From 7b269e4002f52b51b3e03e5cfd8ae969da0812ea Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 11 Oct 2013 13:02:39 +0100
Subject: [PATCH] tidy
---
.../components/genebuilder/cv/GoBox.java | 47 ++++---------------
1 file changed, 8 insertions(+), 39 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java b/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java
index be3f01019..0ee945700 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java
@@ -137,8 +137,6 @@ public class GoBox extends AbstractCvBox
this.value_index = value_index;
this.xBox = Box.createHorizontalBox();
- Vector editable = new Vector(5);
-
String goId = getField("GOid=", qualifierString);
final String term = getField("term=", qualifierString);
CvTerm cvTerm = getGOCvTerm(term);
@@ -147,7 +145,6 @@ public class GoBox extends AbstractCvBox
addGoLabelLiteners(goTermField);
JLabel goAspect = null;
-
Font font = goTermField.getFont().deriveFont(Font.BOLD);
if(cvTerm.getCv().getName().indexOf("molecular_function")>-1)
@@ -190,7 +187,6 @@ public class GoBox extends AbstractCvBox
withTextField.setPreferredSize(dimension);
withTextField.setMaximumSize(dimension);
withTextField.setActionCommand("with=");
- editable.add(withTextField);
xBox.add(withTextField);
@@ -202,7 +198,6 @@ public class GoBox extends AbstractCvBox
dbxrefTextField.setPreferredSize(dimension);
dbxrefTextField.setMaximumSize(dimension);
dbxrefTextField.setActionCommand("db_xref=");
- editable.add(dbxrefTextField);
xBox.add(dbxrefTextField);
// feature_cvterm_prop's
@@ -228,7 +223,6 @@ public class GoBox extends AbstractCvBox
evidenceList.setPreferredSize(evidenceListDimension);
evidenceList.setMaximumSize(evidenceListDimension);
evidenceList.setActionCommand("evidence=");
- editable.add(evidenceList);
xBox.add(evidenceList);
String qual = getField("qualifier=", qualifierString);
@@ -237,13 +231,10 @@ public class GoBox extends AbstractCvBox
qualfTextField.setPreferredSize(dimension);
qualfTextField.setMaximumSize(dimension);
qualfTextField.setActionCommand("qualifier=");
- editable.add(qualfTextField);
xBox.add(qualfTextField);
dateField = new DatePanel( getField("date=", qualifierString),
dimension.height);
-
- editable.add(dateField);
xBox.add(dateField);
}
@@ -320,7 +311,7 @@ public class GoBox extends AbstractCvBox
{
if(dbsLinks.get(i).equals("GO"))
{
- AMIGOURL = (String) dbsLinks.get(i+1);
+ AMIGOURL = dbsLinks.get(i+1);
return;
}
}
@@ -337,14 +328,6 @@ public class GoBox extends AbstractCvBox
evidenceCodes[0][i].equalsIgnoreCase(evidence))
return i;
}
-
- // this is mainly to catch RCA
- // - reviewed computational analysis (inferred from missing)
- /*for(int i=0; i<evidenceCodes[2].length; i++)
- {
- if(evidenceCodes[2][i].indexOf(evidence) > -1)
- return i;
- }*/
return -1;
}
@@ -401,10 +384,10 @@ public class GoBox extends AbstractCvBox
final String goId = getField("GOid=", origQualifierString);
StringVector oldValues = oldQualifier.getValues();
- Vector values_index = new Vector();
+ Vector<Integer> values_index = new Vector<Integer>();
for(int i=0; i<oldValues.size(); i++)
{
- String oldValue = (String)oldValues.get(i);
+ String oldValue = oldValues.get(i);
String newGoId = getField("GOid=", oldValue);
if(newGoId.equals(goId))
values_index.add(new Integer(i));
@@ -412,13 +395,13 @@ public class GoBox extends AbstractCvBox
if(values_index.size() > 0)
{
- String oldValue = (String) oldValues.get(value_index);
+ String oldValue = oldValues.get(value_index);
String oldGoId = getField("GOid=", oldValue);
if(!goId.equals(oldGoId))
{
if(values_index.size() == 1)
- value_index = ((Integer)values_index.get(0)).intValue();
+ value_index = values_index.get(0).intValue();
else
{
final String with = getField("with=", origQualifierString);
@@ -426,9 +409,9 @@ public class GoBox extends AbstractCvBox
final String dbxref = getField("dbxref=", origQualifierString);
for(int i=0; i<values_index.size(); i++)
{
- int ind = ((Integer)values_index.get(i)).intValue();
+ int ind = values_index.get(i).intValue();
value_index = ind;
- String value = (String) oldValues.get(ind);
+ String value = oldValues.get(ind);
if(!with.equals(""))
{
@@ -458,7 +441,6 @@ public class GoBox extends AbstractCvBox
oldValues.remove(value_index);
String updatedQualifierString = updateQualifierString();
-
logger4j.debug(origQualifierString);
logger4j.debug(updatedQualifierString);
oldValues.add(value_index, updatedQualifierString);
@@ -474,39 +456,28 @@ public class GoBox extends AbstractCvBox
String old = getField("with=", origQualifierString);
if(!old.equals(withTextField.getText().trim()))
- {
newQualifierString = changeField("with=", withTextField.getText().trim(),
newQualifierString);
- }
old = getField("db_xref=", origQualifierString);
if(!old.equals(dbxrefTextField.getText().trim()))
- {
newQualifierString = changeField("db_xref=", dbxrefTextField.getText().trim(),
newQualifierString);
- }
old = getField("evidence=", origQualifierString);
if(!old.equals(evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
- {
newQualifierString = changeField("evidence=", evidenceCodes[2][ evidenceList.getSelectedIndex() ],
newQualifierString);
- }
old = getField("qualifier=", origQualifierString);
if(!old.equals(qualfTextField.getText()))
- {
newQualifierString = changeField("qualifier=", qualfTextField.getText().trim(),
newQualifierString);
- }
old = getField("date=", origQualifierString);
if(!old.equals(dateField.getText()))
- {
newQualifierString = changeField("date=", dateField.getText().trim(),
newQualifierString);
- }
-
return newQualifierString;
}
@@ -518,7 +489,6 @@ public class GoBox extends AbstractCvBox
evidenceListDimension = evidenceList.getPreferredSize();
evidenceListDimension = new Dimension(80,(int)evidenceListDimension.getHeight());
}
-
return evidenceListDimension;
}
@@ -548,5 +518,4 @@ public class GoBox extends AbstractCvBox
goText = goText.replaceAll(oldEvidence, newEvidence);
return goText;
}
-
-}
\ No newline at end of file
+}
--
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