diff --git a/uk/ac/sanger/artemis/components/FeatureEdit.java b/uk/ac/sanger/artemis/components/FeatureEdit.java
index 6f16565a14143af9c937eaea6c944b795b209ebd..35e16b40bfdfe2b5151a8a3f6176123cb88ec3bf 100644
--- a/uk/ac/sanger/artemis/components/FeatureEdit.java
+++ b/uk/ac/sanger/artemis/components/FeatureEdit.java
@@ -20,14 +20,14 @@
* 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/FeatureEdit.java,v 1.3 2004-08-13 13:59:20 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureEdit.java,v 1.4 2004-08-26 12:51:56 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.*;
-import uk.ac.sanger.artemis.sequence.*;
+import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.io.OutOfDateException;
import uk.ac.sanger.artemis.io.LocationParseException;
@@ -44,19 +44,21 @@ import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.StreamQualifier;
import uk.ac.sanger.artemis.io.QualifierInfo;
-import uk.ac.sanger.artemis.io.EmblStreamFeature;
+
+import uk.ac.sanger.artemis.components.ProgressThread;
import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.Date;
+import java.util.Vector;
import javax.swing.*;
/**
* FeatureEdit class
*
* @author Kim Rutherford
- * @version $Id: FeatureEdit.java,v 1.3 2004-08-13 13:59:20 tjc Exp $
+ * @version $Id: FeatureEdit.java,v 1.4 2004-08-26 12:51:56 tjc Exp $
**/
public class FeatureEdit extends JFrame
@@ -76,18 +78,18 @@ public class FeatureEdit extends JFrame
private final static int LOCATION_TEXT_WIDTH = 80;
/** The location text - set by updateLocation(). */
- private JTextField location_text = new JTextField (LOCATION_TEXT_WIDTH);
+ private JTextField location_text = new JTextField(LOCATION_TEXT_WIDTH);
- private JButton add_qualifier_button = new JButton ("Add qualifier");
+ private JButton add_qualifier_button = new JButton("Add qualifier");
/** When pressed - apply changes and dispose of the component. */
- private JButton ok_button = new JButton ("OK");
+ private JButton ok_button = new JButton("OK");
/** When pressed - discard changes and dispose of the component. */
- private JButton cancel_button = new JButton ("Cancel");
+ private JButton cancel_button = new JButton("Cancel");
/** When pressed - apply changes and keep the component open. */
- private JButton apply_button = new JButton ("Apply");
+ private JButton apply_button = new JButton("Apply");
/** Edit area for qualifiers - created by createComponents(). */
private QualifierTextArea qualifier_text_area;
@@ -108,7 +110,7 @@ public class FeatureEdit extends JFrame
private EntryGroup entry_group;
/**
- * The datestamp of the RWCorbaFeature when updateFromFeature () was last
+ * The datestamp of the RWCorbaFeature when updateFromFeature() was last
* called or null if this is not a RWCorbaFeature.
**/
private Date datestamp = null;
@@ -128,26 +130,25 @@ public class FeatureEdit extends JFrame
* @param entry_group The EntryGroup that contains this Feature.
* @param selection The Selection operate on. The operations are "Remove
* Range" and "Grab Range"
- * @param goto_event_source The object the we will call gotoBase () on.
+ * @param goto_event_source The object the we will call gotoBase() on.
**/
- public FeatureEdit (final Feature edit_feature,
- final EntryGroup entry_group,
- final Selection selection,
- final GotoEventSource goto_event_source)
+ public FeatureEdit(final Feature edit_feature,
+ final EntryGroup entry_group,
+ final Selection selection,
+ final GotoEventSource goto_event_source)
{
- super("Artemis Feature Edit: " + edit_feature.getIDString () +
- (edit_feature.isReadOnly () ?
+ super("Artemis Feature Edit: " + edit_feature.getIDString() +
+ (edit_feature.isReadOnly() ?
