Changeset 3444

Timestamp:

Oct 14, 2009, 2:58:09 PM (14 years ago)

Author:

Fredrik Levander

Message:

Merging trunk into branch

Location:

branches/testing

Files:

• api/core/src/org/proteios/core/Application.java (modified) (1 diff)
• api/waf/src/se/lu/thep/waf/dom/html/Area.java (copied) (copied from trunk/api/waf/src/se/lu/thep/waf/dom/html/Area.java)
• api/waf/src/se/lu/thep/waf/dom/html/Img.java (modified) (1 diff)
• api/waf/src/se/lu/thep/waf/dom/html/Map.java (copied) (copied from trunk/api/waf/src/se/lu/thep/waf/dom/html/Map.java)
• client/servlet/src/org/proteios/RemoveRequestHandler.java (copied) (copied from trunk/client/servlet/src/org/proteios/RemoveRequestHandler.java)
• client/servlet/src/org/proteios/RequestData.java (copied) (copied from trunk/client/servlet/src/org/proteios/RequestData.java)
• client/servlet/src/org/proteios/RequestHandler.java (copied) (copied from trunk/client/servlet/src/org/proteios/RequestHandler.java)
• client/servlet/src/org/proteios/Service.java (modified) (10 diffs)
• client/servlet/src/org/proteios/action/file/InspectActiveSpectrumFile.java (modified) (15 diffs)
• client/servlet/src/org/proteios/action/hit/ViewActiveHitPDBFile.java (modified) (4 diffs)
• client/servlet/src/org/proteios/action/peakList/PeakAnnotationUtil.java (modified) (5 diffs)
• client/servlet/src/org/proteios/action/peakList/PlotFileSpectrum.java (modified) (3 diffs)
• client/servlet/src/org/proteios/action/peakList/PlotSpectrum.java (modified) (2 diffs)
• client/servlet/src/org/proteios/action/peakList/ViewActivePeakList.java (modified) (4 diffs)
• client/servlet/src/org/proteios/gui/Image.java (modified) (2 diffs)
• client/servlet/src/org/proteios/gui/ImageMap.java (copied) (copied from trunk/client/servlet/src/org/proteios/gui/ImageMap.java)
• client/servlet/src/org/proteios/gui/ImageMapArea.java (copied) (copied from trunk/client/servlet/src/org/proteios/gui/ImageMapArea.java)
• client/servlet/src/org/proteios/gui/web/GUIConverter.java (modified) (4 diffs)
• client/servlet/test/test_webservice.sh (modified) (3 diffs)
• client/servlet/www/static/js/script.js (modified) (1 diff)
• recipe (modified) (1 diff)

branches/testing/api/core/src/org/proteios/core/Application.java

@@ -65 +65 @@
    * The minor version.
    */
-  private static final int MINOR_VERSION = 9;
+  private static final int MINOR_VERSION = 10;
   /**
    * The micro version.

branches/testing/api/waf/src/se/lu/thep/waf/dom/html/Img.java

@@ -40 +40 @@
     return this;
   }
+
+
+  public Img setUsemap(String usemap)
+  {
+    this.setAttribute(new Attribute("usemap", usemap));
+    return this;
+  }
 }

branches/testing/client/servlet/src/org/proteios/Service.java

@@ -49 +49 @@
 import org.proteios.core.Directory;
 import org.proteios.core.File;
+import org.proteios.core.Identifiable;
 import org.proteios.core.ItemAlreadyExistsException;
 import org.proteios.core.ItemFactory;
@@ -54 +55 @@
 import org.proteios.core.ItemQuery;
 import org.proteios.core.ItemResultIterator;
+import org.proteios.core.Nameable;
 import org.proteios.core.Operator;
 import org.proteios.core.Project;
@@ -89 +91 @@
 
 /**
- * Web service that enables clients to fetch and upload data in a tab separated
+ * Web service that enables clients to read and write data through a tab separated
  * format. Exposing items to the service is done in your web.xml. NOTE!!! This
  * service is still under heavy development. Use this feature only in
@@ -128 +130 @@
   {
    RequestData data = startRequest(request, response);
-
-    // Define
-    Removable itemToRemove;
-
-    // Use
-    if (data.item != null)
-
-    {
-      if (data.item instanceof Removable)
-      {
-        itemToRemove = (Removable) data.item;
-        itemToRemove.setRemoved(true);
-        data.dc.commit();
-      }
-      else
-      {
-        response.setStatus(HttpServletResponse.SC_FORBIDDEN);
-      }
-    }
-    else
-    {
-      response.setStatus(HttpServletResponse.SC_NOT_FOUND);
-    }
-
+  RequestHandler remover = new RemoveRequestHandler();
+  remover.handle(data);
     endRequest(data);
   }
@@ -317 +297 @@
  private void applyWhereToQuery(ItemQuery<?> query, List<AttributeDefinition> show, HttpServletRequest request)
  {
-  String paramName,filterString,opStr, valueStr;
+  String subParamName, paramName,filterString,opStr, valueStr, name, key;
     Filter filter;
   Operator operator;
@@ -324 +304 @@
   Class<?> type;
   typeUtil = new TypeUtil();
+  Enumeration en;
+  Map<String,Boolean> whereParams;
+
+  whereParams = new HashMap<String,Boolean>();
+
+  /*
+   Find all where* parameters 
+  */
+  en = request.getParameterNames();
+  while (en.hasMoreElements()) 
+  {
+   name = (String) en.nextElement();
+   if(name.startsWith("where"))
+   {
+     whereParams.put(name, new Boolean(true));
+   }
+  }
 
