Changeset 1575

Timestamp:

Nov 7, 2005, 4:05:24 PM (18 years ago)

Author:

Nicklas Nordborg

Message:

Added IntensityCalculatorUtil? and other classes needed by it:
IntensityCalculator?, IntensityFormula?
Added Java Math Expression Parser package
Changed raw-data-types.xml file and it's dtd

Location:

trunk

Files:

• base2.license.txt (modified) (1 diff)
• doc/3rd-party-components.txt (modified) (1 diff)
• lib/compile/jep-2.3.0.jar (added)
• src/core/net/sf/basedb/core/IntensityFormula.java (added)
• src/core/net/sf/basedb/core/RawDataType.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/RawDataTypes.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/dtd/raw-data-types.dtd (modified) (2 diffs)
• src/core/net/sf/basedb/util/IntensityCalculator.java (added)
• src/core/net/sf/basedb/util/IntensityCalculatorUtil.java (added)
• src/install/includes (modified) (1 diff)
• src/install/initdb.bat (modified) (1 diff)
• src/raw-data-types.xml (modified) (1 diff)
• src/test/TestExperiment.java (modified) (5 diffs)
• src/test/run.bat (modified) (1 diff)
• src/test/run.sh (modified) (1 diff)

trunk/base2.license.txt

@@ -44 +44 @@
 * This product includes software developed by the
   The JDOM(TM) Project (http://www.jdom.org)
+
+* This product includes software developed by
+  Singular Systems (http://www.singularsys.com/)

trunk/doc/3rd-party-components.txt

@@ -134 +134 @@
             commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
 
+
+Java Math Expression Parser
+---------------------------
+Parses and evaluates mathematical expressions in string. Supports
+most operators and funcations as well as variables. 
+
+More info : http://www.singularsys.com/jep/
+Version   : 2.3.0
+License   : GPL (gpl.license.txt)
+Jar files : jep-2.3.0.jar
+

trunk/src/core/net/sf/basedb/core/RawDataType.java

@@ -25 +25 @@
 package net.sf.basedb.core;
 import java.util.List;
-import java.util.ArrayList;
+import java.util.Map;
+import java.util.HashMap;
 import java.util.Collections;
 
@@ -51 +52 @@
   private final String table;
   private final List<RawDataProperty> properties;
+  private final Map<String, RawDataProperty> namedProperties;
+  private final List<IntensityFormula> formulas;
+  private final Map<String, IntensityFormula> namedFormulas;
   
   private final RealTable realTable;
@@ -59 +63 @@
   */
   RawDataType(String id, String name, String description, int channels,
-    String table, List<RawDataProperty> properties)
+    String table, List<RawDataProperty> properties, List<IntensityFormula> formulas)
   {
     this.id = id;
@@ -67 +71 @@
     this.table = table;
     this.properties = Collections.unmodifiableList(properties);
+    this.formulas = formulas;
     this.realTable = new RealTable(table, "raw");
+    
+    this.namedProperties = new HashMap<String, RawDataProperty>(properties.size());
+    for (RawDataProperty property : properties)
+    {
+      if (namedProperties.put(property.getName(), property) != null)
+      {
+        throw new BaseException("RawDataProperty[name="+property.getName()+"] is already defined for raw data type: "+name);
+      }
+    }
+    this.namedFormulas = new HashMap<String, IntensityFormula>(formulas.size());
+    for (IntensityFormula formula : formulas)
+    {
+      if (namedFormulas.put(formula.getName(), formula) != null)
+      {
+        throw new BaseException("IntensityFormula[name="+formula.getName()+"] is already defined for raw data type: "+name);
+      }
+    }
+    
   }
 
@@ -157 +180 @@
     return properties;
   }
+  
+  public RawDataProperty getProperty(String name)
+  {
+    return namedProperties.get(name);
+  }
+
+  public List<IntensityFormula> getIntensityFormulas()
+  {
+    return formulas;
+  }
+  
+  public IntensityFormula getIntensityFormula(String name)
+  {
+    return namedFormulas.get(name);
+  }
 
