diff --git a/uk/ac/sanger/artemis/SimpleEntryGroup.java b/uk/ac/sanger/artemis/SimpleEntryGroup.java
index 63d53fc542cd7a1c401fca324529c640dbf86fc1..2b896b74fed07223dee0fd21d79b7ed653847b83 100644
--- a/uk/ac/sanger/artemis/SimpleEntryGroup.java
+++ b/uk/ac/sanger/artemis/SimpleEntryGroup.java
@@ -20,18 +20,24 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/SimpleEntryGroup.java,v 1.4 2006-03-21 16:05:48 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/SimpleEntryGroup.java,v 1.5 2006-08-07 14:57:10 tjc Exp $
**/
package uk.ac.sanger.artemis;
import uk.ac.sanger.artemis.sequence.*;
+import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.StreamSequence;
import uk.ac.sanger.artemis.io.SimpleDocumentEntry;
+import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
+import uk.ac.sanger.artemis.io.DocumentEntry;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.ReadOnlyException;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.chado.ChadoTransactionManager;
+
+import java.io.IOException;
import java.util.Vector;
import java.util.NoSuchElementException;
@@ -41,7 +47,7 @@ import java.util.NoSuchElementException;
* once. Objects of this class act a bit like single Entry objects.
*
* @author Kim Rutherford
- * @version $Id: SimpleEntryGroup.java,v 1.4 2006-03-21 16:05:48 tjc Exp $
+ * @version $Id: SimpleEntryGroup.java,v 1.5 2006-08-07 14:57:10 tjc Exp $
**/
public class SimpleEntryGroup extends EntryVector
@@ -693,7 +699,32 @@ public class SimpleEntryGroup extends EntryVector
**/
public Entry createEntry()
{
- final Entry new_entry = Entry.newEntry(getBases());
+ Entry new_entry = null;
+ uk.ac.sanger.artemis.io.Entry default_entry =
+ getDefaultEntry().getEMBLEntry();
+ if(default_entry != null &&
+ default_entry instanceof DatabaseDocumentEntry)
+ {
+ DatabaseDocument doc =
+ (DatabaseDocument)((DocumentEntry)getDefaultEntry().getEMBLEntry()).getDocument();
+ DatabaseDocument new_doc = doc.createDatabaseDocument();
+
+ try
+ {
+ DatabaseDocumentEntry new_doc_entry =
+ new DatabaseDocumentEntry();
+ new_doc_entry.setDocument(new_doc);
+ new_entry = new Entry(getBases(), new_doc_entry);
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ }
+ else
+ new_entry = Entry.newEntry(getBases());
+
add(new_entry);
return new_entry;
}
diff --git a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
index baafc54ecb32b1ef7eef3b6872fe01806f7186d8..bac513adc6a431af702f85b82a955fd019503fdd 100644
--- a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
+++ b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
@@ -384,7 +384,7 @@ public class DatabaseEntrySource implements EntrySource
{
DatabaseDocument doc = new DatabaseDocument(location, pfield, id,
schema, splitGFFEntry, progress_listener);
- db_entry = new DatabaseDocumentEntry(doc);
+ db_entry = new DatabaseDocumentEntry(doc, null);
}
final Bases real_bases;
@@ -437,7 +437,7 @@ public class DatabaseEntrySource implements EntrySource
db_entry = new DatabaseDocumentEntry[new_docs.length];
for(int i = 0; i < new_docs.length; i++)
- db_entry[i] = new DatabaseDocumentEntry(new_docs[i]);
+ db_entry[i] = new DatabaseDocumentEntry(new_docs[i], null);
}
catch (EntryInformationException e)
{
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
index 0952586ca9993ec1b459b4557294d14ec4643a60..044bcaa1a15310ec88f02556e896a2fe1afd6f0c 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.11 2006-08-04 11:05:53 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.12 2006-08-07 14:57:10 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -44,6 +44,7 @@ import uk.ac.sanger.artemis.SelectionChangeEvent;
import uk.ac.sanger.artemis.SelectionChangeListener;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.FeatureChangeEvent;
import uk.ac.sanger.artemis.FeatureChangeListener;
import uk.ac.sanger.artemis.GotoEventSource;
@@ -301,16 +302,20 @@ public class GeneBuilderFrame extends JFrame
}
break;
case EntryChangeEvent.FEATURE_ADDED:
+ Qualifier parent_qualifier =
+ qualifiers.getQualifierByName("Parent");
+
+ if(parent_qualifier == null)
+ return;
tree.addNode(event.getFeature());
feature.addFeatureChangeListener(this);
- String parent =
- (String)qualifiers.getQualifierByName("Parent").getValues().get(0);
-
+ String parent = (String)parent_qualifier.getValues().get(0);
String gene_name = null;
try
{
- gene_name = (String)chado_gene.getGene().getQualifierByName("ID").getValues().get(0);
+ gene_name =
+ (String)chado_gene.getGene().getQualifierByName("ID").getValues().get(0);
}
catch(InvalidRelationException e)
{
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
index 36cf912bba4ce02d5a87be2cdd0933e560863b6e..fd115cbdd888aad9e1291adf349ffe444fc7fc87 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.18 2006-08-04 11:05:53 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.19 2006-08-07 14:57:10 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -658,69 +658,69 @@ public class GeneViewerPanel extends JPanel