     for (AttributeDefinition ad : show)
@@ -329 +326 @@
       paramName = "where" + ad.getKey();
       // The filterString is what the user entered
-      filterString = request.getParameter(paramName);
-      log.debug(paramName + "=" + filterString);
-      if (filterString != null && filterString.length() > 1)
-      {
-        // Parse the string for operator
-        filter = null;
-        opStr = filterString.substring(0, 2);
-        valueStr = filterString.substring(2);
-        if (operatorMap.get(opStr) == null)
-        {
-          opStr = filterString.substring(0, 1);
-          valueStr = filterString.substring(1);
-        }
-        if (operatorMap.get(opStr) != null)
-        {
-          if (valueStr != null && valueStr.length() > 0)
-          {
-            // The filter string must be at least
-            // one character long Now convert the string
-            // to the proper type
-            type = ad.getAttributeType();
-            Object value = null;
-            try
-            {
-              value = typeUtil.parse(type, valueStr);
-              log
-                .debug("Value " + valueStr + " is of type " + type + " and typeUtil returned " + value);
-            }
-            catch (Exception e)
-            {
-              log.debug(e.getMessage(), e);
-            }
-            if (value != null)
-            {
-              operator = operatorMap.get(opStr);
-              coreType = typeUtil.getType(type);
-              if (operator.equals(EQ) && typeUtil
-                .isString(type))
-              {
-                // LIKE matching
-                if (((String) value).contains("%"))
-                  operator = LIKE;
-              }
-              filter = new Filter(operator, value,
-                coreType);
-              applyFilter(query, filter, ad);
-            }
-          }
-        }
-      }
-    }
+      filter = createFilter(request, ad.getAttributeType(), paramName);
+   if(filter != null)
+   {
+        applyFilter(query, filter, ad.getKey());
+    }
+    }
+ }
+
+ private Filter createFilter(HttpServletRequest request, Class<?> type, String paramName)
+ {
+
+  Object value = null;
+  Operator operator;
+    Type coreType;
+    TypeUtil typeUtil;
+  String filterString, opStr, valueStr;
+  boolean createFilter;
+  createFilter = false;
+  opStr = null;
+  valueStr = null;
+  
+  filterString = request.getParameter(paramName);
+    log.debug(paramName + "=" + filterString);
+    if (filterString != null && filterString.length() > 1)
+    {
+      // Parse the string for operator
+      opStr = filterString.substring(0, 2);
+      valueStr = filterString.substring(2);
+      if (operatorMap.get(opStr) == null)
+      {
+        opStr = filterString.substring(0, 1);
+        valueStr = filterString.substring(1);
+      }
+      if (operatorMap.get(opStr) != null && valueStr != null && valueStr.length() > 0)
+      {
+    createFilter = true; 
+      }
+    }
+  if(createFilter)
+  {
+   typeUtil = new TypeUtil();
+   try
+    {
+      value = typeUtil.parse(type, valueStr);
+      log.debug("Value " + valueStr + " is of type " + type + " and typeUtil returned " + value);
+     }
+     catch (Exception e)
+     {
+      log.debug(e.getMessage(), e);
+     }
+     if (value != null)
+     {
+      operator = operatorMap.get(opStr);
+      coreType = typeUtil.getType(type);
+      if (operator.equals(EQ) && typeUtil.isString(type))
+      {
+        // LIKE matching
+        if (((String) value).contains("%"))
+        {
+      operator = LIKE;
+     }
+      }
+      return new Filter(operator, value,  coreType);
+   }
+  }
+   return null;
  }
 
@@ -642 +654 @@
     logHeaders(request);
     logParameters(request);
-    data =  new RequestData(request);
+    data =  new RequestData(request, response);
     parsePath(data);
     data.sc = authenticate(request);
@@ -823 +835 @@
 
   private void applyFilter(ItemQuery<?> query, Filter filter,
-      AttributeDefinition attributeDefinition)
-  {
-    String key = attributeDefinition.getKey();
+      String key)
+  {
     String property = key.substring(0, 1).toLowerCase() + key.substring(1);
     Operator operator = filter.getOperator();
@@ -987 +998 @@
 
 
-  /**
-   * @author gregory
-   */
-  private class RequestData
-  {
-    Class<BasicItem> itemClass = null;
-   BasicItem<?> item = null;
-    int itemId = 0;
-    int projectContextId = 0;
-    String context = null;
-    String resource = null;
-    Boolean isValidResource = false;
-   User user = null;
-   SessionControl sc = null;
-   DbControl dc = null;
-   ItemFactory factory = null;
-   ClassDescriptor cd = null;
-   Project activeProject = null;
-  Directory home = null;
-    HttpServletRequest request;
-    BufferedReader reader = null;
-    InputStream stream = null;
-    InputStreamReader streamReader = null;
-
-    public RequestData(HttpServletRequest request)
-    {
-      this.request = request;
-   }
-
-
-
-    @Override
-    public String toString()
-    {
-      StringBuilder sb = new StringBuilder();
-      append(sb, "itemClass", itemClass);
-      append(sb, "itemId", itemId);
-      append(sb, "projectContextId", projectContextId);
-      append(sb, "resource", resource);
-      append(sb, "context", context);
-      return sb.toString();
-    }
-
-
-    private void append(StringBuilder sb, String name, Object value)
-    {
-      sb.append(name);
-      sb.append("=");
-      sb.append(value == null ? null : value.toString());
-      sb.append(",");
-    }
-
-  }
+
 }

branches/testing/client/servlet/src/org/proteios/action/file/InspectActiveSpectrumFile.java

@@ -27 +27 @@
 import org.proteios.action.ProteiosAction;
 import org.proteios.action.peakList.PlotFileSpectrum;
+import org.proteios.action.read.ScrollTo;
 import org.proteios.core.DbControl;
 import org.proteios.core.File;
@@ -32 +33 @@
 import org.proteios.gui.ColumnContainer;
 import org.proteios.gui.Image;
+import org.proteios.gui.ImageMap;
+import org.proteios.gui.ImageMapArea;
 import org.proteios.gui.RowContainer;
+import org.proteios.gui.Scroller;
 import org.proteios.gui.Title;
 import org.proteios.gui.Toolbar;
@@ -38 +42 @@
 import org.proteios.gui.form.Form;
 import org.proteios.gui.form.FormFactory;
+import org.proteios.gui.form.TextField;
 import org.proteios.gui.layout.RowLayout;
 import org.proteios.gui.table.Cell;
@@ -77 +82 @@
     "keepOriginalSpectrum", 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()
@@ -90 +166 @@
     // Check alternative input
     if (files == null)
-    {
-      
+    {     
       Integer fileIdFromSessionAttribute = getSessionAttribute(VSPECTRUMFILEID);
       log.debug("fileIdFromSessionAttribute = " + fileIdFromSessionAttribute );
@@ -165 +240 @@
      */
     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)
     {
@@ -179 +258 @@
     {
       log.debug("spectrumIds.size() = " + spectrumIds.size());
-      for (int i = 0; i < spectrumIds.size(); i++)
+      // 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) + "\"");
@@ -206 +369 @@
      * Spectrum plot
      */
+    PlotFileSpectrum plotFileSpectrum = new PlotFileSpectrum();
+    ImageMap imageMap;
     Image plotOriginal = null;
     if (keepOriginalSpectrum)
@@ -217 +382 @@
       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);
+      log.debug("plotOriginal imagMap = " + imageMap);
     }
     Image plot = new Image();
@@ -228 +398 @@
     plot.setHeight(PlotFileSpectrum.HEIGHT);
     plot.setWidth(PlotFileSpectrum.WIDTH);
+    // Add mass annotation image map
+    imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc, fileId, spectrumId,
+      massCutoffLowStr, massCutoffHighStr);
+    plot.setImageMap(imageMap);
+    log.debug("plot imagMap = " + imageMap);
     /***********************************************************************
      * Spectrum iteration buttons
@@ -367 +542 @@
     //
     setLayout(layout);
-  }
-
-
-  /**
-   * Fetch previous list item from string  list.
+    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 String The previous item, or null if none.
-   */
-  public String fetchPreviousListItem(String currentItem, List<String> inList)
+   * @return Integer The index for the item, or null if none.
+   */
+  public Integer fetchStringListItemIndex(String currentItem, List<String> inList)
   {
     log.debug("currentItem = \"" + currentItem + "\"");
@@ -386 +562 @@
     log.debug("inList.size() = " + inList.size());
     // Find current index
-    int currentIndex = -1;
+    Integer currentIndex = null;
     for (int i = 0; i < inList.size(); i++)
     {
@@ -400 +576 @@
     }
     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;
+    return currentIndex;
   }
 