 }

trunk/src/core/net/sf/basedb/core/RawDataTypes.java

@@ -130 +130 @@
       int channels = XMLUtil.getIntAttribute(el, "channels", 2);
       List<RawDataProperty> properties = loadProperties(el);
-      RawDataType rdt = new RawDataType(id, name, description, channels, table, properties);
+      List<IntensityFormula> formulas = loadIntensityFormulas(el, channels);
+      RawDataType rdt = new RawDataType(id, name, description, channels, table, properties, formulas);
       rawDataTypes.put(id, rdt);
     }
@@ -159 +160 @@
     return properties;
   }
+  
+  /**
+    Load the intensity formulas for the specified raw data type node and
+    return a list of {@link IntensityFormula} objects.
+  */
+  @SuppressWarnings({"unchecked"})
+  private static List<IntensityFormula> loadIntensityFormulas(Element rawDataTypeElement, int channels)
+  {
+    List<IntensityFormula> formulas = new ArrayList<IntensityFormula>();
+    List<Element> children = rawDataTypeElement.getChildren("intensity-formula");
+    for (Element formula : children)
+    {
+      String name = formula.getAttributeValue("name");
+      String title = formula.getAttributeValue("title");
+      if (title == null) title = name;
+      String description = formula.getAttributeValue("description");
+      String[] expressions = new String[channels];
+      for (Element expression :  (List<Element>)formula.getChildren("formula"))
+      {
+        int channel = XMLUtil.getIntAttribute(expression, "channel", 0);
+        if (channel <= 0 || channel > channels)
+        {
+          throw new BaseException("Invalid channel number for expression: "+expression);
+        }
+        if (expressions[channel-1] != null)
+        {
+          throw new BaseException("Expression for channel "+channel+" has already been defined: " +expression);
+        }
+        expressions[channel-1] = expression.getAttributeValue("expression");
+      }
+      formulas.add(new IntensityFormula(name, title, description, expressions));
+    }
+    return formulas;
+  }
+  
 }

trunk/src/core/net/sf/basedb/core/dtd/raw-data-types.dtd

@@ -25 +25 @@
 <!ELEMENT raw-data-types (raw-data-type+) >
 
-<!ELEMENT raw-data-type (property+) >
+<!ELEMENT raw-data-type (property+,intensity-formula*) >
 
 <!ATTLIST raw-data-type
@@ -47 +47 @@
   channel CDATA #IMPLIED
 >
+
+<!ELEMENT intensity-formula (formula+) >
+
+<!ATTLIST intensity-formula
+  name CDATA #REQUIRED
+  title CDATA #IMPLIED
+  description CDATA #IMPLIED
+>
+
+<!ELEMENT formula EMPTY >
+
+<!ATTLIST formula
+  channel CDATA #REQUIRED
+  expression CDATA #REQUIRED
+>

trunk/src/install/includes

@@ -70 +70 @@
 CP=$CP:$WEBINF/lib/jai_core.jar
 CP=$CP:$WEBINF/lib/mlibwrapper_jai.jar
+
+# Java Math Expression Parser
+CP=$CP:$WEBINF/lib/jep-2.3.0.jar
+

trunk/src/install/initdb.bat

@@ -71 +71 @@
 SET CP=%CP%;%WEBINF%/lib/mlibwrapper_jai.jar
 
+REM Java Math Expression Parser
+SET CP=%CP%;%WEBINF%/lib/jep-2.3.0.jar
+
+
 REM Execute install class
 java -cp %CP% net.sf.basedb.install.InitDB %1 %2 %3 %4 %5 %6 %7 %8 %9

trunk/src/raw-data-types.xml

@@ -243 +243 @@
       type="float"
     />
-
+    <intensity-formula
+      name="mean"
+      title="Mean FG - Mean BG"
+      description="Subtract mean background from mean foreground"
+      >
+      <formula 
+        channel="1"
+        expression="ch1FgMean - ch1BgMean"
+      />
+      <formula 
+        channel="2"
+        expression="ch2FgMean - ch2BgMean"
+      />
+    </intensity-formula>
+    <intensity-formula
+      name="median"
+      title="Median FG - Median BG"
+      description="Subtract meadian background from median foreground"
+      >
+      <formula 
+        channel="1"
+        expression="ch1FgMedian - ch1BgMedian"
+      />
+      <formula 
+        channel="2"
+        expression="ch2FgMedian - ch2BgMedian"
+      />
+    </intensity-formula>
   </raw-data-type>
 

trunk/src/test/TestExperiment.java

@@ -34 +34 @@
 import net.sf.basedb.core.query.Selects;
 
