diff --git a/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java b/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java
index 1ceef25159ef8a390c6d5ea81eba81a25c94c42f..fffbcebf985f32eda6f6096a3272c7c4476f985d 100644
--- a/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java
@@ -86,7 +86,7 @@ public class DatabaseDocumentEntry extends SimpleDocumentEntry
if(feature instanceof DatabaseStreamFeature)
return (DatabaseStreamFeature)feature;
else
- return (EmblStreamFeature)feature;
+ return (GFFStreamFeature)feature;
}
else
return new DatabaseStreamFeature(feature);
diff --git a/uk/ac/sanger/artemis/io/DatabaseStreamFeature.java b/uk/ac/sanger/artemis/io/DatabaseStreamFeature.java
index 16e0244414e70b1d7599be6ec832e856e5560b37..0f1d11a3702e88dec949d70b33615840b30a83b2 100644
--- a/uk/ac/sanger/artemis/io/DatabaseStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/DatabaseStreamFeature.java
@@ -31,11 +31,11 @@ import java.io.*;
* This is an implementation of Feature that can read and write itself to a
* CHADO stream.
*
- * @version $Id: DatabaseStreamFeature.java,v 1.1 2005-03-31 12:09:13 tjc Exp $
+ * @version $Id: DatabaseStreamFeature.java,v 1.2 2005-06-13 18:36:49 tjc Exp $
**/
public class DatabaseStreamFeature
- extends SimpleDocumentFeature
+ extends GFFStreamFeature
implements DocumentFeature, StreamFeature, ComparableFeature
{
/**
@@ -151,23 +151,23 @@ public class DatabaseStreamFeature
* @return null if in_stream is at the end of file when the method is
* called
**/
- protected static DatabaseStreamFeature
- readFromStream(LinePushBackReader stream)
- throws IOException
- {
- String line = stream.readLine ();
- return readFromStream(line);
- }
-
- protected static DatabaseStreamFeature
- readFromStream(String line)
- throws IOException
- {
- if(line == null)
- return null;
-
- return new DatabaseStreamFeature(line);
- }
+//protected static DatabaseStreamFeature
+// readFromStream(LinePushBackReader stream)
+// throws IOException
+//{
+// String line = stream.readLine ();
+// return readFromStream(line);
+//}
+
+//protected static DatabaseStreamFeature
+// readFromStream(String line)
+// throws IOException
+//{
+// if(line == null)
+// return null;
+
+// return new DatabaseStreamFeature(line);
+//}
/**
* This is used by readFromStream() as temporary storage. It is a class
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index f829393ba3bfcea2b22dfcbfac5f25107b0f10ac..3c0b03b8200c6771b59c29b4b6b44727d1286c7a 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -115,11 +115,28 @@ public class DatabaseDocument extends Document
* Return a Document with the last element stripped off.
*
**/
- public Document getParent()
+ public String getFeatureName(String feature_id, Connection conn)
+ throws java.sql.SQLException
+ {
+ Statement st = conn.createStatement();
+
+ String sql = "SELECT name FROM feature WHERE feature_id= "+feature_id;
+ appendToLogFile(sql,sqlLog);
+ ResultSet rs = st.executeQuery(sql);
+ rs.next();
+ return rs.getString("name");
+ }
+
+ /**
+ *
+ * Return a Document with the last element stripped off.
+ *
+ **/
+ public Document getParent()
{
return null;
}
-
+
/**
*
* Return true if and only if the Document refered to by this object exists
@@ -157,9 +174,9 @@ public class DatabaseDocument extends Document
Connection conn = getConnection();
System.out.println("Connected");
- String entry = getGene(conn,feature_id) + getSequence(conn);
+ String entry = getGFF(conn,feature_id) + getSequence(conn);
// String entry = getSequence(conn);
-
+ appendToLogFile(entry,sqlLog);
ByteArrayInputStream instream = new ByteArrayInputStream(entry.getBytes());
return instream;
}
@@ -172,45 +189,47 @@ public class DatabaseDocument extends Document
return null;
}
- private String getGene(Connection conn, String parentFeatureID)
+ private String getGFF(Connection conn, String parentFeatureID)
throws java.sql.SQLException
{
Statement st = conn.createStatement();
- String sql = "SELECT strand, fmin, fmax, value, uniquename, featureprop.type_id, strand"+
+ String sql = "SELECT strand, fmin, fmax, value, uniquename, feature.type_id, featureprop.type_id, strand"+
" FROM feature, featureloc, featureprop WHERE srcfeature_id = "+parentFeatureID+
" and featureloc.feature_id=featureprop.feature_id"+
" and featureloc.feature_id=feature.feature_id" +
- " and feature.type_id=cvterm.cvterm_id and cvterm.name='gene'";
+ " and feature.type_id=cvterm.cvterm_id"; // and cvterm.name='gene'";
appendToLogFile(sql,sqlLog);
ResultSet rs = st.executeQuery(sql);
StringBuffer cdsBuffer = new StringBuffer();
+ String parentFeature = getFeatureName(parentFeatureID,conn);
int loop = 1;
while(rs.next())
{
- int fmin = rs.getInt("fmin")+1;
- int fmax = rs.getInt("fmax");
- long type_id = rs.getLong("type_id");
+ int fmin = rs.getInt("fmin")+1;
+ int fmax = rs.getInt("fmax");
+ long type_id = rs.getLong(6);
+ long prop_type_id = rs.getLong(7);
int strand = rs.getInt("strand");
String name = rs.getString("uniquename");
String typeName = getCvtermName(conn,type_id);
-
-// start with uniquename
- cdsBuffer.append("CHADO="+name+" ");
-
- if(strand == -1)
- cdsBuffer.append("complement(");
- cdsBuffer.append(fmin+"..");
- cdsBuffer.append(fmax);
- if(strand == -1)
- cdsBuffer.append(")");
-
- cdsBuffer.append(";");
- cdsBuffer.append("/"+typeName+"=\"");
- cdsBuffer.append(rs.getString("value")+"\"\n");
-
+ String propTypeName = getCvtermName(conn,prop_type_id);
+// make gff format
+
+ cdsBuffer.append(parentFeature+"\t"); // seqid
+ cdsBuffer.append("chado\t"); // source
+ cdsBuffer.append(typeName+"\t"); // type
+ cdsBuffer.append(fmin+"\t"); // start
+ cdsBuffer.append(fmax+"\t"); // end
+ cdsBuffer.append(".\t"); // score
+ if(strand == -1) // strand
+ cdsBuffer.append("-\t");
+ else
+ cdsBuffer.append("+\t");
+ cdsBuffer.append(".\t"); // phase
+ cdsBuffer.append("ID="+name+";"+propTypeName+"="+rs.getString("value")+"\n"); // attributes
progress_listener.progressMade("Read from database: "+name);
}
@@ -276,7 +295,7 @@ public class DatabaseDocument extends Document
rs.next();
name = rs.getString("name");
- return rs.getString("residues");
+ return "##FASTA\n>" + name + "\n" + rs.getString("residues");
}
@@ -378,8 +397,8 @@ public class DatabaseDocument extends Document
try
{
String dat = new java.util.Date().toString();
- bw = new BufferedWriter(new FileWriter(dat+":: "+logFileName, true));
- bw.write(logEntry);
+ bw = new BufferedWriter(new FileWriter(logFileName, true));
+ bw.write(dat+":: "+logEntry);
bw.newLine();
bw.flush();
}