Changeset 2131

Timestamp:

Mar 30, 2006, 12:12:16 PM (17 years ago)

Author:

Nicklas Nordborg

Message:

Replaced special JFreePlotServlet with the generic PlotServlet? which can
now also create correction factor plots.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/servlet/JFreePlotServlet.java (deleted)
• src/clients/web/net/sf/basedb/clients/web/servlet/PlotServlet.java (modified) (5 diffs)
• src/core/net/sf/basedb/util/plot/HistogramPlot.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/plot/ScatterPlot.java (modified) (2 diffs)
• src/web.xml.in (modified) (1 diff)
• www/include/scripts/tabcontrol.js (modified) (1 diff)
• www/views/experiments/bioassaysets/view_bioassayset.jsp (modified) (4 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/servlet/PlotServlet.java

@@ -26 +26 @@
 
 import net.sf.basedb.core.Application;
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioAssay;
 import net.sf.basedb.core.BioAssaySet;
@@ -34 +35 @@
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.VirtualColumn;
+import net.sf.basedb.core.query.Dynamic;
 import net.sf.basedb.core.query.Expression;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.JoinType;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.core.query.Selects;
+import net.sf.basedb.core.query.SqlResult;
+import net.sf.basedb.core.query.SqlResultIterator;
 import net.sf.basedb.clients.web.util.HTML;
 import net.sf.basedb.clients.web.util.Values;
@@ -62 +68 @@
 import java.io.OutputStream;
 import java.io.IOException;
+import java.sql.SQLException;
+import java.util.List;
 