   
   /**
-   * Fetch next list item from string  list.
+   * 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 next item, or null if none.
-   */
-  public String fetchNextListItem(String currentItem, List<String> inList)
+   * @return String The previous item, or null if none.
+   */
+  public String fetchPreviousListItem(String currentItem, List<String> inList)
   {
     log.debug("currentItem = \"" + currentItem + "\"");
@@ -441 +610 @@
     }
     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;
@@ -450 +660 @@
     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);
+  }
 }

branches/testing/client/servlet/src/org/proteios/action/hit/ViewActiveHitPDBFile.java

@@ -281 +281 @@
     }
     log.debug("gene3DUrl = \"" + gene3DUrl + "\"");
+    // ... Gene3D; <a href=http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GotoCath.pl?cath=G3DSA:3.40.605.10>G3DSA:3.40.605.10</a>;
+    // gene3DUrl = "http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GotoCath.pl?cath=G3DSA:3.40.605.10"
+    //
+    // Update 2009-10-07
+    // ... Gene3D; <a href=http://www.cathdb.info/cathnode/G3DSA:3.40.605.10>G3DSA:3.40.605.10</a>; Aldehyde_dehydrogenase_N; 1.
+    // gene3DUrl = "http://www.cathdb.info/cathnode/G3DSA:3.40.605.10"
+    //
     // Get Gene3D server URL string (URL part before /cgi-bin
     String gene3DServerUrlStr = null;
@@ -290 +297 @@
       {
         gene3DServerUrlStr = gene3DUrlStr.substring(0, cgibinIndex);
+      }
+      else
+      {
+        int serverSearchIndex = gene3DUrlStr.indexOf("cathnode/");
+        if (serverSearchIndex > -1)
+        {
+          gene3DServerUrlStr = gene3DUrlStr.substring(0, serverSearchIndex);
+        }
       }
       // Get Gene3D URL title
@@ -297 +312 @@
       {
         gene3DUrlTitleStr = gene3DUrlStr.substring(titleIndex + titlePrecursor.length());
+      }
+      else
+      {
+        titlePrecursor = new String("cathnode/");
+        titleIndex = gene3DUrlStr.indexOf(titlePrecursor);
+        if (titleIndex > -1)
+        {
+          gene3DUrlTitleStr = gene3DUrlStr.substring(titleIndex + titlePrecursor.length());
+        }
       }
     }
@@ -503 +527 @@
   {
     // ... Gene3D; <a href=http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GotoCath.pl?cath=G3DSA:3.40.605.10>G3DSA:3.40.605.10</a>;
+    // gene3DUrl = "http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GotoCath.pl?cath=G3DSA:3.40.605.10"
+    //
+    // Update 2009-10-07
+    // ... Gene3D; <a href=http://www.cathdb.info/cathnode/G3DSA:3.40.605.10>G3DSA:3.40.605.10</a>; Aldehyde_dehydrogenase_N; 1.
+    // gene3DUrl = "http://www.cathdb.info/cathnode/G3DSA:3.40.605.10"
+    //
     String linePattern = new String(".*[Gg][Ee][Nn][Ee]3[Dd];.*");
     // Delimiters for URL string

branches/testing/client/servlet/src/org/proteios/action/peakList/PeakAnnotationUtil.java

@@ -28 +28 @@
 package org.proteios.action.peakList;
 
+import org.proteios.gui.ImageMap;
+import org.proteios.gui.ImageMapArea;
 import org.proteios.io.SpectrumInterface;
 
