Changeset 3541

Timestamp:

Jun 29, 2007, 4:46:10 PM (16 years ago)

Author:

Johan Enell

Message:

Fixes #661, #662

Location:

branches/2.3.2/src/plugins/core/net/sf/basedb/plugins

Files:

• Base1PluginExecuter.java (modified) (3 diffs)
• BioAssaySetExporter.java (modified) (6 diffs)

branches/2.3.2/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -90 +90 @@
 import java.net.URL;
 import java.sql.SQLException;
+import java.util.AbstractSet;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.EnumSet;
 import java.util.HashMap;
@@ -745 +745 @@
       Boolean mergeReporters = (Boolean) configuration.getValue(geneAveragesParameter.getName());
       
-      TreeMap<String, String> parameters = new TreeMap<String, String>(new Comparator<String>()
-      {
-        /**
-         * To make the keys orderd by the same order they are added
-         */
-        public int compare(String o1, String o2)
-        {
-          return 1;
-        }
-      });
+      ListMap<String, String> parameters = new ListMap<String, String>();
       for (PluginParameter<?> pp : getJobParametersFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName()))))
       {
-        if (pp != null)
-        {
-          String name = pp.getName();
-          Object value = job.getValue(name);
-          parameters.put(name, value == null ? "" : value.toString());
-        }
+        String name = pp.getName();
+        Object value = job.getValue(name);
+        parameters.put(name, value == null ? "" : value.toString());
       }
       
@@ -1825 +1813 @@
     }
   }
+  
+  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

branches/2.3.2/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -246 +246 @@
   }
   
-  
   private void exportBaseFileSectionAssays(PrintWriter out, DbControl dc, BioAssaySet bas)
   {
@@ -273 +272 @@
   }
   
-  
   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)
@@ -872 +876 @@
 
 
+  @Override
   public Plugin.MainType getMainType()
   {
@@ -938 +943 @@
   private DbControl dc;
   private BioAssaySet bas;
+  @Override
   protected void begin(DbControl dc)
   {
@@ -943 +949 @@
   } 
   
+  @Override
   @SuppressWarnings("unchecked")
   protected void performExport(ExportOutputStream out, ProgressReporter progress)
@@ -995 +1002 @@
   }
   
+  @Override
   protected void end(boolean success)
   {
     this.dc = null;
   }
+  
+  @Override
   protected String getSuccessMessage()
   {
     return "Bioassay set '" + bas.getName() + "' exported successfully";
   }
-
   
   @Override