From 067c5bbdf6f36a20513f57a3f88210c5f4c3270f Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 27 Mar 2013 10:22:22 +0000
Subject: [PATCH] add getTransferValues() to change evidence code and add
source link to GO and product qualifiers
---
.../components/TransferAnnotationTool.java | 198 +++++++++++++-----
1 file changed, 149 insertions(+), 49 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index 795b21e95..cc44b783d 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -127,16 +127,14 @@ public class TransferAnnotationTool extends JFrame
final EntryGroup entryGroup,
final MatchPanel matchPanel)
{
- super("Transfer Annotation Tool :: "
- + feature.getIDString());
+ super("Transfer Annotation Tool :: "+ feature.getIDString());
this.matchPanel = matchPanel;
List<String> geneNames = null;
if(matchPanel != null)
- geneNames = matchPanel.getGeneNameList();
-
- FlowLayout flow = new FlowLayout(FlowLayout.LEFT);
- JPanel panel = new JPanel(flow);
+ geneNames = matchPanel.getGeneNameList();
+
+ JPanel panel = new JPanel(new FlowLayout(FlowLayout.LEFT));
JPanel pane = new JPanel(new GridBagLayout());
JScrollPane jsp = new JScrollPane(panel);
panel.setBackground(Color.white);
@@ -154,7 +152,6 @@ public class TransferAnnotationTool extends JFrame
geneNameCheckBoxes, geneNames);
addBottomButtons(qualifierPanels, geneNameCheckBoxes,
framePanel, entryGroup);
-
pack();
setVisible(true);
}
@@ -232,7 +229,6 @@ public class TransferAnnotationTool extends JFrame
while(it.hasNext())
{
GFFStreamFeature kid = (GFFStreamFeature)it.next();
-
if(id.equals( GeneUtils.getUniqueName(((GFFStreamFeature)kid)) ))
continue;
addQualifierPanel((Feature)kid.getUserData(), qualifierPanels,
@@ -272,7 +268,7 @@ public class TransferAnnotationTool extends JFrame
{
for(int i=0; i<qualifierPanels.size(); i++)
{
- QualifierPanel qP = (QualifierPanel)qualifierPanels.get(i);
+ QualifierPanel qP = qualifierPanels.get(i);
Enumeration<JCheckBox> enumQualifiers = qP.getQualifierCheckBoxes().keys();
while(enumQualifiers.hasMoreElements())
{
@@ -292,9 +288,10 @@ public class TransferAnnotationTool extends JFrame
{
for(int i = 0; i < geneNameCheckBoxes.size(); i++)
{
- JCheckBox cb = (JCheckBox) geneNameCheckBoxes.get(i);
+ JCheckBox cb = geneNameCheckBoxes.get(i);
cb.setSelected(!cb.isSelected());
}
+ geneNameBox.repaint();
}
});
xBox.add(toggleGeneList);
@@ -330,7 +327,7 @@ public class TransferAnnotationTool extends JFrame
c.gridx = 0;
pane.add(xBox, c);
- final List<String> clusterList = matchPanel.getGeneNameList(true);
+ final List<String> clusterList = (matchPanel == null ? null : matchPanel.getGeneNameList(true));
if(clusterList != null && !geneNames.contains(clusterList.get(0)))
{
final JButton importCluster = new JButton("Import Cluster Names");
@@ -383,7 +380,7 @@ public class TransferAnnotationTool extends JFrame
l.setFont(l.getFont().deriveFont(Font.BOLD));
l.setForeground(STEEL_BLUE);
pane.add(l, c);
-
+
c.gridy = ++nrows;
pane.add(qPanel, c);
c.weightx = 0.d;
@@ -407,7 +404,11 @@ public class TransferAnnotationTool extends JFrame
final JCheckBox overwriteCheckBox = new JCheckBox("Overwrite", false);
overwriteCheckBox.setToolTipText("overwrite rather than append values");
-
+
+ final JCheckBox cvCheckBox = new JCheckBox("Set evidence as ISO and link to source in WITH/FROM", false);