@@ -199 +201 @@
     int ySpectrumOffsetBottom = yInnerAreaOffsetBottom + yInnerAreaPeakBottomOffset;
     int ySpectrumOffsetTop = yInnerAreaOffsetTop + yInnerAreaPeakTopOffset;
-    int spectrumAreaWidth = width- xSpectrumOffsetLeft - xSpectrumOffsetRight;
+    int spectrumAreaWidth = width - xSpectrumOffsetLeft - xSpectrumOffsetRight;
     int spectrumAreaHeight = height - ySpectrumOffsetBottom - ySpectrumOffsetTop;
     log.debug("width = " + width + " height = " + height);
@@ -220 +222 @@
     graphics.drawString("x", (width - xSpectrumOffsetRight), (height - ySpectrumOffsetBottom));
     */
-    // Annotate peaks
+    // Annotate selected peaks
     for (int i = 0; i < topPeaks.size(); i++)
     {
@@ -256 +258 @@
         yCoord = height;
       }
-      log.debug("mass = " + mass + " spectrum offset = " + (xCoord - xSpectrumOffsetLeft) + " xCoord = " + xCoord);
+      log.debug("mass = " + mass + " spectrum offset = " + (xCoord - xSpectrumOffsetLeft) + " xCoord = " + xCoord + " yCoord = " + yCoord);
       // Draw mass value over peak
       graphics.drawString(massStr, xCoord, (height - yCoord));
@@ -402 +404 @@
     return topPeakIndex;
   }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards.
+   * 
+   * @param spectrum SpectrumInterface Input mass spectrum data.
+   * @param imageWidth int Image width in pixels.
+   * @param imageHeight int Image height in pixels.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(SpectrumInterface spectrum, int imageWidth, int imageHeight)
+  {
+    log.debug("spectrum = " + spectrum);
+    log.debug("imageWidth = " + imageWidth);
+    log.debug("imageHeight = " + imageHeight);
+    // If no spectrum, return directly
+    if (spectrum == null)
+    {
+      return null;
+    }
+    //
+    double[] massArray = spectrum.listMass();
+    double[] intensityArray = spectrum.listIntensities();
+    if (massArray == null)
+    {
+      return null;
+    }
+    int size = massArray.length;
+    if (size == 0)
+    {
+      return null;
+    }
+    // Analyze spectrum
+    double massMin = massArray[0];
+    double massMax = massArray[massArray.length - 1];
+    double massRange = 1.0;
+    if (massMin < massMax)
+    {
+      massRange = massMax - massMin;
+    }
+    log.debug("size = " + size + " massMin = " + massMin + " massMax = " + massMax + " massRange = " + massRange);
+    /*
+     * The positioning of mass value markers above (or near)
+     * the top of a mass spectrum peak is determined by
+     * a type of dead reckoning, as use of the JFreeChart
+     * package to draw the mass spectra itself does not
+     * give any feedback for the position of the top of
+     * a mass peak, which depends on the offsets of the
+     * spectrum drawing area in the image, when space for
+     * scales and labels have been allocated. The available
+     * input are the width and height of the image, plus
+     * the mass and intensity values of the spectra.
+     * Based on the graphical output for typical standard
+     * choices of spectra, the needed offsets have been
+     * determined by trial and error to a degree that
+     * hopefully is sufficient for an adequate placement
+     * of the markers.
+     */
+    /*
+     * The following offsets are based on the following input:
+     * width = 400
+     * height = 300
+     * min mass = 110
+     * max mass = 1022
+     * max intensity = 3361
+     */
+    int maxPeakIndex = findMaxValueIndex(intensityArray);
+    double maxIntensity = intensityArray[maxPeakIndex];
+    log.debug("maxPeakIndex = " + maxPeakIndex + " mass = " + massArray[maxPeakIndex] + " intensity = " + maxIntensity);
+    // Use coordinate system with origin at lower left corner
+    // Offsets in pixels for inner drawing area without scales and labels
+    int xInnerAreaOffsetLeft = 58;
+    int xInnerAreaOffsetRight = 12;
+    int yInnerAreaOffsetBottom = 36;
+    int yInnerAreaOffsetTop = 30;
+    // Corrections for intensity scale numbers outside range [1000, 9999]
+    int offsetLeftCorrStep = 7;
+    if (maxIntensity < 1000)
+    {
+      xInnerAreaOffsetLeft -= offsetLeftCorrStep;
+    }
+    if (maxIntensity > 10000)
+    {
+      xInnerAreaOffsetLeft += offsetLeftCorrStep;
+    }
+    if (maxIntensity > 100000)
+    {
+      xInnerAreaOffsetLeft += offsetLeftCorrStep;
+    }
+    if (maxIntensity > 1000000)
+    {
+      xInnerAreaOffsetLeft += offsetLeftCorrStep;
+    }
+    // Offsets in pixels for mass spectrum area relative to inner drawing area
+    int xInnerAreaFirstPeakOffset = 18;
+    int xInnerAreaLastPeakOffset = 13;
+    int yInnerAreaPeakBottomOffset = 0;
+    int yInnerAreaPeakTopOffset = 10;
+    // Offsets in pixels for mass spectrum area relative to full drawing area
+    int xSpectrumOffsetLeft = xInnerAreaOffsetLeft + xInnerAreaFirstPeakOffset;
+    int xSpectrumOffsetRight = xInnerAreaOffsetRight + xInnerAreaLastPeakOffset;
+    int ySpectrumOffsetBottom = yInnerAreaOffsetBottom + yInnerAreaPeakBottomOffset;
+    int ySpectrumOffsetTop = yInnerAreaOffsetTop + yInnerAreaPeakTopOffset;
+    int spectrumAreaWidth = imageWidth - xSpectrumOffsetLeft - xSpectrumOffsetRight;
+    int spectrumAreaHeight = imageHeight - ySpectrumOffsetBottom - ySpectrumOffsetTop;
+    log.debug("imageWidth = " + imageWidth + " imageHeight = " + imageHeight);
+    log.debug("spectrumAreaWidth = " + spectrumAreaWidth + " spectrumAreaHeight = " + spectrumAreaHeight);
+    //
+    // Create mass value annotation tool-tips for all peaks
