diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index 21c8d82c401dc3d598263bde684cf29e237f3081..5b6428efb10f9fa4c0e81171707f9a197a9d7746 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.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/EntryEdit.java,v 1.65 2008-06-16 12:11:01 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryEdit.java,v 1.66 2008-06-17 15:15:54 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -31,6 +31,7 @@ import uk.ac.sanger.artemis.chado.ClusterLazyQualifierValue;
import uk.ac.sanger.artemis.chado.SimilarityLazyQualifierValue;
import uk.ac.sanger.artemis.components.filetree.FileList;
import uk.ac.sanger.artemis.components.filetree.FileManager;
+import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.editor.BigPane;
import uk.ac.sanger.artemis.editor.FastaTextPane;
import uk.ac.sanger.artemis.editor.HitInfo;
@@ -67,7 +68,7 @@ import java.util.Vector;
* Each object of this class is used to edit an EntryGroup object.
*
* @author Kim Rutherford
- * @version $Id: EntryEdit.java,v 1.65 2008-06-16 12:11:01 tjc Exp $
+ * @version $Id: EntryEdit.java,v 1.66 2008-06-17 15:15:54 tjc Exp $
*
*/
public class EntryEdit extends JFrame
@@ -702,69 +703,8 @@ public class EntryEdit extends JFrame
}
- if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry)
- {
- final List lazySimilarityValues = new Vector();
- final List lazyClusterValues = new Vector();
- final FeatureVector features = entry.getAllFeatures();
- // find any lazy values to be loaded
-
-
- for(int i=0; i<features.size(); i++)
- {
- QualifierVector qualifiers = features.elementAt(i).getQualifiers();
- for(int j=0; j<qualifiers.size(); j++)
- {
- Qualifier qualifier = (Qualifier)qualifiers.get(j);
- if(qualifier instanceof QualifierLazyLoading &&
- !((QualifierLazyLoading)qualifier).isAllLazyValuesLoaded())
- {
- if( ((QualifierLazyLoading)qualifier).getValue(0) instanceof SimilarityLazyQualifierValue )
- lazySimilarityValues.addAll( ((QualifierLazyLoading)qualifier).getLazyValues() );
- else if( ((QualifierLazyLoading)qualifier).getValue(0) instanceof ClusterLazyQualifierValue )
- {
- lazyClusterValues.addAll( ((QualifierLazyLoading)qualifier).getLazyValues() );
- }
- else
- ((QualifierLazyLoading)qualifier).setForceLoad(true);
- }
- }
- }
-
- if(lazySimilarityValues.size() > 0 || lazyClusterValues.size() > 0)
- {
- int n = JOptionPane.showConfirmDialog(null,
- "Load and write to file all qualifers from the database?"+
- "\nThis may take a few minutes.",
- "Load All Data",
- JOptionPane.YES_NO_OPTION);
-
- if(n == JOptionPane.YES_OPTION)
- {
- setCursor(new Cursor(Cursor.WAIT_CURSOR));
- final DatabaseDocument document =
- (DatabaseDocument)((DocumentEntry)entry.getEMBLEntry()).getDocument();
-
- if(lazySimilarityValues.size() > 0)
- SimilarityLazyQualifierValue.bulkRetrieve(lazySimilarityValues,document);
-
- if(lazyClusterValues.size() > 0)
- ClusterLazyQualifierValue.setClusterFromValueList(lazyClusterValues, document);
-
- for(int i=0; i<features.size(); i++)
- {
- QualifierVector qualifiers = features.elementAt(i).getQualifiers();
- for(int j=0; j<qualifiers.size(); j++)
- {
- Qualifier qualifier = (Qualifier)qualifiers.get(j);
- if(qualifier instanceof QualifierLazyLoading)
- ((QualifierLazyLoading)qualifier).setForceLoad(true);
- }
- }
- setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
- }
- }
- }
+ if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry)
+ GeneUtils.lazyLoadAll(entry, this);
// if(!System.getProperty("os.arch").equals("alpha"))
diff --git a/uk/ac/sanger/artemis/components/ReadAndWriteEntry.java b/uk/ac/sanger/artemis/components/ReadAndWriteEntry.java
index 646d0fc54faec1b772b40de493f4c197f52ff5b2..63323579e96f47fc30d42784cd715d43eef5c073 100644
--- a/uk/ac/sanger/artemis/components/ReadAndWriteEntry.java
+++ b/uk/ac/sanger/artemis/components/ReadAndWriteEntry.java
@@ -26,9 +26,11 @@ import java.io.File;
import java.io.IOException;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
+import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.io.DocumentEntryFactory;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
@@ -39,13 +41,19 @@ class ReadAndWriteEntry
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(ReadAndWriteEntry.class);
-
-
-
- public static Entry readEntryFromDatabase(final String srcFeatureId)
+
+ /**
+ * Read from the database, given a srcFeature uniquename
+ * @param uniqueName
+ * @return
+ * @throws OutOfRangeException
+ * @throws NoSequenceException
+ * @throws IOException