" - (read only)" :
""));
this.edit_feature = edit_feature;
- this.edit_entry = edit_feature.getEntry ();
+ this.edit_entry = edit_feature.getEntry();
this.entry_group = entry_group;
this.selection = selection;
this.goto_event_source = goto_event_source;
createComponents();
-
updateFromFeature();
orig_qualifier_text = qualifier_text_area.getText();
@@ -157,14 +158,14 @@ public class FeatureEdit extends JFrame
addWindowListener(new WindowAdapter()
{
- public void windowClosing (WindowEvent event)
+ public void windowClosing(WindowEvent event)
{
- stopListening ();
- dispose ();
+ stopListening();
+ dispose();
}
});
- pack ();
+ pack();
final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
setLocation(new Point((screen.width - getSize().width)/2,
@@ -178,8 +179,8 @@ public class FeatureEdit extends JFrame
**/
public void stopListening()
{
- getEntry().removeEntryChangeListener (this);
- getFeature().removeFeatureChangeListener (this);
+ getEntry().removeEntryChangeListener(this);
+ getFeature().removeFeatureChangeListener(this);
}
/**
@@ -187,15 +188,15 @@ public class FeatureEdit extends JFrame
* EntryChange events so we can notify the user if of this component if the
* feature gets deleted.
**/
- public void entryChanged (EntryChangeEvent event)
+ public void entryChanged(EntryChangeEvent event)
{
switch(event.getType())
{
case EntryChangeEvent.FEATURE_DELETED:
- if (event.getFeature () == edit_feature)
+ if(event.getFeature() == edit_feature)
{
- stopListening ();
- dispose ();
+ stopListening();
+ dispose();
}
break;
default:
@@ -225,7 +226,7 @@ public class FeatureEdit extends JFrame
**/
public void addApplyActionListener(final ActionListener l)
{
- apply_button.addActionListener (l);
+ apply_button.addActionListener(l);
}
/**
@@ -245,33 +246,33 @@ public class FeatureEdit extends JFrame
public void featureChanged(FeatureChangeEvent event)
{
// re-read the information from the feature
- switch (event.getType ())
+ switch(event.getType())
{
- case FeatureChangeEvent.LOCATION_CHANGED:
- updateLocation ();
- break;
- case FeatureChangeEvent.KEY_CHANGED:
- updateKey ();
- break;
- case FeatureChangeEvent.QUALIFIER_CHANGED:
- if(qualifier_text_area.getText ().equals (orig_qualifier_text))
- updateFromFeature ();
- else
- {
- final String message =
- "warning: the qualifiers have changed outside the editor - " +
- "view now?";
+ case FeatureChangeEvent.LOCATION_CHANGED:
+ updateLocation();
+ break;
+ case FeatureChangeEvent.KEY_CHANGED:
+ updateKey();
+ break;
+ case FeatureChangeEvent.QUALIFIER_CHANGED:
+ if(qualifier_text_area.getText().equals(orig_qualifier_text))
+ updateFromFeature();
+ else
+ {
+ final String message =
+ "warning: the qualifiers have changed outside the editor - " +
+ "view now?";
- final YesNoDialog yes_no_dialog =
- new YesNoDialog(FeatureEdit.this, message);
+ final YesNoDialog yes_no_dialog =
+ new YesNoDialog(FeatureEdit.this, message);
- if(yes_no_dialog.getResult())
- new FeatureViewer(getFeature());
- }
- break;
- default:
- updateFromFeature ();
- break;
+ if(yes_no_dialog.getResult())
+ new FeatureViewer(getFeature());
+ }
+ break;
+ default:
+ updateFromFeature();
+ break;
}
}
@@ -281,26 +282,24 @@ public class FeatureEdit extends JFrame
**/
private void createComponents()
{
- qualifier_text_area = new QualifierTextArea ();
- qualifier_text_area.setWrapStyleWord (true);
+ qualifier_text_area = new QualifierTextArea();
