diff --git a/uk/ac/sanger/artemis/components/ViewMenu.java b/uk/ac/sanger/artemis/components/ViewMenu.java
index 615a35a0848474fddf940a7b6131a47f990f71a4..79c7eb5f39da6410bab999ce1c1e1413ab3fdc02 100644
--- a/uk/ac/sanger/artemis/components/ViewMenu.java
+++ b/uk/ac/sanger/artemis/components/ViewMenu.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/ViewMenu.java,v 1.10 2007-03-02 12:57:13 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ViewMenu.java,v 1.11 2007-04-05 15:06:11 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -34,6 +34,7 @@ import uk.ac.sanger.artemis.components.filetree.RemoteFileNode;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.InvalidRelationException;
import uk.ac.sanger.artemis.io.Key;
+import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.j2ssh.FTProgress;
import uk.ac.sanger.artemis.j2ssh.FileTransferProgressMonitor;
@@ -50,7 +51,7 @@ import com.sshtools.j2ssh.sftp.FileAttributes;
* A popup menu with viewing commands.
*
* @author Kim Rutherford
- * @version $Id: ViewMenu.java,v 1.10 2007-03-02 12:57:13 tjc Exp $
+ * @version $Id: ViewMenu.java,v 1.11 2007-04-05 15:06:11 tjc Exp $
**/
public class ViewMenu extends SelectionMenu
@@ -1217,114 +1218,127 @@ public class ViewMenu extends SelectionMenu
++i) {
final Feature this_feature = features_to_view.elementAt (i);
- String qualifier_value;
-
- try {
- qualifier_value =
- this_feature.getValueOfQualifier (program_name + "_file");
- } catch (InvalidRelationException e) {
- qualifier_value = null;
+ Qualifier qualifier = null;
+ try
+ {
+ qualifier = this_feature.getQualifierByName(program_name + "_file");
}
-
- String file_name = qualifier_value;
-
- if (file_name == null || file_name.length () == 0) {
+ catch(InvalidRelationException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ StringVector qualifier_values = qualifier.getValues();
+ String qualifier_value;
+ if(qualifier_values == null || qualifier_values.size() == 0) {
new MessageDialog (frame,
"Message",
"No " + program_name + " results for " +
this_feature.getIDString ());
-
continue;
}
-
- // remove the program name string (if any) from the qualifier, so that
- // we can try to read the file with and without the prefix.
- if(file_name.startsWith(program_name + File.separatorChar)||
- file_name.startsWith(program_name + "/"))
+
+ for(int j=0; j<qualifier_values.size(); j++)
{
- file_name = file_name.substring (program_name.length () + 1);
- }
+ qualifier_value = (String) qualifier_values.get(j);
- Document root_document = this_feature.getEntry ().getRootDocument ();
+ // strip off database name
+ int ind;
+ if((ind = qualifier_value.indexOf(':')) > -1)
+ qualifier_value = qualifier_value.substring(ind + 1);
- if (root_document == null) {
- root_document = new FileDocument (new File ("."));
- }
+ String file_name = qualifier_value;
- try {
- Document document = null;
-
- // try the current directory with the program name added:
- // ./fasta/abc.seq.00001.out
- final File dir_name = new File (program_name);
+ // remove the program name string (if any) from the qualifier, so that
+ // we can try to read the file with and without the prefix.
+ if(file_name.startsWith(program_name + File.separatorChar)||
+ file_name.startsWith(program_name + "/"))
+ {
+ file_name = file_name.substring (program_name.length () + 1);
+ }
- final Document [] possible_documents =
- new Document []
- {
- root_document.append (program_name).append (file_name),
- root_document.append (file_name),
- new FileDocument (new File (file_name)),
- new FileDocument (dir_name).append (file_name),
- new FileDocument ( new File(System.getProperty("user.dir")) ).append(program_name).append (file_name)
- };
+ Document root_document = this_feature.getEntry().getRootDocument();
+ if(root_document == null)
+ root_document = new FileDocument(new File("."));
- for (int possible_document_index = 0 ;
- possible_document_index < possible_documents.length ;
- ++possible_document_index) {
+ try
+ {
+ Document document = null;
- final Document this_document =
- possible_documents[possible_document_index];
+ // try the current directory with the program name added:
+ // ./fasta/abc.seq.00001.out
+ final File dir_name = new File(program_name);
- if (this_document.readable ()) {
- document = this_document;
- break;
- } else {
- final File gzip_file =
- new File (this_document.toString () + ".gz");
- final Document gzip_document =
- new FileDocument (gzip_file);
+ final Document[] possible_documents = new Document[] {
+ root_document.append(program_name).append(file_name),
+ root_document.append(file_name),
+ new FileDocument(new File(file_name)),
+ new FileDocument(dir_name).append(file_name),
+ new FileDocument(new File(System.getProperty("user.dir")))
+ .append(program_name).append(file_name) };
+
+ for(int possible_document_index = 0; possible_document_index < possible_documents.length; ++possible_document_index)
+ {
- if (gzip_document.readable ()) {
- document = gzip_document;
+ final Document this_document = possible_documents[possible_document_index];
+
+ if(this_document.readable())
+ {
+ document = this_document;
break;
}
+ else
+ {
+ final File gzip_file = new File(this_document.toString() + ".gz");
+ final Document gzip_document = new FileDocument(gzip_file);
+
+ if(gzip_document.readable())
+ {
+ document = gzip_document;
+ break;
+ }
+ }
}
- }
- // if not found locally check remote side
- if(document == null
- && ((DocumentEntry) (this_feature.getEntry().getEMBLEntry()))
- .getDocument() instanceof RemoteFileDocument)
- {
- document = checkRemoteNode(this_feature, program_name, file_name, dir_name);
- }
-
- if (document == null) {
- final String message_string =
- "No " + program_name + " results for " +
- this_feature.getIDString () + " (file not found: " +
- qualifier_value + ")";
+ // if not found locally check remote side
+ if(document == null
+ && ((DocumentEntry) (this_feature.getEntry().getEMBLEntry()))
+ .getDocument() instanceof RemoteFileDocument)
+ {
+ document = checkRemoteNode(this_feature, program_name, file_name,
+ dir_name);
+ }
- new MessageDialog (frame, message_string);
+ if(document == null)
+ {
+ final String message_string = "No " + program_name
+ + " results for " + this_feature.getIDString()
+ + " (file not found: " + qualifier_value + ")";
- continue;
- }
+ new MessageDialog(frame, message_string);
+
+ continue;
+ }
- if (send_to_browser) {
- SearchResultViewer.sendToBrowser (document.toString ());
- } else {
- new SearchResultViewer (program_name + " results for " +
- this_feature.getIDString () + " from " +
- document,
- document);
+ if(send_to_browser)
+ {
+ SearchResultViewer.sendToBrowser(document.toString());
+ }
+ else
+ {
+ new SearchResultViewer(program_name + " results for "
+ + this_feature.getIDString() + " from " + document, document);
+ }
+ }
+ catch(ExternalProgramException e)
+ {
+ new MessageDialog(frame, "error while open results file: " + e);
+ }
+ catch(IOException e)
+ {
+ new MessageDialog(frame, "error while open results file: " + e);
}
- } catch (ExternalProgramException e) {
- new MessageDialog (frame,
- "error while open results file: " + e);
- } catch (IOException e) {
- new MessageDialog (frame,
- "error while open results file: " + e);
}
}
}