Changeset 3945

Timestamp:

Nov 4, 2010, 2:56:21 PM (13 years ago)

Author:

Gregory Vincic

Message:

Refs #698. Moved method getSpectrumFileInstrumentForm from FormFactory to InspectActiveSpectrumFile, also introducing PropertyRow.

Location:

trunk/client/servlet/src/org/proteios

Files:

• action/file/InspectActiveSpectrumFile.java (modified) (4 diffs)
• gui/form/FormFactory.java (modified) (45 diffs)
• gui/table/Cell.java (modified) (2 diffs)
• gui/table/PropertyRow.java (added)

trunk/client/servlet/src/org/proteios/action/file/InspectActiveSpectrumFile.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 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.List;
 import org.proteios.ActionLink;
 import org.proteios.action.ProteiosAction;
@@ -45 +47 @@
 import org.proteios.gui.table.Cell;
 import org.proteios.gui.table.Column;
+import org.proteios.gui.table.PropertyRow;
 import org.proteios.gui.table.Row;
 import org.proteios.gui.table.Table;
 import org.proteios.io.MgfFileReader;
 import org.proteios.io.PeakListFileInterface;
+import org.proteios.io.SpectrumFileAnalyzerInterface;
 import org.proteios.io.SpectrumFileContactInterface;
 import org.proteios.io.SpectrumFileContactReaderInterface;
@@ -55 +59 @@
 import org.proteios.io.SpectrumIdReaderInterface;
 import org.proteios.io.SpectrumInterface;
-
+import org.proteios.io.StringPairInterface;
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
@@ -61 +65 @@
 import se.lu.thep.waf.constraints.VInteger;
 