+ qualifier_text_area.setWrapStyleWord(true);
key_choice =
new KeyChoice(getEntryInformation(),getFeature().getKey());
final JPanel key_and_qualifier_panel = new JPanel();
-
location_text.setBackground(Color.white);
final JPanel key_panel = new JPanel();
- key_panel.add(new JLabel ("Key:"));
+ key_panel.add(new JLabel("Key:"));
key_panel.add(key_choice);
key_and_qualifier_panel.setLayout(new BorderLayout());
key_and_qualifier_panel.add(key_panel, "West");
qualifier_choice = new QualifierChoice(getEntryInformation(),
- key_choice.getSelectedItem(),
- null);
+ key_choice.getSelectedItem(),null);
final JPanel qualifier_panel = new JPanel();
final JButton qualifier_add_button = new JButton("Add Qualifier:");
@@ -314,7 +313,7 @@ public class FeatureEdit extends JFrame
{
public void itemStateChanged(ItemEvent _)
{
- qualifier_choice.setKey (key_choice.getSelectedItem ());
+ qualifier_choice.setKey(key_choice.getSelectedItem());
}
});
@@ -323,21 +322,19 @@ public class FeatureEdit extends JFrame
public void actionPerformed(ActionEvent e)
{
final String qualifier_name =
- (String)qualifier_choice.getSelectedItem ();
+ (String)qualifier_choice.getSelectedItem();
QualifierInfo qualifier_info =
getEntryInformation().getQualifierInfo(qualifier_name);
if(qualifier_info == null)
- {
qualifier_info = new QualifierInfo(qualifier_name,
QualifierInfo.OPTIONAL_QUOTED_TEXT,
null, null, false);
- }
qualifier_text_area.append("/" + qualifier_name);
- switch (qualifier_info.getType ())
+ switch(qualifier_info.getType())
{
case QualifierInfo.QUOTED_TEXT:
if(qualifier_name.equals("GO"))
@@ -346,8 +343,7 @@ public class FeatureEdit extends JFrame
final java.util.Calendar calendar =
java.util.Calendar.getInstance();
- final java.util.Date current_time =
- calendar.getTime();
+ final Date current_time = calendar.getTime();
final java.text.SimpleDateFormat date_format =
new java.text.SimpleDateFormat("yyyyMMdd");
@@ -357,15 +353,13 @@ public class FeatureEdit extends JFrame
date_format.format(current_time, result_buffer,
new java.text.FieldPosition(java.text.DateFormat.DATE_FIELD));
- final String go_string =
- "aspect=; term=; GOid=GO:; "+
- "evidence=ISS; db_xref=GOC:unpublished; " +
- "with=UNIPROT:; date=" + result_buffer;
+ final String go_string = "aspect=; term=; GOid=GO:; "+
+ "evidence=ISS; db_xref=GOC:unpublished; " +
+ "with=UNIPROT:; date=" + result_buffer;
qualifier_text_area.append("=\"" + go_string + "\"");
}
else
qualifier_text_area.append ("=\"\"");
-
break;
case QualifierInfo.NO_VALUE:
@@ -373,18 +367,18 @@ public class FeatureEdit extends JFrame
break;
default:
- qualifier_text_area.append ("=");
+ qualifier_text_area.append("=");
}
- qualifier_text_area.append ("\n");
+ qualifier_text_area.append("\n");
}
});
final JPanel middle_panel = new JPanel();
- middle_panel.setLayout (new BorderLayout());
+ middle_panel.setLayout(new BorderLayout());
final JPanel lower_panel = new JPanel();
- lower_panel.setLayout (new BorderLayout());
+ lower_panel.setLayout(new BorderLayout());
final JPanel outer_location_button_panel = new JPanel();
lower_panel.add(outer_location_button_panel, "North");
@@ -396,7 +390,7 @@ public class FeatureEdit extends JFrame
final JPanel location_panel = new JPanel();
location_panel.setLayout(new BorderLayout());
location_panel.add(new JLabel("location: "), "West");
- location_panel.add (location_text, "Center");
+ location_panel.add(location_text, "Center");
