diff --git a/uk/ac/sanger/artemis/chado/ArtemisUtils.java b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
index a4f65f0351b6f0bfde916101caa432e717854da3..f0eea5f306acbd15af4d5c04e2f7f0e988c8e2bf 100644
--- a/uk/ac/sanger/artemis/chado/ArtemisUtils.java
+++ b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
@@ -76,23 +76,34 @@ public class ArtemisUtils
*/
public static void inserFeatureCvTerm(GmodDAO dao, FeatureCvTerm featureCvTerm)
{
- List featureCvTerms = dao.getFeatureCvTermsByFeature(featureCvTerm.getFeature());
+ List<FeatureCvTerm> featureCvTerms = dao.getFeatureCvTermsByFeature(featureCvTerm.getFeature());
logger4j.debug("In inserFeatureCvTerm() inserting");
- int rank = 0;
- for(int i=0; i<featureCvTerms.size(); i++)
+
+ boolean isNotProduct = true;
+ try
{
- FeatureCvTerm this_feature_cvterm = (FeatureCvTerm)featureCvTerms.get(i);
-
- if(this_feature_cvterm.getCvTerm().getName().equals(
- featureCvTerm.getCvTerm().getName() ) &&
- this_feature_cvterm.getCvTerm().getCv().getName().equals(
- featureCvTerm.getCvTerm().getCv().getName() ))
+ // product feature_cvterm.rank is used to define alternative products
+ // where there are multiple products, so the rank may already be set
+ if(featureCvTerm.getCvTerm().getCv().getName().equals(
+ DatabaseDocument.PRODUCTS_TAG_CVNAME))
+ isNotProduct = false;
+ } catch(Exception e){}
+
+ if(isNotProduct || featureCvTerm.getRank() == 0)
+ {
+ int rank = 0;
+ for(FeatureCvTerm this_feature_cvterm: featureCvTerms)
{
- rank++;
+ if(this_feature_cvterm.getCvTerm().getName().equals(
+ featureCvTerm.getCvTerm().getName() ) &&
+ this_feature_cvterm.getCvTerm().getCv().getName().equals(
+ featureCvTerm.getCvTerm().getCv().getName() ))
+ {
+ rank++;
+ }
}
+ featureCvTerm.setRank(rank);
}
-
- featureCvTerm.setRank(rank);
dao.persist(featureCvTerm);
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index bc307568d2224454edb69c01b7cf974888d90bef..444080cdba525688245711c67a5080b79db333e8 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -2460,6 +2460,17 @@ public class ChadoTransactionManager
continue;
}
+ // for product use the rank=1 to specify an alternative product
+ // where there are multiple products for a feature
+ if(cvName != null && cvName.equals(PRODUCT_CV) &&
+ this_qualifier_part_lowercase.startsWith("rank="))
+ {
+ if(this_qualifier_part_lowercase.equals("rank=1"))
+ feature_cvterm.setRank(1);
+ else
+ feature_cvterm.setRank(0);
+ continue;
+ }
// feature_cvterm_prop's
if(!this_qualifier_part_lowercase.startsWith("goid=") &&
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java b/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java
index 173760c0b21dba5234ab0c4de611b21e9f3b7770..b8f4f5ec03c657781f3bc5166b91ec89885e532f 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java
@@ -36,7 +36,6 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.Vector;
-
import javax.swing.Box;
import javax.swing.JLabel;
import javax.swing.JTextField;
@@ -180,16 +179,10 @@ public class CVPanel extends JPanel
cvBox.add(xBox);
Dimension go_dimension = null;
- int nGo = 0;
-
-
Box goBox = null;
Box goHeadings = null;
- for(int qualifier_index = 0; qualifier_index < cvQualifiers.size();
- ++qualifier_index)
+ for(Qualifier this_qualifier: cvQualifiers)
{
- Qualifier this_qualifier = (Qualifier)cvQualifiers.elementAt(qualifier_index);
-
if(this_qualifier.getName().equals("GO"))
{
empty = false;
@@ -204,32 +197,24 @@ public class CVPanel extends JPanel
if(goHeadings == null)
goHeadings = Box.createHorizontalBox();
-
- nGo++;
+
final StringVector qualifier_strings = this_qualifier.getValues();
-
- for(int value_index = 0; value_index < qualifier_strings.size();
- ++value_index)
+ for(int i = 0; i < qualifier_strings.size(); ++i)
{
- final int v_index = value_index;
-
