From c0fe92ac89ff83e2bd46724d0ead72df9a99bc18 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 26 Jul 2006 16:04:10 +0000
Subject: [PATCH] Load and save PDB files

---
 src/jalview/gui/Jalview2XML.java |  125 +++++++++++++++++++++++++++++---------
 1 file changed, 97 insertions(+), 28 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1060610..84e3564 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -184,6 +184,7 @@ public class Jalview2XML
         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
         JSeq jseq;
+        Vector pdbfiles = null;
 
         //SAVE SEQUENCES
         int id = 0;
@@ -269,6 +270,39 @@ public class Jalview2XML
                 pdb.setId(entry.getId());
                 pdb.setType(entry.getType());
 
+                if(entry.getFile()!=null)
+                {
+                  if(pdbfiles==null)
+                    pdbfiles = new Vector();
+
+
+                  if(!pdbfiles.contains(entry.getId()))
+                  {
+                    pdbfiles.addElement(entry.getId());
+                    try
+                    {
+                      File file = new File(entry.getFile());
+                      if(file.exists())
+                      {
+                        byte[] data = new byte[ (int) file.length()];
+                        jout.putNextEntry(new JarEntry(entry.getId()));
+                        DataInputStream dis = new DataInputStream(new
+                            FileInputStream(file));
+                        dis.readFully(data);
+
+                        DataOutputStream dout = new DataOutputStream(jout);
+                        dout.write(data, 0, data.length);
+                        jout.closeEntry();
+                      }
+                    }
+                    catch (Exception ex)
+                    {
+                      ex.printStackTrace();
+                    }
+                  }
+                }
+
+
                 if(entry.getProperty()!=null)
                 {
                   PdbentryItem item = new PdbentryItem();
@@ -594,15 +628,6 @@ public class Jalview2XML
           }
         }
 
-        if(av.hasHiddenRows)
-        {
-        //  av.alignment.getHiddenSequences().get
-      //    HiddenSequences hs = new HiddenSequences();
-      //    hs.ad
-      //    view.addHiddenSequences();
-      //    av.showAllHiddenSeqs();.alignment.getHiddenSequences().
-        }
-
         jms.addViewport(view);
 
 
@@ -692,9 +717,7 @@ public class Jalview2XML
      */
     public AlignFrame LoadJalviewAlign(String file)
     {
-
         jalview.gui.AlignFrame af = null;
-
         try
         {
             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
@@ -723,21 +746,9 @@ public class Jalview2XML
                 for (int i = 0; i < entryCount; i++)
                 {
                     jarentry = jin.getNextJarEntry();
+                }
 
-                  }
-
-
-                  class NoDescIDResolver implements IDResolver
-                  {
-                    public Object resolve(String idref)
-                    {
-                      System.out.println(idref+" used");
-                      return null;
-                    }
-                  }
-
-
-                if (jarentry != null)
+                if (jarentry != null && jarentry.getName().endsWith(".xml"))
                 {
                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
                     JalviewModel object = new JalviewModel();
@@ -746,9 +757,14 @@ public class Jalview2XML
                     unmar.setValidation(false);
                     object = (JalviewModel) unmar.unmarshal( in );
 
-                    af = LoadFromObject(object);
+                    af = LoadFromObject(object, file);
                     entryCount++;
                 }
+                else if (jarentry != null)
+                {
+                  //Some other file here.
+                  entryCount++;
+                }
             }
             while (jarentry != null);
         }
@@ -786,7 +802,51 @@ public class Jalview2XML
         return af;
     }
 
-    AlignFrame LoadFromObject(JalviewModel object)
+    String loadPDBFile(String file, String pdbId)
+    {
+      try
+      {
+        JarInputStream jin = null;
+
+        if (file.startsWith("http://"))
+        {
+          jin = new JarInputStream(new URL(file).openStream());
+        }
+        else
+        {
+          jin = new JarInputStream(new FileInputStream(file));
+        }
+
+        JarEntry entry = null;
+        do
+        {
+          entry = jin.getNextJarEntry();
+        }
+        while (!entry.getName().equals(pdbId));
+
+        DataInputStream in = new DataInputStream(jin);
+        File outFile = File.createTempFile("jalview_pdb", ".txt");
+        outFile.deleteOnExit();
+        DataOutputStream out = new DataOutputStream(new FileOutputStream(outFile));
+        int data;
+        while ( (data = in.read()) != -1)
+        {
+          out.write(data);
+        }
+        out.close();
+        return outFile.getAbsolutePath();
+
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
+      return null;
+    }
+
+
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -825,6 +885,7 @@ public class Jalview2XML
         /////////////////////////////////
 
 
+        Hashtable pdbloaded = new Hashtable();
         for (int i = 0; i < vamsasSeq.length; i++)
         {
           if (JSEQ[i].getFeaturesCount() > 0)
@@ -849,9 +910,17 @@ public class Jalview2XML
               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
               entry.setId(ids[p].getId());
               entry.setType(ids[p].getType());
+              if(!pdbloaded.containsKey(ids[p].getId()))
+              {
+                String tmppdb = loadPDBFile(file, ids[p].getId());
+                entry.setFile(tmppdb);
+                pdbloaded.put(ids[p].getId(), tmppdb);
+              }
+              else
+                entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+
               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
             }
-
           }
           if(vamsasSeq[i].getDBRefCount()>0)
           {
-- 
1.7.10.2