final JButton complement_button = new JButton("Complement");
location_button_panel.add(complement_button);
@@ -414,7 +408,7 @@ public class FeatureEdit extends JFrame
{
public void actionPerformed(ActionEvent e)
{
- grabSelectedRange ();
+ grabSelectedRange();
}
});
@@ -430,7 +424,7 @@ public class FeatureEdit extends JFrame
final JButton goto_button = new JButton("Goto Feature");
location_button_panel.add(goto_button);
- goto_button.addActionListener(new ActionListener ()
+ goto_button.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
@@ -448,10 +442,7 @@ public class FeatureEdit extends JFrame
}
});
- final boolean sanger_options =
- Options.getOptions().getPropertyTruthValue("sanger_options");
-
- if(sanger_options)
+ if(Options.getOptions().getPropertyTruthValue("sanger_options"))
{
// a PSU only hack
final JButton tidy_button = new JButton("Tidy");
@@ -462,9 +453,9 @@ public class FeatureEdit extends JFrame
{
try
{
- tidy ();
+ tidy();
}
- catch (QualifierParseException exception)
+ catch(QualifierParseException exception)
{
final String error_string = exception.getMessage();
new MessageDialog(FeatureEdit.this,
@@ -500,37 +491,24 @@ public class FeatureEdit extends JFrame
else
max_fasta_hits = max_fasta_hits_from_options;
- externalEdit(new String[]
- {
- "-fasta",
- "-maxhits",
- max_fasta_hits,
- "-euk"
- });
+ externalEdit(new String[] { "-fasta", "-maxhits",
+ max_fasta_hits, "-euk" });
}
else
{
if(max_fasta_hits_from_options == null)
{
- externalEdit(new String[]
- {
- "-fasta"
- });
+ externalEdit(new String[] { "-fasta" });
}
else
{
- externalEdit(new String[]
- {
- "-fasta",
- "-maxhits",
- max_fasta_hits_from_options
- });
-
+ externalEdit(new String[] { "-fasta", "-maxhits",
+ max_fasta_hits_from_options });
}
}
return;
}
- } catch (InvalidRelationException _) {}
+ } catch(InvalidRelationException _) {}
new MessageDialog(FeatureEdit.this,
"nothing to edit - no /fasta_file qualifier");
@@ -560,22 +538,13 @@ public class FeatureEdit extends JFrame
if(Options.getOptions().isEukaryoticMode())
{
- externalEdit(new String[]
- {
- "-blastp",
- "-maxhits",
- max_blastp_hits,
- "-euk"
- });
+ externalEdit(new String[] { "-blastp", "-maxhits",
+ max_blastp_hits, "-euk" });
}
else
{
- externalEdit(new String[]
- {
- "-blastp",
- "-maxhits",
- max_blastp_hits
- });
+ externalEdit(new String[] { "-blastp", "-maxhits",
+ max_blastp_hits });
}
return;
}
@@ -609,26 +578,17 @@ public class FeatureEdit extends JFrame
if(Options.getOptions().isEukaryoticMode())
{
- externalEdit(new String[]
- {
- "-blastp+go",
- "-maxhits",
- max_go_blast_hits,
- "-euk"
- });
+ externalEdit(new String[] { "-blastp+go", "-maxhits",
+ max_go_blast_hits, "-euk" });
}
else
{
- externalEdit(new String[]
- {
- "-blastp+go",
- "-maxhits",
- max_go_blast_hits
- });
+ externalEdit(new String[] { "-blastp+go", "-maxhits",
+ max_go_blast_hits });
}
return;
}
- } catch (InvalidRelationException _) {}
+ } catch(InvalidRelationException _) {}
new MessageDialog(FeatureEdit.this,
"nothing to edit - no /blastp+go_file qualifier");
@@ -636,8 +596,67 @@ public class FeatureEdit extends JFrame
});
}
- middle_panel.add(location_panel, "North");
+ if(Options.isUnixHost())
+ {
+ JButton oo_edit_button = new JButton("ObjectEdit");
+ location_button_panel.add(oo_edit_button);
+ oo_edit_button.addActionListener(new ActionListener ()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String qualifier_txt = qualifier_text_area.getText();
