X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;fp=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=ec5579cb57bc116f40435f11cab0fcc33dbf61dc;hb=afbff636fa2dfa01daa1f4ec4e8a936e61e3cf16;hp=ae2128bdb016298204c15e708c9efc24caf1a844;hpb=c6df3928336440918d23b4e7cb579f134e2f48dd;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index ae2128b..ec5579c 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -47,6 +47,7 @@ import javax.swing.event.MenuListener;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -155,9 +156,11 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     alignAddedStructures = alignAdded;
   }
-  
+
   /**
-   * called by the binding model to indicate when adding structures is happening or has been completed
+   * called by the binding model to indicate when adding structures is happening
+   * or has been completed
+   * 
    * @param addingStructures
    */
   public synchronized void setAddingStructures(boolean addingStructures)
@@ -442,8 +445,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     {
       return;
     }
-    AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this
-                                                 // cast fails
+    AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error
+                                                         // if this
+    // cast fails
     useAlignmentPanelForSuperposition(alignPanel);
     addStructure(pdbentry, seq, chains, alignPanel.alignFrame);
   }
@@ -580,9 +584,8 @@ public abstract class StructureViewerBase extends GStructureViewer
   public void changeColour_actionPerformed(String colourSchemeName)
   {
     AlignmentI al = getAlignmentPanel().av.getAlignment();
-    ColourSchemeI cs = ColourSchemes.getInstance()
-            .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
-                    null);
+    ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
+            colourSchemeName, getAlignmentPanel().av, al, null);
     getBinding().colourByJalviewColourScheme(cs);
   }
 
@@ -814,7 +817,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         sp.append("'" + alignPanel.getViewName() + "' ");
       }
-      Cache.log.info("Couldn't align structures with the " + sp.toString()
+      Console.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
     }
     return reply;
@@ -1037,14 +1040,17 @@ public abstract class StructureViewerBase extends GStructureViewer
     {
       return false;
     }
-    int p=0;
-    for (String pdbid:pdbids) {
+    int p = 0;
+    for (String pdbid : pdbids)
+    {
       StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
-      if (sm!=null && sm.length>0 && sm[0]!=null) {
+      if (sm != null && sm.length > 0 && sm[0] != null)
+      {
         p++;
       }
     }
-    // only return true if there is a mapping for every structure file we have loaded
+    // only return true if there is a mapping for every structure file we have
+    // loaded
     if (p == 0 || p != pdbids.length)
     {
       return false;
@@ -1136,12 +1142,12 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     String filePath = null;
     Pdb pdbclient = new Pdb();
-    EBIAlfaFold afclient =  new EBIAlfaFold();
+    EBIAlfaFold afclient = new EBIAlfaFold();
     AlignmentI pdbseq = null;
     String pdbid = processingEntry.getId();
     long handle = System.currentTimeMillis()
             + Thread.currentThread().hashCode();
-  
+
     /*
      * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
      */
@@ -1156,29 +1162,36 @@ public abstract class StructureViewerBase extends GStructureViewer
     {
       if (afclient.isValidReference(pdbid))
       {
-        pdbseq = afclient.getSequenceRecords(pdbid,processingEntry.getRetrievalUrl());
-      } else {
-          if (processingEntry.hasRetrievalUrl())
+        pdbseq = afclient.getSequenceRecords(pdbid,
+                processingEntry.getRetrievalUrl());
+      }
+      else
+      {
+        if (processingEntry.hasRetrievalUrl())
+        {
+          String safePDBId = java.net.URLEncoder.encode(pdbid, "UTF-8")
+                  .replace("%", "__");
+
+          // retrieve from URL to new local tmpfile
+          File tmpFile = File.createTempFile(safePDBId,
+                  "." + (PDBEntry.Type.MMCIF.toString().equals(
+                          processingEntry.getType().toString()) ? "cif"
+                                  : "pdb"));
+          String fromUrl = processingEntry.getRetrievalUrl();
+          UrlDownloadClient.download(fromUrl, tmpFile);
+
+          // may not need this check ?
+          String file = tmpFile.getAbsolutePath();
+          if (file != null)
           {
-            String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
-                     
-            // retrieve from URL to new local tmpfile
-            File tmpFile = File.createTempFile(safePDBId,
-                    "." + (PDBEntry.Type.MMCIF.toString().equals(
-                            processingEntry.getType().toString()) ? "cif"
-                                    : "pdb"));
-            String fromUrl = processingEntry.getRetrievalUrl();
-            UrlDownloadClient.download(fromUrl, tmpFile);
-            
-            // may not need this check ?
-            String file = tmpFile.getAbsolutePath();
-            if (file != null)
-            {
-              pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
-            }
-          } else {
-            pdbseq = pdbclient.getSequenceRecords(pdbid);
+            pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,
+                    tmpFile, pdbid, null, null, null);
           }
+        }
+        else
+        {
+          pdbseq = pdbclient.getSequenceRecords(pdbid);
+        }
       }
     } catch (Exception e)
     {
@@ -1212,22 +1225,28 @@ public abstract class StructureViewerBase extends GStructureViewer
    */
   public File saveSession()
   {
-    if (getBinding() == null) { return  null;}
+    if (getBinding() == null)
+    {
+      return null;
+    }
     File session = getBinding().saveSession();
     long l = session.length();
-    int wait=50;
-    do {
-      try {
+    int wait = 50;
+    do
+    {
+      try
+      {
         Thread.sleep(5);
-      } catch (InterruptedException e) {
-      } 
+      } catch (InterruptedException e)
+      {
+      }
       long nextl = session.length();
-      if (nextl!=l)
+      if (nextl != l)
       {
         wait = 50;
-        l=nextl;
+        l = nextl;
       }
-    } while (--wait>0);
+    } while (--wait > 0);
     return session;
   }
 
@@ -1283,20 +1302,26 @@ public abstract class StructureViewerBase extends GStructureViewer
   @Override
   public void showHelp_actionPerformed()
   {
+    /*
     try
     {
-      String url = getBinding().getHelpURL();
-      if (url != null)
-      {
-        BrowserLauncher.openURL(url);
-      }
-    } catch (IOException ex)
+    */
+    String url = getBinding().getHelpURL();
+    if (url != null)
+    {
+      BrowserLauncher.openURL(url);
+    }
+    /* 
+    }
+    catch (IOException ex)
     {
       System.err
               .println("Show " + getViewerName() + " failed with: "
                       + ex.getMessage());
     }
+    */
   }
+
   @Override
   public boolean hasViewerActionsMenu()
   {