-import java.util.ArrayList;
-import java.util.List;
-
 /**
- * This action presents a form with a table of spectrum id values in a selected
- * spectrum file, together with a spectrum corresponding to the first spectrum
- * id value. The user may click on another spectrum id in the table to show that
- * spectrum.
- * 
- * @author olle
- */
+    * This action presents a form with a table of spectrum id values in a selected
+    * spectrum file, together with a spectrum corresponding to the first spectrum
+    * id value. The user may click on another spectrum id in the table to show that
+    * spectrum.
+    * 
+    * @author olle
+*/
 public class InspectActiveSpectrumFile
-    extends ProteiosAction<InspectActiveSpectrumFile>
+extends ProteiosAction<InspectActiveSpectrumFile>
 {
-  public static final VInteger VSPECTRUMFILEID = new VInteger(
-    "spectrumFileId", 0, false);
-  public static final VBoolean VKEEPORIGINALSPECTRUM = new VBoolean(
-    "keepOriginalSpectrum", false);
-  public static final VBoolean VFIRSTMGFTITLESPECTRUM = new VBoolean(
-    "firstMGF", false);
-  private int maxResults = 20;
-  private int itemsFrom = 0;
-  private boolean pageSelectedFromScroller = false;
-
-
-  /**
-   * Get the max number of results to show in list.
-   * 
-   * @return int The max number of results to show in list.
-   */
-  public int getMaxResults()
-  {
-    return this.maxResults;
-  }
-
-
-  /**
-   * Set the max number of results to show in list.
-   * 
-   * @param maxResults int The value to set for the max number of results to
-   *        show in list.
-   */
-  public void setMaxResults(int maxResults)
-  {
-    this.maxResults = maxResults;
-  }
-
-
-  /**
-   * Get the item number to start from in the list.
-   * 
-   * @return int The item number to start from in the list.
-   */
-  public int getItemsFrom()
-  {
-    return this.itemsFrom;
-  }
-
-
-  /**
-   * Set the item number to start from in the list.
-   * 
-   * @param itemsFrom int The value to set for the item number to start from
-   *        in the list.
-   */
-  public void setItemsFrom(int itemsFrom)
-  {
-    this.itemsFrom = itemsFrom;
-  }
-
-
-  /**
-   * Get flag indicating that page is selected from scroller.
-   * 
-   * @return boolean The flag indicating that page is selected from scroller.
-   */
-  public boolean isPageSelectedFromScroller()
-  {
-    return this.pageSelectedFromScroller;
-  }
-
-
-  /**
-   * Set flag indicating that page is selected from scroller.
-   * 
-   * @param pageSelectedFromScroller boolean The value to set for flag
-   *        indicating that page is selected from scroller.
-   */
-  public void setPageSelectedFromScroller(boolean pageSelectedFromScroller)
-  {
-    this.pageSelectedFromScroller = pageSelectedFromScroller;
-  }
-
-
-  @Override
-  protected void runMe()
-      throws ActionException, InvalidParameterValue
-  {
-    /*
-     * Get the id's of all selected files. VSPECTRUMFILEID is the valid
-     * identifier used when rendering the list of files, thus we use it to
-     * get the valid list of item id values.
-     */
-    List<Integer> files = getValidIntegerList(VSPECTRUMFILEID);
-    log.debug("(1) files = " + files);
-    // Check alternative input
-    if (files == null)
-    {
-      Integer fileIdFromSessionAttribute = getSessionAttribute(VSPECTRUMFILEID);
-      log
-        .debug("fileIdFromSessionAttribute = " + fileIdFromSessionAttribute);
-      if (fileIdFromSessionAttribute != null)
-      {
-        files = new ArrayList<Integer>(0);
-        files.add(fileIdFromSessionAttribute);
-      }
-    }
-    log.debug("(2) files = " + files);
-    /*
-     * Make sure at least one file has been selected
-     */
-    if (files == null || files.size() == 0)
-    {
-      setError("Please select a spectrum file to inspect");
-      return;
-    }
-    /*
-     * Inspect first file.
-     */
-    Integer fileId = files.get(0);
-    String spectrumId = getValidString(PlotFileSpectrum.VSPECTRUMID);
-    String massCutoffLowStr = getValidString(PlotFileSpectrum.VMASSCUTOFFLOWSTR);
-    String massCutoffHighStr = getValidString(PlotFileSpectrum.VMASSCUTOFFHIGHSTR);
-    Boolean keepOriginalSpectrum = getValidBoolean(VKEEPORIGINALSPECTRUM);
-    log.debug("(1) spectrumId = " + spectrumId);
-    // Check alternative input
-    if (spectrumId == null)
-    {
-      String spectrumIdFromSessionAttribute = getSessionAttribute(PlotFileSpectrum.VSPECTRUMID);
-      log
-        .debug("spectrumIdFromSessionAttribute = " + spectrumIdFromSessionAttribute);
-      if (spectrumIdFromSessionAttribute != null)
-      {
-        spectrumId = spectrumIdFromSessionAttribute;
-      }
-      // Reset value of spectrum Id from session attribute
-      setSessionAttribute(PlotFileSpectrum.VSPECTRUMID, null);
-    }
-    log.debug("(2) spectrumId = " + spectrumId);
-    log.debug("fileId = " + fileId);
-    log.debug("spectrumId = \"" + spectrumId + "\"");
-    log.debug("massCutoffLowStr = \"" + massCutoffLowStr + "\"");
-    log.debug("massCutoffHighStr = \"" + massCutoffHighStr + "\"");
-    log.debug("(1) keepOriginalSpectrum = " + keepOriginalSpectrum);
-    if (keepOriginalSpectrum == null)
-    {
-      keepOriginalSpectrum = true;
-    }
-    log.debug("(2) keepOriginalSpectrum = " + keepOriginalSpectrum);
-    // Only show one spectrum view if no mass range parameters
-    if ((massCutoffLowStr == null || massCutoffLowStr.equals("")) && (massCutoffHighStr == null || massCutoffHighStr
-      .equals("")))
-    {
-      keepOriginalSpectrum = false;
-    }
-    log.debug("(3) keepOriginalSpectrum = " + keepOriginalSpectrum);
-    DbControl dc = newDbControl();
-    ItemFactory factory = new ItemFactory(dc);
-    File file = factory.getById(File.class, fileId);
-    log.debug("file = " + file);
-    List<String> spectrumIds = null;
-    // Get spectrum id reader
-    SpectrumFileReaderFactory spectrumFileReaderFactory = new SpectrumFileReaderFactory();
-    SpectrumIdReaderInterface spectrumIdReader = spectrumFileReaderFactory
-      .fetchSpectrumIdReader(file);
-    if (spectrumIdReader != null)
-    {
-      spectrumIds = spectrumIdReader.getSpectrumIdList();
-    }
-    /***********************************************************************
-     * Peaklists
-     */
-    Table peakListTable = new Table("peaklists");
-    // Add tool-bar to table to make GUIConverter set
-    // form id for action in hidden field.
-    Toolbar peakListTableToolbar = new Toolbar();
-    peakListTable.setToolbar(peakListTableToolbar);
-    if (spectrumIdReader != null)
-    {
-      if (spectrumIdReader.isSpectrumIdObtainedFromSpectrumOrderNumber())
-      {
-        peakListTable.add(new Column("SpectrumIdOrderNumber3"));
-        /* Special fix to get to the right spectrum id if it is from an MGF title*/
-        if (spectrumId != null && spectrumIdReader instanceof MgfFileReader)
-        {
-          if (!spectrumId.matches("^d+(\\s-\\s.*)?"))
-          {
-            spectrumId = spectrumId.trim();
-            for (String s : spectrumIds)
-            {
-              String toMatch = s.substring(s.indexOf("-") + 2)
-                .trim();
-              if (spectrumId.equals(toMatch))
-              {
-                log.debug("Found spectrum:"+s);
-                spectrumId = s;
-                setSessionAttribute(PlotFileSpectrum.VSPECTRUMID.getName(), spectrumId);
-                break;
-              }
-            }
-          }
-        }
-      }
-      else
-      {
-        peakListTable.add(new Column("Spectrum id"));
-      }
-    }
-    if (spectrumIds != null)
-    {
-      log.debug("spectrumIds.size() = " + spectrumIds.size());
-      // Fetch scroller page selected
-      restoreScrollerState();
-      log
-        .debug("getItemsFrom() = " + getItemsFrom() + " isPageSelectedFromScroller() = " + isPageSelectedFromScroller());
-      if (!isPageSelectedFromScroller())
-      {
-        // Adjust scroller page to include selected spectrum
-        if (spectrumId != null && !spectrumId.equals(""))
-        {
-          // find start of scroller page including selected spectrum
-          Integer currentIndex = fetchStringListItemIndex(spectrumId,
-            spectrumIds);
-          log.debug("currentIndex = " + currentIndex);
-          if (currentIndex != null && currentIndex >= 0)
-          {
-            int pageNo = currentIndex / getMaxResults();
-            int tempStart = pageNo * getMaxResults();
-            log
-              .debug("currentIndex = " + currentIndex + " pageNo = " + pageNo + " tempStart = " + tempStart);
-            // Set start index for displayed list
-            setItemsFrom(tempStart);
-          }
-        }
-      }
-      // Add scroller
-      int count = spectrumIds.size();
-      if (count > getMaxResults())
-      {
-        Scroller scroller = new Scroller();
-        scroller.setFrom(getItemsFrom());
-        scroller.setMax(getMaxResults());
-        scroller.setTotalCount(count);
-        scroller.setScrollActionId(getActionFactory().getId(
-          ScrollTo.class));
-        scroller.setTableConfActionId(getActionFactory().getId(
-          InspectActiveSpectrumFile.class));
-        scroller.setDisplayActionId(getActionFactory().getId(
-          InspectActiveSpectrumFile.class));
-        // scroller.put(FormFactory.VCLASSNAME, itemClass.getName());
-        log.debug("scroller ScrollActionId = \"" + getActionFactory()
-          .getId(ScrollTo.class) + "\"");
-        log
-          .debug("scroller TableConfActionId = \"" + getActionFactory()
-            .getId(InspectActiveSpectrumFile.class) + "\"");
-        log.debug("scroller.getDisplayActionId() = \"" + scroller
-          .getDisplayActionId() + "\"");
-        // Add scroller to table
-        peakListTable.setScroller(scroller);
-      }
-      // Add scroller data
-      log.debug("getItemsFrom() = " + getItemsFrom());
-      log.debug("getMaxResults() = " + getMaxResults());
-      int scrollFrom = getItemsFrom();
-      int scrollMaxResults = getMaxResults();
-      TextField<Integer> scrollFromField = new TextField<Integer>(
-        Scroller.VFROM);
-      TextField<Integer> scrollMaxResultsField = new TextField<Integer>(
-        Scroller.VMAXRESULT);
-      scrollFromField.setValue(scrollFrom);
-      scrollMaxResultsField.setValue(scrollMaxResults);
-      peakListTable.add(scrollFromField);
-      peakListTable.add(scrollMaxResultsField);
-      //
-      // Add spectrum id field
-      TextField<String> spectrumIdField = new TextField<String>(
-        PlotFileSpectrum.VSPECTRUMID);
-      spectrumIdField.setHidden(true);
-      spectrumIdField.setValue(spectrumId);
-      peakListTable.add(spectrumIdField);
-      //
-      // Add mass cut-off low string field
-      TextField<String> massCutOffLowStrField = new TextField<String>(
-        PlotFileSpectrum.VMASSCUTOFFLOWSTR);
-      massCutOffLowStrField.setHidden(true);
-      massCutOffLowStrField.setValue(massCutoffLowStr);
-      peakListTable.add(massCutOffLowStrField);
-      //
-      // Add mass cut-off high string field
-      TextField<String> massCutOffHighStrField = new TextField<String>(
-        PlotFileSpectrum.VMASSCUTOFFHIGHSTR);
-      massCutOffHighStrField.setHidden(true);
-      massCutOffHighStrField.setValue(massCutoffHighStr);
-      peakListTable.add(massCutOffHighStrField);
-      //
-      // Add keep original spectrum flag field
-      TextField<Boolean> keepOriginalSpectrumField = new TextField<Boolean>(
-        VKEEPORIGINALSPECTRUM);
-      keepOriginalSpectrumField.setHidden(true);
-      keepOriginalSpectrumField.setValue(keepOriginalSpectrum);
-      peakListTable.add(keepOriginalSpectrumField);
-      //
-      // Create spectrum list to display
-      int itemStart = getItemsFrom();
-      int itemStop = getItemsFrom() + getMaxResults();
-      for (int i = itemStart; (i < spectrumIds.size() && i < itemStop); i++)
-      {
-        // log.debug("spectrumIds.get(" + i + ") = \"" +
-        // spectrumIds.get(i) + "\"");
-        // Add data
-        Row row = new Row(i);
-        row.addCell(new Cell<String>(spectrumIds.get(i)));
-        // Configure on-click row action to re-run this action with new
-        // spectrum id
-        ActionLink rowAction = getActionFactory().getActionLink(
-          InspectActiveSpectrumFile.class, "View");
-        rowAction.addParameter(VSPECTRUMFILEID, fileId);