+    int numberOfDecimalsForTooltips = 4;
+    ImageMap imageMap = fetchMassPeakAnnotationToolTips(massArray, intensityArray,
+      imageWidth, imageHeight, spectrumAreaWidth, spectrumAreaHeight,
+      xSpectrumOffsetLeft, ySpectrumOffsetBottom, yInnerAreaOffsetBottom,
+      massMin, massRange, maxIntensity, numberOfDecimalsForTooltips);
+    return imageMap;
+  }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards. Input y-coordinates
+   * are expected to to be increasing upwards.
+   * 
+   * @param massArray double[] Array with mass values.
+   * @param intensityArray double[] Array with intensities.
+   * @param width int Width of image area in pixels.
+   * @param height int Height of image area in pixels.
+   * @param spectrumAreaWidth int Width of spectrum area in pixels.
+   * @param spectrumAreaHeight int Height of spectrum area in pixels.
+   * @param xSpectrumOffsetLeft int Left offset in x of spectrum area in pixels.
+   * @param ySpectrumOffsetBottom int Bottom offset in y of spectrum area in pixels.
+   * @param yInnerAreaOffsetBottom int Bottom offset in y of inner area in pixels.
+   * @param massMin double Minimum mass value.
+   * @param massRange double The range of mass values, i.e. maximum - minimum mass value.
+   * @param maxIntensity double Maximum intensity value.
+   * @param numberOfDecimals int The number of decimals to use for mass values in tool-tips.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(double[] massArray, double[] intensityArray,
+      int width, int height, int spectrumAreaWidth, int spectrumAreaHeight,
+      int xSpectrumOffsetLeft, int ySpectrumOffsetBottom, int yInnerAreaOffsetBottom,
+      double massMin, double massRange, double maxIntensity, int numberOfDecimals)
+  {
+    ImageMap imageMap = new ImageMap();
+    ImageMapArea imageMapArea;
+    // Annotate peaks
+    if (numberOfDecimals < 0)
+    {
+      numberOfDecimals = 4;
+    }
+    //
+    // Select peaks for annotation
+    int tempXCoord = -1;
+    double tempMaxIntensity = 0;
+    int tempMaxIntensityIndex = -1;
+    List<Integer> annotationIndexList = new ArrayList<Integer>();
+    int size = massArray.length;
+    for (int i = 0; i < size; i++)
+    {
+      double mass = massArray[i];
+      double intensity = intensityArray[i];
+      int xCoord = xSpectrumOffsetLeft + (int) (spectrumAreaWidth*((mass - massMin)/massRange));
+      // Check if peak has same x-coordinate in pixels as previous peaks
+      if (xCoord == tempXCoord)
+      {
+        // Check if peak is larger than previous peaks with same x-coordinate in pixels
+        if (intensity > tempMaxIntensity)
+        {
+          // Set current peak as annotation candidate for x-coordinate in pixels
+          tempMaxIntensity = intensity;
+          tempMaxIntensityIndex = i;          
+        }
+      }
+      else
+      {
+        if (tempXCoord >= 0)
+        {
+          // Add stored peak for previous x-coordinate in pixels to annotation list
+          annotationIndexList.add(tempMaxIntensityIndex);
+        }
+        // Reset stored peak data to new peak
+        tempXCoord = xCoord;
+        tempMaxIntensity = intensity;
+        tempMaxIntensityIndex = i;
+      }
+    }
+    // Add last stored index to list
+    if (tempXCoord >= 0)
+    {
+      // Add stored peak for previous x-coordinate in pixels to annotation list
+      annotationIndexList.add(tempMaxIntensityIndex);
+    }
+    log.debug("mass array size = " + size + " annotationIndexList.size() = " + annotationIndexList.size());
+    //
+    // Annotate selected mass peaks
+    for (int j = 0; j < annotationIndexList.size(); j++)
+    {
+      int i = (Integer) annotationIndexList.get(j);
+      double mass = massArray[i];
+      double intensity = intensityArray[i];
+      int xCoord = xSpectrumOffsetLeft + (int) (spectrumAreaWidth*((mass - massMin)/massRange));
+      int yCoord = ySpectrumOffsetBottom + (int) (spectrumAreaHeight*(intensity/maxIntensity));
+      // Get mass value marker with desired number of decimals
+      //String massStr = Integer.toString((int) mass);
+      //NumberFormat fixedNumberOfDecimals = NumberFormat.getInstance();
+      NumberFormat fixedNumberOfDecimals = new DecimalFormat("#########.######");
+      fixedNumberOfDecimals.setMinimumFractionDigits(numberOfDecimals);
+      fixedNumberOfDecimals.setMaximumFractionDigits(numberOfDecimals);
+      String massStr = fixedNumberOfDecimals.format(mass).toString();
+      String hrefStr = null;
+      //
+      // Log output for test of tool-tip creation
+      int yCoordFromImageBottom = height - yCoord;
+      int ySpectrumImageBottom = height - yInnerAreaOffsetBottom - 1;
+      // Create image map area with mass annotation tool-tip
+      //log.debug("   <AREA SHAPE=\"RECT\" COORDS=\"" + xCoord + ", " + yCoordFromImageBottom + ", " + (xCoord + 1) + ", " + ySpectrumImageBottom + "\" HREF=\"http://www.proteios.org\" onMouseover=\"showtip(this,event,'" + massStr + "')\" onMouseout=\"hidetip()\">");
+      //log.debug("   <AREA SHAPE=\"RECT\" COORDS=\"" + xCoord + ", " + yCoordFromImageBottom + ", " + (xCoord + 1) + ", " + ySpectrumImageBottom + "\" onMouseover=\"showtip(this,event,'" + massStr + "')\" onMouseout=\"hidetip()\">");
+      imageMapArea = new ImageMapArea(xCoord, yCoordFromImageBottom, (xCoord + 1), ySpectrumImageBottom, hrefStr, massStr);
+      imageMap.addImageMapArea(imageMapArea);     
+    }
+    return imageMap;
+  }
 }

