add phase in

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4164 ee4ac58c-ac51-4696-9907-e4b3aa274f04

artemis_sqlmap/Feature.xml

@@ -23,6 +23,7 @@
         <result property="type_id" column="type_id"/>
         <result property="prop_type_id" column="prop_type_id" nullValue="0"/>
         <result property="value" column="value"/>
+        <result property="phase" column="phase" nullValue="10"/>
      </resultMap>
 
     <resultMap id="select-feature-result" class="uk.ac.sanger.ibatis.Feature">
@@ -62,20 +63,20 @@
                              resultMap="select-feature-properties-result">
         SELECT
           timelastmodified, 
-          feature.feature_id AS id, 
+          f.feature_id AS id, 
           object_id, 
-          strand, 
+          fl.strand, 
           fmin, 
           fmax, 
           uniquename,
-          $schema$.feature.type_id AS type_id,  
-          $schema$.featureprop.type_id AS prop_type_id, 
-          $schema$.featureprop.value AS value
-        FROM  $schema$.featureloc, $schema$.feature
-        LEFT JOIN $schema$.feature_relationship
-              ON $schema$.feature_relationship.subject_id=$schema$.feature.feature_id
-        LEFT JOIN $schema$.featureprop 
-              ON $schema$.featureprop.feature_id=$schema$.feature.feature_id
+          f.type_id,  
+          fp.type_id AS prop_type_id, 
+          fp.value,
+          fl.phase
+        FROM  $schema$.feature f
+        LEFT JOIN $schema$.feature_relationship fr ON fr.subject_id = f.feature_id
+        LEFT JOIN $schema$.featureprop fp          ON fp.feature_id = f.feature_id
+        LEFT JOIN $schema$.featureloc fl           ON f.feature_id  = fl.feature_id
         WHERE
             <dynamic>
              <isGreaterThan property="id" compareValue="0"> 
@@ -85,10 +86,8 @@
                uniquename=#uniquename# AND
              </isNotNull>
            </dynamic>
-           $schema$.featureloc.feature_id=$schema$.feature.feature_id
-           AND ($schema$.featureloc.rank=$schema$.feature_relationship.rank OR 
-                $schema$.feature_relationship.rank IS NULL)
-        ORDER BY $schema$.feature.type_id,  uniquename
+           (fl.rank=fr.rank OR fr.rank IS NULL)
+        ORDER BY f.type_id,  uniquename
      </select>
  
     <select id="getSequence" parameterClass="uk.ac.sanger.ibatis.Feature" 

uk/ac/sanger/artemis/util/DatabaseDocument.java

@@ -386,6 +386,7 @@ public class DatabaseDocument extends Document
       long type_id            = feat.getType_id();
       long prop_type_id       = feat.getProp_type_id();
       int strand              = feat.getStrand();
+      int phase               = feat.getPhase();
       String name             = feat.getUniquename();
       String typeName         = getCvtermName(type_id);
       String propTypeName     = getCvtermName(prop_type_id);
@@ -419,7 +420,11 @@ public class DatabaseDocument extends Document
       else
         this_buff.append(".\t");
 
+      if(phase > 3)
         this_buff.append(".\t");               // phase
+      else
+        this_buff.append(phase+"\t"); 
+
       this_buff.append("ID=" + name + ";");
 
       if(parent_id != null)

uk/ac/sanger/ibatis/Feature.java

@@ -66,6 +66,8 @@ public class Feature
   private String abbreviation;
   /** hashtable of qualifiers */
   private Hashtable qualifiers;
+  /** phase */
+  private int phase;
 
   public int getId()
   {
@@ -227,6 +229,16 @@ public class Feature
     this.srcfeature_id = srcfeature_id;
   }
 
+  public int getPhase()
+  {
+    return phase;  
+  }
+
+  public void setPhase(int phase)
+  {
+    this.phase = phase;
+  }
+
   public void addQualifier(long prop_type_id, String value)
   {
     if(qualifiers == null)

uk/ac/sanger/ibatis/JdbcDAO.java

@@ -110,23 +110,18 @@ public class JdbcDAO
                                         ResultSet.CONCUR_UPDATABLE);
 
     String sql = "SELECT timelastmodified, f.feature_id, object_id, "
-        + "strand, fmin, fmax, uniquename, f.type_id, "
-        + schema + ".featureprop.type_id AS prop_type_id, featureprop.value"
+        + "fl.strand, fmin, fmax, uniquename, f.type_id, "
+        + "fp.type_id AS prop_type_id, fp.value, fl.phase"
         + " FROM  "
-        + schema + ".featureloc fl, "
         + schema + ".feature f"
-        + " LEFT JOIN "
-        + schema + ".feature_relationship fr ON "
-        + "fr.subject_id="
-        + "f.feature_id"
-        + " LEFT JOIN "
-        + schema + ".featureprop ON "
-        + schema + ".featureprop.feature_id="
-        + "f.feature_id"
+        + " LEFT JOIN " + schema + ".feature_relationship fr ON "
+                        + "fr.subject_id=" + "f.feature_id"
+        + " LEFT JOIN " + schema + ".featureprop fp ON "
+                        + "fp.feature_id=" + "f.feature_id"
+        + " LEFT JOIN " + schema + ".featureloc fl ON "
+                        + "f.feature_id=" + "fl.feature_id"
         + " WHERE srcfeature_id = "
-        + parentFeatureID + " AND "
-        + "fl.feature_id="
-        + "f.feature_id"
+        + parentFeatureID 
         + " AND ("
         + "fl.rank="
         + "fr.rank OR "
@@ -146,6 +141,13 @@ public class JdbcDAO
       feature.setType_id( rs.getLong("type_id") );
       feature.setProp_type_id( rs.getLong("prop_type_id") );
       feature.setStrand( rs.getInt("strand") );
+      
+      int phase = rs.getInt("phase");
+      if(rs.wasNull())
+        feature.setPhase(10);
+      else 
+        feature.setPhase( rs.getInt("phase") );
+
       feature.setUniquename( rs.getString("uniquename") );
       feature.setTimelastmodified( rs.getDate("timelastmodified") );
       feature.setId( rs.getInt("feature_id") );