-        rowAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
-          spectrumIds.get(i));
-        row.setActionLink(rowAction);
-        peakListTable.addRow(row);
-      }
-      // Show first spectrum as default
-      if (spectrumId == null || spectrumId.equals(""))
-      {
-        if (spectrumIds != null && spectrumIds.size() > 0)
-        {
-          // Plot first spectrum
-          spectrumId = spectrumIds.get(0);
-        }
-      }
-    }
-    /***********************************************************************
-     * Spectrum plot
-     */
-    PlotFileSpectrum plotFileSpectrum = new PlotFileSpectrum();
-    ImageMap imageMap;
-    Image plotOriginal = null;
-    if (keepOriginalSpectrum)
-    {
-      plotOriginal = new Image();
-      ActionLink viewOriginalAction = getActionFactory().getActionLink(
-        PlotFileSpectrum.class, "ViewOriginal");
-      viewOriginalAction.addParameter(FormFactory.VID, fileId);
-      viewOriginalAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
-        spectrumId);
-      plotOriginal.setViewAction(viewOriginalAction);
-      plotOriginal.setHeight(PlotFileSpectrum.HEIGHT);
-      plotOriginal.setWidth(PlotFileSpectrum.WIDTH);
-      // Add mass annotation image map
-      imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc,
-        fileId, spectrumId, (String) null, (String) null);
-      plotOriginal.setImageMap(imageMap);
-    }
-    Image plot = new Image();
-    ActionLink viewAction = getActionFactory().getActionLink(
-      PlotFileSpectrum.class, "View");
-    viewAction.addParameter(FormFactory.VID, fileId);
-    viewAction.addParameter(PlotFileSpectrum.VSPECTRUMID, spectrumId);
-    viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFLOWSTR,
-      massCutoffLowStr);
-    viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFHIGHSTR,
-      massCutoffHighStr);
-    plot.setViewAction(viewAction);
-    plot.setHeight(PlotFileSpectrum.HEIGHT);
-    plot.setWidth(PlotFileSpectrum.WIDTH);
-    // Add mass annotation image map
-    imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc, fileId,
-      spectrumId, massCutoffLowStr, massCutoffHighStr);
-    plot.setImageMap(imageMap);
-    /***********************************************************************
-     * Spectrum iteration buttons
-     */
-    Form spectrumIterationForm = new Form("spectrumIterationForm");
-    spectrumIterationForm.setTitle("spectrumIterationForm");
-    Fieldset spectrumIterationFS = new Fieldset();
-    spectrumIterationFS.setTitle("SpectrumIteration");
-    spectrumIterationForm.addFieldset(spectrumIterationFS);
-    Toolbar spectrumIterationToolbar = new Toolbar();
-    spectrumIterationForm.setToolbar(spectrumIterationToolbar);
-    //
-    // Add button for previous spectrum
-    String previousSpectrumId = fetchPreviousListItem(spectrumId,
-      spectrumIds);
-    log.debug("previousSpectrumId = \"" + previousSpectrumId + "\"");
-    ActionLink previousSpectrumAction = getActionLink(
-      InspectActiveSpectrumFile.class, "PreviousSpectrum");
-    previousSpectrumAction.addParameter(FormFactory.VID, fileId);
-    previousSpectrumAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
-      previousSpectrumId);
-    previousSpectrumAction.addParameter(VKEEPORIGINALSPECTRUM, true);
-    if (previousSpectrumId == null)
-    {
-      previousSpectrumAction.disable();
-    }
-    spectrumIterationToolbar.add(previousSpectrumAction);
-    //
-    // Add button for next spectrum
-    String nextSpectrumId = fetchNextListItem(spectrumId, spectrumIds);
-    log.debug("nextSpectrumId = \"" + nextSpectrumId + "\"");
-    ActionLink nextSpectrumAction = getActionLink(
-      InspectActiveSpectrumFile.class, "NextSpectrum");
-    nextSpectrumAction.addParameter(FormFactory.VID, fileId);
-    nextSpectrumAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
-      nextSpectrumId);
-    nextSpectrumAction.addParameter(VKEEPORIGINALSPECTRUM, true);
-    if (nextSpectrumId == null)
-    {
-      nextSpectrumAction.disable();
-    }
-    spectrumIterationToolbar.add(nextSpectrumAction);
-    /***********************************************************************
-     * Spectrum mass range selection form
-     */
-    Form massRangeSelectionForm = getFormFactory()
-      .getSpectrumMassRangeSelectionForm(massCutoffLowStr,
-        massCutoffHighStr, spectrumId);
-    Toolbar toolbar = new Toolbar();
-    massRangeSelectionForm.setToolbar(toolbar);
-    //
-    ActionLink zoomWithOriginalAction = getActionLink(
-      InspectActiveSpectrumFile.class, "ZoomedAndOriginalSpectrum");
-    zoomWithOriginalAction.addParameter(FormFactory.VID, fileId);
-    zoomWithOriginalAction.addParameter(VKEEPORIGINALSPECTRUM, true);
-    toolbar.add(zoomWithOriginalAction);
-    //
-    ActionLink zoomAction = getActionLink(InspectActiveSpectrumFile.class,
-      "ZoomedSpectrum");
-    zoomAction.addParameter(FormFactory.VID, fileId);
-    zoomAction.addParameter(VKEEPORIGINALSPECTRUM, false);
-    toolbar.add(zoomAction);
-    /***********************************************************************
-     * Spectrum properties
-     */
-    SpectrumInterface spectrum = null;
-    Form propertiesForm = null;
-    if (file != null)
-    {
-      // Get new list file reader
-      PeakListFileInterface peakListFileReader = spectrumFileReaderFactory
-        .fetchPeakListFileReader(file);
-      if (peakListFileReader != null && spectrumId != null)
-      {
-        spectrum = peakListFileReader.getSpectrum(spectrumId);
-      }
-      // Spectrum properties form
-      propertiesForm = getFormFactory().getSpectrumPropertiesForm(file,
-        spectrumId, spectrum);
-    }
-    /***********************************************************************
-     * Spectrum file instrument data
-     */
-    List<SpectrumFileInstrumentInterface> spectrumFileInstrumentList = null;
-    Form instrumentForm = null;
-    if (file != null)
-    {
-      // Get new spectrum file instrument reader
-      SpectrumFileInstrumentReaderInterface spectrumFileInstrumentReader = spectrumFileReaderFactory
-        .fetchSpectrumFileInstrumentReader(file);
-      if (spectrumFileInstrumentReader != null)
-      {
-        spectrumFileInstrumentList = spectrumFileInstrumentReader
-          .getSpectrumFileInstrumentList();
-      }
-      // Spectrum file instrument form
-      instrumentForm = getFormFactory().getSpectrumFileInstrumentForm(
-        spectrumFileInstrumentList);
-    }
-    /***********************************************************************
-     * Spectrum file contact data
-     */
-    SpectrumFileContactInterface spectrumContact = null;
-    Form contactForm = null;
-    if (file != null)
-    {
-      // Get new spectrum file contact reader
-      SpectrumFileContactReaderInterface spectrumFileContactReader = spectrumFileReaderFactory
-        .fetchSpectrumFileContactReader(file);
-      if (spectrumFileContactReader != null)
-      {
-        spectrumContact = spectrumFileContactReader
-          .getSpectrumContact();
-      }
-      // Spectrum file contacts form
-      contactForm = getFormFactory().getSpectrumFileContactForm(
-        spectrumContact);
-    }
-    /***********************************************************************
-     * Layout
-     */
-    // GridLayout layout = getLayoutFactory().getGridLayout(1, 2, 1, 1);
-    RowLayout layout = getLayoutFactory().getRowLayout();
-    // Adapt title to file type
-    String titleHeader = spectrumFileReaderFactory
-      .fetchFileTypeTitleString(file);
-    Title title = new Title(titleHeader);
-    title.setSubtitle("" + file.getName() + " [" + fileId + "]");
-    layout.add(title);
-    // Row container for plot and properties form
-    RowContainer rc = new RowContainer();
-    if (plotOriginal != null)
-    {
-      rc.add(plotOriginal);
-    }
-    rc.add(plot);
-    rc.add(spectrumIterationForm);
-    rc.add(massRangeSelectionForm);
-    rc.add(propertiesForm);
-    if (instrumentForm != null)
-    {
-      rc.add(instrumentForm);
-    }
-    if (contactForm != null)
-    {
-      rc.add(contactForm);
-    }
-    //
-    ColumnContainer cc = new ColumnContainer();
-    cc.add(peakListTable);
-    if (plot != null || propertiesForm != null)
-    {
-      cc.add(rc);
-    }
-    layout.add(cc);
-    //
-    setLayout(layout);
-    log.debug("End");
-  }
-
-
-  /**
-   * Fetch index for item from from string list.
-   * 
-   * @param currentItem String The current item.
-   * @param inList List<String> The string list to use.
-   * @return Integer The index for the item, or null if none.
-   */
-  public Integer fetchStringListItemIndex(String currentItem,
-      List<String> inList)
-  {
-    log.debug("currentItem = \"" + currentItem + "\"");
-    if (currentItem == null || inList == null)
-    {
-      return null;
-    }
-    log.debug("inList.size() = " + inList.size());
-    // Find current index
-    Integer currentIndex = null;
-    for (int i = 0; i < inList.size(); i++)
-    {
-      String item = (String) inList.get(i);
-      if (item != null)
-      {
-        if (item.equals(currentItem))
-        {
-          currentIndex = i;
-          break;
-        }
-      }
-    }
-    log.debug("currentIndex = " + currentIndex);
-    return currentIndex;
-  }
-
-
-  /**
-   * Fetch previous list item from string list.
-   * 
-   * @param currentItem String The current item.
-   * @param inList List<String> The string list to use.
-   * @return String The previous item, or null if none.
-   */
-  public String fetchPreviousListItem(String currentItem, List<String> inList)
-  {
-    log.debug("currentItem = \"" + currentItem + "\"");
-    if (currentItem == null || inList == null)
-    {
-      return null;
-    }
-    log.debug("inList.size() = " + inList.size());
-    // Find current index
-    int currentIndex = -1;
-    for (int i = 0; i < inList.size(); i++)
-    {
-      String item = (String) inList.get(i);
-      if (item != null)
-      {
-        if (item.equals(currentItem))
-        {
-          currentIndex = i;
-          break;
-        }
-      }
-    }
-    log.debug("currentIndex = " + currentIndex);
-    // Find previous item
-    String previousItem = null;
-    if (currentIndex > 0)
-    {
-      previousItem = (String) inList.get(currentIndex - 1);
-    }
-    log.debug("previousItem = \"" + previousItem + "\"");
-    return previousItem;
-  }
-
-
-  /**
-   * Fetch next list item from string list.
-   * 
-   * @param currentItem String The current item.
-   * @param inList List<String> The string list to use.
-   * @return String The next item, or null if none.
-   */
-  public String fetchNextListItem(String currentItem, List<String> inList)
-  {
-    log.debug("currentItem = \"" + currentItem + "\"");
-    if (currentItem == null || inList == null)
-    {
-      return null;
-    }
-    log.debug("inList.size() = " + inList.size());
-    // Find current index
-    int currentIndex = -1;
-    for (int i = 0; i < inList.size(); i++)
-    {
-      String item = (String) inList.get(i);
-      if (item != null)
-      {
-        if (item.equals(currentItem))
-        {
-          currentIndex = i;
-          break;
-        }
-      }
-    }
-    log.debug("currentIndex = " + currentIndex);
-    // Find next item
-    String nextItem = null;
-    if (currentIndex < (inList.size() - 1))
-    {
-      nextItem = (String) inList.get(currentIndex + 1);
-    }
-    log.debug("nextItem = \"" + nextItem + "\"");
-    return nextItem;
-  }
-
-
-  /**
-   * Restores table scroller settings (stored as valid parameters).
-   */
-  private void restoreScrollerState()
-      throws InvalidParameterValue
-  {
-    // Get scroller data from valid parameters set to table
-    Integer scrollFrom = getValidInteger(Scroller.VFROM);
-    Integer scrollMaxResults = getValidInteger(Scroller.VMAXRESULT);
-    // Update scroller settings
-    if (scrollFrom != null)
-    {
-      setItemsFrom(scrollFrom);
-      setPageSelectedFromScroller(true);
-    }
-    if (scrollMaxResults != null)
-    {
-      setMaxResults(scrollMaxResults);
-    }
-    log
-      .debug("scrollFrom = " + scrollFrom + " isPageSelectedFromScroller() = " + isPageSelectedFromScroller());
-    log.debug("scrollMaxResults = " + scrollMaxResults);
-  }
-}
+    public static final VInteger VSPECTRUMFILEID = new VInteger(
+    "spectrumFileId", 0, false);
+    public static final VBoolean VKEEPORIGINALSPECTRUM = new VBoolean(