+ */
+ public static Entry readEntryFromDatabase(final String uniqueName)
throws OutOfRangeException, NoSequenceException, IOException
{
- DatabaseEntrySource entry_source = new DatabaseEntrySource();
+ final DatabaseEntrySource entry_source = new DatabaseEntrySource();
boolean promptUser = true;
if(System.getProperty("read_only") != null)
promptUser = false;
@@ -60,6 +68,8 @@ class ReadAndWriteEntry
if(userName.startsWith("user="))
userName = userName.substring(5);
+ final String srcFeatureId = getFeatureId(entry_source, uniqueName);
+
final InputStreamProgressListener stream_progress_listener =
new InputStreamProgressListener()
{
@@ -75,26 +85,47 @@ class ReadAndWriteEntry
}
};
return entry_source.getEntry(srcFeatureId, userName,
- stream_progress_listener);
+ stream_progress_listener);
}
- public static void writeEntry(final Entry entry)
+ /**
+ * Write entry to a file
+ * @param entry
+ * @param file
+ * @throws IOException
+ * @throws EntryInformationException
+ */
+ public static void writeEntry(final Entry entry, final File file)
throws IOException, EntryInformationException
{
- File file = new File("x");
+ System.out.println(file.getAbsolutePath());
+ GeneUtils.lazyLoadAll(entry, null);
entry.save(file, DocumentEntryFactory.EMBL_FORMAT, false);
}
+ /**
+ * Get feature id
+ * @param entry_source
+ * @param srcUniqueName
+ * @return
+ */
+ public static String getFeatureId(
+ final DatabaseEntrySource entry_source, final String srcUniqueName)
+ {
+ final DatabaseDocument doc = entry_source.getDatabaseDocument();
+ org.gmod.schema.sequence.Feature feature = doc.getFeatureByUniquename(srcUniqueName);
+ return Integer.toString(feature.getFeatureId());
+ }
+
public static void main(final String args[])
{
try
{
- Entry entry = ReadAndWriteEntry.readEntryFromDatabase("1");
- ReadAndWriteEntry.writeEntry(entry);
+ Entry entry = ReadAndWriteEntry.readEntryFromDatabase("Pf3D7_03");
+ ReadAndWriteEntry.writeEntry(entry,new File("Pf3D7_03"));
}
catch(Exception e)
{
- // TODO Auto-generated catch block
e.printStackTrace();
}
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
index b53ff5c2a82feb5d2fde95132105b010aace42cc..639560e761960478aaf8ccc339ad86a8de0f2bab 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java
@@ -21,6 +21,7 @@
package uk.ac.sanger.artemis.components.genebuilder;
import java.awt.BorderLayout;
+import java.awt.Cursor;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Collection;
@@ -47,11 +48,14 @@ import org.gmod.schema.sequence.FeatureDbXRef;
import org.gmod.schema.sequence.FeaturePub;
import org.gmod.schema.sequence.FeatureSynonym;
+import uk.ac.sanger.artemis.chado.ClusterLazyQualifierValue;
+import uk.ac.sanger.artemis.chado.SimilarityLazyQualifierValue;
import uk.ac.sanger.artemis.components.EditMenu;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.SelectionMenu;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
+import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.Feature;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
@@ -60,6 +64,7 @@ import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.KeyVector;
import uk.ac.sanger.artemis.io.Location;
import uk.ac.sanger.artemis.io.Qualifier;
+import uk.ac.sanger.artemis.io.QualifierLazyLoading;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
@@ -270,6 +275,71 @@ public class GeneUtils
feature.setQualifier(new Qualifier("ID", feature.getSegmentID( rv )));
}
+ public static void lazyLoadAll(final Entry entry, final JFrame parent)
+ {
+ final List lazySimilarityValues = new Vector();
+ final List lazyClusterValues = new Vector();
+ final FeatureVector features = entry.getAllFeatures();
+ // find any lazy values to be loaded
+
+
+ for(int i=0; i<features.size(); i++)
+ {
+ QualifierVector qualifiers = features.elementAt(i).getQualifiers();
+ for(int j=0; j<qualifiers.size(); j++)
+ {
+ Qualifier qualifier = (Qualifier)qualifiers.get(j);
+ if(qualifier instanceof QualifierLazyLoading &&
+ !((QualifierLazyLoading)qualifier).isAllLazyValuesLoaded())
+ {
+ if( ((QualifierLazyLoading)qualifier).getValue(0) instanceof SimilarityLazyQualifierValue )
+ lazySimilarityValues.addAll( ((QualifierLazyLoading)qualifier).getLazyValues() );
+ else if( ((QualifierLazyLoading)qualifier).getValue(0) instanceof ClusterLazyQualifierValue )
+ {
+ lazyClusterValues.addAll( ((QualifierLazyLoading)qualifier).getLazyValues() );
+ }
+ else
+ ((QualifierLazyLoading)qualifier).setForceLoad(true);
+ }
+ }
+ }
+
