JAL-2944 remove modal prompt logic and expose methods for adding structure data to...

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index af25653..29f02d6 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -44,7 +44,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -162,8 +161,9 @@ public class AppJmol extends StructureViewerBase
   {
     return progressBar;
   }
+  
   /**
-   * add a single PDB structure to a new or existing Jmol view
+   * display a single PDB structure in a new Jmol view
    * 
    * @param pdbentry
    * @param seq
@@ -174,29 +174,7 @@ public class AppJmol extends StructureViewerBase
           final AlignmentPanel ap)
   {
     progressBar = ap.alignFrame;
-    String pdbId = pdbentry.getId();
 
-    /*
-     * If the PDB file is already loaded, the user may just choose to add to an
-     * existing viewer (or cancel)
-     */
-    if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * Check if there are other Jmol views involving this alignment and prompt
-     * user about adding this molecule to one of them
-     */
-    if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * If the options above are declined or do not apply, open a new viewer
-     */
     openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
   }
 
@@ -209,11 +187,9 @@ public class AppJmol extends StructureViewerBase
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
-    if (pdbentrys.length > 1)
-    {
-      alignAddedStructures = true;
+    alignAddedStructures = true;
       useAlignmentPanelForSuperposition(ap);
-    }
+
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();