From 377e254ff2867c1f006039ca15eae2058ca9af10 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 9 Aug 2013 14:58:57 +0100
Subject: [PATCH] add paste qualifiers option
---
.../components/UserDefinedQualifiers.java | 122 +++++++++++++-----
1 file changed, 88 insertions(+), 34 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
index 62a5b6a08..6f0b1e6d5 100644
--- a/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
+++ b/uk/ac/sanger/artemis/components/UserDefinedQualifiers.java
@@ -30,6 +30,7 @@ import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.BufferedWriter;
+import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
@@ -84,7 +85,7 @@ class UserDefinedQualifier extends JFrame
org.apache.log4j.Logger.getLogger(UserDefinedQualifier.class);
/* collection of loaded files */
- private Vector<OBO> obos = new Vector<OBO>();
+ private Vector<QualifierList> obos = new Vector<QualifierList>();
/* component containing list of available values */
private Box qualifierBox = Box.createHorizontalBox();
@@ -120,7 +121,7 @@ class UserDefinedQualifier extends JFrame
importFile.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
- importObo();
+ importFromFile();
}
});
fileMenu.add(importFile);
@@ -134,7 +135,29 @@ class UserDefinedQualifier extends JFrame
});
fileMenu.add(importURL);
+ final JMenuItem pasteQualifiers = new JMenuItem("Paste qualifiers ...");
+ pasteQualifiers.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent arg0)
+ {
+ final QualifierTextArea qualifierText = new QualifierTextArea();
+ int status = JOptionPane.showConfirmDialog(UserDefinedQualifier.this,
+ qualifierText, "Paste in qualifier lists in the format: name = value",
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if(status == JOptionPane.OK_OPTION)
+ {
+ QualifierList obo = new QualifierList();
+ obo.qualifiers = loadText(new ByteArrayInputStream(qualifierText.getText().getBytes()));
+ obos.add(obo);
+ createComponentToAddCvTerm();
+ mainPanel.revalidate();
+
+ writeQualifierList(qualifierText.getText());
+ }
+ }
+ });
+ fileMenu.add(pasteQualifiers);
fileMenu.addSeparator();
final JMenu removeFile = new JMenu("Qualifier source(s)");
@@ -145,7 +168,7 @@ class UserDefinedQualifier extends JFrame
public void menuSelected(MenuEvent e)
{
removeFile.removeAll();
- for(final OBO obo: obos)
+ for(final QualifierList obo: obos)
{
final JCheckBoxMenuItem oboMenu =
new JCheckBoxMenuItem(obo.doc.getName(), obo.isAcive);
@@ -154,7 +177,6 @@ class UserDefinedQualifier extends JFrame
public void actionPerformed(ActionEvent e)
{
obo.isAcive = oboMenu.isSelected();
- mainPanel.removeAll();
createComponentToAddCvTerm();
mainPanel.revalidate();
mainPanel.repaint();
@@ -173,6 +195,7 @@ class UserDefinedQualifier extends JFrame
*/
private void createComponentToAddCvTerm()
{
+ mainPanel.removeAll();
mainPanel.setLayout(new GridBagLayout());
final GridBagConstraints c = new GridBagConstraints();
@@ -261,7 +284,7 @@ class UserDefinedQualifier extends JFrame
mainPanel.add(Box.createVerticalStrut(15), c);
}
- private StringVector searchOboQualifiers(final OBO obo,
+ private StringVector searchOboQualifiers(final QualifierList obo,
final String qName,
final String keyWord,
final boolean ignoreCase)
@@ -300,7 +323,7 @@ class UserDefinedQualifier extends JFrame
{
final String qName = (String) nameCombo.getSelectedItem();
final StringVector results = new StringVector();
- for(OBO obo: obos)
+ for(QualifierList obo: obos)
{
if(!obo.isAcive)
continue;
@@ -354,7 +377,7 @@ class UserDefinedQualifier extends JFrame
private Vector<String> getQualiferNames()
{
final Vector<String> names = new Vector<String>();
- for(OBO obo: obos)
+ for(QualifierList obo: obos)
{
if(!obo.isAcive)
continue;
@@ -516,11 +539,11 @@ class UserDefinedQualifier extends JFrame
/**
* Import OBO
*/
- private void importObo()
+ private void importFromFile()
{
