Skip to content
Snippets Groups Projects
Commit 067c5bbd authored by tcarver's avatar tcarver
Browse files

add getTransferValues() to change evidence code and add source link to 

GO and product qualifiers
parent 2f5978a4
No related branches found
No related tags found
No related merge requests found
Show whitespace changes
Inline Side-by-side
uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+ 149
− 49
View file @ 067c5bbd
......@@ -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);
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");
......@@ -408,6 +405,10 @@ 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");
......@@ -509,6 +512,7 @@ public class TransferAnnotationTool extends JFrame
final EntryGroup entryGroup,
final boolean sameKey,
final boolean overwrite,
final boolean setEvidenceAndWithFrom,
final StringBuffer buff,
final StringBuffer genesUpdated)
{
......@@ -523,13 +527,13 @@ 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());
......@@ -539,6 +543,10 @@ public class TransferAnnotationTool extends JFrame
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();
......@@ -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();
......@@ -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);
}
......@@ -846,14 +944,14 @@ 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,
private int addQualifierComponents(
final Qualifier qualifier,
final Hashtable<JCheckBox, Vector<JCheckBox>> qualifierCheckBoxes,
final GridBagConstraints c,
int 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());
}
}
......@@ -943,17 +1041,19 @@ 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;
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment