Load and save PDB files

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