X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=684d7a41ad9ce8fe09c5139caa16f909a9689589;hb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;hp=fce50fe01b7eed25210665beabad05992e760521;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index fce50fe..684d7a4 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -3200,55 +3200,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @param viewer
    *          JmolViewer instance
    * @param sequenceIds
-   *          - sequence Ids to search for associations
-   * This method doesn't work. See http://issues.jalview.org/browse/JAL-621
+   *          - sequence Ids to search for associations This method doesn't
+   *          work. See http://issues.jalview.org/browse/JAL-621
    * 
-  public SequenceStructureBinding addStructureViewInstance(Object jmolviewer, String[] sequenceIds)
-  {
-    org.jmol.api.JmolViewer viewer=null;
-    try {
-      viewer = (org.jmol.api.JmolViewer) jmolviewer;
-    } 
-    catch (ClassCastException ex) {
-      System.err.println("Unsupported viewer object :"+jmolviewer.getClass());
-    }
-    if (viewer==null)
-    {
-      System.err.println("Can't use this object as a structure viewer:"+jmolviewer.getClass());
-      return null;
-    }
-    SequenceI[] seqs=null;
-    if (sequenceIds==null || sequenceIds.length==0)
-    {
-      seqs = viewport.getAlignment().getSequencesArray();
-    } else {
-      Vector sqi=new Vector();
-      AlignmentI al = viewport.getAlignment();
-      for (int sid=0;sid<sequenceIds.length;sid++) {
-        SequenceI sq = al.findName(sequenceIds[sid]);
-        if (sq!=null) {
-          sqi.addElement(sq);
-        }
-      }
-      if (sqi.size()>0) {
-        seqs = new SequenceI[sqi.size()];
-        for (int sid=0,sSize=sqi.size();sid<sSize;sid++)
-        {
-          seqs[sid] = (SequenceI) sqi.elementAt(sid);
-        }
-      } else {
-        return null;
-      }
-    }
-    ExtJmol jmv=null;
-    // TODO: search for a jmv that involves viewer
-    if (jmv==null){
-      // create a new viewer/jalview binding.
-      jmv = new ExtJmol(viewer, alignPanel, seqs);
-    }
-    return jmv;
-    
-  }
+   *          public SequenceStructureBinding addStructureViewInstance(Object
+   *          jmolviewer, String[] sequenceIds) { org.jmol.api.JmolViewer
+   *          viewer=null; try { viewer = (org.jmol.api.JmolViewer) jmolviewer;
+   *          } catch (ClassCastException ex) {
+   *          System.err.println("Unsupported viewer object :"
+   *          +jmolviewer.getClass()); } if (viewer==null) {
+   *          System.err.println("Can't use this object as a structure viewer:"
+   *          +jmolviewer.getClass()); return null; } SequenceI[] seqs=null; if
+   *          (sequenceIds==null || sequenceIds.length==0) { seqs =
+   *          viewport.getAlignment().getSequencesArray(); } else { Vector
+   *          sqi=new Vector(); AlignmentI al = viewport.getAlignment(); for
+   *          (int sid=0;sid<sequenceIds.length;sid++) { SequenceI sq =
+   *          al.findName(sequenceIds[sid]); if (sq!=null) { sqi.addElement(sq);
+   *          } } if (sqi.size()>0) { seqs = new SequenceI[sqi.size()]; for (int
+   *          sid=0,sSize=sqi.size();sid<sSize;sid++) { seqs[sid] = (SequenceI)
+   *          sqi.elementAt(sid); } } else { return null; } } ExtJmol jmv=null;
+   *          // TODO: search for a jmv that involves viewer if (jmv==null){ //
+   *          create a new viewer/jalview binding. jmv = new ExtJmol(viewer,
+   *          alignPanel, seqs); } return jmv;
+   * 
+   *          }
    **/
   public boolean addPdbFile(String sequenceId, String pdbEntryString,
           String pdbFile)
@@ -3292,14 +3267,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       if (needtoadd)
       {
         // make a note of the access mode and add
-        if (pdbentry.getProperty()==null)
-          {pdbentry.setProperty(new Hashtable());}
+        if (pdbentry.getProperty() == null)
+        {
+          pdbentry.setProperty(new Hashtable());
+        }
         pdbentry.getProperty().put("protocol", protocol);
         toaddpdb.addPDBId(pdbentry);
       }
     }
     return true;
   }
+
   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
   {
     if (seqs != null)
@@ -3309,7 +3287,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         if (seqs[i] != null)
         {
-          sequences.addElement(new Object[] { seqs[i], (chains!=null) ? chains[i] : null});
+          sequences.addElement(new Object[]
+          { seqs[i], (chains != null) ? chains[i] : null });
         }
       }
       seqs = new SequenceI[sequences.size()];
@@ -3322,9 +3301,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         chains[i] = (String) oj[1];
       }
     }
-    return new Object[] { seqs, chains};
+    return new Object[]
+    { seqs, chains };
 
   }
+
   public void newStructureView(JalviewLite applet, PDBEntry pdb,
           SequenceI[] seqs, String[] chains, String protocol)
   {
@@ -3364,9 +3345,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           break;
         }
       }
-      if (ajm!=null)
+      if (ajm != null)
       {
-        System.err.println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+        System.err
+                .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
         // try and add the pdb structure
         // ajm.addS
         ajm = null;