branches/testing/client/servlet/src/org/proteios/action/peakList/PlotFileSpectrum.java

@@ -37 +37 @@
 import org.proteios.core.File;
 import org.proteios.core.ItemFactory;
+import org.proteios.gui.ImageMap;
 import org.proteios.gui.form.FormFactory;
 import org.proteios.io.PeakListFileInterface;
@@ -250 +251 @@
       {
         // Trim plot header to fit on one line
-        int maxNumChars = 40;
+        int maxNumChars = 35;
         if (plotHeader.length() > maxNumChars)
         {
@@ -286 +287 @@
       throw new ActionException(e);
     }
+  }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param spectrumFileId Integer The spectrum file id. 
+   * @param spectrumId String The spectrum id. 
+   * @param massCutoffLowStr String The lower cutoff mass value string.
+   * @param massCutoffHighStr String The upper cutoff mass value string.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(DbControl dc, Integer spectrumFileId, String spectrumId,
+      String massCutoffLowStr, String massCutoffHighStr)
+  {
+    Float massCutoffLow = null;
+    if (massCutoffLowStr != null)
+    {
+      try
+      {
+        massCutoffLow = Float.parseFloat(massCutoffLowStr);
+      }
+      catch (Exception e)
+      {
+        log.debug("Exception when parsing string \"" + massCutoffLowStr + "\" to Float: " + e);
+      }
+    }
+    Float massCutoffHigh = null;
+    if (massCutoffHighStr != null)
+    {
+      try
+      {
+        massCutoffHigh = Float.parseFloat(massCutoffHighStr);
+      }
+      catch (Exception e)
+      {
+        log.debug("Exception when parsing string \"" + massCutoffHighStr + "\" to Float: " + e);
+      }
+    }
+    log.debug("spectrumFileId = " + spectrumFileId);
+    log.debug("spectrumId = \"" + spectrumId + "\"");
+    log.debug("massCutoffLowStr = \"" + massCutoffLowStr + "\"");
+    log.debug("massCutoffHighStr = \"" + massCutoffHighStr + "\"");
+    log.debug("massCutoffLow = " + massCutoffLow);
+    log.debug("massCutoffHigh = " + massCutoffHigh);
+    //
+    SpectrumInterface spectrum = fetchSpectrum(dc, spectrumFileId, spectrumId, massCutoffLow, massCutoffHigh);
+    PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
+    ImageMap imageMap = peakAnnotationUtil.fetchMassPeakAnnotationToolTips(spectrum, WIDTH, HEIGHT);
+    return imageMap;
+  }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param spectrumFileId Integer The spectrum file id. 
+   * @param spectrumId String The spectrum id. 
+   * @param massCutoffLow Float The lower cutoff mass value.
+   * @param massCutoffHigh Float The upper cutoff mass value.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(DbControl dc, Integer spectrumFileId, String spectrumId,
+      Float massCutoffLow, Float massCutoffHigh)
+  {
+    log.debug("spectrumFileId = " + spectrumFileId);
+    log.debug("spectrumId = \"" + spectrumId + "\"");
+    log.debug("massCutoffLow = " + massCutoffLow);
+    log.debug("massCutoffHigh = " + massCutoffHigh);
+    SpectrumInterface spectrum = fetchSpectrum(dc, spectrumFileId, spectrumId, massCutoffLow, massCutoffHigh);
+    PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
+    ImageMap imageMap = peakAnnotationUtil.fetchMassPeakAnnotationToolTips(spectrum, WIDTH, HEIGHT);
+    return imageMap;
+  }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param spectrumFileId Integer The spectrum file id. 
+   * @param spectrumId String The spectrum id. 
+   * @param massCutoffLow Float The lower cutoff mass value.
+   * @param massCutoffHigh Float The upper cutoff mass value.
+   * @param imageWidth int Image width in pixels.
+   * @param imageHeight int Image height in pixels.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(DbControl dc, Integer spectrumFileId, String spectrumId,
+      Float massCutoffLow, Float massCutoffHigh, int imageWidth, int imageHeight)
+  {
+    SpectrumInterface spectrum = fetchSpectrum(dc, spectrumFileId, spectrumId, massCutoffLow, massCutoffHigh);
+    PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
+    ImageMap imageMap = peakAnnotationUtil.fetchMassPeakAnnotationToolTips(spectrum, imageWidth, imageHeight);
+    return imageMap;
+  }
+
+
+  /**
+   * Fetches spectrum given spectrum file id, spectrum id,
+   * and zoom limit parameters.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param spectrumFileId Integer The spectrum file id. 
+   * @param spectrumId String The spectrum id. 
+   * @param massCutoffLow Float The lower cutoff mass value.
+   * @param massCutoffHigh Float The upper cutoff mass value.
+   * @return SpectrumInterface The possibly pruned spectrum.
+   */
+  public SpectrumInterface fetchSpectrum(DbControl dc, Integer spectrumFileId, String spectrumId, Float massCutoffLow, Float massCutoffHigh)
+  {
+    log.debug("spectrumFileId = " + spectrumFileId);
+    log.debug("spectrumId = \"" + spectrumId + "\"");
+    log.debug("massCutoffLow = " + massCutoffLow);
+    log.debug("massCutoffHigh = " + massCutoffHigh);
+    /***********************************************************************
+     * Get peakListFile data
+     */
+    ItemFactory factory = new ItemFactory(dc);
+    // Get peak list file
+    File spectrumFile = null;
+    if (spectrumFileId != null && spectrumFileId > 0)
+    {
+      spectrumFile = factory.getById(File.class, spectrumFileId);
+    }
+    // Get peak list file reader
+    boolean useTitle = true;
+    // Use string id if it exists
+    if (spectrumId != null)
+    {
+      // If the stringId is just a number, it could have been parsed,
+      // so use the int instead...
+      try
+      {
+        Integer titleNumber = Integer.parseInt(spectrumId);
+        if (titleNumber != null)
+        {
+          useTitle = false;
+          log.debug("spectrumId is a number, useTitle = " + useTitle);
+        }
+      }
+      catch (NumberFormatException e)
+      {}
+      // Special case: A spectrum id starting with a number should be treated as a number
+      String stringId = null;
+      int strIndex = spectrumId.indexOf(" ");
+      if (strIndex >= 0)
+      {
+        // Remove part beginning with first blank
+        stringId = spectrumId.substring(0, strIndex);
+      }
+      if (stringId != null)
+      {
+        try
+        {
+          Integer titleNumber = Integer.parseInt(stringId);
+          if (titleNumber != null)
+          {
+            useTitle = false;
+            log.debug("spectrumId begins with a number, useTitle = " + useTitle);
+          }
+        }
+        catch (NumberFormatException e)
+        {}        
+      }
+    }
+    SpectrumFileReaderFactory spectrumFileReaderFactory = new SpectrumFileReaderFactory();
+    PeakListFileInterface peakListFileReader = spectrumFileReaderFactory.fetchPeakListFileReader(spectrumFile, useTitle);
+    SpectrumInterface spectrum = null;
+    if (peakListFileReader != null && spectrumId != null)
+    {
+      // Get spectrum
+      int size = 0;
+      log.debug("useTitle = " + useTitle + " spectrumId = \"" + spectrumId + "\"");
+      spectrum = peakListFileReader.getSpectrum(spectrumId);
+      // Restrict spectrum to specified mass range, if defined
+      spectrum = zoomSpectrum(spectrum, massCutoffLow, massCutoffHigh);
+    }
+    else
+    {
+      log.warn("Couldn't find peak list (Peaklist file: " + spectrumFile + " Spectrum Id: " + spectrumId + ")");
+    }
+    return spectrum;
   }
 

branches/testing/client/servlet/src/org/proteios/action/peakList/PlotSpectrum.java

