField<String> contactInfoF = new TextField<String>(
-        VNONREQUIRED_CONTACT_INFO);
-        contactInfoF.setValue(defaultContactInfo);
-        contactInfoF.setLabel("ContactInfo");
-        contactInputFS.add(contactInfoF);
-        //
-        TextField<String> addressF = new TextField<String>(VNONREQUIRED_ADDRESS);
-        addressF.setValue(defaultAddress);
-        addressF.setLabel("Address");
-        contactInputFS.add(addressF);
-        //
-        TextField<String> urlF = new TextField<String>(VNONREQUIRED_URL);
-        urlF.setValue("");
-        urlF.setLabel("URL");
-        contactInputFS.add(urlF);
-        //
-        TextField<String> emailF = new TextField<String>(VNONREQUIRED_EMAIL);
-        emailF.setValue(defaultEmail);
-        emailF.setLabel("email");
-        contactInputFS.add(emailF);
-        //
-        Fieldset contactOutputFS = new Fieldset();
-        contactOutputFS.setTitle("SpectrumFileContactOutput");
-        form.addFieldset(contactOutputFS);
-        //
-        TextField<String> outputDirNameF = new TextField<String>(
-        VNONREQUIRED_FILENAME);
-        outputDirNameF.setValue(outputDirNameDefault);
-        outputDirNameF.setLabel("OutputDirectoryName");
-        contactOutputFS.add(outputDirNameF);
-        //
-        /*
-            * Checkbox<VBoolean> overwriteExistingContactDataCB = new Checkbox<VBoolean>(
-            * SpectrumFileContactDataAdder.VOVERWRITEEXISTINGCONTACTDATAFLAG);
-            * overwriteExistingContactDataCB.setLabel("OverwriteExistingContactData");
-            * overwriteExistingContactDataCB.setValue("true");
-            * overwriteExistingContactDataCB.isChecked(true);
-            * contactOutputFS.add(overwriteExistingContactDataCB);
-        */
-        //
-        return form;
-    }
-    
-    /**
-        * Adds an element of data to contact info string.
-        * 
-        * @param contactInfo String Current contact info string.
-        * @param elementName String Name of contact info element.
-        * @param elementValue String Contents of contact info element.
-        * @return String Contact info string with the added info data.
-    */
-    private String addContactInfoElement(String contactInfo,
-    String elementName, String elementValue)
-    {
-        if (elementValue != null && !elementValue.equals(""))
-        {
-            if (!contactInfo.equals(""))
-            {
-                contactInfo += ", ";
-            }
-            contactInfo += elementName + ": " + elementValue;
-        }
-        return contactInfo;
-    }
-    
-    /**
-        * Returns a form for adding spectrum file sample data for a spectrum file.
-        * 
-        * @param project Project The project in whose directory a new output
-        *        directory is created.
-        * @param outputDirNameDefault String The default name of the output
-        *        directory.
-        * @return Form for displaying spectrum file contact data.
+        Returns a form for adding spectrum file sample data for a spectrum file.
+        
+        @param project Project The project in whose directory a new output
+               directory is created.
+        @param outputDirNameDefault String The default name of the output
+               directory.
+        @return Form for displaying spectrum file contact data.
     */
     public Form getSpectrumFileSampleInputForm(Project project,
@@ -1830 +1689 @@
         //
         /*
-            * TextField<String> stateF = new TextField<String>(VNONREQUIRED_SAMPLE_STATE);
-            * stateF.setValue(""); stateF.setLabel("SampleState");
-            * sampleInputFS.add(stateF);
+            TextField<String> stateF = new TextField<String>(VNONREQUIRED_SAMPLE_STATE);
+            stateF.setValue(""); stateF.setLabel("SampleState");
+            sampleInputFS.add(stateF);
         */
         // Sample state select box
@@ -1890 +1749 @@
         //
         /*
-            * Checkbox<VBoolean> overwriteExistingSampleDataCB = new Checkbox<VBoolean>(
-            * SpectrumFileSampleDataAdder.VOVERWRITEEXISTINGSAMPLEDATAFLAG);
-            * overwriteExistingSampleDataCB.setLabel("OverwriteExistingSampleData");
-            * overwriteExistingSampleDataCB.setValue("true");
-            * overwriteExistingSampleDataCB.isChecked(true);
-            * sampleOutputFS.add(overwriteExistingSampleDataCB);
+            Checkbox<VBoolean> overwriteExistingSampleDataCB = new Checkbox<VBoolean>(
+            SpectrumFileSampleDataAdder.VOVERWRITEEXISTINGSAMPLEDATAFLAG);
+            overwriteExistingSampleDataCB.setLabel("OverwriteExistingSampleData");
+            overwriteExistingSampleDataCB.setValue("true");
+            overwriteExistingSampleDataCB.isChecked(true);
+            sampleOutputFS.add(overwriteExistingSampleDataCB);
         */
         //
@@ -1913 +1772 @@
     {
         /***********************************************************************
-            * Properties fieldset
+            Properties fieldset
         */
         Fieldset properties = new Fieldset();
@@ -1927 +1786 @@
         properties.add(descrF);
         /***********************************************************************
-            * Hardware configuration
+            Hardware configuration
         */
         Fieldset instrumentFS = new Fieldset();
         instrumentFS.setTitle("Instrument");
         /***********************************************************************
-            * Analyzers
+            Analyzers
         */
         Fieldset analyzersFS = new Fieldset();
         analyzersFS.setTitle("Analyzers");
         /***********************************************************************
-            * Set field values
+            Set field values
         */
         if (pls != null)
@@ -1946 +1805 @@
             instrumentFS.add(newTextField("Hardware", hw.getName()));
             /*******************************************************************
-                * Analyzer annotation values
+                Analyzer annotation values
             */
             List<HardwareConfiguration> analyzerList = pls.getAnalyzers();
@@ -1961 +1820 @@
             }
             /*******************************************************************
-                * PeakListSet values
+                PeakListSet values
             */
             itemIdF.setValue(pls.getId());
@@ -1968 +1827 @@
         }
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("peakListSetForm");
@@ -1981 +1840 @@
     {
         /***********************************************************************
-            * Properties
+            Properties
         */
         Fieldset fs = new Fieldset();
@@ -2018 +1877 @@
         fs.add(nameF);
         /***********************************************************************
-            * Form
+            Form
         */
         Form form = new Form("exportPeakListSetForm");
@@ -2125 +1984 @@
     