+    "keepOriginalSpectrum", false);
+    public static final VBoolean VFIRSTMGFTITLESPECTRUM = new VBoolean(
+    "firstMGF", false);
+    private int maxResults = 20;
+    private int itemsFrom = 0;
+    private boolean pageSelectedFromScroller = false;
+                
+    /**
+        * Get the max number of results to show in list.
+        * 
+        * @return int The max number of results to show in list.
+    */
+    public int getMaxResults()
+    {
+        return this.maxResults;
+    }
+                
+    /**
+        * Set the max number of results to show in list.
+        * 
+        * @param maxResults int The value to set for the max number of results to
+        *        show in list.
+    */
+    public void setMaxResults(int maxResults)
+    {
+        this.maxResults = maxResults;
+    }
+                
+    /**
+        * Get the item number to start from in the list.
+        * 
+        * @return int The item number to start from in the list.
+    */
+    public int getItemsFrom()
+    {
+        return this.itemsFrom;
+    }
+                
+    /**
+        * Set the item number to start from in the list.
+        * 
+        * @param itemsFrom int The value to set for the item number to start from
+        *        in the list.
+    */
+    public void setItemsFrom(int itemsFrom)
+    {
+        this.itemsFrom = itemsFrom;
+    }
+                
+    /**
+        * Get flag indicating that page is selected from scroller.
+        * 
+        * @return boolean The flag indicating that page is selected from scroller.
+    */
+    public boolean isPageSelectedFromScroller()
+    {
+        return this.pageSelectedFromScroller;
+    }
+                
+    /**
+        * Set flag indicating that page is selected from scroller.
+        * 
+        * @param pageSelectedFromScroller boolean The value to set for flag
+        *        indicating that page is selected from scroller.
+    */
+    public void setPageSelectedFromScroller(boolean pageSelectedFromScroller)
+    {
+        this.pageSelectedFromScroller = pageSelectedFromScroller;
+    }
+                
+    @Override
+    protected void runMe()
+    throws ActionException, InvalidParameterValue
+    {
+        /*
+            * Get the id's of all selected files. VSPECTRUMFILEID is the valid
+            * identifier used when rendering the list of files, thus we use it to
+            * get the valid list of item id values.
+        */
+        List<Integer> files = getValidIntegerList(VSPECTRUMFILEID);
+        log.debug("(1) files = " + files);
+        // Check alternative input
+        if (files == null)
+        {
+            Integer fileIdFromSessionAttribute = getSessionAttribute(VSPECTRUMFILEID);
+            log
+            .debug("fileIdFromSessionAttribute = " + fileIdFromSessionAttribute);
+            if (fileIdFromSessionAttribute != null)
+            {
+                files = new ArrayList<Integer>(0);
+                files.add(fileIdFromSessionAttribute);
+            }
+        }
+        log.debug("(2) files = " + files);
+        /*
+            * Make sure at least one file has been selected
+        */
+        if (files == null || files.size() == 0)
+        {
+            setError("Please select a spectrum file to inspect");
+            return;
+        }
+        /*
+            * Inspect first file.
+        */
+        Integer fileId = files.get(0);
+        String spectrumId = getValidString(PlotFileSpectrum.VSPECTRUMID);
+        String massCutoffLowStr = getValidString(PlotFileSpectrum.VMASSCUTOFFLOWSTR);
+        String massCutoffHighStr = getValidString(PlotFileSpectrum.VMASSCUTOFFHIGHSTR);
+        Boolean keepOriginalSpectrum = getValidBoolean(VKEEPORIGINALSPECTRUM);
+        log.debug("(1) spectrumId = " + spectrumId);
+        // Check alternative input
+        if (spectrumId == null)
+        {
+            String spectrumIdFromSessionAttribute = getSessionAttribute(PlotFileSpectrum.VSPECTRUMID);
+            log
+            .debug("spectrumIdFromSessionAttribute = " + spectrumIdFromSessionAttribute);
+            if (spectrumIdFromSessionAttribute != null)
+            {
+                spectrumId = spectrumIdFromSessionAttribute;
+            }
+            // Reset value of spectrum Id from session attribute
+            setSessionAttribute(PlotFileSpectrum.VSPECTRUMID, null);
+        }
+        log.debug("(2) spectrumId = " + spectrumId);
+        log.debug("fileId = " + fileId);
+        log.debug("spectrumId = \"" + spectrumId + "\"");
+        log.debug("massCutoffLowStr = \"" + massCutoffLowStr + "\"");
+        log.debug("massCutoffHighStr = \"" + massCutoffHighStr + "\"");
+        log.debug("(1) keepOriginalSpectrum = " + keepOriginalSpectrum);
+        if (keepOriginalSpectrum == null)
+        {
+            keepOriginalSpectrum = true;
+        }
+        log.debug("(2) keepOriginalSpectrum = " + keepOriginalSpectrum);
+        // Only show one spectrum view if no mass range parameters
+        if ((massCutoffLowStr == null || massCutoffLowStr.equals("")) && (massCutoffHighStr == null || massCutoffHighStr
+        .equals("")))
+        {
+            keepOriginalSpectrum = false;
+        }
+        log.debug("(3) keepOriginalSpectrum = " + keepOriginalSpectrum);
+        DbControl dc = newDbControl();
+        ItemFactory factory = new ItemFactory(dc);
+        File file = factory.getById(File.class, fileId);
+        log.debug("file = " + file);
+        List<String> spectrumIds = null;
+        // Get spectrum id reader
+        SpectrumFileReaderFactory spectrumFileReaderFactory = new SpectrumFileReaderFactory();
+        SpectrumIdReaderInterface spectrumIdReader = spectrumFileReaderFactory
+        .fetchSpectrumIdReader(file);
+        if (spectrumIdReader != null)
+        {
+            spectrumIds = spectrumIdReader.getSpectrumIdList();
+        }
+        /***********************************************************************
+            * Peaklists
+        */
+        Table peakListTable = new Table("peaklists");
+        // Add tool-bar to table to make GUIConverter set
+        // form id for action in hidden field.
+        Toolbar peakListTableToolbar = new Toolbar();
+        peakListTable.setToolbar(peakListTableToolbar);
+        if (spectrumIdReader != null)
+        {
+            if (spectrumIdReader.isSpectrumIdObtainedFromSpectrumOrderNumber())
+            {
+                peakListTable.add(new Column("SpectrumIdOrderNumber3"));
+                /* Special fix to get to the right spectrum id if it is from an MGF title*/
+                    if (spectrumId != null && spectrumIdReader instanceof MgfFileReader)
+                    {
+                        if (!spectrumId.matches("^d+(\\s-\\s.*)?"))
+                        {
+                            spectrumId = spectrumId.trim();
+                            for (String s : spectrumIds)
+                            {
+                                String toMatch = s.substring(s.indexOf("-") + 2)
+                                .trim();
+                                if (spectrumId.equals(toMatch))
+                                {
+                                    log.debug("Found spectrum:"+s);
+                                    spectrumId = s;
+                                    setSessionAttribute(PlotFileSpectrum.VSPECTRUMID.getName(), spectrumId);
+                                    break;
+                                }
+                            }
+                        }
+                    }
+                }
+                else
+                {
+                    peakListTable.add(new Column("Spectrum id"));
+                }
+            }
+            if (spectrumIds != null)
+            {
+                log.debug("spectrumIds.size() = " + spectrumIds.size());
+                // Fetch scroller page selected
+                restoreScrollerState();
+                log
+                .debug("getItemsFrom() = " + getItemsFrom() + " isPageSelectedFromScroller() = " + isPageSelectedFromScroller());
+                if (!isPageSelectedFromScroller())
+                {
+                    // Adjust scroller page to include selected spectrum
+                    if (spectrumId != null && !spectrumId.equals(""))
+                    {
+                        // find start of scroller page including selected spectrum
+                        Integer currentIndex = fetchStringListItemIndex(spectrumId,
+                        spectrumIds);
+                        log.debug("currentIndex = " + currentIndex);
+                        if (currentIndex != null && currentIndex >= 0)
+                        {
+                            int pageNo = currentIndex / getMaxResults();
+                            int tempStart = pageNo * getMaxResults();
+                            log
+                            .debug("currentIndex = " + currentIndex + " pageNo = " + pageNo + " tempStart = " + tempStart);
+                            // Set start index for displayed list
+                            setItemsFrom(tempStart);
+                        }
+                    }
+                }
+                // Add scroller
+                int count = spectrumIds.size();
+                if (count > getMaxResults())
+                {
+                    Scroller scroller = new Scroller();
+                    scroller.setFrom(getItemsFrom());
+                    scroller.setMax(getMaxResults());
+                    scroller.setTotalCount(count);
+                    scroller.setScrollActionId(getActionFactory().getId(
+                    ScrollTo.class));
+                    scroller.setTableConfActionId(getActionFactory().getId(
+                    InspectActiveSpectrumFile.class));
+                    scroller.setDisplayActionId(getActionFactory().getId(
+                    InspectActiveSpectrumFile.class));
+                    // scroller.put(FormFactory.VCLASSNAME, itemClass.getName());
+                    log.debug("scroller ScrollActionId = \"" + getActionFactory()
+                    .getId(ScrollTo.class) + "\"");
+                    log
+                    .debug("scroller TableConfActionId = \"" + getActionFactory()
+                    .getId(InspectActiveSpectrumFile.class) + "\"");
+                    log.debug("scroller.getDisplayActionId() = \"" + scroller
+                    .getDisplayActionId() + "\"");
+                    // Add scroller to table
+                    peakListTable.setScroller(scroller);
+                }
+                // Add scroller data
+                log.debug("getItemsFrom() = " + getItemsFrom());
+                log.debug("getMaxResults() = " + getMaxResults());
+                int scrollFrom = getItemsFrom();
+                int scrollMaxResults = getMaxResults();
+                TextField<Integer> scrollFromField = new TextField<Integer>(
+                Scroller.VFROM);
+                TextField<Integer> scrollMaxResultsField = new TextField<Integer>(
+                Scroller.VMAXRESULT);
+                scrollFromField.setValue(scrollFrom);
+                scrollMaxResultsField.setValue(scrollMaxResults);
+                peakListTable.add(scrollFromField);
+                peakListTable.add(scrollMaxResultsField);
+                //
+                // Add spectrum id field
+                TextField<String> spectrumIdField = new TextField<String>(
+                PlotFileSpectrum.VSPECTRUMID);
+                spectrumIdField.setHidden(true);
+                spectrumIdField.setValue(spectrumId);
+                peakListTable.add(spectrumIdField);
+                //
+                // Add mass cut-off low string field
+                TextField<String> massCutOffLowStrField = new TextField<String>(
+                PlotFileSpectrum.VMASSCUTOFFLOWSTR);
+                massCutOffLowStrField.setHidden(true);
+                massCutOffLowStrField.setValue(massCutoffLowStr);
+                peakListTable.add(massCutOffLowStrField);
+                //
+                // Add mass cut-off high string field
+                TextField<String> massCutOffHighStrField = new TextField<String>(
+                PlotFileSpectrum.VMASSCUTOFFHIGHSTR);
+                massCutOffHighStrField.setHidden(true);
+                massCutOffHighStrField.setValue(massCutoffHighStr);
+                peakListTable.add(massCutOffHighStrField);
