X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=4b1149406ab99dc1a613dddbd2a65c78ccb453f8;hb=d622d93ba5a3e596a4ea29bc1ba75bf2acacfdf0;hp=44d698dafe9f27282aead9cf00cab8af2be94fce;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 44d698d..4b11494 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,8 +20,6 @@
  */
 package jalview.structures.models;
 
-import java.util.Locale;
-
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
@@ -31,6 +29,7 @@ import java.util.BitSet;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import javax.swing.SwingUtilities;
@@ -43,6 +42,7 @@ import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.PDBEntry;
@@ -780,7 +780,7 @@ public abstract class AAStructureBindingModel
 
     if (waiting)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Timed out waiting for structure viewer to load file "
                       + notLoaded);
       return false;
@@ -871,21 +871,39 @@ public abstract class AAStructureBindingModel
     {
       AlignmentI alignment = view.getAlignment();
       HiddenColumns hiddenCols = alignment.getHiddenColumns();
-
       /*
        * 'matched' bit i will be set for visible alignment columns i where
        * all sequences have a residue with a mapping to their PDB structure
        */
-      BitSet matched = new BitSet();
       final int width = alignment.getWidth();
-      for (int m = 0; m < width; m++)
+      BitSet matched = new BitSet();
+      ColumnSelection cs = view.getAlignViewport().getColumnSelection();
+      // restrict to active column selection, if there is one
+      if (cs != null && cs.hasSelectedColumns()
+              && cs.getSelected().size() >= 4)
       {
-        if (hiddenCols == null || hiddenCols.isVisible(m))
+        for (int s : cs.getSelected())
         {
-          matched.set(m);
+          if (hiddenCols == null)
+          {
+            matched.set(s);
+          }
+          else
+          {
+            matched.set(hiddenCols.visibleToAbsoluteColumn(s));
+          }
+        }
+      }
+      else
+      {
+        for (int m = 0; m < width; m++)
+        {
+          if (hiddenCols == null || hiddenCols.isVisible(m))
+          {
+            matched.set(m);
+          }
         }
       }
-
       AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
       for (int f = 0; f < files.length; f++)
       {
@@ -928,6 +946,8 @@ public abstract class AAStructureBindingModel
       AtomSpecType backbone = structures[refStructure].isRna
               ? AtomSpecType.PHOSPHATE
               : AtomSpecType.ALPHA;
+      List<AtomSpecModel> models = new ArrayList<AtomSpecModel>();
+      models.add(refAtoms);
       /*
        * superpose each (other) structure to the reference in turn
        */
@@ -948,10 +968,16 @@ public abstract class AAStructureBindingModel
               error += "; " + reply;
             }
           }
+          models.add(atomSpec);
         }
       }
+      List<StructureCommandI> finalView = commandGenerator
+              .centerViewOn(models);
+      if (finalView != null && finalView.size() > 0)
+      {
+        executeCommands(finalView, false, "Centered on Superposition");
+      }
     }
-
     return error;
   }
 
@@ -1072,7 +1098,7 @@ public abstract class AAStructureBindingModel
    * @param getReply
    * @param msg
    */
-  protected List<String> executeCommands(List<StructureCommandI> commands,
+  public List<String> executeCommands(List<StructureCommandI> commands,
           boolean getReply, String msg)
   {
     return executeCommand(getReply, msg,
@@ -1280,6 +1306,12 @@ public abstract class AAStructureBindingModel
   @Override
   public void updateColours(Object source)
   {
+    if (getViewer() == null)
+    {
+      // can happen if a viewer was not instantiated or cleaned up and is still
+      // registered - mostly during tests
+      return;
+    }
     AlignmentViewPanel ap = (AlignmentViewPanel) source;
     // ignore events from panels not used to colour this view
     if (!getViewer().isUsedForColourBy(ap))
@@ -1514,6 +1546,31 @@ public abstract class AAStructureBindingModel
     return f;
   }
 
+
+  /**
+   * Use restoreSession when you want to restore a previously saved sesssion to
+   * the running viewer instance.
+   * 
+   * @param absolutePath
+   */
+  public void restoreSession(String absolutePath)
+  {
+    String prefix = getViewerType().toString();
+    try {
+
+      StructureCommandI cmd = commandGenerator.restoreSession(absolutePath);
+      if (cmd != null)
+      {
+        executeCommand(cmd, false);
+      }
+    } catch (Throwable e)
+    {
+      Console.error(String.format("Error restoring %s session: %s", prefix,
+              e.toString()));
+    }
+
+  }
+
   /**
    * Saves the structure viewer session to the given file
    *