     /**
-        * Creates and adds a hidden field with an Integer value to the given form.
-        * Introduced to solve problem in #623
+        Creates and adds a hidden field with an Integer value to the given form.
+        Introduced to solve problem in #623
     */
     public void addHiddenField(Form form, VInteger param, Integer value)
@@ -2137 +1996 @@
     
     /**
-        * Creates and adds a hidden field with an Integer value to the given table.
-        * Introduced to solve problem in #623
+        Creates and adds a hidden field with an Integer value to the given table.
+        Introduced to solve problem in #623
     */
     public void addHiddenField(Table table, VInteger param, Integer value)
@@ -2335 +2194 @@
         properties.add(filterValueF);
         /*
-            * The following section stores information on previous settings in
-            * hidden fields, to be retrieved when the form is verified.
+            The following section stores information on previous settings in
+            hidden fields, to be retrieved when the form is verified.
         */
         // Add forward action id
@@ -2372 +2231 @@
                 String filterVal = null;
                 /*
-                    * Note that the list and hash maps may be null here, even
-                    * though filter list size > 0. This happens after the form has
-                    * been displayed, and a following action verifies the form to
-                    * have the form fields filled in with data stored in the
-                    * request.
+                    Note that the list and hash maps may be null here, even
+                    though filter list size > 0. This happens after the form has
+                    been displayed, and a following action verifies the form to
+                    have the form fields filled in with data stored in the
+                    request.
                 */
                 if (getFilterKeyColumnList() != null)
@@ -2442 +2301 @@
 