List exons = chado_gene.getExonsOfTranscript(
getFeatureID( embl_transcript ));
- if(exons == null)
- return;
-
ypos += border*2;
- boolean last_segment = false;
-
- // build from artemis objects
- for(int i=0; i<exons.size(); i++)
+ if(exons != null)
{
- int last_ex_start = 0;
- int last_ex_end = 0;
- int last_ypos = 0;
-
- Feature embl_exon = (Feature)exons.get(i);
+ boolean last_segment = false;
+
+ // build from artemis objects
+ for(int i=0; i<exons.size(); i++)
+ {
+ int last_ex_start = 0;
+ int last_ex_end = 0;
+ int last_ypos = 0;
- uk.ac.sanger.artemis.Feature exon =
- (uk.ac.sanger.artemis.Feature)embl_exon.getUserData();
+ Feature embl_exon = (Feature) exons.get(i);
- RangeVector ranges = exon.getLocation().getRanges();
- FeatureSegmentVector segments = null;
-
- try
- {
- segments = exon.getSegments();
- }
- catch(NullPointerException npe){}
-
- float selected_size;
- for(int j=0; j<ranges.size(); j++)
- {
- Range range = (Range)ranges.get(j);
+ uk.ac.sanger.artemis.Feature exon =
+ (uk.ac.sanger.artemis.Feature)embl_exon.getUserData();
- int ex_start = border+(int)((range.getStart()-start)*fraction);
- int ex_end = border+(int)((range.getEnd()-start)*fraction);
+ RangeVector ranges = exon.getLocation().getRanges();
+ FeatureSegmentVector segments = null;
- if(exon.getColour() != null)
- g2d.setColor( exon.getColour() );
+ try
+ {
+ segments = exon.getSegments();
+ }
+ catch(NullPointerException npe)
+ {
+ }
- if(j == ranges.size()-1)
- last_segment = true;
-
- selected_size = 2.f;
- if(segments != null)
+ float selected_size;
+ for(int j = 0; j < ranges.size(); j++)
{
- for(int k=0; k<segments.size(); k++)
+ Range range = (Range) ranges.get(j);
+
+ int ex_start = border + (int)((range.getStart() - start) * fraction);
+ int ex_end = border + (int)((range.getEnd() - start) * fraction);
+
+ if(exon.getColour() != null)
+ g2d.setColor(exon.getColour());
+
+ if(j == ranges.size() - 1)
+ last_segment = true;
+
+ selected_size = 2.f;
+ if(segments != null)
{
- FeatureSegment segment = segments.elementAt(k);
- if(range.equals(segment.getRawRange()) &&
- selection.contains(segment))
- selected_size = 4.f;
+ for(int k = 0; k < segments.size(); k++)
+ {
+ FeatureSegment segment = segments.elementAt(k);
+ if(range.equals(segment.getRawRange())
+ && selection.contains(segment))
+ selected_size = 4.f;
+ }
}
- }
-
- drawExons(g2d, ex_start, ex_end,
- last_ex_start, last_ex_end, last_ypos,
- 0, ypos, exon.getColour(),
- 2, exon.isForwardFeature(),
- last_segment, selection.contains(exon), selected_size);
- last_ex_end = ex_end;
- last_ex_start = ex_start;
- last_ypos = ypos;
+ drawExons(g2d, ex_start, ex_end, last_ex_start, last_ex_end,
+ last_ypos, 0, ypos, exon.getColour(), 2, exon.isForwardFeature(),
+ last_segment, selection.contains(exon), selected_size);
+
+ last_ex_end = ex_end;
+ last_ex_start = ex_start;
+ last_ypos = ypos;
+ }
}
}
@@ -1255,8 +1255,6 @@ public class GeneViewerPanel extends JPanel
*/
class PopupListener extends MouseAdapter
{
- private JMenuItem exonMenu = new JMenuItem();
- private ActionListener exonListener;
public void mousePressed(MouseEvent e)
{
maybeShowPopup(e);
@@ -1271,39 +1269,10 @@ public class GeneViewerPanel extends JPanel
{
if(e.isPopupTrigger())
{
- exonMenu.removeActionListener(exonListener);
final Feature embl_transcript = getTranscriptAt(e.getPoint());
if(embl_transcript == null)
return;
- try
- {
- final String uniquename =
- (String)(embl_transcript.getQualifierByName("ID").getValues().get(0));
-
- exonMenu.setText("Show exon list for "+uniquename);
- exonListener = new ActionListener()
- {
- public void actionPerformed(ActionEvent event)
- {
- try
- {
- showExonsList(uniquename);
- }
- catch(InvalidRelationException e)
- {
- e.printStackTrace();
- }
- }
- };
- exonMenu.addActionListener(exonListener);
- popup.add(exonMenu);
- }
- catch(InvalidRelationException e1)
- {
- e1.printStackTrace();
- }
-
popup.show(e.getComponent(),
e.getX(), e.getY());
}
diff --git a/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java b/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java
index 46bf3ec584d9624689b3920429ea38d23bee132c..051e6c92942dd7adb492ddb9a5270e35c57cd37a 100644
--- a/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java
@@ -38,12 +38,18 @@ public class DatabaseDocumentEntry extends GFFDocumentEntry
implements DocumentEntry
{
- public DatabaseDocumentEntry(final Document doc)
+ public DatabaseDocumentEntry(final Document doc,
+ final ReadListener listener)
throws EntryInformationException, IOException
{
- super(doc,null);
+ super(doc,listener);
}
+ public DatabaseDocumentEntry()
+ {
+ super(new GFFEntryInformation());
+ }
+
/**
* Returns true if and only if this entry is read only. For now this
* always returns true - BlastDocumentEntry objects can't be changed.