+ cvCheckBox.setToolTipText("for GO and Product qualifiers set the evidence as ISO (Inferred from\n"+
+ "Sequence Orthology) and add a link to the source in the WITH/FROM field");
+
Box buttonBox = Box.createHorizontalBox();
final JButton transfer = new JButton(">>TRANSFER");
transfer.setToolTipText("transfer annotation");
@@ -418,8 +419,7 @@ public class TransferAnnotationTool extends JFrame
if(overwriteCheckBox.isSelected())
{
int res = JOptionPane.showConfirmDialog(TransferAnnotationTool.this,
- "Overwrite selected annotation?",
- "Overwrite", JOptionPane.OK_CANCEL_OPTION);
+ "Overwrite selected annotation?", "Overwrite", JOptionPane.OK_CANCEL_OPTION);
if(res == JOptionPane.CANCEL_OPTION)
return;
}
@@ -429,11 +429,13 @@ public class TransferAnnotationTool extends JFrame
StringBuffer summary = new StringBuffer();
for(int i = 0; i < qualifierPanels.size(); i++)
{
- QualifierPanel qP = (QualifierPanel) qualifierPanels.get(i);
+ QualifierPanel qP = qualifierPanels.get(i);
int res = transferAnnotation(qP.getQualifierCheckBoxes(),
geneNameCheckBoxes, qP.getFeature(), entryGroup,
sameKeyCheckBox.isSelected(),
- overwriteCheckBox.isSelected(), buff, summary);
+ overwriteCheckBox.isSelected(),
+ cvCheckBox.isSelected(),
+ buff, summary);
if(res == -1)
break;
}
@@ -458,6 +460,7 @@ public class TransferAnnotationTool extends JFrame
yBox.add(transfer);
yBox.add(sameKeyCheckBox);
yBox.add(overwriteCheckBox);
+ yBox.add(cvCheckBox);
buttonBox.add(yBox);
final JButton close = new JButton("CLOSE");
@@ -503,19 +506,20 @@ public class TransferAnnotationTool extends JFrame
* @param overwrite
*/
protected static int transferAnnotation(
- final Hashtable<JCheckBox, Vector<JCheckBox>> qualifierCheckBoxes,
- final Vector<JCheckBox> geneNameCheckBoxes,
- final Feature orginatingFeature,
- final EntryGroup entryGroup,
- final boolean sameKey,
- final boolean overwrite,
- final StringBuffer buff,
- final StringBuffer genesUpdated)
+ final Hashtable<JCheckBox, Vector<JCheckBox>> qualifierCheckBoxes,
+ final Vector<JCheckBox> geneNameCheckBoxes,
+ final Feature orginatingFeature,
+ final EntryGroup entryGroup,
+ final boolean sameKey,
+ final boolean overwrite,
+ final boolean setEvidenceAndWithFrom,
+ final StringBuffer buff,
+ final StringBuffer genesUpdated)
{
// transfer selected annotation to genes
final QualifierVector qualifiers = orginatingFeature.getQualifiers();
final QualifierVector qualifiersToTransfer = new QualifierVector();
-
+
Enumeration<JCheckBox> enumQualifiers = qualifierCheckBoxes.keys();
while(enumQualifiers.hasMoreElements())
{
@@ -523,22 +527,26 @@ public class TransferAnnotationTool extends JFrame
if (cb.isSelected())
{
Vector<JCheckBox> qualifierValuesCheckBox = qualifierCheckBoxes.get(cb);
- StringVector values = qualifiers.getQualifierByName(cb.getText()).getValues();
+ final StringVector values = qualifiers.getQualifierByName(cb.getText()).getValues();
StringVector valuesToTransfer = new StringVector(values);
logger4j.debug("TRANSFER "+cb.getText());
for(int i=0; i<qualifierValuesCheckBox.size(); i++)
{
- JCheckBox valuesCb = (JCheckBox) qualifierValuesCheckBox.get(i);
+ JCheckBox valuesCb = qualifierValuesCheckBox.get(i);
if(!valuesCb.isSelected())
{
valuesToTransfer.remove(valuesCb.getText());
logger4j.debug("NOT TRANSFERING "+valuesCb.getText());
}
}
-
+
if(valuesToTransfer.size() < 1)
continue;
+