- final String qualifierString =
- (String)qualifier_strings.elementAt(value_index);
-
- GoBox go_box = new GoBox(this_qualifier, qualifierString, value_index,
+ GoBox go_box = new GoBox(this_qualifier, qualifier_strings.elementAt(i), i,
go_dimension, dimension);
go_dimension = go_box.getGoDimension();
editableComponents.add(go_box);
xBox = go_box.getBox();
xBox.add(Box.createHorizontalGlue());
- xBox.add(getRemoveButton(this_qualifier, v_index));
+ xBox.add(getRemoveButton(this_qualifier, i));
goBox.add(xBox);
}
// add column headings
- JLabel lab = new JLabel("GO terms");
+ final JLabel lab = new JLabel("GO terms");
lab.setPreferredSize(go_dimension);
lab.setFont(lab.getFont().deriveFont(Font.BOLD));
goHeadings.add(lab);
@@ -248,9 +233,7 @@ public class CVPanel extends JPanel
final JLabel qualLabel = new JLabel("Qualifier");
qualLabel.setPreferredSize(dimension);
goHeadings.add(qualLabel);
-
- final JLabel dateLabel = new JLabel("Date");
- goHeadings.add(dateLabel);
+ goHeadings.add(new JLabel("Date"));
goHeadings.add(Box.createHorizontalGlue());
goHeadings.add(hide_show_GO);
@@ -261,34 +244,24 @@ public class CVPanel extends JPanel
}
int n = 0;
- for(int qualifier_index = 0; qualifier_index < cvQualifiers.size();
- ++qualifier_index)
+ for(Qualifier this_qualifier: cvQualifiers)
{
- final Qualifier this_qualifier = (Qualifier)cvQualifiers.elementAt(qualifier_index);
if(this_qualifier.getName().equals("product"))
{
final StringVector qualifier_strings = this_qualifier.getValues();
-
- for(int value_index = 0; value_index < qualifier_strings.size(); ++value_index)
+ for(int i = 0; i < qualifier_strings.size(); ++i)
{
- final int v_index = value_index;
-
- xBox = Box.createHorizontalBox();
- final String qualifierString = (String) qualifier_strings
- .elementAt(value_index);
-
empty = false;
-
- xBox = Box.createHorizontalBox();
final ProductBox productBox = new ProductBox(
- this_qualifier,
- qualifierString, value_index,
- dimension, go_dimension);
+ this_qualifier, qualifier_strings.elementAt(i),
+ i, dimension, go_dimension);
editableComponents.add(productBox);
-
+
+ if(qualifier_strings.size() == 1)
+ productBox.getRecommended().setEnabled(false);
xBox = productBox.getBox();
xBox.add(Box.createHorizontalGlue());
- xBox.add(getRemoveButton(this_qualifier, v_index));
+ xBox.add(getRemoveButton(this_qualifier, i));
n++;
cvBox.add(productBox.getHeadingsBox());
cvBox.add(xBox);
@@ -301,35 +274,25 @@ public class CVPanel extends JPanel
// history field
n = 0;
- for(int qualifier_index = 0; qualifier_index < cvQualifiers.size();
- ++qualifier_index)
+ for(Qualifier this_qualifier: cvQualifiers)
{
- final Qualifier this_qualifier =
- (Qualifier)cvQualifiers.elementAt(qualifier_index);
if(this_qualifier.getName().equals("history"))
{
final StringVector qualifier_strings = this_qualifier.getValues();
- for(int value_index = 0; value_index < qualifier_strings.size(); ++value_index)
+ for(int i = 0; i < qualifier_strings.size(); ++i)
{
- final int v_index = value_index;
-
- xBox = Box.createHorizontalBox();
- final String qualifierString = (String) qualifier_strings
- .elementAt(value_index);
-
empty = false;
-
- xBox = Box.createHorizontalBox();
+
final HistoryBox historyBox = new HistoryBox(
this_qualifier,
- qualifierString, value_index,
+ qualifier_strings.elementAt(i), i,
dimension, go_dimension);
editableComponents.add(historyBox);
xBox = historyBox.getBox();
xBox.add(Box.createHorizontalGlue());
- xBox.add(getRemoveButton(this_qualifier, v_index));
+ xBox.add(getRemoveButton(this_qualifier, i));
if(n == 0)
{
@@ -359,15 +322,12 @@ public class CVPanel extends JPanel
n = 0;
- for(int qualifier_index = 0; qualifier_index < cvQualifiers.size();
- ++qualifier_index)
+ for(Qualifier this_qualifier: cvQualifiers)
{