+                //
+                // Add keep original spectrum flag field
+                TextField<Boolean> keepOriginalSpectrumField = new TextField<Boolean>(
+                VKEEPORIGINALSPECTRUM);
+                keepOriginalSpectrumField.setHidden(true);
+                keepOriginalSpectrumField.setValue(keepOriginalSpectrum);
+                peakListTable.add(keepOriginalSpectrumField);
+                //
+                // Create spectrum list to display
+                int itemStart = getItemsFrom();
+                int itemStop = getItemsFrom() + getMaxResults();
+                for (int i = itemStart; (i < spectrumIds.size() && i < itemStop); i++)
+                {
+                    // log.debug("spectrumIds.get(" + i + ") = \"" +
+                    // spectrumIds.get(i) + "\"");
+                    // Add data
+                    Row row = new Row(i);
+                    row.addCell(new Cell<String>(spectrumIds.get(i)));
+                    // Configure on-click row action to re-run this action with new
+                    // spectrum id
+                    ActionLink rowAction = getActionFactory().getActionLink(
+                    InspectActiveSpectrumFile.class, "View");
+                    rowAction.addParameter(VSPECTRUMFILEID, fileId);
+                    rowAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
+                    spectrumIds.get(i));
+                    row.setActionLink(rowAction);
+                    peakListTable.addRow(row);
+                }
+                // Show first spectrum as default
+                if (spectrumId == null || spectrumId.equals(""))
+                {
+                    if (spectrumIds != null && spectrumIds.size() > 0)
+                    {
+                        // Plot first spectrum
+                        spectrumId = spectrumIds.get(0);
+                    }
+                }
+            }
+            /***********************************************************************
+                * Spectrum plot
+            */
+            PlotFileSpectrum plotFileSpectrum = new PlotFileSpectrum();
+            ImageMap imageMap;
+            Image plotOriginal = null;
+            if (keepOriginalSpectrum)
+            {
+                plotOriginal = new Image();
+                ActionLink viewOriginalAction = getActionFactory().getActionLink(
+                PlotFileSpectrum.class, "ViewOriginal");
+                viewOriginalAction.addParameter(FormFactory.VID, fileId);
+                viewOriginalAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
+                spectrumId);
+                plotOriginal.setViewAction(viewOriginalAction);
+                plotOriginal.setHeight(PlotFileSpectrum.HEIGHT);
+                plotOriginal.setWidth(PlotFileSpectrum.WIDTH);
+                // Add mass annotation image map
+                imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc,
+                fileId, spectrumId, (String) null, (String) null);
+                plotOriginal.setImageMap(imageMap);
+            }
+            Image plot = new Image();
+            ActionLink viewAction = getActionFactory().getActionLink(
+            PlotFileSpectrum.class, "View");
+            viewAction.addParameter(FormFactory.VID, fileId);
+            viewAction.addParameter(PlotFileSpectrum.VSPECTRUMID, spectrumId);
+            viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFLOWSTR,
+            massCutoffLowStr);
+            viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFHIGHSTR,
+            massCutoffHighStr);
+            plot.setViewAction(viewAction);
+            plot.setHeight(PlotFileSpectrum.HEIGHT);
+            plot.setWidth(PlotFileSpectrum.WIDTH);
+            // Add mass annotation image map
+            imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc, fileId,
+            spectrumId, massCutoffLowStr, massCutoffHighStr);
+            plot.setImageMap(imageMap);
+            /***********************************************************************
+                * Spectrum iteration buttons
+            */
+            Form spectrumIterationForm = new Form("spectrumIterationForm");
+            spectrumIterationForm.setTitle("spectrumIterationForm");
+            Fieldset spectrumIterationFS = new Fieldset();
+            spectrumIterationFS.setTitle("SpectrumIteration");
+            spectrumIterationForm.addFieldset(spectrumIterationFS);
+            Toolbar spectrumIterationToolbar = new Toolbar();
+            spectrumIterationForm.setToolbar(spectrumIterationToolbar);
+            //
+            // Add button for previous spectrum
+            String previousSpectrumId = fetchPreviousListItem(spectrumId,
+            spectrumIds);
+            log.debug("previousSpectrumId = \"" + previousSpectrumId + "\"");
+            ActionLink previousSpectrumAction = getActionLink(
+            InspectActiveSpectrumFile.class, "PreviousSpectrum");
+            previousSpectrumAction.addParameter(FormFactory.VID, fileId);
+            previousSpectrumAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
+            previousSpectrumId);
+            previousSpectrumAction.addParameter(VKEEPORIGINALSPECTRUM, true);
+            if (previousSpectrumId == null)
+            {
+                previousSpectrumAction.disable();
+            }
+            spectrumIterationToolbar.add(previousSpectrumAction);
+            //
+            // Add button for next spectrum
+            String nextSpectrumId = fetchNextListItem(spectrumId, spectrumIds);
+            log.debug("nextSpectrumId = \"" + nextSpectrumId + "\"");
+            ActionLink nextSpectrumAction = getActionLink(
+            InspectActiveSpectrumFile.class, "NextSpectrum");
+            nextSpectrumAction.addParameter(FormFactory.VID, fileId);
+            nextSpectrumAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
+            nextSpectrumId);
+            nextSpectrumAction.addParameter(VKEEPORIGINALSPECTRUM, true);
+            if (nextSpectrumId == null)
+            {
+                nextSpectrumAction.disable();
+            }
+            spectrumIterationToolbar.add(nextSpectrumAction);
+            /***********************************************************************
+                * Spectrum mass range selection form
+            */
+            Form massRangeSelectionForm = getFormFactory().getSpectrumMassRangeSelectionForm(massCutoffLowStr,
+            massCutoffHighStr, spectrumId);
+            Toolbar toolbar = new Toolbar();
+            massRangeSelectionForm.setToolbar(toolbar);
+            //
+            ActionLink zoomWithOriginalAction = getActionLink(
+            InspectActiveSpectrumFile.class, "ZoomedAndOriginalSpectrum");
+            zoomWithOriginalAction.addParameter(FormFactory.VID, fileId);
+            zoomWithOriginalAction.addParameter(VKEEPORIGINALSPECTRUM, true);
+            toolbar.add(zoomWithOriginalAction);
+            //
+            ActionLink zoomAction = getActionLink(InspectActiveSpectrumFile.class,
+            "ZoomedSpectrum");
+            zoomAction.addParameter(FormFactory.VID, fileId);
+            zoomAction.addParameter(VKEEPORIGINALSPECTRUM, false);
+            toolbar.add(zoomAction);
+            /***********************************************************************
+                * Spectrum properties
+            */
+            SpectrumInterface spectrum = null;
+            Form propertiesForm = null;
+            if (file != null)
+            {
+                // Get new list file reader
+                PeakListFileInterface peakListFileReader = spectrumFileReaderFactory
+                .fetchPeakListFileReader(file);
+                if (peakListFileReader != null && spectrumId != null)
+                {
+                    spectrum = peakListFileReader.getSpectrum(spectrumId);
+                }
+                // Spectrum properties form
+                propertiesForm = getFormFactory().getSpectrumPropertiesForm(file,
+                spectrumId, spectrum);
+            }
+            /***********************************************************************
+                * Spectrum file instrument data
+            */
+            List<SpectrumFileInstrumentInterface> spectrumFileInstrumentList = null;
+            Form instrumentForm = null;
+            if (file != null)
+            {
+                // Get new spectrum file instrument reader
+                SpectrumFileInstrumentReaderInterface spectrumFileInstrumentReader = spectrumFileReaderFactory
+                .fetchSpectrumFileInstrumentReader(file);
+                if (spectrumFileInstrumentReader != null)
+                {
+                    spectrumFileInstrumentList = spectrumFileInstrumentReader
+                    .getSpectrumFileInstrumentList();
+                }
+                // Spectrum file instrument form
+                instrumentForm = getSpectrumFileInstrumentForm(spectrumFileInstrumentList);
+            }
+            /***********************************************************************
+                * Spectrum file contact data
+            */
+            SpectrumFileContactInterface spectrumContact = null;
+            Form contactForm = null;
+            if (file != null)
+            {
+                // Get new spectrum file contact reader
+                SpectrumFileContactReaderInterface spectrumFileContactReader = spectrumFileReaderFactory
+                .fetchSpectrumFileContactReader(file);
+                if (spectrumFileContactReader != null)
+                {
+                    spectrumContact = spectrumFileContactReader
+                    .getSpectrumContact();
+                }
+                // Spectrum file contacts form
+                contactForm = getFormFactory().getSpectrumFileContactForm(
+                spectrumContact);
+            }
+            /***********************************************************************
+                * Layout
+            */
+            // GridLayout layout = getLayoutFactory().getGridLayout(1, 2, 1, 1);
+            RowLayout layout = getLayoutFactory().getRowLayout();
+            // Adapt title to file type
+            String titleHeader = spectrumFileReaderFactory
+            .fetchFileTypeTitleString(file);
+            Title title = new Title(titleHeader);
+            title.setSubtitle("" + file.getName() + " [" + fileId + "]");
+            layout.add(title);
+            // Row container for plot and properties form
+            RowContainer rc = new RowContainer();
+            if (plotOriginal != null)
+            {
+                rc.add(plotOriginal);
+            }
+            rc.add(plot);
+            rc.add(spectrumIterationForm);
+            rc.add(massRangeSelectionForm);
+            rc.add(propertiesForm);
+            if (instrumentForm != null)
+            {
+                rc.add(instrumentForm);
+            }
+            if (contactForm != null)
+            {
+                rc.add(contactForm);
+            }
+            //
+            ColumnContainer cc = new ColumnContainer();
+            cc.add(peakListTable);
+            if (plot != null || propertiesForm != null)
+            {
+                cc.add(rc);
+            }
+            layout.add(cc);
+            //
+            setLayout(layout);
+            log.debug("End");
+        }
+                                
+        /**
+            * Fetch index for item from from string list.
+            * 
+            * @param currentItem String The current item.
+            * @param inList List<String> The string list to use.
+            * @return Integer The index for the item, or null if none.
+        */
+        public Integer fetchStringListItemIndex(String currentItem,
+        List<String> inList)
+        {
+            log.debug("currentItem = \"" + currentItem + "\"");
+            if (currentItem == null || inList == null)
+            {
+                return null;
+            }
+            log.debug("inList.size() = " + inList.size());
+            // Find current index
+            Integer currentIndex = null;
+            for (int i = 0; i < inList.size(); i++)
+            {
+                String item = (String) inList.get(i);
+                if (item != null)
+                {
+                    if (item.equals(currentItem))
+                    {
+                        currentIndex = i;
