diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java b/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java index be3f01019a22fee43d226948b80f0537b574e5e0..0ee945700b7435fc8328247fc495f2c65b25d11a 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 +}