From cca59534ea7c3550143a958a0d8e4b79c8c17346 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 12 Aug 2013 14:08:21 +0100
Subject: [PATCH] add user qualifier to selected features options
---
.../artemis/components/FeatureEdit.java | 1 +
.../components/UserDefinedQualifiers.java | 95 +++++++++++++++----
2 files changed, 79 insertions(+), 17 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/FeatureEdit.java b/uk/ac/sanger/artemis/components/FeatureEdit.java
index 613999b3b..fc55c7084 100644
--- a/uk/ac/sanger/artemis/components/FeatureEdit.java
+++ b/uk/ac/sanger/artemis/components/FeatureEdit.java
@@ -802,6 +802,7 @@ public class FeatureEdit extends JPanel
userDefinedQualifierFrame.setLocation(p);
userDefinedQualifierFrame.setQualifierTextArea(qualifier_text_area);
+ userDefinedQualifierFrame.setSelection(selection);
userDefinedQualifierFrame.setVisible(true);
}
});
diff --git a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
index 6f0b1e6d5..9b069ff70 100644
--- a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
+++ b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
@@ -62,15 +62,19 @@ import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.swing.filechooser.FileFilter;
+import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.components.genebuilder.JExtendedComboBox;
import uk.ac.sanger.artemis.components.genebuilder.cv.DatePanel;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;
+import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.FileDocument;
import uk.ac.sanger.artemis.util.LinePushBackReader;
+import uk.ac.sanger.artemis.util.ReadOnlyException;
import uk.ac.sanger.artemis.util.StringVector;
import uk.ac.sanger.artemis.util.URLDocument;
@@ -95,6 +99,7 @@ class UserDefinedQualifier extends JFrame
/* text area in the feature editor to add qualifiers to */
private QualifierTextArea qualifier_text_area;
+ private Selection selection;
private JPanel mainPanel;
/* line pattern for tag=value */
@@ -200,10 +205,11 @@ class UserDefinedQualifier extends JFrame
final GridBagConstraints c = new GridBagConstraints();
final JCheckBox ignoreCase = new JCheckBox("Ignore case",true);
- final JComboBox nameCombo = new JComboBox(getQualiferNames());
+ final Vector<String> names = getQualiferNames();
+ final JComboBox nameCombo = new JComboBox(names);
final JButton addButton = new JButton("ADD");
- //final JScrollPane jspNames = new JScrollPane(nameCombo);
-
+ final JCheckBox addToAllSelected = new JCheckBox("add to all selected features", false);
+ final JTextField keyWord = new JTextField(45);
final Dimension d = new Dimension(500, ignoreCase.getPreferredSize().height);
final Dimension d2 = new Dimension(300, ignoreCase.getPreferredSize().height);
@@ -211,17 +217,30 @@ class UserDefinedQualifier extends JFrame
c.gridx = 0;
c.gridy = row;
c.anchor = GridBagConstraints.EAST;
- mainPanel.add(new JLabel("Name: "), c);
- c.gridx = 1;
- c.anchor = GridBagConstraints.WEST;
- mainPanel.add(nameCombo, c);
-
+ if(names.size() < 1)
+ {
+ c.gridwidth = 2;
+ mainPanel.add(new JLabel("Import a list of qualifiers from the File menu."), c);
+ c.gridwidth = 1;
+ ignoreCase.setEnabled(false);
+ nameCombo.setEnabled(false);
+ addButton.setEnabled(false);
+ addToAllSelected.setEnabled(false);
+ keyWord.setEnabled(false);
+ }
+ else
+ {
+ mainPanel.add(new JLabel("Name: "), c);
+ c.gridx = 1;
+ c.anchor = GridBagConstraints.WEST;
+ mainPanel.add(nameCombo, c);
+ }
+
c.gridx = 2;
mainPanel.add(Box.createHorizontalStrut(150), c);