+ valuesToTransfer = new StringVector( getTransferValues(
+ setEvidenceAndWithFrom, orginatingFeature, cb.getText(), valuesToTransfer) );
+
qualifiersToTransfer.addElement(new Qualifier(cb.getText(), valuesToTransfer));
}
}
@@ -546,14 +554,13 @@ public class TransferAnnotationTool extends JFrame
int count = 0;
for(int i =0; i<geneNameCheckBoxes.size(); i++)
{
- if( ((JCheckBox)geneNameCheckBoxes.get(i)).isSelected() )
+ if( geneNameCheckBoxes.get(i).isSelected() )
count++;
}
if(count < 1)
{
- JOptionPane.showMessageDialog(null,
- "No genes selected.",
+ JOptionPane.showMessageDialog(null, "No genes selected.",
"Warning", JOptionPane.WARNING_MESSAGE);
return -1;
}
@@ -562,7 +569,7 @@ public class TransferAnnotationTool extends JFrame
count = 0;
for(int i =0; i<geneNameCheckBoxes.size(); i++)
{
- JCheckBox cb = (JCheckBox)geneNameCheckBoxes.get(i);
+ JCheckBox cb = geneNameCheckBoxes.get(i);
if( cb.isSelected() )
{
geneNames[count] = cb.getText();
@@ -576,7 +583,7 @@ public class TransferAnnotationTool extends JFrame
// transfer selected annotation
entryGroup.getActionController().startAction();
- geneNames = transfer(features, qualifiersToTransfer, key, sameKey, overwrite,
+ geneNames = transfer(features, qualifiersToTransfer, key, sameKey, overwrite,
GeneUtils.isDatabaseEntry(entryGroup), geneNames, genesUpdated);
entryGroup.getActionController().endAction();
@@ -584,7 +591,8 @@ public class TransferAnnotationTool extends JFrame
// Commit changes to genes not in Artemis but in the database
//
Vector<String> genesNotFound = null;
- if (orginatingFeature.getEntry().getEMBLEntry() instanceof DatabaseDocumentEntry)
+ if (geneNames != null &&
+ orginatingFeature.getEntry().getEMBLEntry() instanceof DatabaseDocumentEntry)
{
DatabaseDocumentEntry db_entry =
(DatabaseDocumentEntry) orginatingFeature.getEntry().getEMBLEntry();
@@ -638,7 +646,7 @@ public class TransferAnnotationTool extends JFrame
// GeneEdit.showGeneEditor(null, geneNames[i], newDbEntry);
}
}
-
+
if(genesNotFound != null)
JOptionPane.showMessageDialog(null,
"Gene(s) Not Found:\n"+genesNotFound.toString(),
@@ -676,7 +684,7 @@ public class TransferAnnotationTool extends JFrame
StringBuffer qualifierBuffer = new StringBuffer();
for (int j = 0; j < qualifiersToTransfer.size(); j++)
{
- Qualifier newQualifier = (Qualifier) qualifiersToTransfer.elementAt(j);
+ Qualifier newQualifier = qualifiersToTransfer.elementAt(j);
String qualifierName = newQualifier.getName();
try
{
@@ -709,6 +717,7 @@ public class TransferAnnotationTool extends JFrame
e1.printStackTrace();
}
}
+
geneNames = removeArrayElement(geneNames, predicate.getGeneName());
if(qualifierBuffer.length() > 0)
genesUpdated.append(thisFeature.getSystematicName()+
@@ -782,7 +791,11 @@ public class TransferAnnotationTool extends JFrame
private static String[] removeArrayElement(final String strArr[], final String str)
{
if(strArr.length == 1)
+ {
+ if(strArr[0].equals(str))
+ return null;
return strArr;
+ }
String[] newarray = new String[strArr.length - 1];
int count = 0;
for (int i = 0; i < strArr.length; i++)
@@ -803,9 +816,94 @@ public class TransferAnnotationTool extends JFrame
System.arraycopy(newarray, 0, tmparray, 0, count);
newarray = tmparray;
}
-
return newarray;
}
+
+ /**
+ * Optionally transfer GO fields with evidence code ISO and link back to
+ * the original source in the WITH/FROM column.
