From bc5214395905c64ca2a05df5f43a6dd67dd3dd20 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 3 May 2007 12:57:01 +0000
Subject: [PATCH] fixes and updates
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5999 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../genebuilder/GeneComponentTree.java | 8 +-
.../genebuilder/GeneViewerPanel.java | 9 +-
.../components/genebuilder/cv/CVPanel.java | 83 +++++++++++++++-
.../genebuilder/cv/ControlledCurationBox.java | 98 +++++++++++++++++--
.../components/genebuilder/cv/GoBox.java | 14 ++-
5 files changed, 193 insertions(+), 19 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java b/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
index 9036142a6..ab2d1eca8 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.18 2007-05-01 09:36:42 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.19 2007-05-03 12:57:01 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -351,7 +351,11 @@ public class GeneComponentTree extends JTree
if(feature == null)
feature = new uk.ac.sanger.artemis.Feature(embl_feature);
- gene_builder.setActiveFeature(feature, true);
+ boolean isSet = true;
+ if(feature.isReadOnly())
+ isSet = false;
+
+ gene_builder.setActiveFeature(feature, isSet);
if(selection != null)
selection.set(feature);
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
index 5ebfb1cfb..dd0279de5 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.50 2007-05-01 15:02:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.51 2007-05-03 12:57:01 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -1654,8 +1654,13 @@ public class GeneViewerPanel extends JPanel
{
selection.set(
(uk.ac.sanger.artemis.Feature)((Feature)feature).getUserData());
+
+ boolean isSet = true;
+ if(((Feature)feature).isReadOnly())
+ isSet = false;
+
gene_builder.setActiveFeature(
- (uk.ac.sanger.artemis.Feature)((Feature)feature).getUserData(), true);
+ (uk.ac.sanger.artemis.Feature)((Feature)feature).getUserData(), isSet);
}
else
{
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java b/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java
index 02b0fddb8..f3d11fe57 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/CVPanel.java
@@ -77,6 +77,10 @@ public class CVPanel extends JPanel
private JExtendedComboBox evidenceList;
+ private JButton hide_show_CC;
+ private JButton hide_show_GO;
+
+
public CVPanel(final Feature feature)
{
super(new BorderLayout());
@@ -141,6 +145,21 @@ public class CVPanel extends JPanel
if(this_qualifier.getName().equals("GO"))
{
+ final Box yBox = Box.createVerticalBox();
+ if(hide_show_GO == null)
+ hide_show_GO = new JButton("-");
+
+ addHideShowButton(yBox, hide_show_GO);
+
+ Box xLabel = Box.createHorizontalBox();
+ JLabel lab = new JLabel("GO terms");
+ lab.setFont(lab.getFont().deriveFont(Font.BOLD));
+ xLabel.add(lab);
+ xLabel.add(Box.createHorizontalGlue());
+ xLabel.add(hide_show_GO);
+
+ cvBox.add(xLabel);
+
n++;
final StringVector qualifier_strings = this_qualifier.getValues();
@@ -161,8 +180,11 @@ public class CVPanel extends JPanel
xBox.add(Box.createHorizontalGlue());
xBox.add(getRemoveButton(this_qualifier, v_index));
- cvBox.add(xBox);
+ yBox.add(xBox);
}
+ cvBox.add(yBox);
+ if(hide_show_GO.getText().equals("+"))
+ yBox.setVisible(false);
}
}
@@ -179,7 +201,21 @@ public class CVPanel extends JPanel
if(this_qualifier.getName().equals("controlled_curation"))
{
final StringVector qualifier_strings = this_qualifier.getValues();
-
+
+ final Box yBox = Box.createVerticalBox();
+ if(hide_show_CC == null)
+ hide_show_CC = new JButton("-");
+
+ addHideShowButton(yBox, hide_show_CC);
+
+ Box xLabel = Box.createHorizontalBox();