// keyword
- final JTextField keyWord = new JTextField(45);
keyWord.setSelectionStart(0);
keyWord.setSelectionEnd(keyWord.getText().length());
keyWord.setSelectedTextColor(Color.blue);
@@ -231,7 +250,7 @@ class UserDefinedQualifier extends JFrame
public void actionPerformed(ActionEvent event)
{
searchQualifiers(keyWord.getText(), nameCombo,
- ignoreCase.isSelected(), addButton, d);
+ ignoreCase.isSelected(), addButton, addToAllSelected, d);
}
});
c.gridy = ++row;
@@ -254,7 +273,7 @@ class UserDefinedQualifier extends JFrame
public void actionPerformed(ActionEvent arg0)
{
searchQualifiers(keyWord.getText(), nameCombo,
- ignoreCase.isSelected(), addButton, d);
+ ignoreCase.isSelected(), addButton, addToAllSelected, d);
}
});
mainPanel.add(search,c);
@@ -268,8 +287,8 @@ class UserDefinedQualifier extends JFrame
c.gridx = 0;
c.gridy = ++row;
c.gridwidth = 1;
- mainPanel.add(addButton, c);
-
+ mainPanel.add(addButton, c);
+
c.gridx = 1;
final JButton closeButton = new JButton("CLOSE");
mainPanel.add(closeButton, c);
@@ -280,6 +299,11 @@ class UserDefinedQualifier extends JFrame
}
});
+ c.gridx = 0;
+ c.gridy = ++row;
+ c.gridwidth = 2;
+ mainPanel.add(addToAllSelected,c);
+
c.gridy = ++row;
mainPanel.add(Box.createVerticalStrut(15), c);
}
@@ -319,6 +343,7 @@ class UserDefinedQualifier extends JFrame
final JComboBox nameCombo,
final boolean ignoreCase,
final JButton addButton,
+ final JCheckBox addToAllSelected,
final Dimension d)
{
final String qName = (String) nameCombo.getSelectedItem();
@@ -361,8 +386,38 @@ class UserDefinedQualifier extends JFrame
qval = "/GO=aspect=C;"+qval+";date="+DatePanel.getDate();
else
qval = "/"+qName+"="+qval;
-
- qualifier_text_area.append(qval+"\n");
+
+ if(addToAllSelected.isSelected())
+ {
+ final FeatureVector features = selection.getAllFeatures();
+ if(!Options.isBlackBeltMode() && features.size() > 1)
+ {
+ int status = JOptionPane.showConfirmDialog(UserDefinedQualifier.this,
+ "Add "+qName+" to "+features.size()+" selected features?",
+ "Add Qualifier To Selected Features",
+ JOptionPane.OK_CANCEL_OPTION);
+ if(status == JOptionPane.CANCEL_OPTION)
+ return;
+ }
+ final int idx = qval.indexOf("=");
+ final Qualifier q = new Qualifier(qval.substring(1, idx), qval.substring( idx+1 ));
+
+ try
+ {
+ for(int i=0; i<features.size(); i++)
+ features.elementAt(i).addQualifierValues(q);
+ }
+ catch (ReadOnlyException e)
+ {
+ e.printStackTrace();
+ }
+ catch (EntryInformationException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ else
+ qualifier_text_area.append(qval+"\n");
}
};
addButton.addActionListener(addListener);
@@ -565,7 +620,7 @@ class UserDefinedQualifier extends JFrame
createComponentToAddCvTerm();
mainPanel.revalidate();
-
+ mainPanel.repaint();
//if(autoImport.isSelected())
writeQualifierList(fc.getSelectedFile().getAbsolutePath());
}
@@ -587,6 +642,7 @@ class UserDefinedQualifier extends JFrame
createObo(new URLDocument(new URL(urlStr)));
createComponentToAddCvTerm();
mainPanel.revalidate();
+ mainPanel.repaint();
writeQualifierList(urlStr);
}
@@ -739,11 +795,16 @@ class UserDefinedQualifier extends JFrame
}
}
- protected void setQualifierTextArea(QualifierTextArea qualifier_text_area)
+ protected void setQualifierTextArea(final QualifierTextArea qualifier_text_area)
{
this.qualifier_text_area = qualifier_text_area;
}
+ protected void setSelection(final Selection selection)
+ {
+ this.selection = selection;
+ }
+
private class ComboMouseListener extends MouseAdapter
{
private JComboBox cb;
--
GitLab