- final Qualifier this_qualifier = (Qualifier)cvQualifiers.elementAt(qualifier_index);
if(this_qualifier.getName().equals("controlled_curation"))
{
empty = false;
- final StringVector qualifier_strings = this_qualifier.getValues();
-
+
final Box yBox = Box.createVerticalBox();
if(hide_show_CC == null)
hide_show_CC = new JButton("-");
@@ -423,23 +383,20 @@ public class CVPanel extends JPanel
xHeadings.add(Box.createHorizontalGlue());
}
- for(int value_index = 0; value_index < qualifier_strings.size();
- ++value_index)
+ final StringVector qualifier_strings = this_qualifier.getValues();
+ for(int i = 0; i < qualifier_strings.size(); ++i)
{
n++;
- xBox = Box.createHorizontalBox();
- final String qualifierString =
- (String)qualifier_strings.elementAt(value_index);
final ControlledCurationBox ccBox = new ControlledCurationBox(
this_qualifier,
- qualifierString, value_index,
+ qualifier_strings.elementAt(i), i,
dimension, go_dimension);
editableComponents.add(ccBox);
xBox = ccBox.getBox();
xBox.add(Box.createHorizontalGlue());
- xBox.add(getRemoveButton(this_qualifier, value_index));
+ xBox.add(getRemoveButton(this_qualifier, i));
yBox.add(xBox);
yBox.add(Box.createVerticalStrut(2));
}
@@ -461,43 +418,39 @@ public class CVPanel extends JPanel
if(go_dimension == null)
go_dimension = new JLabel("product ").getPreferredSize();
n = 0;
- for(int qualifier_index = 0; qualifier_index < cvQualifiers.size(); ++qualifier_index)
+ for(Qualifier this_qualifier: cvQualifiers)
{
- final Qualifier this_qualifier = (Qualifier) cvQualifiers
- .elementAt(qualifier_index);
if(this_qualifier.getName().equals("class"))
{
empty = false;
final StringVector qualifier_strings = this_qualifier.getValues();
n++;
- for(int value_index = 0; value_index < qualifier_strings.size(); ++value_index)
+ for(int i = 0; i < qualifier_strings.size(); ++i)
{
- final int v_index = value_index;
-
xBox = Box.createHorizontalBox();
- final String qualifierString = (String) qualifier_strings.elementAt(value_index);
+ final String qualifierStr = qualifier_strings.elementAt(i);
JLabel label = new JLabel("class");
if(go_dimension != null)
label.setPreferredSize(go_dimension);
xBox.add(label);
- int index = qualifierString.indexOf("::");
- String classStr = qualifierString.substring(0, index);
+ int index = qualifierStr.indexOf("::");
+ String classStr = qualifierStr.substring(0, index);
JLabel termTextField = new JLabel(classStr);
termTextField.setOpaque(false);
termTextField
.setToolTipText(DatabaseDocument.getCvTermByCvTermId(
- Integer.parseInt(qualifierString.substring(index + 2)), feature.getEmblFeature())
+ Integer.parseInt(qualifierStr.substring(index + 2)), feature.getEmblFeature())
.getDefinition());
termTextField.setPreferredSize(dimension);
termTextField.setMaximumSize(dimension);
xBox.add(termTextField);
xBox.add(Box.createHorizontalGlue());
- xBox.add(getRemoveButton(this_qualifier, v_index));
+ xBox.add(getRemoveButton(this_qualifier, i));
cvBox.add(xBox);
}
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/ProductBox.java b/uk/ac/sanger/artemis/components/genebuilder/cv/ProductBox.java
index c9983887e33ca7fa8390a2bb2f45daa9c9597056..bc027a5fce437e7354ceb4a224924858956bd182 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/ProductBox.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/ProductBox.java
@@ -28,6 +28,7 @@ import java.awt.Dimension;
import java.awt.Font;
import javax.swing.Box;
+import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JTextField;
@@ -38,7 +39,11 @@ import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.util.StringVector;
/**
- * Product display box
+ * Product display box.
+ *
+ * Where there are multiple products associated with a feature assume
+ * the product is the recommended product unless rank=1 which means it
+ * is an alternative product.
