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Commit afedbd8c authored by tjc's avatar tjc
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append abbreviation to GO evidence codes

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5205 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent d503ac93
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......@@ -382,7 +382,7 @@ public class CVPanel extends JPanel
cv_qualifier.addValue("GOid=GO:"+cvterm.getDbXRef().getAccession()+";"+
"aspect="+cv_name+";"+
"term="+cvterm.getName()+";"+
"evidence="+evidenceList.getSelectedItem());
"evidence="+ GoBox.evidenceCodes[2][ evidenceList.getSelectedIndex() ]);
else if(cv_type.equals("controlled_curation"))
cv_qualifier.addValue("term="+cvterm.getName());
else if(cv_type.equals("product"))
......@@ -601,7 +601,7 @@ public class CVPanel extends JPanel
{
final String options[] = { "<PREV", "CANCEL", "NEXT>"};
evidenceList = new JExtendedComboBox(GoBox.evidenceCodes[1]);
evidenceList.setSelectedItem("not recorded");
evidenceList.setSelectedItem("NR \t:: not recorded");
xBox.add(evidenceList);
int select = JOptionPane.showOptionDialog(null, xBox,
......
......@@ -48,6 +48,19 @@ class GoBox extends CvBoxA
{
{"IC", "IDA", "IEA", "IEP", "IGI", "IMP", "IPI", "ISS",
"NAS", "ND", "RCA", "TAS", "NR" },
{"IC \t:: inferred by curator",
"IDA\t:: inferred from direct assay",
"IEA\t:: inferred from electronic annotation",
"IEP\t:: inferred from expression pattern",
"IGI\t:: inferred from genetic interaction",
"IMP\t:: inferred from mutant phenotype",
"IPI\t:: inferred from physical interaction",
"ISS\t:: inferred from sequence or structural similarity",
"NAS\t:: non-traceable author statement",
"ND \t:: no biological data available",
"RCA\t:: inferred from reviewed computational analysis",
"TAS\t:: traceable author statement",
"NR \t:: not recorded"},
{"inferred by curator",
"inferred from direct assay",
"inferred from electronic annotation",
......@@ -133,10 +146,10 @@ class GoBox extends CvBoxA
evidenceList = new JExtendedComboBox(evidenceCodes[1]);
evidenceList.setToolTipText("evidence column");
evidenceList.setSelectedItem(evidence);
evidenceList.setSelectedIndex( getEvidenceIndex(evidence) );
Dimension d = evidenceList.getPreferredSize();
d = new Dimension(150,(int)d.getHeight());
d = new Dimension(80,(int)d.getHeight());
evidenceList.setPreferredSize(d);
evidenceList.setMaximumSize(d);
evidenceList.setActionCommand("evidence=");
......@@ -165,6 +178,16 @@ class GoBox extends CvBoxA
xBox.add(dateField);
}
private int getEvidenceIndex(String evidence)
{
for(int i=0; i<evidenceCodes[2].length; i++)
{
if(evidenceCodes[2][i].equals(evidence))
return i;
}
return -1;
}
protected Dimension getGoDimension()
{
return go_dimension;
......@@ -186,7 +209,7 @@ class GoBox extends CvBoxA
return true;
old = getField("evidence=", origQualifierString);
if(!old.equals(evidenceList.getSelectedItem()))
if(!old.equals(evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
return true;
old = getField("qualifier=", origQualifierString);
......@@ -241,9 +264,9 @@ class GoBox extends CvBoxA
}
old = getField("evidence=", origQualifierString);
if(!old.equals(evidenceList.getSelectedItem()))
if(!old.equals(evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
{
newQualifierString = changeField("evidence=", (String)evidenceList.getSelectedItem(),
newQualifierString = changeField("evidence=", evidenceCodes[2][ evidenceList.getSelectedIndex() ],
newQualifierString);
}
......
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