final StickyFileChooser fc = new StickyFileChooser();
- final JCheckBox autoImport = new JCheckBox("Automatically import", true);
- fc.setAccessory(autoImport);
+ //final JCheckBox autoImport = new JCheckBox("Automatically import", true);
+ //fc.setAccessory(autoImport);
OboFileFilter oboFilter = new OboFileFilter(new String[]{"obo", "OBO"}, "OBO files");
fc.addChoosableFileFilter(oboFilter);
@@ -540,12 +563,11 @@ class UserDefinedQualifier extends JFrame
createObo(doc);
- mainPanel.removeAll();
createComponentToAddCvTerm();
mainPanel.revalidate();
- if(autoImport.isSelected())
- writeProperties(fc.getSelectedFile().getAbsolutePath());
+ //if(autoImport.isSelected())
+ writeQualifierList(fc.getSelectedFile().getAbsolutePath());
}
private void importFromUrl()
@@ -563,16 +585,10 @@ class UserDefinedQualifier extends JFrame
{
String urlStr = s.trim();
createObo(new URLDocument(new URL(urlStr)));
- mainPanel.removeAll();
createComponentToAddCvTerm();
mainPanel.revalidate();
- int status = JOptionPane.showConfirmDialog(
- UserDefinedQualifier.this,
- "Automatically import:\n"+urlStr+"\nbetween session?",
- "Import Option", JOptionPane.YES_NO_OPTION);
- if(status == JOptionPane.YES_OPTION)
- writeProperties(urlStr);
+ writeQualifierList(urlStr);
}
catch (MalformedURLException e)
{
@@ -585,7 +601,7 @@ class UserDefinedQualifier extends JFrame
try
{
logger4j.debug("Reading qualifiers from: "+doc.getName());
- OBO obo = new OBO();
+ final QualifierList obo = new QualifierList();
obo.doc = doc;
obo.qualifiers = loadQualifiers(doc);
obos.add(obo);
@@ -599,15 +615,34 @@ class UserDefinedQualifier extends JFrame
JOptionPane.ERROR_MESSAGE);
}
}
-
-
+
+
/**
- * Write or re-write properties and insert/update the user.dir property
- * @param jemProp properties file
- * @param uHome user working directory
- */
- private static void writeProperties(final String loc)
+ * Write or append to artemis qualifiers list
+ * @param loc
+ * @param isOBO
+ */
+ private static void writeQualifierList(final String loc)
{
+ int status = JOptionPane.showConfirmDialog(
+ null,
+ "Automatically import:\n"+loc+"\nbetween session?",
+ "Import Option", JOptionPane.YES_NO_OPTION);
+ if(status != JOptionPane.YES_OPTION)
+ return;
+
+ final boolean isOBO;
+ if(loc.toLowerCase().endsWith(".obo"))
+ isOBO = true;
+ else
+ {
+ File f = new File(loc);
+ if(f.exists())
+ isOBO = true;
+ else
+ isOBO = false;
+ }
+
final String qualPath = System.getProperty("user.home") + File.separator + ".artemis.qualifiers";
try
{
@@ -639,12 +674,30 @@ class UserDefinedQualifier extends JFrame
}
}
+ final File qualFile = new File(qualPath);
+ final boolean exists = qualFile.exists();
final BufferedWriter bufferedwriter = new BufferedWriter(
- new FileWriter(new File(qualPath), true));
- if(loc.startsWith("http://"))
- bufferedwriter.append("\nimport: "+loc+"\n");
+ new FileWriter(qualFile, true));
+
+ if(!exists)
+ {
+ bufferedwriter.append("# User defined list of qualifiers in the format of:\n");
+ bufferedwriter.append("# name=value\n");
+ bufferedwriter.append("# The qualifiers are separated by lines.\n");
+ bufferedwriter.append("# OBO files can be used by defining import statements:\n");
+ bufferedwriter.append("#import: http://www.geneontology.org/GO_slims/goslim_generic.obo\n\n");
+ }
+
+ if(isOBO)
+ {
+ if(loc.startsWith("http://"))
+ bufferedwriter.append("\nimport: "+loc+"\n");
+ else
+ bufferedwriter.append("\nimport: file://"+loc+"\n");
+ }
else
- bufferedwriter.append("\nimport: file://"+loc+"\n");
+ bufferedwriter.append(loc+"\n");
+
bufferedwriter.close();
}
catch (FileNotFoundException filenotfoundexception)
@@ -719,8 +772,9 @@ class UserDefinedQualifier extends JFrame
return buff.toString();
}
}
-
- private class OBO
+
+
+ private class QualifierList
{
Document doc;
QualifierVector qualifiers;
--
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