+
+ StringReader strRead = new StringReader(qualifier_txt);
+ BufferedReader buff = new BufferedReader(strRead);
+ String line;
+ final Vector dataFile = new Vector();
+ try
+ {
+ while((line = buff.readLine()) != null)
+ {
+ if(line.startsWith("/fasta_file="))
+ {
+ int ind = line.lastIndexOf("\"");
+ if(ind > -1)
+ dataFile.add(line.substring(13,ind));
+ }
+ else if(line.startsWith("/blastp_file="))
+ {
+ int ind = line.lastIndexOf("\"");
+ if(ind > -1)
+ dataFile.add(line.substring(14,ind));
+ }
+ else if(line.startsWith("/blastp+go_file="))
+ {
+ int ind = line.lastIndexOf("\"");
+ if(ind > -1)
+ dataFile.add(line.substring(17,ind));
+ }
+ }
+ }
+ catch(IOException ioe){}
+
+ FeatureEdit.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ final ProgressThread progress = new ProgressThread(null,
+ "Loading Data....");
+ progress.start();
+ SwingWorker ooEd = new SwingWorker()
+ {
+ public Object construct()
+ {
+ new uk.ac.sanger.artemis.editor.BigPane(dataFile.toArray(),
+ qualifier_text_area);
+ progress.finished();
+ FeatureEdit.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ return null;
+ }
+ };
+ ooEd.start();
+ }
+ });
+ }
+ middle_panel.add(location_panel, "North");
getContentPane().add(key_and_qualifier_panel, "North");
cancel_button.addActionListener(new ActionListener()
@@ -678,12 +697,12 @@ public class FeatureEdit extends JFrame
final JPanel ok_cancel_update_panel = new JPanel(flow_layout);
if(!getFeature().isReadOnly())
- ok_cancel_update_panel.add (ok_button);
+ ok_cancel_update_panel.add(ok_button);
- ok_cancel_update_panel.add (cancel_button);
+ ok_cancel_update_panel.add(cancel_button);
if(!getFeature().isReadOnly())
- ok_cancel_update_panel.add (apply_button);
+ ok_cancel_update_panel.add(apply_button);
getContentPane().add(ok_cancel_update_panel, "South");
@@ -724,24 +743,24 @@ public class FeatureEdit extends JFrame
if(location_text.getText().startsWith("complement("))
{
final String new_text = location_text.getText().substring(11);
- if (new_text.endsWith (")"))
+ if (new_text.endsWith(")"))
{
final String new_text2 =
- new_text.substring (0, new_text.length () - 1);
- location_text.setText (new_text2);
+ new_text.substring(0, new_text.length () - 1);
+ location_text.setText(new_text2);
}
else
- location_text.setText (new_text);
+ location_text.setText(new_text);
}
else
{
final String new_text = location_text.getText ();
- location_text.setText ("complement(" + new_text + ")");
+ location_text.setText("complement(" + new_text + ")");
}
}
else
- new MessageDialog (this, "complement failed - " +
- "current location cannot be parsed");
+ new MessageDialog(this, "complement failed - " +
+ "current location cannot be parsed");
}
/**
@@ -860,9 +879,8 @@ public class FeatureEdit extends JFrame
if(!rationalizeLocation())
{
location_text.setText (old_location_text);
- new MessageDialog (this,
- "grab failed - location cannot be parsed after " +
- "grabbing");
+ new MessageDialog(this, "grab failed - location cannot be parsed after " +
+ "grabbing");
}
}
@@ -900,17 +918,17 @@ public class FeatureEdit extends JFrame
try
{
- location = new Location (location_text.getText ());
+ location = new Location(location_text.getText ());
}
catch (LocationParseException e)
{
// this shouldn't happen because we called rationalizeLocation ()
- throw new Error ("internal error - unexpected exception: " + e);
+ throw new Error("internal error - unexpected exception: " + e);
