X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=6a29ecd027e64d3601f3280dd95be2cc4d6c7662;hb=4674dbf3f27eee61a7e21174649aa4c9ec7a04dd;hp=7bf1a5f6b687455de3a70d5518186c2d00f4414a;hpb=05c04b298565cdc668027027e13d0ac6f8bc8517;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 7bf1a5f..6a29ecd 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -334,7 +334,7 @@ public class JalviewLite extends Applet
 
   public boolean jmolAvailable = false;
 
-  private boolean alignPdbStructures=false;
+  private boolean alignPdbStructures = false;
 
   public static boolean debug = false;
 
@@ -901,10 +901,11 @@ public class JalviewLite extends Applet
           }
         }
         /*
-         * <param name="alignpdbfiles" value="false/true"/>
-         * Undocumented for 2.6 - related to JAL-434
+         * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
+         * - related to JAL-434
          */
-        applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",false));
+        applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+                false));
         /*
          * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
          * PDB|1GAQ|1GAQ|C">
@@ -913,10 +914,11 @@ public class JalviewLite extends Applet
          * 
          * <param name="PDBfile3" value="1q0o Q45135_9MICO">
          */
-        
+
         int pdbFileCount = 0;
-        // Accumulate pdbs here if they are heading for the same view (if alignPdbStructures is true)
-        Vector pdbs=new Vector();
+        // Accumulate pdbs here if they are heading for the same view (if
+        // alignPdbStructures is true)
+        Vector pdbs = new Vector();
         do
         {
           if (pdbFileCount > 0)
@@ -1008,25 +1010,29 @@ public class JalviewLite extends Applet
                   }
                 }
               }
-              
-              if (!alignPdbStructures) {
+
+              if (!alignPdbStructures)
+              {
                 newAlignFrame.newStructureView(applet, pdb, seqs, chains,
-                      protocol);
-              } else {
-                pdbs.add(new Object[] { pdb, seqs, chains, new String(protocol)});
+                        protocol);
+              }
+              else
+              {
+                pdbs.addElement(new Object[]
+                { pdb, seqs, chains, new String(protocol) });
               }
             }
           }
 
           pdbFileCount++;
         } while (pdbFileCount < 10);
-        if (pdbs.size()>0)
+        if (pdbs.size() > 0)
         {
           SequenceI[][] seqs = new SequenceI[pdbs.size()][];
           PDBEntry[] pdb = new PDBEntry[pdbs.size()];
           String[][] chains = new String[pdbs.size()][];
           String[] protocols = new String[pdbs.size()];
-          for (int pdbsi=0,pdbsiSize=pdbs.size(); pdbsi<pdbsiSize;pdbsi++)
+          for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
           {
             Object[] o = (Object[]) pdbs.elementAt(pdbsi);
             pdb[pdbsi] = (PDBEntry) o[0];
@@ -1034,8 +1040,9 @@ public class JalviewLite extends Applet
             chains[pdbsi] = (String[]) o[2];
             protocols[pdbsi] = (String) o[3];
           }
-          newAlignFrame.alignedStructureView(applet, pdb, seqs, chains, protocols);
-          
+          newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
+                  protocols);
+
         }
         // ///////////////////////////
         // modify display of features
@@ -1190,7 +1197,7 @@ public class JalviewLite extends Applet
   public String arrayToSeparatorList(String[] list)
   {
     StringBuffer v = new StringBuffer();
-    if (list != null)
+    if (list != null && list.length > 0)
     {
       for (int i = 0, iSize = list.length - 1; i < iSize; i++)
       {
@@ -1365,7 +1372,8 @@ public class JalviewLite extends Applet
   }
 
   /**
-   * get all components associated with the applet of the given type 
+   * get all components associated with the applet of the given type
+   * 
    * @param class1
    * @return
    */
@@ -1373,19 +1381,19 @@ public class JalviewLite extends Applet
   {
     Vector wnds = new Vector();
     Component[] cmp = getComponents();
-    if (cmp!=null)
-    {
-    for (int i=0;i<cmp.length;i++)
+    if (cmp != null)
     {
-      if (class1.isAssignableFrom(cmp[i].getClass()))
+      for (int i = 0; i < cmp.length; i++)
       {
-        wnds.addElement(cmp);
+        if (class1.isAssignableFrom(cmp[i].getClass()))
+        {
+          wnds.addElement(cmp);
+        }
       }
-    }}
+    }
     return wnds;
   }
 
-
   /**
    * bind structures in a viewer to any matching sequences in an alignFrame (use
    * sequenceIds to limit scope of search to specific sequences)
@@ -1394,21 +1402,13 @@ public class JalviewLite extends Applet
    * @param viewer
    * @param sequenceIds
    * @return TODO: consider making an exception structure for indicating when
-   *         binding fails
-  public SequenceStructureBinding addStructureViewInstance(
-          AlignFrame alFrame, Object viewer, String sequenceIds)
-  {
-
-    if (sequenceIds != null && sequenceIds.length() > 0)
-    {
-      return alFrame.addStructureViewInstance(viewer,
-              separatorListToArray(sequenceIds));
-    }
-    else
-    {
-      return alFrame.addStructureViewInstance(viewer, null);
-    }
-    // return null;
-  }
+   *         binding fails public SequenceStructureBinding
+   *         addStructureViewInstance( AlignFrame alFrame, Object viewer, String
+   *         sequenceIds) {
+   * 
+   *         if (sequenceIds != null && sequenceIds.length() > 0) { return
+   *         alFrame.addStructureViewInstance(viewer,
+   *         separatorListToArray(sequenceIds)); } else { return
+   *         alFrame.addStructureViewInstance(viewer, null); } // return null; }
    */
 }