X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=a9df882856dbd18dba7352710e35b145efe76f9e;hb=534653c4f58440e1ee709e60d93854161e879ed0;hp=85ea20b69e39e9c6487d87a4bf4a1d49b2d5fb88;hpb=65675b2d016736f8ca4dfb2493863c4d53cec591;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 85ea20b..a9df882 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -31,6 +31,7 @@ import jalview.fts.service.uniprot.UniprotFTSPanel;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -42,6 +43,7 @@ import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -201,8 +203,19 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private IProgressIndicator progressIndicator;
 
+  private volatile boolean _isConstructing = false;
+
+  private List<AlignFrame> newAlframes = null;
+
   public SequenceFetcher(IProgressIndicator guiIndic)
   {
+    this(guiIndic, null, null);
+  }
+
+  public SequenceFetcher(IProgressIndicator guiIndic,
+          final String selectedDb, final String queryString)
+  {
+    this._isConstructing=true;
     this.progressIndicator = guiIndic;
     final SequenceFetcher us = this;
     // launch initialiser thread
@@ -214,7 +227,8 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         if (getSequenceFetcherSingleton(progressIndicator) != null)
         {
-          us.initGui(progressIndicator);
+          us.initGui(progressIndicator, selectedDb, queryString);
+          us._isConstructing=false;
         }
         else
         {
@@ -240,6 +254,26 @@ public class SequenceFetcher extends JPanel implements Runnable
     });
     sf.start();
   }
+  /**
+   * blocking call which creates a new sequence fetcher panel, configures it and presses the OK button with the given database and query.
+   * @param database
+   * @param query
+   */
+  public static List<AlignFrame> fetchAndShow(String database, String query)
+  {
+    final SequenceFetcher sf = new SequenceFetcher(Desktop.instance, database, query);
+    while (sf._isConstructing)
+    {
+      try { Thread.sleep(50);
+      } catch (Exception q)
+      {
+        return Collections.emptyList();
+      }
+    }
+    sf.newAlframes = new ArrayList<AlignFrame>();
+    sf.run();
+    return sf.newAlframes;
+  }
 
   private class DatabaseAuthority extends DefaultMutableTreeNode
   {
@@ -250,13 +284,51 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
 
   };
+  
+  /**
+   * initialise the database and query for this fetcher panel
+   * 
+   * @param selectedDb
+   *          - string that should correspond to a sequence fetcher
+   * @param queryString
+   *          - string that will be entered in the query dialog
+   * @return true if UI was configured with valid database and query string
+   */
+  protected boolean setInitialQuery(String selectedDb, String queryString)
+  {
+    if (selectedDb == null || selectedDb.trim().length() == 0)
+    {
+      return false;
+    }
+    try
+    {
+      List<DbSourceProxy> sp = sfetch.getSourceProxy(selectedDb);
+      if (sp == null || sp.size() != 1)
+      {
+        System.err.println("Ignoring fetch parameter db='" + selectedDb
+                + "'");
+        return false;
+      }
+      database.selection = sp;
+      textArea.setText(queryString);
+    } catch (Exception q)
+    {
+      System.err.println("Ignoring fetch parameter db='" + selectedDb
+              + "' and query='" + queryString + "'");
+      return false;
+    }
+    return true;
+  }
 
   /**
    * called by thread spawned by constructor
    * 
    * @param guiWindow
+   * @param queryString
+   * @param selectedDb
    */
-  private void initGui(IProgressIndicator guiWindow)
+  private void initGui(IProgressIndicator guiWindow, String selectedDb,
+          String queryString)
   {
     this.guiWindow = guiWindow;
     if (guiWindow instanceof AlignFrame)
@@ -267,6 +339,16 @@ public class SequenceFetcher extends JPanel implements Runnable
     try
     {
       jbInit();
+      /*
+       * configure the UI with any query parameters we were called with
+       */
+      if (!setInitialQuery(selectedDb, queryString))
+      {
+        /*
+         * none provided, so show the database chooser
+         */
+        database.waitForInput();
+      }
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -274,13 +356,13 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
+      Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240);
     }
     else
     {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+      Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180);
     }
   }
 
@@ -365,7 +447,19 @@ public class SequenceFetcher extends JPanel implements Runnable
     jPanel1.add(close);
     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
     jPanel2.setLayout(borderLayout3);
-    databaseButt = database.getDatabaseSelectorButton();
+    databaseButt = /*database.getDatabaseSelectorButton();
+                   final JButton viewdbs =*/new JButton(
+            MessageManager.getString("action.select_ddbb"));
+    databaseButt.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        hidePanel();
+        database.showDialog();
+      }
+    });
     databaseButt.setFont(JvSwingUtils.getLabelFont());
     database.addActionListener(new ActionListener()
     {
@@ -374,6 +468,12 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         debounceTrap++;
         String currentSelection = database.getSelectedItem();
+        if (currentSelection == null)
+        {
+          close_actionPerformed(null);
+        }
+
+        showPanel();
 
         if (currentSelection.equalsIgnoreCase("pdb")
                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
@@ -406,11 +506,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     this.add(jPanel3, java.awt.BorderLayout.CENTER);
     this.add(jPanel2, java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textArea);
-
-    /*
-     * open the database tree
-     */
-    database.waitForInput();
   }
 
   private void pdbSourceAction()
@@ -923,7 +1018,10 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);
         }
-
+        if (newAlframes != null)
+        {
+          newAlframes.add(af);
+        }
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
@@ -970,4 +1068,22 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
     this.progressIndicator = progressIndicator;
   }
+
+  /**
+   * Make this panel visible (after a selection has been made in the database
+   * chooser)
+   */
+  void showPanel()
+  {
+    frame.setVisible(true);
+  }
+
+  /**
+   * Hide this panel (on clicking the database button to open the database
+   * chooser)
+   */
+  void hidePanel()
+  {
+    frame.setVisible(false);
+  }
 }