*/
class ProductBox extends AbstractCvBox
{
@@ -48,33 +53,34 @@ class ProductBox extends AbstractCvBox
private JTextField withTextField;
private JTextField dbxrefTextField;
private JExtendedComboBox evidenceList;
- private String origQualifierString;
+ private JCheckBox recommended = new JCheckBox();
+ private String origQualifierStr;
private Qualifier origQualifier;
private Box xHeadings = Box.createHorizontalBox();
public ProductBox(final Qualifier qualifier,
- final String qualifierString,
+ final String qualifierStr,
final int value_index,
final Dimension dimension,
final Dimension go_dimension)
{
this.origQualifier = qualifier;
- this.origQualifierString = qualifierString;
+ this.origQualifierStr = qualifierStr;
this.value_index = value_index;
this.xBox = Box.createHorizontalBox();
- String term = getField("term=", qualifierString);
+ String term = getField("term=", qualifierStr);
// this may not be stored as a CV (product_cv=no?)
if(term.equals(""))
- term = qualifierString;
+ term = qualifierStr;
termTextField = new WrapTextArea(term, go_dimension, dimension.width*2);
xBox.add(termTextField);
// the WITH column is associated with one or more FeatureCvTermDbXRef
- String with = getField("with=", qualifierString);
+ String with = getField("with=", qualifierStr);
withTextField = new JTextField(with);
withTextField.setToolTipText("with/from column");
withTextField.setPreferredSize(dimension);
@@ -85,7 +91,7 @@ class ProductBox extends AbstractCvBox
// N.B. for /GO the db_xref is a Pub (for primary pubs)
// or FeatureCvTermPub (for others) in /GO
- String dbxref = getField("db_xref=", qualifierString);
+ String dbxref = getField("db_xref=", qualifierStr);
dbxrefTextField = new JTextField(dbxref);
dbxrefTextField.setToolTipText("dbxref column");
dbxrefTextField.setPreferredSize(dimension);
@@ -95,7 +101,7 @@ class ProductBox extends AbstractCvBox
xBox.add(dbxrefTextField);
// feature_cvterm_prop's
- String evidence = getField("evidence=", qualifierString);
+ String evidence = getField("evidence=", qualifierStr);
evidenceList = new JExtendedComboBox(GoBox.evidenceCodes[1]);
evidenceList.setOpaque(false);
@@ -109,23 +115,38 @@ class ProductBox extends AbstractCvBox
evidenceList.setActionCommand("evidence=");
xBox.add(evidenceList);
-
- JLabel lab = new JLabel("Product");
- lab.setFont(lab.getFont().deriveFont(Font.BOLD));
- xHeadings.add(lab);
-
- xHeadings.add(Box.createRigidArea(new Dimension(
- termTextField.getPreferredSize().width-lab.getPreferredSize().width,0)));
- JLabel withLabel = new JLabel("WITH/FROM");
- withLabel.setPreferredSize(dimension);
- withLabel.setMaximumSize(dimension);
- xHeadings.add(withLabel);
-
- JLabel dbxrefLabel = new JLabel("Dbxref");
- dbxrefLabel.setPreferredSize(dimension);
- dbxrefLabel.setMaximumSize(dimension);
- xHeadings.add(dbxrefLabel);
- xHeadings.add(Box.createHorizontalGlue());
+ // check box for recommended product
+ final String rank = getField("rank=", qualifierStr);
+ recommended.setSelected( (rank.length() == 0 || rank.equals("0")) ? true : false );
+ evidenceList.setActionCommand("rank=");
+ xBox.add(recommended);
+
+ if (value_index == 0)
+ {
+ JLabel lab = new JLabel("Product");
+ lab.setFont(lab.getFont().deriveFont(Font.BOLD));
+ xHeadings.add(lab);
+
+ xHeadings.add(Box.createRigidArea(new Dimension(termTextField
+ .getPreferredSize().width - lab.getPreferredSize().width, 0)));
+ JLabel withLabel = new JLabel("WITH/FROM");
+ withLabel.setPreferredSize(dimension);
+ withLabel.setMaximumSize(dimension);
+ xHeadings.add(withLabel);
+
+ JLabel dbxrefLabel = new JLabel("Dbxref");
+ dbxrefLabel.setPreferredSize(dimension);
+ dbxrefLabel.setMaximumSize(dimension);
+ xHeadings.add(dbxrefLabel);
+
+ xHeadings.add(Box.createHorizontalStrut(de.width));
+ JLabel recommendedLabel = new JLabel("Recommended");
+ recommendedLabel.setPreferredSize(dimension);