+ JLabel lab = new JLabel("Controlled Curation");
+ lab.setFont(lab.getFont().deriveFont(Font.BOLD));
+ xLabel.add(lab);
+ xLabel.add(Box.createHorizontalGlue());
+ xLabel.add(hide_show_CC);
+ cvBox.add(xLabel);
+
for(int value_index = 0; value_index < qualifier_strings.size();
++value_index)
{
@@ -192,14 +228,17 @@ public class CVPanel extends JPanel
ControlledCurationBox ccBox = new ControlledCurationBox(this_qualifier,
qualifierString, value_index,
- dimension4, go_dimension);
+ dimension, go_dimension);
editableComponents.add(ccBox);
xBox = ccBox.getBox();
xBox.add(Box.createHorizontalGlue());
xBox.add(getRemoveButton(this_qualifier, v_index));
- cvBox.add(xBox);
+ yBox.add(xBox);
}
+ cvBox.add(yBox);
+ if(hide_show_CC.getText().equals("+"))
+ yBox.setVisible(false);
}
}
@@ -306,6 +345,42 @@ public class CVPanel extends JPanel
return cvBox;
}
+ /**
+ * Add hide/show button to CV section
+ * @param box
+ */
+ private void addHideShowButton(final Box box, final JButton hide_show)
+ {
+ hide_show.setOpaque(false);
+
+ // remove any old listeners
+ ActionListener l[] = hide_show.getActionListeners();
+ if(l != null)
+ for(int i=0;i<l.length;i++)
+ hide_show.removeActionListener(l[i]);
+
+ hide_show.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if(hide_show.getText().equals("-"))
+ {
+ hide_show.setText("+");
+ box.setVisible(false);
+ }
+ else
+ {
+ hide_show.setText("-");
+ box.setVisible(true);
+ }
+ }
+ });
+ }
+
+ /**
+ * Separator between CV's
+ * @param cvBox
+ */
private void addSeparator(final Box cvBox)
{
JSeparator separator = new JSeparator();
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/ControlledCurationBox.java b/uk/ac/sanger/artemis/components/genebuilder/cv/ControlledCurationBox.java
index a7e292efc..2fdc9ec40 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/ControlledCurationBox.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/ControlledCurationBox.java
@@ -27,10 +27,10 @@ package uk.ac.sanger.artemis.components.genebuilder.cv;
import java.awt.Dimension;
import javax.swing.Box;
-import javax.swing.JLabel;
import javax.swing.JTextField;
import uk.ac.sanger.artemis.components.Splash;
+import uk.ac.sanger.artemis.components.genebuilder.JExtendedComboBox;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.util.StringVector;
@@ -40,6 +40,9 @@ class ControlledCurationBox extends AbstractCvBox
private Box xBox;
private int value_index;
private JTextField termTextField;
+ private JTextField dbxrefTextField;
+ private JExtendedComboBox evidenceList;
+ private JTextField qualfTextField;
private DatePanel dateField;
private String origQualifierString;
private Qualifier origQualifier;
@@ -55,23 +58,66 @@ class ControlledCurationBox extends AbstractCvBox
this.value_index = value_index;
this.xBox = Box.createHorizontalBox();
- JLabel cclabel = new JLabel("controlled_curation");
- if(go_dimension != null)
- cclabel.setPreferredSize(go_dimension);
+ //JLabel cclabel = new JLabel("controlled_curation");
+ //if(go_dimension != null)
+ // cclabel.setPreferredSize(go_dimension);
- xBox.add(cclabel);
+ //xBox.add(cclabel);
String term = getField("term=", qualifierString);
termTextField = new JTextField(term);
termTextField.setOpaque(false);
termTextField.setEditable(false);
termTextField.setToolTipText("term column");
- termTextField.setPreferredSize(dimension);
- termTextField.setMaximumSize(dimension);
+
+ if(go_dimension != null)
+ {
+ final Dimension d = new Dimension(go_dimension.width+dimension.width,
+ dimension.height);
+ termTextField.setPreferredSize(d);
+ termTextField.setMaximumSize(d);
+ }
+ else
+ {
+ termTextField.setPreferredSize(dimension);
+ termTextField.setMaximumSize(dimension);