@@ -39 +39 @@
 import org.proteios.core.Peak;
 import org.proteios.core.PeakList;
+import org.proteios.gui.ImageMap;
 import org.proteios.io.SpectrumImpl;
 import org.proteios.io.SpectrumInterface;
@@ -245 +246 @@
       throw new ActionException(e);
     }
+  }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param peakListId Integer The peak list id. 
+   * @param massCutoffLowStr String The lower cutoff mass value string.
+   * @param massCutoffHighStr String The upper cutoff mass value string.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(DbControl dc, Integer peakListId,
+      String massCutoffLowStr, String massCutoffHighStr)
+  {
+    Float massCutoffLow = null;
+    if (massCutoffLowStr != null)
+    {
+      try
+      {
+        massCutoffLow = Float.parseFloat(massCutoffLowStr);
+      }
+      catch (Exception e)
+      {
+        log.debug("Exception when parsing string \"" + massCutoffLowStr + "\" to Float: " + e);
+      }
+    }
+    Float massCutoffHigh = null;
+    if (massCutoffHighStr != null)
+    {
+      try
+      {
+        massCutoffHigh = Float.parseFloat(massCutoffHighStr);
+      }
+      catch (Exception e)
+      {
+        log.debug("Exception when parsing string \"" + massCutoffHighStr + "\" to Float: " + e);
+      }
+    }
+    log.debug("peakListId = " + peakListId);
+    log.debug("massCutoffLowStr = \"" + massCutoffLowStr + "\"");
+    log.debug("massCutoffHighStr = \"" + massCutoffHighStr + "\"");
+    log.debug("massCutoffLow = " + massCutoffLow);
+    log.debug("massCutoffHigh = " + massCutoffHigh);
+    //
+    SpectrumInterface spectrum = fetchSpectrum(dc, peakListId, massCutoffLow, massCutoffHigh);
+    PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
+    ImageMap imageMap = peakAnnotationUtil.fetchMassPeakAnnotationToolTips(spectrum, WIDTH, HEIGHT);
+    return imageMap;
+  }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param peakListId Integer The peak list id. 
+   * @param massCutoffLow Float The lower cutoff mass value.
+   * @param massCutoffHigh Float The upper cutoff mass value.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(DbControl dc, Integer peakListId,
+      Float massCutoffLow, Float massCutoffHigh)
+  {
+    log.debug("peakListId = " + peakListId);
+    log.debug("massCutoffLow = " + massCutoffLow);
+    log.debug("massCutoffHigh = " + massCutoffHigh);
+    SpectrumInterface spectrum = fetchSpectrum(dc, peakListId, massCutoffLow, massCutoffHigh);
+    PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
+    ImageMap imageMap = peakAnnotationUtil.fetchMassPeakAnnotationToolTips(spectrum, WIDTH, HEIGHT);
+    return imageMap;
+  }
+
+
+  /**
+   * Create mass peak annotation tool-tips for HTML.
+   * Note that y-coordinates for drawing purposes
+   * increases upwards, while tool-tip y-coordinates
+   * in HTML increases downwards.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param peakListId Integer The peak list id. 
+   * @param massCutoffLow Float The lower cutoff mass value.
+   * @param massCutoffHigh Float The upper cutoff mass value.
+   * @param imageWidth int Image width in pixels.
+   * @param imageHeight int Image height in pixels.
+   * @return ImageMap An HTML image map with mass value annotations for mass peaks as tool-tips.
+   */
+  public ImageMap fetchMassPeakAnnotationToolTips(DbControl dc, Integer peakListId,
+      Float massCutoffLow, Float massCutoffHigh, int imageWidth, int imageHeight)
+  {
+    SpectrumInterface spectrum = fetchSpectrum(dc, peakListId, massCutoffLow, massCutoffHigh);
+    PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
+    ImageMap imageMap = peakAnnotationUtil.fetchMassPeakAnnotationToolTips(spectrum, imageWidth, imageHeight);
+    return imageMap;
+  }
+
+
+  /**
+   * Fetches spectrum given peak list id,
+   * and zoom limit parameters.
+   * 
+   * @param dc DbControl The DbControl to use.
+   * @param peakListId Integer The peak list id. 
+   * @param massCutoffLow Float The lower cutoff mass value.
+   * @param massCutoffHigh Float The upper cutoff mass value.
+   * @return SpectrumInterface The possibly pruned spectrum.
+   */
+  public SpectrumInterface fetchSpectrum(DbControl dc, Integer peakListId, Float massCutoffLow, Float massCutoffHigh)
+  {
+    log.debug("peakListId = " + peakListId);
+    log.debug("massCutoffLow = " + massCutoffLow);
+    log.debug("massCutoffHigh = " + massCutoffHigh);
+    /***********************************************************************
+     * Get peakList data
+     */
+    PeakList pl = PeakList.getById(dc, peakListId);
+    ItemQuery<Peak> query = pl.getPeaksQuery();
+    // query.include(Include.MINE);
+    ItemResultList<Peak> peaksList = query.list(dc);
+    int size = 0;
+    if (!peaksList.isEmpty())
+    {
+      size = peaksList.size();
+    }
+    // Store mass and intensity values in arrays for peak annotation
+    double[] massArray = null;
+    double[] intensityArray = null;
+    if (size > 0)
+    {
+      massArray = new double[size];
+      intensityArray = new double[size];
+    }
+    // Load peak values
+    for (int i = 0; i < size; i++)
+    {
+      Peak p = peaksList.get(i);
+      double x = p.getMassToChargeRatio();
+      double y = p.getIntensity();
+      massArray[i] = x;
+      intensityArray[i] = y;
+    }
+    SpectrumImpl spectrumOrig = null;
+    if (size > 0)
+    {
+      spectrumOrig = new SpectrumImpl();
+      spectrumOrig.setMass(massArray);
+      spectrumOrig.setIntensities(intensityArray);
+    }
+    // Restrict spectrum to specified mass range, if defined
+    SpectrumInterface spectrum = zoomSpectrum(spectrumOrig, massCutoffLow, massCutoffHigh);
+    return spectrum;
   }
 

branches/testing/client/servlet/src/org/proteios/action/peakList/ViewActivePeakList.java

@@ -38 +38 @@
 import org.proteios.gui.ColumnContainer;
 import org.proteios.gui.Image;
+import org.proteios.gui.ImageMap;
+import org.proteios.gui.ImageMapArea;
 import org.proteios.gui.RowContainer;
 import org.proteios.gui.Toolbar;
@@ -120 +122 @@
      * Spectrum plot
      */
+    PlotSpectrum plotSpectrum = new PlotSpectrum();
+    ImageMap imageMap;
     Image plotOriginal = null;
     if (keepOriginalSpectrum)
@@ -130 +134 @@
       plotOriginal.setHeight(PlotSpectrum.HEIGHT);
       plotOriginal.setWidth(PlotSpectrum.WIDTH);
+      // Add mass annotation image map
+      imageMap = plotSpectrum.fetchMassPeakAnnotationToolTips(dc, peakListId,
+        (String) null, (String) null);
+      plotOriginal.setImageMap(imageMap);
+      log.debug("plotOriginal imagMap = " + imageMap);
     }
     Image plot = new Image();
@@ -140 +149 @@
     plot.setHeight(PlotSpectrum.HEIGHT);
     plot.setWidth(PlotSpectrum.WIDTH);
+    // Add mass annotation image map
+    imageMap = plotSpectrum.fetchMassPeakAnnotationToolTips(dc, peakListId,
+      massCutoffLowStr, massCutoffHighStr);
+    plot.setImageMap(imageMap);
+    log.debug("plot imagMap = " + imageMap);
     /***********************************************************************
      * Spectrum mass range selection form

branches/testing/client/servlet/src/org/proteios/gui/Image.java

@@ -39 +39 @@
   private Integer width = 0;
   private Integer height = 0;
+  private ImageMap imageMap = null;
   /**
    * If true draw a kind of frame around this image
@@ -107 +108 @@
     this.framed = framed;
   }
+
+
+  public ImageMap getImageMap()
+  {
+    return this.imageMap;
+  }
+
+
+  public void setImageMap(ImageMap imageMap)
+  {
+    this.imageMap = imageMap;
+  }
 }