}
final Range location_total_range = location.getTotalRange();
- if(!selected_range.overlaps (location_total_range))
+ if(!selected_range.overlaps(location_total_range))
{
new MessageDialog(this, "remove range failed - the range you " +
"selected does not overlap the feature");
@@ -937,27 +955,27 @@ public class FeatureEdit extends JFrame
{
final Range this_range = location_ranges.elementAt(i);
- if(selected_range.overlaps (this_range))
+ if(selected_range.overlaps(this_range))
{
try
{
- if(this_range.contains (selected_range) &&
- this_range.getStart () != selected_range.getStart () &&
- this_range.getEnd () != selected_range.getEnd ())
+ if(this_range.contains(selected_range) &&
+ this_range.getStart() != selected_range.getStart() &&
+ this_range.getEnd() != selected_range.getEnd())
{
// chop a piece out of the middle and make two new ranges
final Range new_start_range =
- this_range.change(selected_range.getEnd () + 1,
- this_range.getEnd ());
+ this_range.change(selected_range.getEnd() + 1,
+ this_range.getEnd());
new_ranges.add(new_start_range);
final Range new_end_range =
- this_range.change(this_range.getStart (),
- selected_range.getStart () - 1);
+ this_range.change(this_range.getStart(),
+ selected_range.getStart() - 1);
new_ranges.add(new_end_range);
}
else
{
- if(selected_range.contains (this_range)) {
+ if(selected_range.contains(this_range)) {
// delete (ie. don't copy) the range
}
else
@@ -998,7 +1016,7 @@ public class FeatureEdit extends JFrame
final Location new_location =
new Location(new_ranges, location_is_complemented);
- location_text.setText(new_location.toStringShort ());
+ location_text.setText(new_location.toStringShort());
}
/**
@@ -1011,8 +1029,8 @@ public class FeatureEdit extends JFrame
{
try
{
- final Location location = new Location(location_text.getText ());
- location_text.setText(location.toStringShort ());
+ final Location location = new Location(location_text.getText());
+ location_text.setText(location.toStringShort());
return true;
}
catch(LocationParseException e)
@@ -1037,7 +1055,7 @@ public class FeatureEdit extends JFrame
final String pre_edit_text = qualifier_text_area.getText();
// write to a temporary file
- final java.util.Date current_time = calendar.getTime();
+ final Date current_time = calendar.getTime();
final String temp_file_name =
"/tmp/artemis_temp." + current_time.getTime();
@@ -1086,7 +1104,6 @@ public class FeatureEdit extends JFrame
new ProcessWatcher(process, "editor", false);
final Thread watcher_thread = new Thread(process_watcher);
-
watcher_thread.start();
final ProcessWatcherListener listener = new ProcessWatcherListener()
@@ -1096,21 +1113,17 @@ public class FeatureEdit extends JFrame
try
{
final FileReader file_reader = new FileReader(temp_file);
-
final BufferedReader buffered_reader =
new BufferedReader(file_reader);
final StringBuffer buffer = new StringBuffer();
-
String line;
while((line = buffered_reader.readLine()) != null)
buffer.append(line + "\n");
- final String current_qualifier_text =
- qualifier_text_area.getText();
-
- if(!current_qualifier_text.equals(pre_edit_text))
+ //ensure current qualifier text has not changed
+ if(!qualifier_text_area.getText().equals(pre_edit_text))
{
final String message =
"the qualifiers have changed - apply changes from the " +
@@ -1164,7 +1177,6 @@ public class FeatureEdit extends JFrame
private String getQualifierString()
{
