@@ -82,9 +82,6 @@ public class AlignmentGui extends JFrame{
8282 JProgressBar progress ;
8383
8484
85- private DBSearchGUI dbsearch ;
86-
87-
8885 public static void main (String [] args ){
8986
9087 AlignmentGui .getInstance ();
@@ -163,10 +160,6 @@ protected AlignmentGui() {
163160
164161 masterPane .addTab ("Pairwise Comparison" , vBox );
165162
166- dbsearch = new DBSearchGUI ();
167-
168- masterPane .addTab ("Database Search" ,dbsearch );
169-
170163 //JPanel dir = tab1.getPDBDirPanel(pdbDir);
171164
172165 Box vBoxMain = Box .createVerticalBox ();
@@ -278,8 +271,6 @@ public void actionPerformed(ActionEvent evt) {
278271 int selectedIndex = masterPane .getSelectedIndex ();
279272 if (selectedIndex == 0 )
280273 calcAlignment ();
281- else if ( selectedIndex == 1 )
282- calcDBSearch ();
283274 else {
284275 System .err .println ("Unknown TAB: " + selectedIndex );
285276 }
@@ -408,110 +399,6 @@ private void calcAlignment() {
408399
409400 }
410401
411-
412- private void calcDBSearch () {
413-
414- JTabbedPane tabPane = dbsearch .getTabPane ();
415- System .out .println ("run DB search " + tabPane .getSelectedIndex ());
416-
417- Structure s = null ;
418- boolean domainSplit = dbsearch .isDomainSplit ();
419-
420- StructurePairSelector tab = null ;
421- int pos = tabPane .getSelectedIndex ();
422-
423- if (pos == 0 ){
424-
425- tab = dbsearch .getSelectPDBPanel ();
426-
427- } else if (pos == 1 ){
428-
429- tab = dbsearch .getScopSelectPanel ();
430-
431-
432- } else if (pos == 2 ){
433-
434- tab = dbsearch .getPDBUploadPanel ();
435-
436- }
437-
438- try {
439-
440- s = tab .getStructure1 ();
441-
442- if ( s == null ) {
443- JOptionPane .showMessageDialog (null ,"please select structure 1" );
444- return ;
445- }
446-
447- } catch (Exception e ){
448- e .printStackTrace ();
449- }
450-
451- String name1 = s .getName ();
452- if ( name1 == null || name1 .equals ("" ))
453- name1 = s .getPDBCode ();
454-
455-
456-
457- System .out .println ("name1 in alig gui:" + name1 );
458- String file = dbsearch .getOutFileLocation ();
459- if ( file == null || file .equals ("" ) ){
460- JOptionPane .showMessageDialog (null ,"Please select a directory to contain the DB search results." );
461- return ;
462- }
463- File outFile = new File (file );
464- if ( !outFile .exists () ) {
465- outFile .mkdirs ();
466- }
467- if ( !outFile .isDirectory () || !outFile .canWrite ()) {
468- JOptionPane .showMessageDialog (null ,"Unable to write to " +outFile .getAbsolutePath ());
469- return ;
470- }
471-
472- UserConfiguration config = WebStartMain .getWebStartConfig ();
473-
474- int totalNrCPUs = Runtime .getRuntime ().availableProcessors ();
475-
476- int useNrCPUs = 1 ;
477- if ( totalNrCPUs > 1 ){
478- Object [] options = new Integer [totalNrCPUs ];
479- int posX = 0 ;
480- for ( int i = totalNrCPUs ; i > 0 ; i --){
481- options [posX ] = i ;
482- posX ++;
483- }
484- int n = JOptionPane .showOptionDialog (null ,
485- "How many would you like to use for the calculations?" ,
486- "We detected " + totalNrCPUs + " processors on your system." ,
487- JOptionPane .OK_CANCEL_OPTION ,
488- JOptionPane .QUESTION_MESSAGE ,
489- null ,
490- options ,
491- options [0 ]);
492-
493- if ( n < 0 )
494- return ;
495- useNrCPUs = (Integer ) options [n ];
496- System .out .println ("will use " + useNrCPUs + " CPUs." );
497- }
498- System .out .println ("using domainSplit data" );
499- alicalc = new AlignmentCalcDB (this , s , name1 ,config ,file , domainSplit );
500- alicalc .setNrCPUs (useNrCPUs );
501- abortB .setEnabled (true );
502- progress .setIndeterminate (true );
503- ProgressThreadDrawer drawer = new ProgressThreadDrawer (progress );
504- drawer .start ();
505-
506- Thread t = new Thread (alicalc );
507- t .start ();
508- }
509-
510-
511- public DBSearchGUI getDBSearch (){
512- return dbsearch ;
513- }
514-
515402 public void notifyCalcFinished (){
516403 abortB .setEnabled (false );
517404 thread = null ;
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