+ }
termTextField.setCaretPosition(0);
xBox.add(termTextField);
+ String dbxref = getField("db_xref=", qualifierString);
+ dbxrefTextField = new JTextField(dbxref);
+ dbxrefTextField.setToolTipText("dbxref column");
+ dbxrefTextField.setPreferredSize(dimension);
+ dbxrefTextField.setMaximumSize(dimension);
+ dbxrefTextField.setActionCommand("db_xref=");
+ xBox.add(dbxrefTextField);
+
+ // feature_cvterm_prop's
+ String evidence = getField("evidence=", qualifierString);
+
+ evidenceList = new JExtendedComboBox(GoBox.evidenceCodes[1]);
+ evidenceList.setOpaque(false);
+ evidenceList.setToolTipText("evidence column");
+ evidenceList.setSelectedIndex( GoBox.getEvidenceIndex(evidence) );
+
+ Dimension d = evidenceList.getPreferredSize();
+ d = new Dimension(80,(int)d.getHeight());
+ evidenceList.setPreferredSize(d);
+ evidenceList.setMaximumSize(d);
+ evidenceList.setActionCommand("evidence=");
+ xBox.add(evidenceList);
+
+ String qual = getField("qualifier=", qualifierString);
+ qualfTextField = new JTextField(qual);
+ qualfTextField.setToolTipText("qualifier column");
+ qualfTextField.setPreferredSize(dimension);
+ qualfTextField.setMaximumSize(dimension);
+ qualfTextField.setActionCommand("qualifier=");
+ xBox.add(qualfTextField);
+
+
dateField = new DatePanel(getField("date=", qualifierString),
dimension.height);
@@ -82,9 +128,23 @@ class ControlledCurationBox extends AbstractCvBox
protected boolean isQualifierChanged()
{
- String old = getField("date=", origQualifierString);
+ String old = getField("db_xref=", origQualifierString);
+ if(!old.equals(dbxrefTextField.getText().trim()))
+ return true;
+
+ old = getField("evidence=", origQualifierString);
+ if(!(old.equals("") && evidenceList.getSelectedIndex() == -1) )
+ if(!old.equals(GoBox.evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
+ return true;
+
+ old = getField("qualifier=", origQualifierString);
+ if(!old.equals(qualfTextField.getText()))
+ return true;
+
+ old = getField("date=", origQualifierString);
if(!old.equals(dateField.getText()))
return true;
+
return false;
}
@@ -116,6 +176,28 @@ class ControlledCurationBox extends AbstractCvBox
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(evidenceList.getSelectedIndex() > -1 &&
+ !old.equals(GoBox.evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
+ {
+ newQualifierString = changeField("evidence=", GoBox.evidenceCodes[2][ evidenceList.getSelectedIndex() ],
+ newQualifierString);
+ }
+
+ old = getField("qualifier=", origQualifierString);
+ if(!old.equals(qualfTextField.getText()))
+ {
+ newQualifierString = changeField("qualifier=", qualfTextField.getText().trim(),
+ newQualifierString);
+ }
+
return newQualifierString;
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java b/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java
index 35dd50d43..6453a0d2d 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java
@@ -198,13 +198,21 @@ class GoBox extends AbstractCvBox
xBox.add(dateField.getDateSpinner());
}
- private int getEvidenceIndex(String evidence)
+ protected static int getEvidenceIndex(String evidence)
{
for(int i=0; i<evidenceCodes[2].length; i++)
{
- if(evidenceCodes[2][i].equals(evidence))
+ if(evidenceCodes[2][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;
}
@@ -229,7 +237,7 @@ class GoBox extends AbstractCvBox
return true;
old = getField("evidence=", origQualifierString);
- if(!old.equals(evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
+ if(!old.equalsIgnoreCase(evidenceCodes[2][ evidenceList.getSelectedIndex() ]))
return true;
old = getField("qualifier=", origQualifierString);
--
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