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Commit 3b41b3de authored by tjc's avatar tjc
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updates 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9708 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+ 198
− 48
View file @ 3b41b3de
......@@ -38,14 +38,25 @@ import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextArea;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeaturePredicate;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.SimpleEntryGroup;
import uk.ac.sanger.artemis.chado.ChadoTransactionManager;
import uk.ac.sanger.artemis.components.genebuilder.GeneEdit;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.PartialSequence;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
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;
class TransferAnnotationTool extends JFrame
{
......@@ -62,9 +73,12 @@ class TransferAnnotationTool extends JFrame
"orthologous_to",
"paralogous_to",
"fasta_file",
"blastp_file"
"blastp_file",
"blastn_file",
"systematic_id",
"previous_systematic_id"
};
public TransferAnnotationTool(final Feature feature,
final EntryGroup entryGroup)
{
......@@ -106,6 +120,8 @@ class TransferAnnotationTool extends JFrame
c.gridy = ++nrows;
}
c.gridx = 1;
c.gridy = 1;
c.gridheight = nrows;
......@@ -132,16 +148,23 @@ class TransferAnnotationTool extends JFrame
});
pane.add(toggle, c);
final JCheckBox sameKeyCheckBox = new JCheckBox("Add to feature of same key", true);
final JButton transfer = new JButton(">>TRANSFER");
transfer.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
transferAnnotation(qualifierCheckBoxes, geneNameTextArea, feature, entryGroup);
transferAnnotation(qualifierCheckBoxes, geneNameTextArea, feature,
entryGroup, sameKeyCheckBox.isSelected());
}
});
c.gridx = 1;
pane.add(transfer, c);
c.gridy = ++nrows;
c.gridx = 1;
pane.add(sameKeyCheckBox, c);
final JButton close = new JButton("CLOSE");
close.addActionListener(new ActionListener()
......@@ -182,11 +205,12 @@ class TransferAnnotationTool extends JFrame
*/
private void transferAnnotation(final Vector qualifierCheckBoxes,
final JTextArea geneNameTextArea,
final Feature feature,
final EntryGroup entryGroup)
final Feature orginatingFeature,
final EntryGroup entryGroup,
final boolean sameKey)
{
// transfer selected annotation to genes
final QualifierVector qualifiers = feature.getQualifiers();
final QualifierVector qualifiers = orginatingFeature.getQualifiers();
final QualifierVector qualifiersToTransfer = new QualifierVector();
for(int i = 0; i < qualifierCheckBoxes.size(); i++)
{
......@@ -198,59 +222,185 @@ class TransferAnnotationTool extends JFrame
}
}
final String geneNames[] = geneNameTextArea.getText().split("\\s");
final String key = feature.getKey().getKeyString();
String geneNames[] = geneNameTextArea.getText().split("\\s");
final String key = orginatingFeature.getKey().getKeyString();
final FeatureVector features = entryGroup.getAllFeatures();
final FeaturePredicate predicate = new FeaturePredicate()
// transfer selected annotation
entryGroup.getActionController().startAction();
geneNames = transfer(features, qualifiersToTransfer, key,
sameKey, GeneUtils.isDatabaseEntry(entryGroup), geneNames);
entryGroup.getActionController().endAction();
//
// Commit changes to genes not in Artemis but in the database
//
/* DatabaseDocumentEntry db_entry =
(DatabaseDocumentEntry) orginatingFeature.getEntry().getEMBLEntry();
DatabaseDocument doc = (DatabaseDocument) db_entry.getDocument();
for(int i=0; i<geneNames.length; i++)
{
public boolean testPredicate(Feature feature)
System.out.println(geneNames[i]);
DatabaseDocumentEntry newDbEntry = GeneEdit.makeGeneEntry(null, geneNames[i], doc, null);
char[] c = new char[1];
PartialSequence ps = new PartialSequence(c, 100, 0, null, null);
newDbEntry.setPartialSequence(ps);
Entry entry = null;
try
{
entry = new Entry(newDbEntry);
}
catch(Exception e) { e.printStackTrace(); }
SimpleEntryGroup entry_group = new SimpleEntryGroup();
entry_group.addElement(entry);
ChadoTransactionManager ctm = new ChadoTransactionManager();
entry_group.addFeatureChangeListener(ctm);
entry_group.addEntryChangeListener(ctm);
ctm.setEntryGroup(entry_group);