 /**
@@ -144 +152 @@
     try
     {
-      // Functions for parsing ch(n) and raw(property)
-      JepFunction ch = new ChannelFunction();
-      JepFunction raw = new RawFunction();
-      
-      // Convert formulas to Expression:s
-      Expression[] x = xFormulas == null ? null : new Expression[xFormulas.length];
-      Expression[] y = yFormulas == null ? null : new Expression[yFormulas.length];
-      if (xFormulas != null)
-      {
-        for (int i = 0; i < xFormulas.length; ++i)
-        {
-          x[i] = Jep.formulaToExpression(xFormulas[i], ch, raw);
-          if (xLog) x[i] = Expressions.log2(x[i]);
-        }
-      }
-      if (yFormulas != null)
-      {
-        for (int i = 0; i < yFormulas.length; ++i)
-        {
-          y[i] = Jep.formulaToExpression(yFormulas[i], ch, raw);
-          if (yLog) y[i] = Expressions.log2(y[i]);
-        }
-      }
-
-      // Get the query
       final SessionControl sc = Application.getSessionControl(ID, request.getRemoteAddr());
       dc = sc.newDbControl();
       BioAssay ba = bioAssayId == 0 ? null : BioAssay.getById(dc, bioAssayId);
       BioAssaySet bas = ba == null ? BioAssaySet.getById(dc, bioAssaySetId) : ba.getBioAssaySet();
-
-      DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
-
+      
       JFreeChart chart = null;
-      if ("scatter".equals(type))
-      {
-        ScatterPlot plot = new ScatterPlot(xLabel, yLabel);
-        for (int i = 0; i < x.length; ++i)
-        {
-          query.reset();
-          query.joinRawData(JoinType.INNER); // TODO - only join if used in query
-          query.select(Selects.expression(x[i], "x"));
-          query.select(Selects.expression(y[i], "y"));
-          plot.addData(query.iterate(dc), Integer.toString(i));
-        }
-        chart = plot.getChart();
+      if ("cfplot".equals(type))
+      {
+        chart = generateCFPlot(ba, xLabel, yLabel);
       }
       else
       {
-        HistogramPlot plot = new HistogramPlot(xLabel, yLabel);
-        query.setReturnTotalCount(true);
-        for (int i = 0; i < x.length; ++i)
-        {
-          query.reset();
-          query.joinRawData(JoinType.INNER); // TODO - only join if used in query
-          query.select(Selects.expression(x[i], "x"));
-          if (!isCount) query.select(Selects.expression(y[i], "y"));
-          plot.addData(query.iterate(dc), Integer.toString(i), binSize, 
-            HistogramPlot.YAggregate.valueOf(yAggregate.toUpperCase()));
-        }
-        chart = plot.getChart();
-      }
+        // Functions for parsing ch(n) and raw(property)
+        JepFunction ch = new ChannelFunction();
+        JepFunction raw = new RawFunction();
+        
+        // Convert formulas to Expression:s
+        Expression[] x = xFormulas == null ? null : new Expression[xFormulas.length];
+        Expression[] y = yFormulas == null ? null : new Expression[yFormulas.length];
+        if (xFormulas != null)
+        {
+          for (int i = 0; i < xFormulas.length; ++i)
+          {
+            x[i] = Jep.formulaToExpression(xFormulas[i], ch, raw);
+            if (xLog) x[i] = Expressions.log2(x[i]);
+          }
+        }
+        if (yFormulas != null)
+        {
+          for (int i = 0; i < yFormulas.length; ++i)
+          {
+            y[i] = Jep.formulaToExpression(yFormulas[i], ch, raw);
+            if (yLog) y[i] = Expressions.log2(y[i]);
+          }
+        }
+  
+        // Get the query
+        DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
+  
+        if ("scatter".equals(type))
+        {
+          ScatterPlot plot = new ScatterPlot(xLabel, yLabel);
+          for (int i = 0; i < x.length; ++i)
+          {
+            query.reset();
+            query.joinRawData(JoinType.INNER); // TODO - only join if used in query
+            query.select(Selects.expression(x[i], "x"));
+            query.select(Selects.expression(y[i], "y"));
+            plot.addData(query.iterate(dc), Integer.toString(i));
+          }
+          chart = plot.getChart();
+        }
+        else
+        {
+          HistogramPlot plot = new HistogramPlot(xLabel, yLabel);
+          query.setReturnTotalCount(true);
+          for (int i = 0; i < x.length; ++i)
+          {
+            query.reset();
+            query.joinRawData(JoinType.INNER); // TODO - only join if used in query
+            query.select(Selects.expression(x[i], "x"));
+            if (!isCount) query.select(Selects.expression(y[i], "y"));
+            plot.addData(query.iterate(dc), Integer.toString(i), binSize, 
+              HistogramPlot.YAggregate.valueOf(yAggregate.toUpperCase()));
+          }
+          chart = plot.getChart();
+        }
+      }
+      
       if (title != null) chart.setTitle(title);
       chart.removeLegend();
@@ -301 +317 @@
     doGet(request, response);
   }
+  
+  
+  private JFreeChart generateCFPlot(BioAssay ba, String xLabel, String yLabel)
+    throws Exception
+  {
+    DbControl dc = ba.getDbControl();
+    // Get parent bioassay
+    List<BioAssay> parents = ba.getParents().list(dc);
+    
+    if (parents.size() != 1)
+    {
+      throw new BaseException("A bioassay must have exactly one parent to generate a correction factor plot");
+    }
+    
+    BioAssay parent = parents.get(0);
+    
+    // Generate MA-data for it
+    JepFunction ch = new ChannelFunction();
+    JepFunction raw = new RawFunction();
+    
+    Expression m = Jep.formulaToExpression("log2(ch(1) / ch(2))", ch);
+    Expression a = Jep.formulaToExpression("log(ch(1) * ch(2)) / 2", ch);
+    Expression position = Dynamic.column(VirtualColumn.POSITION);
+    
+    DynamicSpotQuery parentQuery = parent.getSpotData();
+    parentQuery.select(Selects.expression(position, "pos"));
+    parentQuery.select(Selects.expression(m, "m"));
+    parentQuery.select(Selects.expression(a, "a"));
+    parentQuery.order(Orders.asc(position));
+
+    DynamicSpotQuery query = ba.getSpotData();
+    query.select(Selects.expression(position, "pos"));
+    query.select(Selects.expression(m, "m"));
+    query.order(Orders.asc(position));
+    
+    // Add CF-data to the plot
+    
+    SqlResultIterator cf = new CFResultIterator(parentQuery.iterate(dc), query.iterate(dc));
+    
+    ScatterPlot plot = new ScatterPlot(xLabel, yLabel);
+    plot.addData(cf, "ma", "cf");
+    return plot.getChart(); 
+  }
+  
+  
+  private static class CFResultIterator
+    implements SqlResultIterator
+  {
+    
+    private final SqlResultIterator parent;
+    private final SqlResultIterator child;
+    private final CFSqlResult next;
+    
+    CFResultIterator(SqlResultIterator parent, SqlResultIterator child)
+    {
+      this.parent = parent;
+      this.child = child;
+      this.next = new CFSqlResult();
+    }
+
+    /*
+      From the Iterator interface
+      -------------------------------------------
+    */
+    public boolean hasNext()
+    {
+      return child.hasNext();
+    }
+    public SqlResult next()
+    {
+      try
+      {
+        SqlResult nextChild = child.next();
+        while (parent.hasNext())
+        {
+          SqlResult nextParent = parent.next();
+          if (nextChild.getInt(1) == nextParent.getInt(1))
+          {
+            next.setResult(nextParent, nextChild);
+            return next;
+          }
+        }
+      }
+      catch (SQLException ex)
+      {
+        throw new BaseException(ex);
+      }
+      return null;
+    }
+    /**
+      Not supported.
+      @throws UnsupportedOperationException Always
+    */
+    public void remove()
+    {
+      throw new UnsupportedOperationException("remove");
+    }
+    // -------------------------------------------
+
+    /*
+      From the QueryResult interface
+      -------------------------------------------
+    */
+    public int getTotalCount()
+    {
+      return child.getTotalCount();
+    }
+    // -------------------------------------------
+
+    /*
+      From the ResultIterator interface
+      -------------------------------------------
+    */
+    public void close()
+    {
+      parent.close();
+      child.close();
+    }
+    public boolean isClosed()
+    {
+      return child.isClosed();
+    }
+    // -------------------------------------------
+
+    /*
+      From the SqlResultIterator interface
+      -------------------------------------------
+    */
+    public int getIndex(String name) 
+      throws SQLException
+    {
+      if ("a".equals(name))
+      {
+        return 1;
+      }
+      else if ("m".equals(name))
+      {
+        return 2;
+      }
+      else if ("cf".equals(name))
+      {
+        return 3;
+      }
+      throw new SQLException("Unknown column name: " + name);
+    }
+    // -------------------------------------------
+    
+  }
+  
+  private static class CFSqlResult
+    implements SqlResult
+  {
+    
+    private SqlResult parent;
+    private SqlResult child;
+    
+    CFSqlResult()
+    {}
+
+    void setResult(SqlResult parent, SqlResult child)
+    {
+      this.parent = parent;
+      this.child = child;
+    }
+    
+    public float getFloat(int index)
+      throws SQLException
+    {
+      switch (index)
+      {
+        case 1:
+          return parent.getFloat(3);
+        case 2:
+          return parent.getFloat(2);
+        case 3: 
+          return parent.getFloat(2) - child.getFloat(2);
+        default:
+          throw new ArrayIndexOutOfBoundsException(index);
+      }
+    }
+    public int getInt(int index) 
+      throws SQLException
+    {
+      return (int)getFloat(index);
+    }
+    public Object getObject(int index) 
+      throws SQLException
+    {
+      return getFloat(index);
+    }
+    public short getShort(int index) 
+      throws SQLException
+    {
+      return (short)getFloat(index);
+    }
+    public String getString(int index) 
+      throws SQLException
+    {
+      return String.valueOf(getFloat(index));
+    }
+    
+  }
 }