+import net.sf.basedb.util.IntensityCalculatorUtil;
+import net.sf.basedb.util.IntensityCalculator;
+
 import java.util.Date;
 import java.util.Set;
@@ -82 +85 @@
     test_list_rawbioassays(id, 2);
     
-    int rootBasId = test_create_root_bioassayset(id, rbaId1, rbaId2);
+    int rootBasId = test_create_root_bioassayset(id, "mean", rbaId1, rbaId2);
     int filterBasId = test_filter_bioassayset(rootBasId);
     int basId = test_create_bioassayset(filterBasId);
@@ -413 +416 @@
   }
   
-  static int test_create_root_bioassayset(int experimentId, int... rawBioAssays)
+
+  static int test_create_root_bioassayset(int experimentId, String intensityFormulaName, int... rawBioAssays)
   {
     if (experimentId == 0) return 0;
     int id = 0;
     DbControl dc = null;
+    long time;
     try
     {
@@ -429 +434 @@
       }
       
-      Transformation t = e.newTransformation(null, rbaCollection);
-      BioAssaySet bas = t.newProduct(null, null);
-      bas.setName("Root bioassayset");
-      dc.saveItem(t);
-      dc.saveItem(bas);
-
-      boolean first = true;
-      PositionBatcher posBatcher = bas.getPositionBatcher();
-      SpotBatcher spotBatcher = bas.getSpotBatcher();
-      MappingBatcher rawBatcher = bas.getMappingBatcher();
-      int numSpots = 0;
-      for (RawBioAssay rba : rbaCollection)
-      {
-        BioAssay ba = bas.newRootBioAssay(Collections.singleton(rba));
-        short column = ba.getDataCubeColumnNo();
-        DataResultIterator<RawData> rawData = rba.getRawData().iterate(dc);
-        while (rawData.hasNext())
-        {
-          RawData rd = rawData.next();
-          int position = rd.getPosition();
-          float[] intensities = new float[2];
-          intensities[0] = (Float)rd.getExtended("ch1FgMean") - (Float)rd.getExtended("ch1BgMean");
-          intensities[1] = (Float)rd.getExtended("ch2FgMean") - (Float)rd.getExtended("ch2BgMean");
-          if (first)
-          {
-            posBatcher.insert(position, rd.getReporter());
-          }
-          rawBatcher.insert(column, position, rd);
-          spotBatcher.insert(column, position, intensities);
-          numSpots++;
-        }
-        dc.saveItem(ba);
-        first = false;
-      }
-      posBatcher.close();
-      spotBatcher.close();
-      rawBatcher.close();
-
+      RawDataType rdt = e.getRawDataType();
+      IntensityCalculator iCalc = IntensityCalculatorUtil.createJepIntensityCalculator(
+        rdt, rdt.getIntensityFormula(intensityFormulaName).getExpressions());
+      
+      time = System.currentTimeMillis();
+      BioAssaySet root = IntensityCalculatorUtil.createRootBioAssaySet(
+        dc, e, rbaCollection, null, iCalc);
       dc.commit();
-      id = bas.getId();
-      dc = TestUtil.getDbControl();
-      dc.reattachItem(bas);
-      write_item(0, bas);
-      write("--Create root bioassayset OK ("+numSpots+" spots inserted)");
+      
+      time = System.currentTimeMillis()-time;
+      int numSpots = root.getNumSpots();
+      id = root.getId();
+      dc = TestUtil.getDbControl();
+      dc.reattachItem(root);
+      write_item(0, root);
+      write("--Create root bioassayset OK ("+numSpots+" spots inserted; "+time+" ms)");
     }
     catch (Throwable ex)
@@ -486 +463 @@
     return id;
   }
-
+  
   static int test_create_bioassayset(int bioAssaySetId)
   {

trunk/src/test/run.bat

@@ -64 +64 @@
 SET CP=%CP%;../../lib/compile/mlibwrapper_jai.jar
 
+REM Java Math Expression Parser
+SET CP=%CP%;../../lib/compile/jep-2.3.0.jar
+
 REM Execute test class
 java -ea -cp %CP% %1 %2 %3 %4 %5 %6 %7 %8 %9

trunk/src/test/run.sh

@@ -63 +63 @@
 CP=$CP:../../lib/compile/mlibwrapper_jai.jar
 
+# Java Math Expression Parser
+CP=$CP:../../lib/compile/jep-2.3.0.jar
+
 # Execute test class
 java -ea -cp $CP $*