+                        break;
+                    }
+                }
+            }
+            log.debug("currentIndex = " + currentIndex);
+            return currentIndex;
+        }
+                                
+        /**
+            * Fetch previous list item from string list.
+            * 
+            * @param currentItem String The current item.
+            * @param inList List<String> The string list to use.
+            * @return String The previous item, or null if none.
+        */
+        public String fetchPreviousListItem(String currentItem, List<String> inList)
+        {
+            log.debug("currentItem = \"" + currentItem + "\"");
+            if (currentItem == null || inList == null)
+            {
+                return null;
+            }
+            log.debug("inList.size() = " + inList.size());
+            // Find current index
+            int currentIndex = -1;
+            for (int i = 0; i < inList.size(); i++)
+            {
+                String item = (String) inList.get(i);
+                if (item != null)
+                {
+                    if (item.equals(currentItem))
+                    {
+                        currentIndex = i;
+                        break;
+                    }
+                }
+            }
+            log.debug("currentIndex = " + currentIndex);
+            // Find previous item
+            String previousItem = null;
+            if (currentIndex > 0)
+            {
+                previousItem = (String) inList.get(currentIndex - 1);
+            }
+            log.debug("previousItem = \"" + previousItem + "\"");
+            return previousItem;
+        }
+                                
+        /**
+            * Fetch next list item from string list.
+            * 
+            * @param currentItem String The current item.
+            * @param inList List<String> The string list to use.
+            * @return String The next item, or null if none.
+        */
+        public String fetchNextListItem(String currentItem, List<String> inList)
+        {
+            log.debug("currentItem = \"" + currentItem + "\"");
+            if (currentItem == null || inList == null)
+            {
+                return null;
+            }
+            log.debug("inList.size() = " + inList.size());
+            // Find current index
+            int currentIndex = -1;
+            for (int i = 0; i < inList.size(); i++)
+            {
+                String item = (String) inList.get(i);
+                if (item != null)
+                {
+                    if (item.equals(currentItem))
+                    {
+                        currentIndex = i;
+                        break;
+                    }
+                }
+            }
+            log.debug("currentIndex = " + currentIndex);
+            // Find next item
+            String nextItem = null;
+            if (currentIndex < (inList.size() - 1))
+            {
+                nextItem = (String) inList.get(currentIndex + 1);
+            }
+            log.debug("nextItem = \"" + nextItem + "\"");
+            return nextItem;
+        }
+                                
+        /**
+            * Restores table scroller settings (stored as valid parameters).
+        */
+        private void restoreScrollerState()
+        throws InvalidParameterValue
+        {
+            // Get scroller data from valid parameters set to table
+            Integer scrollFrom = getValidInteger(Scroller.VFROM);
+            Integer scrollMaxResults = getValidInteger(Scroller.VMAXRESULT);
+            // Update scroller settings
+            if (scrollFrom != null)
+            {
+                setItemsFrom(scrollFrom);
+                setPageSelectedFromScroller(true);
+            }
+            if (scrollMaxResults != null)
+            {
+                setMaxResults(scrollMaxResults);
+            }
+            log
+            .debug("scrollFrom = " + scrollFrom + " isPageSelectedFromScroller() = " + isPageSelectedFromScroller());
+            log.debug("scrollMaxResults = " + scrollMaxResults);
+        }
+                                
+        /**
+            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(
+        List<SpectrumFileInstrumentInterface> spectrumFileInstrumentList)
+        {
+            if (spectrumFileInstrumentList == null || spectrumFileInstrumentList
+            .size() == 0)
+            {
+                return null;
+            }
+            /***********************************************************************
+                Instrument fieldset
+            */
+            Fieldset instrumentFS = new Fieldset();
+            int instrumentNo = 0;
+            for (SpectrumFileInstrumentInterface spectrumFileInstrument : spectrumFileInstrumentList)
+            {
+                instrumentNo++;
+                List<StringPairInterface> dataList;
+                /*
+                    Name field.
+                */
+                Table instrumentGeneralTable = new Table(
+                "InstrumentGeneralInformation");
+                // Only print table header for first table
+                if (instrumentNo == 1)
+                {
+                    instrumentGeneralTable.setTitle("InstrumentInformation");
+                }
+                // instrumentGeneralTable.add(new Column<String>("Property"));
+                instrumentGeneralTable.add(new Column<String>("InstrumentGeneral"));
+                instrumentGeneralTable.add(new Column<String>("Value"));
+                String instrumentName = null;
+                if (spectrumFileInstrument != null)
+                {
+                    instrumentName = spectrumFileInstrument.getInstrumentName();
+                }
+                instrumentGeneralTable.addRow(new PropertyRow(0, "InstrumentName", instrumentName, null));
+                /*
+                    Serial No field.
+                */
+                String instrumentSerialNo = null;
+                if (spectrumFileInstrument != null)
+                {
+                    instrumentSerialNo = spectrumFileInstrument
+                    .getInstrumentSerialNo();
+                }
+                instrumentGeneralTable.addRow(new PropertyRow(0, "InstrumentSerialNo", instrumentSerialNo, null));
+                instrumentFS.add(instrumentGeneralTable);
+                /*
+                    Source field.
+                */
+                Table sourceTable = new Table("SourceInformation");
+                // sourceTable.setTitle("SourceInformation");
+                // sourceTable.add(new Column<String>("Property"));
+                sourceTable.add(new Column<String>("SourceInformation"));
+                sourceTable.add(new Column<String>("Value"));
+                dataList = spectrumFileInstrument.getSource();
+                if (dataList != null)
+                {
+                    for (int i = 0; i < dataList.size(); i++)
+                    {
+                        StringPairInterface data = dataList.get(i);
+                        if (data != null)
+                        {
+                            String name = data.getName();
+                            String value = data.getValue();
+                            if (name != null && !name.equals(""))
+                            {
+                                sourceTable.addRow(new PropertyRow(0, name, value, null));
+                            }
+                        }
+                    }
+                }
+                instrumentFS.add(sourceTable);
+                /*
+                    AnalyzerList field.
+                */
+                List<SpectrumFileAnalyzerInterface> analyzerList = spectrumFileInstrument
+                .getAnalyzers();
+                if (analyzerList != null)
+                {
+                    for (int j = 0; j < analyzerList.size(); j++)
+                    {
+                        Table analyzerTable = new Table("AnalyzerListInformation");
+                        /*
+                            // Only add table title header for first table if (j ==
+                            0) { analyzerTable.setTitle("AnalyzerListInformation"); }
+                        */
+                        // analyzerTable.add(new Column<String>("Property"));
+                        analyzerTable
+                        .add(new Column<String>("AnalyzerInformation"));
+                        analyzerTable.add(new Column<String>("Value"));
+                        SpectrumFileAnalyzerInterface analyzer = analyzerList
+                        .get(j);
+                        if (analyzer != null)
+                        {
+                            dataList = analyzer.getAnalyzer();
+                            if (dataList != null)
+                            {
+                                for (int i = 0; i < dataList.size(); i++)
+                                {
+                                    StringPairInterface data = dataList.get(i);
+                                    if (data != null)
+                                    {
+                                        String name = data.getName();
+                                        String value = data.getValue();
+                                        if (name != null && !name.equals(""))
+                                        {
+                                            analyzerTable.addRow(new PropertyRow(0, name, value, null));
+                                        }
+                                    }
+                                }
+                            }
+                        }
+                        instrumentFS.add(analyzerTable);
+                    }
+                }
+                /*
+                    Detector field.
+                */
+                Table detectorTable = new Table("DetectorInformation");
+                // detectorTable.setTitle("DetectorInformation");
+                // detectorTable.add(new Column<String>("Property"));
+                detectorTable.add(new Column<String>("DetectorInformation"));
+                detectorTable.add(new Column<String>("Value"));
+                dataList = spectrumFileInstrument.getDetector();
+                if (dataList != null)
+                {
+                    for (int i = 0; i < dataList.size(); i++)
+                    {
+                        StringPairInterface data = dataList.get(i);
+                        if (data != null)
+                        {
+                            String name = data.getName();
+                            String value = data.getValue();
+                            if (name != null && !name.equals(""))
+                            {
+                                detectorTable.addRow(new PropertyRow(0, name, value, null));
+                            }
+                        }
+                    }
+                }
+                instrumentFS.add(detectorTable);
+                /*
+                    Additional field.
+                */
+                Table additionalTable = new Table("AdditionalInformation");
+                additionalTable.add(new Column<String>("AdditionalInformation"));
+                additionalTable.add(new Column<String>("Value"));
+                dataList = spectrumFileInstrument.getAdditional();
+                if (dataList != null)
+                {
+                    for (int i = 0; i < dataList.size(); i++)
+                    {
+                        StringPairInterface data = dataList.get(i);
+                        if (data != null)
+                        {
+                            String name = data.getName();
+                            String value = data.getValue();
+                            if (name != null && !name.equals(""))
+                            {
+                                additionalTable.addRow(new PropertyRow(0, name, value, null));
+                            }
+                        }
+                    }
+                }
+                instrumentFS.add(additionalTable);
+            }
+            /***********************************************************************
+                Form
+            */
+            Form form = new Form("InstrumentInformation");
+            form.addFieldset(instrumentFS);
+            return form;
+        }
+    }