trunk/src/core/net/sf/basedb/util/plot/HistogramPlot.java

@@ -25 +25 @@
 package net.sf.basedb.util.plot;
 
-import net.sf.basedb.core.DynamicResultIterator;
 import net.sf.basedb.core.query.SqlResult;
+import net.sf.basedb.core.query.SqlResultIterator;
 
 import org.jfree.chart.JFreeChart;
@@ -70 +70 @@
   }
 
-  public void addData(DynamicResultIterator data, String name, float binSize, YAggregate yAggregate)
+  public void addData(SqlResultIterator data, String name, float binSize, YAggregate yAggregate)
     throws SQLException
   {

trunk/src/core/net/sf/basedb/util/plot/ScatterPlot.java

@@ -25 +25 @@
 package net.sf.basedb.util.plot;
 
-import net.sf.basedb.core.DynamicResultIterator;
 import net.sf.basedb.core.query.SqlResult;
+import net.sf.basedb.core.query.SqlResultIterator;
 
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.plot.SeriesRenderingOrder;
 import org.jfree.chart.plot.XYPlot;
 import org.jfree.chart.renderer.xy.XYDotRenderer;
@@ -61 +62 @@
 
       plot = new XYPlot(allSeries, domainAxis, rangeAxis, new XYDotRenderer());
+      plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
     chart = new JFreeChart(plot);
     chart.setAntiAlias(false);
   }
 
-  public void addData(DynamicResultIterator data, String name)
+  public void addData(SqlResultIterator data, String... names)
     throws SQLException
   {
-    XYSeries series = new XYSeries(name);
+    XYSeries[] series = new XYSeries[names.length];
+    for (int i = 0; i < names.length; ++i)
+    {
+      series[i] = new XYSeries(names[i]);
+    }
     while (data.hasNext())
     {
       SqlResult r = data.next();
-      series.add(r.getFloat(1), r.getFloat(2));
+      float x = r.getFloat(1);
+      for (int i = 0; i < series.length; ++i)
+      {
+        series[i].add(x, r.getFloat(2+i));
+      }
     }
-    allSeries.addSeries(series);
+    for (int i = 0; i < series.length; ++i)
+    {
+      allSeries.addSeries(series[i]);
+    }
   }
   

