JAL-629 move SubId to more logical place. Attempt removal of annotations in a better...

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 3f5f39c..d38f39f 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -24,6 +24,7 @@ package jalview.gui;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
+import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -116,11 +117,19 @@ public class StructureChooser extends GStructureChooser
 
   List<SequenceI> seqsWithoutSourceDBRef = null;
 
+  private boolean noChooserGUI = false;
+
   private static StructureViewer lastTargetedView = null;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
+    this(selectedSeqs, selectedSeq, ap, false);
+  }
+
+  public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+          AlignmentPanel ap, boolean noChooserGUI)
+  {
     // which FTS engine to use
     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
     initDialog();
@@ -129,6 +138,7 @@ public class StructureChooser extends GStructureChooser
     this.selectedSequence = selectedSeq;
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
+    this.noChooserGUI = noChooserGUI;
     init();
 
   }
@@ -244,7 +254,7 @@ public class StructureChooser extends GStructureChooser
     populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
     discoverStructureViews();
     updateProgressIndicator(null, startTime);
-    mainFrame.setVisible(true);
+    mainFrame.setVisible(noChooserGUI);
     updateCurrentView();
   }
 
@@ -321,6 +331,7 @@ public class StructureChooser extends GStructureChooser
       @Override
       public void run()
       {
+        btn_queryTDB.setEnabled(false);
         populateSeqsWithoutSourceDBRef();
 
         final int y = seqsWithoutSourceDBRef.size();
@@ -333,6 +344,7 @@ public class StructureChooser extends GStructureChooser
                   { new jalview.ws.dbsources.Uniprot() }, null, false);
           dbRefFetcher.addListener(afterDbRefFetch);
           // ideally this would also gracefully run with callbacks
+
           dbRefFetcher.fetchDBRefs(true);
         }
         else
@@ -354,7 +366,7 @@ public class StructureChooser extends GStructureChooser
         }
       };
     };
-    int threshold = Cache.getDefault("THRESHOLD_WARN_UNIPROT_FETCH",
+    int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
             THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
     Console.debug("Using Uniprot fetch threshold of " + threshold);
     if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
@@ -365,7 +377,9 @@ public class StructureChooser extends GStructureChooser
     }
     // need cancel and no to result in the discoverPDB action - mocked is
     // 'cancel' TODO: mock should be OK
-    JvOptionPane.newOptionDialog(this)
+
+    StructureChooser thisSC = this;
+    JvOptionPane.newOptionDialog(thisSC.getFrame())
             .setResponseHandler(JvOptionPane.OK_OPTION,
                     discoverCanonicalDBrefs)
             .setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
@@ -379,7 +393,7 @@ public class StructureChooser extends GStructureChooser
                     null, new Object[]
                     { MessageManager.getString("action.ok"),
                         MessageManager.getString("action.cancel") },
-                    MessageManager.getString("action.ok"));
+                    MessageManager.getString("action.ok"), false);
   }
 
   /**
@@ -1387,6 +1401,7 @@ public class StructureChooser extends GStructureChooser
   {
     if (selectedSequences != null)
     {
+      lbl_loading.setVisible(true);
       Thread refreshThread = new Thread(new Runnable()
       {
         @Override
@@ -1398,6 +1413,7 @@ public class StructureChooser extends GStructureChooser
           filterResultSet(
                   ((FilterOption) cmb_filterOption.getSelectedItem())
                           .getValue());
+          lbl_loading.setVisible(false);
         }
       });
       refreshThread.start();
@@ -1570,4 +1586,34 @@ public class StructureChooser extends GStructureChooser
   {
     return notQueriedTDBYet;
   }
+
+  /**
+   * Open a single structure file for a given sequence
+   */
+  public static void openStructureFileForSequence(AlignmentPanel ap,
+          SequenceI seq, File sFile)
+  {
+    StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
+            ap, true);
+    StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    PDBEntry fileEntry = null;
+    try
+    {
+      fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+              sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
+              Desktop.instance);
+    } catch (Exception e)
+    {
+      Console.error("Could not open structure file '"
+              + sFile.getAbsolutePath() + "'");
+      return;
+    }
+
+    StructureViewer sViewer = sc.launchStructureViewer(ssm,
+            new PDBEntry[]
+            { fileEntry }, ap, new SequenceI[] { seq });
+
+    sc.mainFrame.dispose();
+    sc.noChooserGUI = false;
+  }
 }