diff --git a/uk/ac/sanger/artemis/components/RunMenu.java b/uk/ac/sanger/artemis/components/RunMenu.java
index 8a6760af32b52ee0169c253ae5448e1e5f98fd69..a0cbf87db6d83fb6a257ee879496edafc2679db5 100644
--- a/uk/ac/sanger/artemis/components/RunMenu.java
+++ b/uk/ac/sanger/artemis/components/RunMenu.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/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;
-//}
}