final StringBuffer buffer = new StringBuffer();
-
final QualifierVector qualifiers = getFeature().getQualifiers();
for(int qualifier_index = 0; qualifier_index < qualifiers.size();
@@ -1199,7 +1211,6 @@ public class FeatureEdit extends JFrame
private boolean setFeature()
{
final Key key = key_choice.getSelectedItem();
-
final KeyVector possible_keys = getEntryInformation().getValidKeys();
if(possible_keys != null && !possible_keys.contains(key))
@@ -1214,7 +1225,6 @@ public class FeatureEdit extends JFrame
}
final Location location;
-
try
{
location = new Location(location_text.getText());
@@ -1223,10 +1233,8 @@ public class FeatureEdit extends JFrame
{
final String error_string = exception.getMessage ();
System.out.println(error_string);
- new MessageDialog(this,
- "Cannot apply changes because of location error: " +
+ new MessageDialog(this, "Cannot apply changes because of location error: " +
error_string);
-
return false;
}
@@ -1242,8 +1250,7 @@ public class FeatureEdit extends JFrame
{
final String error_string = exception.getMessage();
System.out.println(error_string);
- new MessageDialog(this,
- "Cannot apply changes because of a qualifier " +
+ new MessageDialog(this, "Cannot apply changes because of a qualifier " +
"error: " + error_string);
return false;
}
@@ -1259,8 +1266,7 @@ public class FeatureEdit extends JFrame
catch(OutOfDateException e)
{
final YesNoDialog dialog =
- new YesNoDialog(this,
- "the feature has changed since the edit " +
+ new YesNoDialog(this, "the feature has changed since the edit " +
"window was opened, continue?");
if(dialog.getResult()) // yes - ignore the datestamp
@@ -1278,15 +1284,13 @@ public class FeatureEdit extends JFrame
}
catch(OutOfRangeException e)
{
- new MessageDialog(this,
- "Cannot apply changes - the location is out of " +
+ new MessageDialog(this, "Cannot apply changes - the location is out of " +
"range for this sequence");
return false;
}
catch(ReadOnlyException e)
{
- new MessageDialog(this,
- "Cannot apply changes - the feature is " +
+ new MessageDialog(this, "Cannot apply changes - the feature is " +
"read only");
return false;
}
@@ -1314,7 +1318,7 @@ public class FeatureEdit extends JFrame
**/
private void dribble()
{
- if(!Options.isUnixHost ())
+ if(!Options.isUnixHost())
return;
final String dribble_file_name;
diff --git a/uk/ac/sanger/artemis/components/ProgressThread.java b/uk/ac/sanger/artemis/components/ProgressThread.java
index 54c585e60319a41cd6fffec93e824b4d23ea02be..73608fee83ef86fbe1cbb2102c3a1946a3611a8e 100644
--- a/uk/ac/sanger/artemis/components/ProgressThread.java
+++ b/uk/ac/sanger/artemis/components/ProgressThread.java
@@ -35,6 +35,7 @@ public class ProgressThread extends Thread
private String msg;
private JProgressBar progressBar = new JProgressBar();
+
public ProgressThread(JFrame frame, String msg)
{
this.frame = frame;
@@ -45,7 +46,7 @@ public class ProgressThread extends Thread
{
try
{
- progress_frame = new JFrame("Loading...");
+ progress_frame = new JFrame(msg);
Dimension d = progress_frame.getToolkit().getScreenSize();
progressBar.setIndeterminate(true);
progressBar.setBackground(Color.white);
diff --git a/uk/ac/sanger/artemis/editor/Annotation.java b/uk/ac/sanger/artemis/editor/Annotation.java
index c3187e6adca9e50089f599ed1845961f0ef499a9..fcd89aa37be738dc4bb6307fb45474e4f8d1669d 100644
--- a/uk/ac/sanger/artemis/editor/Annotation.java
+++ b/uk/ac/sanger/artemis/editor/Annotation.java