     /**
-        * Get generic form for object.
-        * 
-        * @param template template for generic form
-        * @return Form for editing the object
+        Get generic form for object.
+        
+        @param template template for generic form
+        @return Form for editing the object
     */
     public Form getForm(Template template)
     {
         /***********************************************************************
-            * Analyze template
+            Analyze template
         */
         Form form = null;
@@ -2462 +2321 @@
     
     /**
-        * Get generic form for object.
-        * 
-        * @param template template for generic form
-        * @return Form for editing the object
+        Get generic form for object.
+        
+        @param template template for generic form
+        @return Form for editing the object
     */
     private Form getFormImpl(FormTemplateInterface formTemplate)
     {
         /***********************************************************************
-            * Analyze object class
+            Analyze object class
         */
         
         /*
-            * Get class from formTemplate itemObject or itemClass.
+            Get class from formTemplate itemObject or itemClass.
         */
         Object itemObject = null;
@@ -2488 +2347 @@
         }
         /*
-            * Add optional extra formTemplate list of methods to be excluded.
+            Add optional extra formTemplate list of methods to be excluded.
         */
         if (formTemplate != null && formTemplate.getExcludedDeclMethods() != null)
@@ -2501 +2360 @@
         
         /***********************************************************************
-            * Main fieldset
+            Main fieldset
         */
         Fieldset mainFS = new Fieldset();
@@ -2507 +2366 @@
         mainFS.setTitle(mainFsName);
         /*
-            * Add forward actionId field as first field, for external use.
+            Add forward actionId field as first field, for external use.
         */
         TextField<String> fwdactionF = new ForwardField();
         mainFS.add(fwdactionF);
         /*
-            * Get item id, if any.
+            Get item id, if any.
         */
         int itemId = 0;
@@ -2541 +2400 @@
         }
         /*
-            * Add itemId field idF (hidden) if itemId value ok.
+            Add itemId field idF (hidden) if itemId value ok.
         */
         if (itemId > 0)
@@ -2552 +2411 @@
         }
         /*
-            * Add class name field cnF.
+            Add class name field cnF.
         */
         String classNameFull = new String("");
@@ -2566 +2425 @@
         cnF.setDisabled(true);
         /*
-            * Add readOnlyForm field rofF (hidden).
+            Add readOnlyForm field rofF (hidden).
         */
         TextField<Boolean> rofF = newHiddenReadOnlyFormField();
@@ -2574 +2433 @@
         rofF.setDisabled(true);
         /*
-            * Keep track on whether public setter methods exist, in order to know
-            * if a "Save" button should be added.
+            Keep track on whether public setter methods exist, in order to know
+            if a "Save" button should be added.
         */
         boolean hasSetterMethods = false;
         /*
-            * Methods, declared and inherited
+            Methods, declared and inherited
         */
         Method[] methodArr = new Method[0];
@@ -2588 +2447 @@
         