trunk/src/web.xml.in

@@ -96 +96 @@
   </servlet-mapping>
 
-  <!-- The PlotServlet used to generate overiew and correction factor plots -->
-  <servlet>
-    <servlet-name>jfreeplot</servlet-name>
-    <servlet-class>
-      net.sf.basedb.clients.web.servlet.JFreePlotServlet
-    </servlet-class>
-  </servlet>
-   <servlet-mapping>
-    <servlet-name>jfreeplot</servlet-name>
-    <url-pattern>/views/experiments/plotter/jfreeplot/*</url-pattern>
-  </servlet-mapping>
-  
   <!-- The Generic PlotServlet for the HTML plot tool -->
   <servlet>

trunk/www/include/scripts/tabcontrol.js

@@ -90 +90 @@
     }
   }
+  
+  this.isActive = function(tabControlId, tabId)
+  {
+    var realTabId = tabControlId+'.'+tabId;
+    var tabControl = document.getElementById(tabControlId);
+    var tab = document.getElementById(realTabId);
+    return tabControl.activeTab == tab;
+  }
 
   this.mouseEnter = function(tabControlId, tabId)

trunk/www/views/experiments/bioassaysets/view_bioassayset.jsp

@@ -150 +150 @@
     function switchTab(tabControlId, tabId)
     {
+      if (TabControl.isActive(tabControlId, tabId)) return;
       if (tabId == 'bioassays')
       {
@@ -369 +370 @@
       
       <t:tab id="overviewplots" title="Overview plots" 
+        tooltip="MA-plots of each bioassay in this bioassay set"
         visible="<%=rawDataType.getChannels() == 2%>">
       <%
       if ("overviewplots".equals(tabId))
       {
-        /*
-        TODO - replace jfreeplot with generic plot servlet
         String M = HTML.urlEncode("log2(ch(1) / ch(2))");
         String A = HTML.urlEncode("log(ch(1) * ch(2)) / 2");
-        String xName = HTML.urlEncode("A, log10(ch1 * ch2) / 2");
-        String yName = HTML.urlEncode("M, log2(ch1 / ch2)");
-        */
+        String xLabel = HTML.urlEncode("A, log10(ch1 * ch2) / 2");
+        String yLabel = HTML.urlEncode("M, log2(ch1 / ch2)");
         ItemQuery<BioAssay> bioAssayQuery = bioAssaySet.getBioAssays();
         bioAssayQuery.order(Orders.asc(Hql.property("name")));
         for (BioAssay bioAssay : bioAssayQuery.list(dc))
         {
-          /*
           String url = "../plotter/plot?ID="+ID+"&bioassay_id="+bioAssay.getId();
           url += "&type=scatter&width=400&height=300";
-          url += "&x="+A+"&y="+M+"&xaxis="+xName+"&yaxis="+yName;
-          */
-          String url = "../plotter/jfreeplot/"+ID+"/"+bioAssaySet.getId()+"/"+bioAssay.getId()+"/overviewPlot";
+          url += "&x="+A+"&y="+M+"&xLabel="+xLabel+"&yLabel="+yLabel;
+          url += "&title="+HTML.urlEncode(bioAssay.getName());
           %>
-          <img src="<%=url%>">
+          <img src="<%=url%>" width="400" height="300" 
+            title="MA-plot for bioassay <%=HTML.encodeTags(bioAssay.getName())%>">
           <%
         }
@@ -399 +397 @@
       
       <t:tab id="cfplots" title="Correction factor plots" 
+        tooltip="MA-plot of the parent bioassays together with a correction factor for each spot in the current bioassayset."
         visible="<%=rawDataType.getChannels() == 2 && bioAssaySet.getTransformation().getSource() != null %>">
       <%
@@ -405 +404 @@
         ItemQuery<BioAssay> bioAssayQuery = bioAssaySet.getBioAssays();
         bioAssayQuery.order(Orders.asc(Hql.property("name")));
+        String xLabel = HTML.urlEncode("A, log10(ch1 * ch2) / 2");
+        String yLabel = HTML.urlEncode("M, log2(ch1 / ch2)");
         for (BioAssay bioAssay : bioAssayQuery.list(dc))
         {
-          String url = "../plotter/jfreeplot/"+ID+"/"+bioAssaySet.getId()+"/"+bioAssay.getId()+"/correctionFactorPlot";
+          String url = "../plotter/plot?ID="+ID+"&bioassay_id="+bioAssay.getId();
+          url += "&type=cfplot&width=400&height=300";
+          url += "&xLabel="+xLabel+"&yLabel="+yLabel;
+          url += "&title="+HTML.urlEncode(bioAssay.getName());
           %>
-          <img src="<%=url%>">
+          <img src="<%=url%>" width="400" height="300"
+            title="Correction factor plot for bioassay <%=HTML.encodeTags(bioAssay.getName())%>">
           <%
         }