@@ -120,7 +120,7 @@ public class Annotation extends JEditorPane
text = getDatabaseHTML(text,"SWALL:");
text = getDatabaseHTML(text,"UNIPROT:");
text = getDatabaseHTML(text,"EMBL:");
- setText("<html><body>"+text+"</html></body>");
+ setText("<html><body><font size=3>"+text+"</font></html></body>");
startRange = getDocument().getLength();
}
diff --git a/uk/ac/sanger/artemis/editor/BigPane.java b/uk/ac/sanger/artemis/editor/BigPane.java
index c634a74093cc1a86a772f46066fc955d36cc2436..8c2b48363adbba80d4c546a56794d3f9ff7f2e2a 100644
--- a/uk/ac/sanger/artemis/editor/BigPane.java
+++ b/uk/ac/sanger/artemis/editor/BigPane.java
@@ -28,10 +28,14 @@ import java.awt.event.ActionListener;
import java.awt.event.ActionEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
import java.awt.Dimension;
-import java.awt.Toolkit;
import java.awt.Font;
-import java.awt.Component;
+import java.awt.Insets;
+import java.awt.Toolkit;
+
import java.util.Vector;
import javax.swing.*;
@@ -75,7 +79,7 @@ public class BigPane extends JFrame
addWindowListener(new winExit());
// data set
- int hgt = getHeight()-60;
+ int hgt = getHeight()-85;
int wid = getWidth()-100;
dataView = new DataViewInternalFrame(dataFile,desktop,
wid,qualifier_txt);
@@ -87,9 +91,43 @@ public class BigPane extends JFrame
JMenuBar menuBar = createMenuBar(desktop);
setJMenuBar(menuBar);
+// toolbar
+ JToolBar toolBar = createToolbar();
+ getContentPane().add(toolBar,BorderLayout.NORTH);
+
setVisible(true);
}
+
+ /**
+ *
+ * Create a toolbar
+ * @return toolbar.
+ *
+ */
+ private JToolBar createToolbar()
+ {
+ JToolBar toolBar = new JToolBar();
+
+ JButton applyButt = new JButton("APPLY");
+ applyButt.setToolTipText("Apply annotation changed to feature editor");
+ applyButt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ qualifier.setText(dataView.getFeatureText());
+ }
+ });
+ applyButt.setBackground(new Color(0,0,81));
+ applyButt.setForeground(Color.white);
+ applyButt.setBorderPainted(false);
+ applyButt.setMargin(new Insets(0,0,0,0));
+ applyButt.setFont(font);
+ toolBar.add(applyButt);
+
+ return toolBar;
+ }
+
/**
*
* Create a menu bar.
@@ -133,7 +171,17 @@ public class BigPane extends JFrame
if(qualifier == null)
System.exit(0);
- qualifier.setText(dataView.getFeatureText());
+ int ok = JOptionPane.showConfirmDialog(BigPane.this,
+ "Apply changes now?",
+ "Apply Changes",
+ JOptionPane.YES_NO_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+
+ if(ok == JOptionPane.CANCEL_OPTION)
+ return;
+
+ if(ok == JOptionPane.OK_OPTION)
+ qualifier.setText(dataView.getFeatureText());
BigPane.srsFrame = null;
dispose();
}
diff --git a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
index 2dcfa74217df9967e89d2b021c60443f0aea96c8..44330904ee10643bc871cbcafa65ae25dcc660d2 100644
--- a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
+++ b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
@@ -118,11 +118,11 @@ public class DataViewInternalFrame extends JInternalFrame
// add annotator text pane
ann.setAnnotation(annFormat.toString().trim());
JScrollPane annotationScroll = new JScrollPane(ann);
- annotationScroll.setPreferredSize(new Dimension(500,300));
+ annotationScroll.setPreferredSize(new Dimension(500,150));
JSplitPane split = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
annotationScroll,tabPane);
- split.setDividerLocation(250);
+ split.setDividerLocation(150);
getContentPane().add(split);
setVisible(true);