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Commit 51fe33b1 authored by tjc's avatar tjc
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group blast programs into there own submenus 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8348 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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uk/ac/sanger/artemis/components/RunMenu.java
+ 34
− 96
View file @ 51fe33b1
......@@ -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/RunMenu.java,v 1.9 2007-02-28 15:47:56 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/RunMenu.java,v 1.10 2008-07-24 13:49:00 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
......@@ -31,15 +31,19 @@ import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.InvalidKeyException;
import java.io.IOException;
import java.util.Hashtable;
import java.awt.event.*;
import javax.swing.*;
import javax.swing.JFrame;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
/**
* A JMenu of external commands/functions.
*
* @author Kim Rutherford
* @version $Id: RunMenu.java,v 1.9 2007-02-28 15:47:56 tjc Exp $
* @version $Id: RunMenu.java,v 1.10 2008-07-24 13:49:00 tjc Exp $
**/
public class RunMenu extends SelectionMenu
......@@ -49,8 +53,8 @@ public class RunMenu extends SelectionMenu
private static final long serialVersionUID = 1L;
private JMenu fastaMenu = null;
private JMenu fastaMenuOptions = null;
private JMenu blastpMenu = null;
private JMenu blastpMenuOptions = null;
private Hashtable blastMenu = null;
private Hashtable blastMenuOptions = null;
/**
* Create a new RunMenu object.
......@@ -78,34 +82,6 @@ public class RunMenu extends SelectionMenu
for(int i = 0; i < external_programs_size; ++i)
makeOptionsMenuItem(external_programs.elementAt(i));
// if(Options.getOptions().getProperty("jcon_min_jobs") != null)
// {
// addSeparator();
// final JMenuItem jcon_status = new JMenuItem("Show Job Status ...");
// jcon_status.addActionListener(new ActionListener()
// {
// public void actionPerformed(ActionEvent event)
// {
// try
// {
// final int ids[] = getIds();
// TaskViewerFrame tvf = new TaskViewerFrame(ids);
// tvf.setSize(400, 600);
// tvf.setVisible(true);
// }
// catch(Exception e)
// {
// e.printStackTrace();
// new MessageDialog(frame, "unable to view job status: " + e);
// }
// }
// });
// add(jcon_status);
// }
}
/**
......@@ -140,7 +116,7 @@ public class RunMenu extends SelectionMenu
if(options_string.length() > 0)
{
if(program_name.startsWith("fasta") ||
program_name.startsWith("blastp"))
program_name.indexOf("blast")>-1)
new_menu = new JMenuItem(options_string);
else
new_menu = new JMenuItem("Run " + program_name + " (" +
......@@ -225,14 +201,21 @@ public class RunMenu extends SelectionMenu
}
fastaMenu.add(new_menu);
}
else if(program.getName().startsWith("blastp"))
else if(program.getName().indexOf("blast")>-1)
{
if(blastpMenu == null)
if(blastMenu == null)
blastMenu = new Hashtable();
if(!blastMenu.containsKey(program.getName()))
{
blastpMenu = new JMenu("Run blastp on selected features against");
add(blastpMenu);
JMenu topMenu = new JMenu("Run "+program.getName()+
" on selected features against");
blastMenu.put(program.getName(), topMenu);
add(topMenu);
}
blastpMenu.add(new_menu);
JMenu topMenu = (JMenu) blastMenu.get(program.getName());
topMenu.add(new_menu);
}
else
add(new_menu);
......@@ -261,15 +244,22 @@ public class RunMenu extends SelectionMenu
new_options_menu = new JMenuItem(program.getProgramOptions());
fastaMenuOptions.add(new_options_menu);
}
else if(program_name.startsWith("blastp"))
else if(program_name.indexOf("blast")>-1)
{
if(blastpMenuOptions == null)
if(blastMenuOptions == null)
blastMenuOptions = new Hashtable();
String menuStr = "Set " + program_name + " options";
if(!blastMenuOptions.containsKey(menuStr))
{
blastpMenuOptions = new JMenu("Set " + program_name + " options");
add(blastpMenuOptions);
JMenu topMenu = new JMenu(menuStr);
blastMenuOptions.put(menuStr, topMenu);
add(topMenu);
}
JMenu topMenu = (JMenu) blastMenuOptions.get(menuStr);
new_options_menu = new JMenuItem(program.getProgramOptions());
blastpMenuOptions.add(new_options_menu);
topMenu.add(new_options_menu);
}
else
{
......@@ -286,56 +276,4 @@ public class RunMenu extends SelectionMenu
});
}
/**
*
**/
//private int[] getIds()
//{
// final FeatureVector selected_features = getSelection().getAllFeatures();
// final Vector ids_vector = new Vector();
// for(int feature_index = 0; feature_index < selected_features.size();
// ++feature_index)
// {
// final Feature this_feature = selected_features.elementAt(feature_index);
// try
// {
// final Qualifier job_qualifier =
// this_feature.getQualifierByName("job");
//
// final StringVector values = job_qualifier.getValues();
// if(values != null && values.size() > 0)
// {
// for(int value_index=0; value_index<values.size();
// ++value_index)
// {
// final String job_value = values.elementAt(value_index);
// final StringVector bits = StringVector.getStrings(job_value);
// if(bits.size() > 4 && bits.elementAt(2).equals("task:"))
// {
// try
// {
// final Integer task_id = Integer.valueOf(bits.elementAt(3));
// if(!ids_vector.contains(task_id))
// ids_vector.add(task_id);
// }
// catch(NumberFormatException e) {}
// }
// }
// }
// }
// catch(InvalidRelationException e) {}
// }
// final int[] ids = new int[ids_vector.size()];
// for(int i=0 ; i<ids.length ; ++i)
// ids[i] =((Integer)ids_vector.elementAt(i)).intValue();
// return ids;
//}
}
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