geneNames = transfer(entry.getAllFeatures(), qualifiersToTransfer, key,
sameKey, true, geneNames);
ChadoTransactionManager.commit(
(DatabaseDocument)newDbEntry.getDocument(), false, ctm);
//if(newDbEntry != null)
// GeneEdit.showGeneEditor(null, geneNames[i], newDbEntry);
}*/
}
/**
*
* @param features
* @param qualifiersToTransfer
* @param key
* @param sameKey
* @param isDatabaseEntry
* @param geneNames
* @return
*/
private String[] transfer(final FeatureVector features,
final QualifierVector qualifiersToTransfer,
final String key,
final boolean sameKey,
final boolean isDatabaseEntry,
String[] geneNames)
{
final TransferFeaturePredicate predicate = new TransferFeaturePredicate(
key, sameKey, isDatabaseEntry, geneNames);
for (int i = 0; i < features.size(); i++)
{
Feature thisFeature = features.elementAt(i);
if (predicate.testPredicate(thisFeature))
{
String chadoGeneName = null;
if(GeneUtils.isDatabaseEntry(entryGroup))
{
GFFStreamFeature gffFeature = ((GFFStreamFeature)feature.getEmblFeature());
if(gffFeature.getChadoGene() != null)
chadoGeneName = gffFeature.getChadoGene().getGeneUniqueName();
}
String thisFeatureSystematicName = feature.getSystematicName();
for(int i=0;i<geneNames.length;i++)
for (int j = 0; j < qualifiersToTransfer.size(); j++)
{
if(feature.getKey().getKeyString().equals(key))
Qualifier qualifier = (Qualifier) qualifiersToTransfer.elementAt(j);
try
{
if( geneNames[i].equals(thisFeatureSystematicName) ||
(chadoGeneName != null && geneNames[i].equals(chadoGeneName)) )
{
return true;
}
thisFeature.addQualifierValues(qualifier);
} catch (Exception e1)
{
e1.printStackTrace();
}
}
return false;
geneNames = removeArrayElement(geneNames, predicate.getGeneName());
}
};
}
return geneNames;
}
/**
* Remove a string from an array of strings. If the string appears multiple
* times in the array this method will delete all occurrences.
* @param strArr
* @param str
* @return
*/
private String[] removeArrayElement(final String strArr[], final String str)
{
String[] newarray = new String[strArr.length - 1];
int count = 0;
for(int i=0;i<strArr.length; i++)
{
if(strArr[i].equals(str))
continue;
// not found str return original array
if(count>=newarray.length)
return strArr;
newarray[count] = strArr[i];
count++;
}
// transfer selected annotation
entryGroup.getActionController().startAction();
for(int i=0; i<features.size(); i++)
if(count < newarray.length)
{
Feature thisFeature = features.elementAt(i);
if(predicate.testPredicate(thisFeature))
{
for(int j=0; j<qualifiersToTransfer.size(); j++)
{
Qualifier qualifier = (Qualifier) qualifiersToTransfer.elementAt(j);
try
{
thisFeature.addQualifierValues(qualifier);
}
catch (Exception e1)
{
e1.printStackTrace();
}
}
}
String[] tmparray = new String[count];
System.arraycopy(newarray, 0, tmparray, 0, count);
newarray = tmparray;
}
entryGroup.getActionController().endAction();
return newarray;
}
/**
* Test if the feature is nominated to have annotation transferred
* to it.
*/
class TransferFeaturePredicate implements FeaturePredicate
{
private String geneName;
private String key;
private boolean sameKey;
private boolean isDatabaseEntry;
private String[] geneNames;
public TransferFeaturePredicate(final String key,
final boolean sameKey,
final boolean isDatabaseEntry,
final String[] geneNames)
{
this.key = key;
this.sameKey = sameKey;
this.isDatabaseEntry = isDatabaseEntry;
this.geneNames = geneNames;
}
public boolean testPredicate(Feature targetFeature)
{
String targetKey = targetFeature.getKey().getKeyString();
if(!sameKey || !targetKey.equals(key))
return false;
String chadoGeneName = null;
if(isDatabaseEntry)
{
GFFStreamFeature gffFeature = ((GFFStreamFeature)targetFeature.getEmblFeature());
if(gffFeature.getChadoGene() != null)
chadoGeneName = gffFeature.getChadoGene().getGeneUniqueName();
}
String thisFeatureSystematicName = targetFeature.getSystematicName();
for(int i=0;i<geneNames.length;i++)
{
if( geneNames[i].equals(thisFeatureSystematicName) ||
(chadoGeneName != null && geneNames[i].equals(chadoGeneName)) )
{
geneName = geneNames[i];
return true;
}
}
return false;
}
public String getGeneName()
{
return geneName;
}
}
}
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