From 3b41b3dee4bba29ebd7c94b631e5a48228bc747c Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 9 Jan 2009 16:18:57 +0000
Subject: [PATCH] updates
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9708 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../components/TransferAnnotationTool.java | 246 ++++++++++++++----
1 file changed, 198 insertions(+), 48 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index 74e92767f..fdb113c41 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -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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