+ * @param setEvidenceAndWithFrom
+ * @param feature
+ * @param qName
+ * @param values
+ * @return
+ */
+ private static StringVector getTransferValues(final boolean setEvidenceAndWithFrom,
+ final Feature feature,
+ final String qName,
+ final StringVector values)
+ {
+ if(!setEvidenceAndWithFrom)
+ return values;
+
+ if(qName.equals("GO") || qName.equals("product"))
+ {
+ final StringVector tvalues = new StringVector();
+ final String gene = getGeneName(feature);
+ for (int i = 0; i < values.size(); i++)
+ {
+ String val = changeField("evidence=",
+ "Inferred from Sequence Orthology",
+ null, values.get(i));
+
+ if(gene != null)
+ val = changeField("with=",
+ "GeneDB:"+gene, "|", val);
+ tvalues.add(val);
+ }
+ return tvalues;
+ }
+ return values;
+ }
+
+ private static String getGeneName(Feature feature)
+ {
+ try
+ {
+ return
+ ((GFFStreamFeature)feature.getEmblFeature()).getChadoGene().getGeneUniqueName();
+ }
+ catch(Exception e){}
+ return null;
+ }
+
+ /**
+ * Replace or add the value of a field in a qualifier string
+ * @param fieldName
+ * @param newFieldStr
+ * @param separator
+ * @param qualStr
+ * @return
+ */
+ private static String changeField(final String fieldName,
+ final String newFieldStr,
+ final String separator,
+ String qualStr)
+ {
+ int idx1 = qualStr.toLowerCase().indexOf(fieldName.toLowerCase());
+ int idx2 = qualStr.indexOf(";", idx1);
+ int len = fieldName.length();
+ if(idx2 > idx1 && idx1 > -1)
+ {
+ if(separator != null)
+ qualStr = qualStr.substring(0, idx2) + separator + newFieldStr +
+ qualStr.substring(idx2);
+ else
+ qualStr = qualStr.substring(0, idx1+len) + newFieldStr +
+ qualStr.substring(idx2);
+ }
+ else if(idx1 > -1)
+ {
+ if(separator != null)
+ qualStr = qualStr + separator + newFieldStr;
+ else
+ qualStr = qualStr.substring(0, idx1+len) + newFieldStr;
+ }
+ else if(!newFieldStr.equals(""))
+ qualStr = qualStr + ";" +
+ fieldName + newFieldStr;
+ return qualStr;
+ }
}
class QualifierPanel extends JPanel
@@ -835,7 +933,7 @@ class QualifierPanel extends JPanel
for(int i = 0; i < qualifiers.size(); i++)
{
nrows =
- addQualifierComponents((Qualifier) qualifiers.get(i),
+ addQualifierComponents(qualifiers.get(i),
qualifierCheckBoxes, c, nrows);
}
@@ -846,17 +944,17 @@ class QualifierPanel extends JPanel
/**
* Add a qualifier to the list of transferable annotation
- * @param pane
* @param qualifier
* @param qualifierCheckBoxes
* @param c
* @param nrows
* @return
*/
- private int addQualifierComponents(final Qualifier qualifier,
- final Hashtable<JCheckBox, Vector<JCheckBox>> qualifierCheckBoxes,
- final GridBagConstraints c,
- int nrows)
+ private int addQualifierComponents(
+ final Qualifier qualifier,
+ final Hashtable<JCheckBox, Vector<JCheckBox>> qualifierCheckBoxes,
+ final GridBagConstraints c,
+ int nrows)
{
if(TransferAnnotationTool.isNonTransferable(qualifier.getName()))
return nrows;
@@ -887,7 +985,7 @@ class QualifierPanel extends JPanel
for(int i=0; i<qualifierValuesCheckBox.size(); i++)
{
- JCheckBox cb = (JCheckBox) qualifierValuesCheckBox.get(i);
+ JCheckBox cb = qualifierValuesCheckBox.get(i);
cb.setSelected(qualifierNameCheckBox.isSelected());
}
}
@@ -943,20 +1041,22 @@ class QualifierPanel extends JPanel
// set-up qualifier values list
qualifierValueBox.setVisible(false);
- Vector<JCheckBox> qualifierValuesCheckBox = new Vector<JCheckBox>();
- StringVector values = qualifier.getValues();
+ final Vector<JCheckBox> qualifierValuesCheckBox = new Vector<JCheckBox>();
+ final StringVector values = qualifier.getValues();
if(values != null)
+ {
for (int i = 0; i < values.size(); i++)
{
- JCheckBox cb = new JCheckBox((String) values.get(i),
+ final JCheckBox cb = new JCheckBox(values.get(i),
qualifierNameCheckBox.isSelected());
cb.setFont(cb.getFont().deriveFont(Font.ITALIC));
qualifierValueBox.add(cb);
qualifierValuesCheckBox.add(cb);
}
+ }
return qualifierValuesCheckBox;
}
-
+
protected Hashtable<JCheckBox, Vector<JCheckBox>> getQualifierCheckBoxes()
{
return qualifierCheckBoxes;
--
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