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 4e05ce75a745dc65d3da4ea3bb40d9c45cac2831..c8bb170ba51266e30b3851ee8c2112bcca8e5fc9 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.42 2006-08-04 11:00:30 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.43 2006-08-07 14:57:10 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -40,7 +40,7 @@ import java.text.SimpleDateFormat;
* A StreamFeature that thinks it is a GFF feature.
*
* @author Kim Rutherford
- * @version $Id: GFFStreamFeature.java,v 1.42 2006-08-04 11:00:30 tjc Exp $
+ * @version $Id: GFFStreamFeature.java,v 1.43 2006-08-07 14:57:10 tjc Exp $
**/
public class GFFStreamFeature extends SimpleDocumentFeature
@@ -86,6 +86,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
setKey(key);
setLocation(location);
setQualifiers(qualifiers);
+
+ /*
if(getQualifierByName("score") == null)
setQualifier(new Qualifier("score", "."));
@@ -94,7 +96,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(getQualifierByName("gff_seqname") == null)
setQualifier(new Qualifier("gff_seqname", "."));
-
+ */
if(getQualifierByName("ID") == null)
setQualifier(new Qualifier("ID", "to_be_set"));
@@ -207,11 +209,14 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
}
- final Qualifier gff_seqname =
- new Qualifier("gff_seqname", decode((String)line_bits.elementAt(0)));
-
- setQualifier(gff_seqname);
+ if( !((String)line_bits.elementAt(0)).equals("null") )
+ {
+ final Qualifier gff_seqname =
+ new Qualifier("gff_seqname", decode((String)line_bits.elementAt(0)));
+ setQualifier(gff_seqname);
+ }
+
final Key key = new Key((String)line_bits.elementAt(2));
setKey(key);
@@ -219,10 +224,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
new Qualifier("gff_source", (String)line_bits.elementAt(1));
setQualifier(source_qualifier);
- final Qualifier score_qualifier =
- new Qualifier("score", (String)line_bits.elementAt(5));
- setQualifier(score_qualifier);
-
+ if( !((String)line_bits.elementAt(5)).equals(".") )
+ {
+ final Qualifier score_qualifier =
+ new Qualifier("score", (String)line_bits.elementAt(5));
+ setQualifier(score_qualifier);
+ }
+
String frame = (String)line_bits.elementAt(7);
if(frame.equals ("0"))
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 58a4195c12fb4765bd2216fbd4db6cde86fb77f7..96836b2b6833f33e3522559135330f89d5144e6f 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -109,6 +109,7 @@ public class DatabaseDocument extends Document
}
}
+
/**
*
* Create a new Document from a database.
@@ -244,14 +245,13 @@ public class DatabaseDocument extends Document
this.name = name;
}
- /**
- * Return a Document with the last element stripped off.
- */
- public Document getParent()
+
+ public DatabaseDocument createDatabaseDocument()
{
- return null;
+ return new DatabaseDocument( (String)getLocation(), pfield,
+ feature_id, schema );
}
-
+
/**
* Return true if and only if the Document refered to by this object exists
* and is readable. Always returns true.
@@ -310,7 +310,7 @@ public class DatabaseDocument extends Document
if(gff_buffer[0].size() > 0)
entry.append(gff_buffer[0]);
- getSequence(dao, entry);
+ getChadoSequence(dao, entry);
}
else
{
@@ -320,7 +320,7 @@ public class DatabaseDocument extends Document
entry.append(gff_buffer[i]);
}
- getSequence(dao, entry);
+ getChadoSequence(dao, entry);
}
instream = new ByteArrayInputStream(entry.getBytes());
@@ -784,7 +784,7 @@ public class DatabaseDocument extends Document
* @return the resulting buffer
* @throws java.sql.SQLException
*/
- private ByteBuffer getSequence(ChadoDAO dao, ByteBuffer buff)
+ private ByteBuffer getChadoSequence(ChadoDAO dao, ByteBuffer buff)
throws java.sql.SQLException
{
ChadoFeature feature = dao.getSequence(Integer.parseInt(feature_id),
@@ -1173,4 +1173,9 @@ public class DatabaseDocument extends Document
e.printStackTrace();
}
}
+
+ public Document getParent()
+ {
+ return null;
+ }
}