X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=198aa626baa97f7b4e470ebcb59396cac130cb1f;hb=d7e95f458ebcbbdcc13f8b07357542ab2d7e4547;hp=452677e9d75046b9fd9d3a625ff34f7ef2a6513a;hpb=c169d9e5208916dd465ad8837b31004e45a2e938;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 452677e..198aa62 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -21,6 +21,7 @@
 
 package jalview.gui;
 
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Jalview;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -53,6 +54,8 @@ import java.util.Vector;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
 
 /**
@@ -728,16 +731,65 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
+   * select structures for viewing by their PDB IDs
+   * 
+   * @param pdbids
+   * @return true if structures were found and marked as selected
+   */
+  public boolean selectStructure(String... pdbids)
+  {
+    boolean found = false;
+
+    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+            .getSelectedItem());
+    String currentView = selectedFilterOpt.getView();
+    JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+            : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
+
+    if (restable == null)
+    {
+      // can't select (enter PDB ID, or load file - need to also select which
+      // sequence to associate with)
+      return false;
+    }
+
+    int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
+    for (int r = 0; r < restable.getRowCount(); r++)
+    {
+      for (int p = 0; p < pdbids.length; p++)
+      {
+        if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
+                .equalsIgnoreCase(pdbids[p]))
+        {
+          restable.setRowSelectionInterval(r, r);
+          found = true;
+        }
+      }
+    }
+    return found;
+  }
+  /**
    * Handles action event for btn_ok
    */
   @Override
   public void ok_ActionPerformed()
   {
+    showStructures(false);
+  }
+
+  /**
+   * structure viewer opened by this dialog, or null
+   */
+  private StructureViewer sViewer = null;
+
+  public void showStructures(boolean waitUntilFinished)
+  {
+
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 
     final int preferredHeight = pnl_filter.getHeight();
 
-    new Thread(new Runnable()
+    Runnable viewStruc = new Runnable()
     {
       @Override
       public void run()
@@ -783,7 +835,8 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+                  selectedSeqs);
         }
         else if (currentView == VIEWS_LOCAL_PDB)
         {
@@ -806,7 +859,8 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+                  selectedSeqs);
         }
         else if (currentView == VIEWS_ENTER_ID)
         {
@@ -835,7 +889,7 @@ public class StructureChooser extends GStructureChooser
           }
 
           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
-          launchStructureViewer(ssm, pdbEntriesToView, ap,
+          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
                   new SequenceI[]
                   { selectedSequence });
         }
@@ -852,14 +906,40 @@ public class StructureChooser extends GStructureChooser
                           DataSourceType.FILE, selectedSequence, true,
                           Desktop.instance);
 
-          launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+          sViewer = launchStructureViewer(
+                  ssm, new PDBEntry[]
+                  { fileEntry }, ap,
                   new SequenceI[]
                   { selectedSequence });
         }
-        closeAction(preferredHeight);
-        mainFrame.dispose();
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            closeAction(preferredHeight);
+            mainFrame.dispose();
+          }
+        });
+      }
+    };
+    Thread runner = new Thread(viewStruc);
+    runner.start();
+    if (waitUntilFinished)
+    {
+      while (sViewer == null ? runner.isAlive()
+              : (sViewer.sview == null ? true
+                      : !sViewer.sview.hasMapping()))
+      {
+        try
+        {
+          Thread.sleep(300);
+        } catch (InterruptedException ie)
+        {
+
+        }
       }
-    }).start();
+    }
   }
 
   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
@@ -877,7 +957,8 @@ public class StructureChooser extends GStructureChooser
     return foundEntry;
   }
 
-  private void launchStructureViewer(StructureSelectionManager ssm,
+  private StructureViewer launchStructureViewer(
+          StructureSelectionManager ssm,
           final PDBEntry[] pdbEntriesToView,
           final AlignmentPanel alignPanel, SequenceI[] sequences)
   {
@@ -951,6 +1032,7 @@ public class StructureChooser extends GStructureChooser
       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
     }
     setProgressBar(null, progressId);
+    return sViewer;
   }
 
   /**
@@ -1181,4 +1263,9 @@ public class StructureChooser extends GStructureChooser
   {
     return progressBar.operationInProgress();
   }
+
+  public JalviewStructureDisplayI getOpenedStructureViewer()
+  {
+    return sViewer == null ? null : sViewer.sview;
+  }
 }