Changeset 3545

Timestamp:

Jul 2, 2007, 3:45:01 PM (16 years ago)

Author:

Johan Enell

Message:

Merged log:branches/2.3.2#3537:3542 to trunk.

Location:

trunk/src/plugins/core/net/sf/basedb/plugins

Files:

• Base1PluginExecuter.java (modified) (7 diffs)
• BioAssaySetExporter.java (modified) (6 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -93 +93 @@
 import java.net.URL;
 import java.sql.SQLException;
+import java.util.AbstractSet;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -104 +105 @@
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -744 +746 @@
       Boolean mergeReporters = (Boolean) configuration.getValue(geneAveragesParameter.getName());
       
-      Map<String, String> parameters = new HashMap<String, String>();
+      ListMap<String, String> parameters = new ListMap<String, String>();
       for (PluginParameter<?> pp : getJobParametersFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName()))))
       {
@@ -908 +910 @@
     try
     {
-      List<PluginParameter<?>> p = new ArrayList<PluginParameter<?>>();
       String doctype = "<!DOCTYPE jobparameters SYSTEM \"base1-plugin-configuration-file.dtd\">";
       Document doc = XMLUtil.getValidatedXml(doctype+xml, dtdFile);
@@ -923 +924 @@
         }
       });
+      
+      TreeMap<Integer, PluginParameter<?>> positionParameter = new TreeMap<Integer, PluginParameter<?>>();
       while (it.hasNext())
       {
         Element e = it.next();
         JobParameter jp = new JobParameter(e);
-        p.add(jp.getPluginParameter());
-      }
-      return p;
+        if (positionParameter.containsKey(jp.getPosition()))
+        {
+          throw new BaseException("Duplicate parameter at position "+jp.getPosition());
+        }
+        positionParameter.put(jp.getPosition(), jp.getPluginParameter());
+      }
+      return new ArrayList<PluginParameter<?>>(positionParameter.values());
     }
     catch (JDOMException e1)
@@ -1430 +1437 @@
 
                 // int2 = 10^a / 2^(0.5*m)
-                // int1 = int2  2^m
+                // int1 = int2 * 2^m
                 intensities[1] = new Float(Math.pow(10, a) / Math.pow(2, 0.5 * m));
-                intensities[0] = new Float(intensities[1] * Math.pow(2, m));
+                intensities[0] = new Float(intensities[1] * Math.pow(2, m));
               }
 
@@ -1848 +1855 @@
     }
   }
+  
+  private class ListMap<K, V> extends java.util.AbstractMap<K, V>
+  {
+    private List<K> keys = new ArrayList<K>();
+    private List<V> values = new ArrayList<V>();
+
+    @Override
+    public Set<java.util.Map.Entry<K, V>> entrySet()
+    {
+      throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public V put(K key, V value)
+    {
+      V ret = null;
+      int index = keys.indexOf(key);
+      if (index == -1)
+      {
+        keys.add(key);
+        values.add(value);
+      }
+      else
+      {
+        keys.set(index, key);
+        ret = values.set(index, value);
+      }
+      return ret;
+    }
+
+    @Override
+    public V get(Object key)
+    {
+      if (key == null) throw new NullPointerException();
+      int index = keys.indexOf(key);
+      V ret = null;
+      if (index != -1)
+      {
+        ret = values.get(index);
+      }
+      return ret;
+    }
+
+    @Override
+    public boolean isEmpty()
+    {
+      return keys.isEmpty();
+    }
+
+    @Override
+    public Set<K> keySet()
+    {
+      return new AbstractSet<K>()
+      {
+        @Override
+        public Iterator<K> iterator()
+        {
+          return Collections.unmodifiableList(keys).iterator();
+        }
+
+        @Override
+        public int size()
+        {
+          return keys.size();
+        }
+      };
+    }
+    
+  }
 
   private enum Base1JobParameterType

trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -302 +302 @@
   }
   
-  
   private void exportBaseFileSectionAssays(PrintWriter out, DbControl dc, BioAssaySet bas)
   {
@@ -329 +328 @@
   }
   
-  
   private void exportBaseFileSectionHead(PrintWriter out, Map<String, String> parameters)
   {
     out.println("BASEfile");
+    
     if (!parameters.isEmpty())
     {
-      Set<String> keys = new HashSet<String>(parameters.keySet());
-      if (keys.remove("section"))
+      List<String> keys = new ArrayList<String>(parameters.keySet());
+      if ("section".equals(keys.get(0)))
       {
         out.println("section\t"+parameters.get("section"));
+        keys = keys.subList(1, keys.size());
+      }
+      if (keys.contains("section"))
+      {
+        throw new BaseException("The parameters can't have a parameter 'section' in the middle of the list.");
       }
       for (String key : keys)
@@ -1025 +1029 @@
 
 
+  @Override
   public Plugin.MainType getMainType()
   {
@@ -1092 +1097 @@
   private DbControl dc;
   private BioAssaySet bas;
+  @Override
   protected void begin(DbControl dc)
   {
@@ -1097 +1103 @@
   } 
   
+  @Override
   @SuppressWarnings("unchecked")
   protected void performExport(ExportOutputStream out, ProgressReporter progress)
@@ -1150 +1157 @@
   }
   
+  @Override
   protected void end(boolean success)
   {
     this.dc = null;
   }
+  
+  @Override
   protected String getSuccessMessage()
   {
     return "Bioassay set '" + bas.getName() + "' exported successfully";
   }
-
   
   @Override