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

@@ -1 +1 @@
 /*
     $Id$
-                        
+                                        
     Copyright (C) 2006, 2007 Fredrik Levander, Gregory Vincic, Olle Mansson
-                        
+                                        
     Files are copyright by their respective authors. The contributions to
     files where copyright is not explicitly stated can be traced with the
     source code revision system.
-                        
+                                        
     This file is part of Proteios.
     Available at http://www.proteios.org/
-                        
+                                        
     proteios-2.x 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
@@ -68 +68 @@
     private HttpServletRequest request = null;
     private SessionControl sc = null;
-        
+                        
     private Localizer locale = null;
     private String forwardActionId = null;
@@ -160 +160 @@
     private static final org.apache.log4j.Logger log = org.apache.log4j.LogManager
     .getLogger("org.proteios.gui.form");
-                        
+                                        
     public void setActionFactory(ActionFactory af)
     {
         this.actionFactory = af;
     }
-                        
+                                        
     public String getForwardActionId()
     {
         return this.forwardActionId;
     }
-                        
+                                        
     public void setForwardActionId(String forwardActionId)
     {
         this.forwardActionId = forwardActionId;
     }
-                        
+                                        
     public HttpServletRequest getRequest()
     {
         return request;
     }
-                        
+                                        
     public void setRequest(HttpServletRequest request)
     {
         this.request = request;
     }
-                        
+                                        
     public void modifyForPopup(Fieldset fs)
     {
         actionFactory.modifyForPopup(fs);
     }
-                        
+                                        
     private FileField newFileField()
     {
@@ -197 +197 @@
         return fileF;
     }
-                        
+                                        
     public TextField<Integer> newIdField()
     {
@@ -205 +205 @@
         return idF;
     }
-                        
+                                        
     public TextField<String> newValueField(String setValueMethodName,
     Class<?> valueClass)
@@ -237 +237 @@
         return valueF;
     }
-                        
+                                        
     public TextField<Integer> newHiddenItemIdField()
     {
@@ -243 +243 @@
         return field;
     }
-                        
+                                        
     private TextField<Integer> newHiddenIntegerField(VInteger vInteger)
     {
@@ -250 +250 @@
         return field;
     }
-                        
+                                        
     private TextField<String> newHiddenStringField(VString vString)
     {
@@ -257 +257 @@
         return field;
     }
-                        
+                                        
     public <D extends BasicItem<?>, E extends ProteiosAction<?>> Form getAnnotationsForm(
     DbControl dc, D item, Class<E> forwardAction)
@@ -307 +307 @@
         return form;
     }
-                        
+                                        
     /**
         @return Hidden
@@ -317 +317 @@
         return field;
     }
-                        
+                                        
     /**
         Form for user preferences configuration settings. Arguments
@@ -323 +323 @@
         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.
@@ -341 +341 @@
         return form;
     }
-                        
+                                        
     /**
         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.
@@ -398 +398 @@
         return properties;
     }
-                        
+                                        
     /**
         Creates a select box for notification mode.
-                                                
+                                                                                
         @param modeValue int Mode value for default selection.
         @return Select<VInteger> Select box for notification mode selection
@@ -426 +426 @@
         return modeS;
     }
-                        
+                                        
     /**
         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.
@@ -461 +461 @@
         return properties;
     }
-                        
+                                        
     /**
         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
@@ -489 +489 @@
         return modeS;
     }
-                        
+                                        
     /**
         @param a annotation
@@ -502 +502 @@
         return sb.toString();
     }
-        
+                        
     /**
         This will probably be removed when fixint #691
@@ -601 +601 @@
         return form;
     }
-                        
+                                        
     /**
         @param hit Current Hit
@@ -817 +817 @@
         return form;
     }
-                        
+                                        
     /**
         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.
@@ -866 +866 @@
         return form;
     }
-                        
+                                        
     /**
         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.
@@ -1079 +1079 @@
         return form;
     }
-                        
-    /**
-        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(
-    List<SpectrumFileInstrumentInterface> spectrumFileInstrumentList)
-    {
-        if (spectrumFileInstrumentList == null || spectrumFileInstrumentList
-        .size() == 0)
-        {
-            return null;
-        }
-        /***********************************************************************
-            Instrument fieldset
-        */
-        Fieldset instrumentFS = new Fieldset();
-        int instrumentNo = 0;
-        for (SpectrumFileInstrumentInterface spectrumFileInstrument : spectrumFileInstrumentList)
-        {
-            instrumentNo++;
-            List<StringPairInterface> dataList;
-            /*
-                Name field.
-            */
-            Table instrumentGeneralTable = new Table(
-            "InstrumentGeneralInformation");
-            // Only print table header for first table
-            if (instrumentNo == 1)
-            {
-                instrumentGeneralTable.setTitle("InstrumentInformation");
-            }
-            // instrumentGeneralTable.add(new Column<String>("Property"));
-            instrumentGeneralTable.add(new Column<String>("InstrumentGeneral"));
-            instrumentGeneralTable.add(new Column<String>("Value"));
-            String instrumentName = null;
-            if (spectrumFileInstrument != null)
-            {
-                instrumentName = spectrumFileInstrument.getInstrumentName();
-            }
-            addTableRow(instrumentGeneralTable, "InstrumentName",
-            instrumentName, null, 0);
-            // instrumentFS.add(instrumentGeneralTable);
-            /*
-                Serial No field.
-            */
-            String instrumentSerialNo = null;
-            if (spectrumFileInstrument != null)
-            {
-                instrumentSerialNo = spectrumFileInstrument
-                .getInstrumentSerialNo();
-            }
-            addTableRow(instrumentGeneralTable, "InstrumentSerialNo",
-            instrumentSerialNo, null, 0);
-            instrumentFS.add(instrumentGeneralTable);
-            /*
-                Source field.
-            */
-            Table sourceTable = new Table("SourceInformation");
-            // sourceTable.setTitle("SourceInformation");
-            // sourceTable.add(new Column<String>("Property"));
-            sourceTable.add(new Column<String>("SourceInformation"));
-            sourceTable.add(new Column<String>("Value"));
-            dataList = spectrumFileInstrument.getSource();
-            if (dataList != null)
-            {
-                for (int i = 0; i < dataList.size(); i++)
-                {
-                    StringPairInterface data = dataList.get(i);
-                    if (data != null)
-                    {
-                        String name = data.getName();
-                        String value = data.getValue();
-                        if (name != null && !name.equals(""))
-                        {
-                            addTableRow(sourceTable, name, value, null, 0);
-                        }
-                    }
-                }
-            }
-            instrumentFS.add(sourceTable);
-            /*
-                AnalyzerList field.
-            */
-            List<SpectrumFileAnalyzerInterface> analyzerList = spectrumFileInstrument
-            .getAnalyzers();
-            if (analyzerList != null)
-            {
-                for (int j = 0; j < analyzerList.size(); j++)
-                {
-                    Table analyzerTable = new Table("AnalyzerListInformation");
-                    /*
-                        // Only add table title header for first table if (j ==
-                        0) { analyzerTable.setTitle("AnalyzerListInformation"); }
-                    */
-                    // analyzerTable.add(new Column<String>("Property"));
-                    analyzerTable
-                    .add(new Column<String>("AnalyzerInformation"));
-                    analyzerTable.add(new Column<String>("Value"));
-                    SpectrumFileAnalyzerInterface analyzer = analyzerList
-                    .get(j);
-                    if (analyzer != null)
-                    {
-                        dataList = analyzer.getAnalyzer();
-                        if (dataList != null)
-                        {
-                            for (int i = 0; i < dataList.size(); i++)
-                            {
-                                StringPairInterface data = dataList.get(i);
-                                if (data != null)
-                                {
-                                    String name = data.getName();
-                                    String value = data.getValue();
-                                    if (name != null && !name.equals(""))
-                                    {
-                                        addTableRow(analyzerTable, name, value,
-                                        null, 0);
-                                    }
-                                }
-                            }
-                        }
-                    }
-                    instrumentFS.add(analyzerTable);
-                }
-            }
-            /*
-                Detector field.
-            */
-            Table detectorTable = new Table("DetectorInformation");
-            // detectorTable.setTitle("DetectorInformation");
-            // detectorTable.add(new Column<String>("Property"));
-            detectorTable.add(new Column<String>("DetectorInformation"));
-            detectorTable.add(new Column<String>("Value"));
-            dataList = spectrumFileInstrument.getDetector();
-            if (dataList != null)
-            {
-                for (int i = 0; i < dataList.size(); i++)
-                {
-                    StringPairInterface data = dataList.get(i);
-                    if (data != null)
-                    {
-                        String name = data.getName();
-                        String value = data.getValue();
-                        if (name != null && !name.equals(""))
-                        {
-                            addTableRow(detectorTable, name, value, null, 0);
-                        }
-                    }
-                }
-            }
-            instrumentFS.add(detectorTable);
-            /*
-                Additional field.
-            */
-            Table additionalTable = new Table("AdditionalInformation");
-            // additionalTable.setTitle("AdditionalInformation");
-            // additionalTable.add(new Column<String>("Property"));
-            additionalTable.add(new Column<String>("AdditionalInformation"));
-            additionalTable.add(new Column<String>("Value"));
-            dataList = spectrumFileInstrument.getAdditional();
-            if (dataList != null)
-            {
-                for (int i = 0; i < dataList.size(); i++)
-                {
-                    StringPairInterface data = dataList.get(i);
-                    if (data != null)
-                    {
-                        String name = data.getName();
-                        String value = data.getValue();
-                        if (name != null && !name.equals(""))
-                        {
-                            addTableRow(additionalTable, name, value, null, 0);
-                        }
-                    }
-                }
-            }
-            instrumentFS.add(additionalTable);
-        }
-        /***********************************************************************
-            Form
-        */
-        Form form = new Form("InstrumentInformation");
-        form.addFieldset(instrumentFS);
-        return form;
-    }
-                        
+                                        
     /**
         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.
@@ -1308 +1120 @@
         table.addRow(row);
     }
-                        
+                                        
     /**
         Returns a form with spectrum file contact data for a spectrum file.
-                                                
+                                                                                
         @param spectrumContact Spectrum file contact
         data.
@@ -1394 +1206 @@
         return form;
     }
-                            
+                                            
     /**
         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.
@@ -1487 +1299 @@
         return form;
     }
-                        
+                                        
     private <D extends Object> TextField<D> newTextField(String name, D value)
     {
@@ -1496 +1308 @@
         return field;
     }
-                        
+                                        
     public Form getPeakListSetForm(PeakListSet pls)
     {
@@ -1564 +1376 @@
         return form;
     }
-                        
-                        
+                                        
     private void addAnnotationsAsFields(Fieldset to, Annotatable item,
     DbControl dc)
@@ -1580 +1391 @@
         }
     }
-                        
+                                        
     public Fieldset getProteinAssemblyFieldset(Project project)
     {
@@ -1603 +1414 @@
         return properties;
     }
-                        
+                                        
     public Select<VString> selectLocalSampleIdWithAllOption(DbControl dc,
     Project project)
@@ -1617 +1428 @@
         return select;
     }
-                        
+                                        
     private Select<VInteger> newSelectLabel(LabeledExtract le, DbControl dc)
     {
@@ -1638 +1449 @@
         return select;
     }
-                        
+                                        
     /**
         Creates and adds a hidden field with an Integer value to the given form.
@@ -1650 +1461 @@
         form.getFieldsets().get(0).add(field);
     }
-                        
+                                        
     /**
         Creates and adds a hidden field with an Integer value to the given table.
@@ -1662 +1473 @@
         table.add(field);
     }
-                        
+                                        
     public Fieldset getUsedSampleFieldset(Sample sample)
     {
@@ -1680 +1491 @@
         return fs;
     }
-                        
+                                        
     public Fieldset getUsedExtractFieldset(Extract extract)
     {
@@ -1695 +1506 @@
         return fs;
     }
-                        
+                                        
     public Fieldset getUsedLabeledExtractFieldset(LabeledExtract extract)
     {
@@ -1713 +1524 @@
         return fs;
     }
-                        
+                                        
     public Form getSecondaryLabeledExtractForm(LabeledExtract extract,
     DbControl dc, LabeledExtract fromExtract)
@@ -1776 +1587 @@
         return form;
     }
-
+                
     public TextField<Float> newOriginalQuantityField()
     {
@@ -1784 +1595 @@
         return field;
     }
-                        
+                                        
     public TextField<Float> newRemainingQuantityField(Float remainingQuantity)
     {
@@ -1795 +1606 @@
         return field;
     }
-                        
+                                        
     private Localizer getLocale()
     {
         return locale;
     }
-                        
+                                        
     public void setLocale(Localizer locale)
     {
         this.locale = locale;
     }
-                        
+                                        
     //Cleaning up from here        
-                    
+                                    
     /**
         Form for new Protocol item. The difference between calling
@@ -1818 +1629 @@
         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.
@@ -1903 +1714 @@
         return form;
     }
-                        
+                                        
     public Form getForm(Class<?> cls)
     {
@@ -1993 +1804 @@
             loginF.setDisabled(true);
             fs.add(fs.size()-2, loginF); // After the itemId field
-                                                            
+                                                                                                            
             TextField<String> emailF = new EmailField();
             fs.add(fs.size()-1, emailF);
-                                                                        
+                                                                                                                        
             TextField<String> phoneF = new PhoneField();
             fs.add(phoneF);
-                                                                        
+                                                                                                                        
             TextField<String> addressF = new AddressField();
             fs.add(addressF);
-                                                                        
+                                                                                                                        
             TextField<String> organisationF = new OrganisationField();
             fs.add(organisationF);
-                                                                        
+                                                                                                                        
             if (obj != null)
             {
@@ -2336 +2147 @@
         return form;
     }
-                        
+                                        
     /**
         Creates a select box for protocols. If the class for which the protocol
@@ -2344 +2155 @@
         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
@@ -2451 +2262 @@
         return protocolS;
     }
-                        
+                                        
     public void setSc(SessionControl sc)
     {