         /*
-            * Methods declared in object class (not inherited)
+            Methods declared in object class (not inherited)
         */
         Method[] declaredMethodArr = new Method[0];
@@ -2602 +2461 @@
             String methodReturnType = method.getReturnType().getName();
             /*
-                * Only process declared methods not in exclude list.
+                Only process declared methods not in exclude list.
             */
             if (!getExcludedDeclMethods().contains(methodName))
@@ -2612 +2471 @@
                 Class<?> returnTypeOfGetterMethod = null;
                 /*
-                    * Check if getter access method.
+                    Check if getter access method.
                 */
                 if (methodName.startsWith("get"))
                 {
                     /*
-                        * Assume that attribute name can optained by skipping "get"
-                        * in method name.
+                        Assume that attribute name can optained by skipping "get"
+                        in method name.
                     */
                     attrName = methodName.substring(3);
@@ -2639 +2498 @@
                 {
                     /*
-                        * Assume that attribute name can optained by skipping "is"
-                        * in method name.
+                        Assume that attribute name can optained by skipping "is"
+                        in method name.
                     */
                     attrName = methodName.substring(2);
@@ -2664 +2523 @@
                             {
                                 /*
-                                    * Return date values in "YYYY-MM-DD HH:mm:ss"
-                                    * 24-hour format.
+                                    Return date values in "YYYY-MM-DD HH:mm:ss"
+                                    24-hour format.
                                 */
                                 if (method.getReturnType().getName().equals(
@@ -2695 +2554 @@
                     }
                     /*
-                        * Check if public accessor method for setting value exists.
+                        Check if public accessor method for setting value exists.
                     */
                     boolean isSettable = false;
@@ -2710 +2569 @@
                     .debug("FormFactory::getFormImpl(): attrName = \"" + attrName + "\" publMethodName = \"" + publMethodName + "\" isSettable = " + isSettable);
                     /*
-                        * Use TextArea for Description, else TextField
+                        Use TextArea for Description, else TextField
                     */
                     if (attrName.equals("Description"))
                     {
                         /*
-                            * Value text area
+                            Value text area
                         */
                         TextArea valueF = null;
@@ -2735 +2594 @@
                     {
                         /*
-                            * Value field
+                            Value field
                         */
                         TextField<String> valueF = null;
@@ -2757 +2616 @@
         
         /*
-            * Check if object supports method getAnnotationSet().
+            Check if object supports method getAnnotationSet().
         */
         Fieldset annotationFS = null;
@@ -2773 +2632 @@
             {
                 /***************************************************************
-                    * Annotation fieldset
+                    Annotation fieldset
                 */
                 annotationFS = new Fieldset();
                 annotationFS.setTitle("Annotations");
                 /*
-                    * Get DbControl
+                    Get DbControl
                 */
                 DbControl dc = getDbControlForObject(itemObject);
                 /*
-                    * Fetch annotations
+                    Fetch annotations
                 */
                 if (itemObject != null)
@@ -2794 +2653 @@
                         {
                             /*
-                                * Only add annotations that contain something.
+                                Only add annotations that contain something.
                             */
                             String value = joinAnnotationValues(a);
@@ -2800 +2659 @@
                             {
                                 /*
-                                    * Value (description) field - optional scroll
-                                    * bar
+                                    Value (description) field - optional scroll
+                                    bar
                                 */
                                 TextArea descrF = new DescriptionField();
@@ -2826 +2685 @@
         }
         /***********************************************************************
-            * Form
+            Form
         */
         String formName = new String("newForm");
@@ -2837 +2696 @@
         form.setTitle(clsName);
         /***********************************************************************
-            * Add fieldsets to form
+            Add fieldsets to form
         */
         form.addFieldset(mainFS);
@@ -2845 +2704 @@
         }
         /*
-            * Return generated form.
+            Return generated form.
         */
         return form;
@@ -2851 +2710 @@
     
     /**
-        * Get DbControl for object.
-        * 
-        * @return DbControl for the object
+        Get DbControl for object.
+        
+        @return DbControl for the object
     */
     public DbControl getDbControlForObject(Object itemObject)
     {
         /*
-            * Get class from itemObject.
+            Get class from itemObject.
         */
         Class<? extends Object> cls = null;
@@ -2871 +2730 @@
         String clsName = cls.getSimpleName();
         /*
-            * Check if object supports method getDbControl().
+            Check if object supports method getDbControl().
         */
         DbControl dc = null;
@@ -2882 +2741 @@
             {
                 /*
-                    * Get DbControl for object
+                    Get DbControl for object
                 */
                 try
@@ -2903 +2762 @@
         }
         /*
-            * Return DbControl.
+            Return DbControl.
         */
         return dc;
@@ -2909 +2768 @@
     