+ recommendedLabel.setMaximumSize(dimension);
+ xHeadings.add(recommendedLabel);
+
+ xHeadings.add(Box.createHorizontalGlue());
+ }
}
/**
@@ -133,29 +154,40 @@ class ProductBox extends AbstractCvBox
*/
protected boolean isQualifierChanged()
{
- String old = getField("with=", origQualifierString);
+ String old = getField("with=", origQualifierStr);
if(!old.equals(withTextField.getText().trim()))
return true;
- old = getField("db_xref=", origQualifierString);
+ old = getField("db_xref=", origQualifierStr);
if(!old.equals(dbxrefTextField.getText().trim()))
return true;
- old = getField("evidence=", origQualifierString);
+ old = getField("evidence=", origQualifierStr);
if(evidenceList.getSelectedIndex() > -1 &&
!old.equalsIgnoreCase(GoBox.evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
return true;
+ // test rank change for recommended/alternative product
+ if(recommended.isEnabled())
+ {
+ old = getField("rank=", origQualifierStr);
+ if( !recommended.isSelected() && (old.equals("0") || old.equals("")) )
+ return true;
+ else if(recommended.isSelected() && !old.equals("0"))
+ return true;
+ }
return false;
}
protected void updateQualifier(QualifierVector qv)
{
- StringVector values = origQualifier.getValues();
+ Qualifier oldQualifier = qv.getQualifierByName(origQualifier.getName());
+ StringVector values = oldQualifier.getValues();
+
values.remove(value_index);
String updatedQualifierString = updateQualifierString();
- Splash.logger4j.debug(origQualifierString);
+ Splash.logger4j.debug(origQualifierStr);
Splash.logger4j.debug(updatedQualifierString);
values.add(value_index, updatedQualifierString);
@@ -168,23 +200,23 @@ class ProductBox extends AbstractCvBox
private String updateQualifierString()
{
- String newQualifierString = origQualifierString;
+ String newQualifierString = origQualifierStr;
- String old = getField("with=", origQualifierString);
+ String old = getField("with=", origQualifierStr);
if(!old.equals(withTextField.getText().trim()))
{
newQualifierString = changeField("with=", withTextField.getText().trim(),
newQualifierString);
}
- old = getField("db_xref=", origQualifierString);
+ old = getField("db_xref=", origQualifierStr);
if(!old.equals(dbxrefTextField.getText().trim()))
{
newQualifierString = changeField("db_xref=", dbxrefTextField.getText().trim(),
newQualifierString);
}
- old = getField("evidence=", origQualifierString);
+ old = getField("evidence=", origQualifierStr);
if(evidenceList.getSelectedIndex() > -1 &&
!old.equals(GoBox.evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
{
@@ -192,6 +224,19 @@ class ProductBox extends AbstractCvBox
GoBox.evidenceCodes[2][ evidenceList.getSelectedIndex() ],
newQualifierString);
}
+
+ // test rank change
+ old = getField("rank=", origQualifierStr);
+ if( !recommended.isSelected() )
+ {
+ if(old.equals("0") || old.equals(""))
+ newQualifierString = changeField("rank=", "1", newQualifierString);
+ }
+ else
+ {
+ if(recommended.isEnabled() && !old.equals("0") && !old.equals(""))
+ newQualifierString = changeField("rank=", "0", newQualifierString);
+ }
return newQualifierString;
}
@@ -205,6 +250,12 @@ class ProductBox extends AbstractCvBox
{
return xHeadings;
}
-
+ /**
+ * @return the recommended
+ */
+ protected JCheckBox getRecommended()
+ {
+ return recommended;
+ }
}
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index f1a889b1d2e6017cd99cf2451c13de772821be71..6cba75df3449f18a6ac8c27112ac66ae89d5f06d 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -1595,6 +1595,9 @@ public class DatabaseDocument extends Document
{
attr_buff.append("product=");
+ // use the rank=1 to specify an alternative product where there is more than one
+ if(feature_cvterm.getRank() > 0)
+ attr_buff.append("rank="+feature_cvterm.getRank()+"%3B");
constructCvTermString(attr_buff, dao, feature_cvterm, featureCvTermDbXRefs,
featureCvTermPubs, dbXRef, false, gene_builder);
}