+ if(lazySimilarityValues.size() > 0 || lazyClusterValues.size() > 0)
+ {
+ int n = JOptionPane.showConfirmDialog(null,
+ "Load and write to file all qualifers from the database?"+
+ "\nThis may take a few minutes.",
+ "Load All Data",
+ JOptionPane.YES_NO_OPTION);
+
+ if(n == JOptionPane.YES_OPTION)
+ {
+ if(parent != null)
+ parent.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ final DatabaseDocument document =
+ (DatabaseDocument)((DocumentEntry)entry.getEMBLEntry()).getDocument();
+
+ if(lazySimilarityValues.size() > 0)
+ SimilarityLazyQualifierValue.bulkRetrieve(lazySimilarityValues,document);
+
+ if(lazyClusterValues.size() > 0)
+ ClusterLazyQualifierValue.setClusterFromValueList(lazyClusterValues, document);
+
+ for(int i=0; i<features.size(); i++)
+ {
+ QualifierVector qualifiers = features.elementAt(i).getQualifiers();
+ for(int j=0; j<qualifiers.size(); j++)
+ {
+ Qualifier qualifier = (Qualifier)qualifiers.get(j);
+ if(qualifier instanceof QualifierLazyLoading)
+ ((QualifierLazyLoading)qualifier).setForceLoad(true);
+ }
+ }
+ if(parent != null)
+ parent.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ }
+ }
+ }
/**
* Sorts the elements of the vector using a simple O(n^2) selection
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index 2c751d3efe3d722ad1ff4e29b97b77de0e3bb82a..423e2e65615fbfef5005d821db87f433301c06da 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.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/PublicDBDocumentEntry.java,v 1.9 2008-06-16 12:13:14 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java,v 1.10 2008-06-17 15:15:54 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -36,7 +36,7 @@ import java.io.IOException;
* entry.
*
* @author Kim Rutherford
- * @version $Id: PublicDBDocumentEntry.java,v 1.9 2008-06-16 12:13:14 tjc Exp $
+ * @version $Id: PublicDBDocumentEntry.java,v 1.10 2008-06-17 15:15:54 tjc Exp $
**/
public class PublicDBDocumentEntry extends SimpleDocumentEntry
@@ -165,24 +165,27 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
qualifiers.addAll(chadoGene.getGene().getQualifiers().copy());
}
+
+ final String[][] QUALIFIERS_TO_MAP =
+ {
+ {"comment", "note"},
+ {"Dbxref", "db_xref"},
+ {"private", "note"},
+ {"orthologous_to", "ortholog"},
+ {"paralogous_to", "paralog"}
+ };
+
try
{
- int index = qualifiers.indexOfQualifierWithName("comment");
-
- if(index > -1)
- {
- StringVector comments = ((Qualifier)qualifiers.get(index)).getValues();
- Qualifier noteQualifier = new Qualifier("note", comments);
- qualifiers.setQualifier(noteQualifier);
- }
+ for(int i=0; i<QUALIFIERS_TO_MAP.length; i++)
+ changeQualifierName(qualifiers, QUALIFIERS_TO_MAP[i][0], QUALIFIERS_TO_MAP[i][1]);
for(int i=0; i<QUALIFIERS_TO_REMOVE.length; i++)
{
- index = qualifiers.indexOfQualifierWithName(QUALIFIERS_TO_REMOVE[i]);
- if(index > -1)
- qualifiers.removeElementAt(index);
+ qualifiers.removeQualifierByName(QUALIFIERS_TO_REMOVE[i]);
+ qualifiers.removeQualifierByName(QUALIFIERS_TO_REMOVE[i]);
+ qualifiers.removeQualifierByName(QUALIFIERS_TO_REMOVE[i]);
}
-
if(key.getKeyString().equals(DatabaseDocument.EXONMODEL))
key = new Key("CDS");
@@ -196,6 +199,8 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
return null;
else if(key.getKeyString().equals("gene"))
return null;
+ else if(key.getKeyString().equals("centromere"))
+ return null;
else if(key.getKeyString().equals("transcript") ||
key.getKeyString().equals("mRNA"))
return null;
@@ -273,6 +278,27 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
}
}
+ /**
+ * Change the name of a qualifier
+ * @param qualifiers
+ * @param oldName
+ * @param newName
+ */
+ private void changeQualifierName(final QualifierVector qualifiers,
+ final String oldName,
+ final String newName)
+ {
+ int index = qualifiers.indexOfQualifierWithName(oldName);
+
+ if(index > -1)
+ {
+ StringVector values = ((Qualifier)qualifiers.get(index)).getValues();
+ qualifiers.removeQualifierByName(oldName);
+ Qualifier newQualifier = new Qualifier(newName, values);
+ qualifiers.setQualifier(newQualifier);
+ }
+ }
+
/**
* If the given Sequence can be added directly to this Entry, then return a
* copy of it, otherwise create and return a new feature of the appropriate
@@ -280,7 +306,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
**/
protected StreamSequence makeNativeSequence (final Sequence sequence)
{
- if(this instanceof EmblDocumentEntry)
+ if(this instanceof EmblDocumentEntry)
return new EmblStreamSequence (sequence);
else
return new GenbankStreamSequence (sequence);