     /**
-        * Fetch public method for object, or null if not found.
-        * 
-        * @param publMethodName String Name of public method to search for.
-        * @return Method public method for object with desired name, or null if not
-        *         found.
+        Fetch public method for object, or null if not found.
+        
+        @param publMethodName String Name of public method to search for.
+        @return Method public method for object with desired name, or null if not
+                found.
     */
     private Method fetchPublicMethodForObject(String publMethodName,
@@ -2924 +2783 @@
         String clsName = cls.getSimpleName();
         /*
-            * Check if object supports public method with desired name.
+            Check if object supports public method with desired name.
         */
         Method publMethod = null;
@@ -2935 +2794 @@
             {
                 /*
-                    * Check if method is public.
+                    Check if method is public.
                 */
                 int methodMod = method.getModifiers();
@@ -2948 +2807 @@
     
     /**
-        * Returns a String corresponding to the method modifier: "static",
-        * "public", "protected", or "private".
-        * 
-        * @param method
-        * @return String for method modifier
+        Returns a String corresponding to the method modifier: "static",
+        "public", "protected", or "private".
+        
+        @param method
+        @return String for method modifier
     */
     private String methodModifierString(Method method)
@@ -2990 +2849 @@
 
     /**
-        * Form for new Protocol item. The difference between calling
-        * getNewProtocolForm(protocol) and getForm(Protocol.class, protocol) when
-        * protocol != null, is that getForm(Protocol.class, protocol) assumes that
-        * the protocol argument is stored in the database, i.e. that
-        * protocol.getId() is a valid item id, that can be used as value for a
-        * newIdField(), without an exception being thrown. Method
-        * getNewProtocolForm() on the other hand only uses the protocol argument as
-        * a convenient place holder for default values for the Protocol form
-        * fields.
-        * 
-        * @param protocol Protocol object (need not be stored in database) with
-        *        default field values.
-        * @return Form A form for setting protocol values.
+        Form for new Protocol item. The difference between calling
+        getNewProtocolForm(protocol) and getForm(Protocol.class, protocol) when
+        protocol != null, is that getForm(Protocol.class, protocol) assumes that
+        the protocol argument is stored in the database, i.e. that
+        protocol.getId() is a valid item id, that can be used as value for a
+        newIdField(), without an exception being thrown. Method
+        getNewProtocolForm() on the other hand only uses the protocol argument as
+        a convenient place holder for default values for the Protocol form
+        fields.
+        
+        @param protocol Protocol object (need not be stored in database) with
+               default field values.
+        @return Form A form for setting protocol values.
     */
     public Form getNewProtocolForm(Protocol protocol)
@@ -3267 +3126 @@
             // Forward field
             /*
-                * This hidden forward field sets action id used by the directory
-                * selection action called by MoveFile1.
+                This hidden forward field sets action id used by the directory
+                selection action called by MoveFile1.
             */
             TextField<String> forwardF = new ForwardField();
@@ -3515 +3374 @@
     
     /**
-        * Creates a select box for protocols. If the class for which the protocol
-        * is intended is supported by the method, only protocols with correct
-        * protocol type are included. If an input object with attached protocol
-        * exists, the latter protocol should appear in the list and be selected, if
-        * if the protocol is tagged to be removed. However, no other protocols
-        * tagged to be removed should be included in the list.
-        * 
-        * @param cls Class Class for which a protocol should be selected.
-        * @param obj Object Optional object with attached protocol for setting
-        *        default protocol.
-        * @return Select<VInteger> Select box for protocol selection
+        Creates a select box for protocols. If the class for which the protocol
+        is intended is supported by the method, only protocols with correct
+        protocol type are included. If an input object with attached protocol
+        exists, the latter protocol should appear in the list and be selected, if
+        if the protocol is tagged to be removed. However, no other protocols
+        tagged to be removed should be included in the list.
+        
+        @param cls Class Class for which a protocol should be selected.
+        @param obj Object Optional object with attached protocol for setting
+               default protocol.
+        @return Select<VInteger> Select box for protocol selection
     */
     private Select<VInteger> getProtocolSelectBox(Class cls, Object obj)