trunk/client/servlet/src/org/proteios/gui/table/Cell.java

@@ -1 +1 @@
 /*
- $Id$
- 
- Copyright (C) 2006, 2007 Gregory Vincic
- 
- Files are copyright by their respective authors. The contributions to
- files where copyright is not explicitly stated can be traced with the
- source code revision system.
- 
- 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) 2006, 2007 Gregory Vincic
+                 
+    Files are copyright by their respective authors. The contributions to
+    files where copyright is not explicitly stated can be traced with the
+    source code revision system.
+                 
+    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.gui.table;
 
@@ -31 +31 @@
 
 /**
- * Describes a cell within a table.
- * 
- * @author gregory
- */
+    * Describes a cell within a table.
+    * 
+    * @author gregory
+*/
 public class Cell<D extends Object>
 {
-  /**
-   * Displayed in this cell
-   */
-  private D value = null;
-  /**
-   * Flag telling any converter that the value should be wrapped, default is
-   * false.
-   */
-  private boolean wrap = false;
-  /**
-   * What happens when a user clicks the value in this column
-   */
-  private AbstractLink actionLink = null;
-  /**
-   * If clicking on this cell should invoke a javascript action
-   */
-  private String jsAction = null;
-
-
-  public String getJsAction()
-  {
-    return jsAction;
-  }
-
-
-  public void setJsAction(String jsAction)
-  {
-    this.jsAction = jsAction;
-  }
-
-
-  public AbstractLink getActionLink()
-  {
-    return actionLink;
-  }
-
-
-  public void setActionLink(AbstractLink actionLink)
-  {
-    this.actionLink = actionLink;
-  }
-
-
-  public boolean isWrap()
-  {
-    return wrap;
-  }
-
-
-  public Cell<D> setWrap(boolean wrap)
-  {
-    this.wrap = wrap;
-    return this;
-  }
-
-
-  public Cell(D value)
-  {
-    this.value = value;
-  }
-
-
-  public D getValue()
-  {
-    return value;
-  }
-
-
-  public void setValue(D value)
-  {
-    this.value = value;
-  }
+    /**
+        * Displayed in this cell
+    */
+    private D value = null;
+    /**
+        * Flag telling any converter that the value should be wrapped, default is
+        * false.
+    */
+    private boolean wrap = false;
+    /**
+        * What happens when a user clicks the value in this column
+    */
+    private AbstractLink actionLink = null;
+    /**
+        * If clicking on this cell should invoke a javascript action
+    */
+    private String jsAction = null;
+                
+    /**
+        If true then the value within this cell should be translated before presented to the client. Default is false.
+    */
+    private boolean translate = false;
+                
+    /** 
+        @param translate true if you want the value within this cell should be translated before presented to the client.
+    */
+    public void setTranslate(boolean translate)
+    {
+        this.translate = translate;
+    }
+                
+    /**
+        @return true if the value within this cell should be translated, false otherwise.
+    */
+    public boolean getTranslate()
+    {
+        return this.translate;
+    }
+                
+    public String getJsAction()
+    {
+        return jsAction;
+    }
+                
+    public void setJsAction(String jsAction)
+    {
+        this.jsAction = jsAction;
+    }
+                
+    public AbstractLink getActionLink()
+    {
+        return actionLink;
+    }
+                
+    public void setActionLink(AbstractLink actionLink)
+    {
+        this.actionLink = actionLink;
+    }
+                
+    public boolean isWrap()
+    {
+        return wrap;
+    }
+                
+    public Cell<D> setWrap(boolean wrap)
+    {
+        this.wrap = wrap;
+        return this;
+    }
+                
+    public Cell(D value)
+    {
+        this.value = value;
+    }
+                
+    public D getValue()
+    {
+        return value;
+    }
+                
+    public void setValue(D value)
+    {
+        this.value = value;
+    }
 }