branches/testing/client/servlet/src/org/proteios/gui/web/GUIConverter.java

@@ -45 +45 @@
 import org.proteios.gui.IFrame;
 import org.proteios.gui.Image;
+import org.proteios.gui.ImageMap;
+import org.proteios.gui.ImageMapArea;
 import org.proteios.gui.ListItem;
 import org.proteios.gui.Listing;
@@ -72 +74 @@
 
 import se.lu.thep.waf.dom.html.A;
+import se.lu.thep.waf.dom.html.Area;
 import se.lu.thep.waf.dom.html.Attribute;
 import se.lu.thep.waf.dom.html.CData;
@@ -83 +86 @@
 import se.lu.thep.waf.dom.html.Input;
 import se.lu.thep.waf.dom.html.Li;
+import se.lu.thep.waf.dom.html.Map;
 import se.lu.thep.waf.dom.html.Option;
 import se.lu.thep.waf.dom.html.Select;
@@ -187 +191 @@
     // First we show the loading img
     imgT.setSrc(loadingImgSrc);
+    //
+    if (img.getImageMap() != null && img.getImageMap().getImageMapAreaList() != null)
+    {
+      String imageMapStr = "ImageMap" + imgId;
+      imgT.setUsemap("#" + imageMapStr);
+      // Create image map
+      Map map = new Map();
+      map.setParent(div);
+      div.add(map);
+      map.setName(imageMapStr);
+      List<ImageMapArea> imageMapAreaList = img.getImageMap().getImageMapAreaList();
+      for (int i = 0; i < imageMapAreaList.size(); i++)
+      {
+        // Get image map area data from image object
+        ImageMapArea imageMapArea = (ImageMapArea) imageMapAreaList .get(i);
+        int xTopLeft = imageMapArea.getXTopLeft();
+        int yTopLeft = imageMapArea.getYTopLeft();
+        int xBottomRight = imageMapArea.getXBottomRight();
+        int yBottomRight = imageMapArea.getYBottomRight();
+        String hrefStr = imageMapArea.getHrefStr();
+        String toolTipStr = imageMapArea.getToolTipStr();
+        String onMouseoverStr = null;
+        String onMouseoutStr = null;
+        if (toolTipStr != null && !toolTipStr.equals(""))
+        {
+          onMouseoverStr = new String("showtip(this,event,'" + toolTipStr + "')");
+          onMouseoutStr = new String("hidetip()");
+        }
+        // Create new image map area
+        Area area = new Area();
+        area.setParent(map);
+        map.add(area);
+        area.setShape("RECT");
+        area.setCoords(xTopLeft, yTopLeft, xBottomRight, yBottomRight);
+        if (hrefStr != null && !hrefStr.equals(""))
+        {
+          area.setHref(hrefStr);
+        }
+        if (onMouseoverStr != null && !onMouseoverStr.equals(""))
+        {
+          area.setOnMousover(onMouseoverStr);
+        }
+        if (onMouseoutStr != null && !onMouseoutStr.equals(""))
+        {
+          area.setOnMousout(onMouseoutStr);
+        }
+      }
+    }
     script = div.newScript();
     script.newCData("var " + imgId + " = new Image();");

branches/testing/client/servlet/test/test_webservice.sh

@@ -49 +49 @@
 }
 
+DELETE() 
+{
+  url=$1
+  curlit "-X DELETE" $url
+}
+
+ 
 PUT()
 {
@@ -71 +78 @@
 fail()
 {
-    echo "Failed[$test_no]: $1"
-    echo "Message: $2"
+  date >> /dev/stderr
+    echo "Failed[$test_no]: $1" >> /dev/stderr
+    echo "Message: $2" >> /dev/stderr
+  echo "" >> /dev/stderr
   exit
 }
@@ -84 +93 @@
 case $1 in
   9)
-    test "Cross table search"
-    GET "$A" "$resource/extracts?$auth"
+    test "Mark file for deletion"
+    generate_name
+    echo -e "Name\tDescription" > $A
+    echo -e "${i}_$name\tThis is the ${i}:th file" >> $A
+    PUT "$A" "$resource/files?$auth" 
+    GET "$B" "$resource/files?$auth&select=Id&whereName==${i}_$name"
+    lastid=`tail -n 1 $B | perl -ane '/(\d+)/; print \$1;'`
+    DELETE "$resource/files/$lastid?$auth"
+    GET "$C" "$resource/files?$auth&select=Name,Removed&whereName==${i}_$name"
+    removed=`grep $name $C`
+    if [ "$removed" != "" ]; then
+      fail "$test" "File should have been marked as removed, but was not."
+    fi
     ;;
   8)

branches/testing/client/servlet/www/static/js/script.js

@@ -378 +378 @@
 }
 
+/* http://www.dynamicdrive.com/dynamicindex5/texttool.htm */
+function showtip(current,e,text)
+{
+   if (document.all || document.getElementById)
+   {
+      thetitle = text.split('<br>');
+      if (thetitle.length > 1)
+      {
+         thetitles = '';
+         for (i=0; i < thetitle.length; i++)
+         {
+            thetitles += thetitle[i];
+         }
+         current.title = thetitles;
+      }
+      else
+      {
+         current.title = text;
+      }
+   }
+   else if (document.layers)
+   {
+      document.tooltip.document.write('<layer bgColor="white" style="border:1px solid black;font-size:12px;">'+text+'</layer>');
+      document.tooltip.document.close();
+      document.tooltip.left = e.pageX + 5;
+      document.tooltip.top = e.pageY + 5;
+      document.tooltip.visibility = "show";
+   }
+}
+
+function hidetip()
+{
+   if (document.layers)
+   {
+      document.tooltip.visibility = "hidden";
+   }
+}
+
 // this will resize all iframes every
 // time you change the size of the window.

branches/testing/recipe

@@ -9 +9 @@
 # Run 'bake web' to generate and copy web related files
 WEB_PATH=/home/tom/wwwroot/proteios
-VERSION=2.7.0
+VERSION=2.9.0
 MD5_GZ=`cat /home/tom/trac/proteios/htdocs/downloads/$VERSION/ProteiosSE-$VERSION.tar.gz.MD5`
 MD5_ZIP=`cat /home/tom/trac/proteios/htdocs/downloads/$VERSION/ProteiosSE-$VERSION.zip.MD5`