Dont set pdb file if it doenst exist

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 84e3564..562d5cb 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -804,6 +804,7 @@ public class Jalview2XML
 \r
     String loadPDBFile(String file, String pdbId)\r
     {\r
+      System.out.println("load file "+file);\r
       try\r
       {\r
         JarInputStream jin = null;\r
@@ -824,14 +825,15 @@ public class Jalview2XML
         }\r
         while (!entry.getName().equals(pdbId));\r
 \r
-        DataInputStream in = new DataInputStream(jin);\r
+        BufferedReader in = new BufferedReader(new InputStreamReader(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
+        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+        String data;\r
+\r
+        while ( (data = in.readLine()) != null)\r
         {\r
-          out.write(data);\r
+          out.println(data);\r
         }\r
         out.close();\r
         return outFile.getAbsolutePath();\r
@@ -910,14 +912,17 @@ 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
+              if (ids[p].getFile() != null)\r
               {\r
-                String tmppdb = loadPDBFile(file, ids[p].getId());\r
-                entry.setFile(tmppdb);\r
-                pdbloaded.put(ids[p].getId(), tmppdb);\r
+                if (!pdbloaded.containsKey(ids[p].getFile()))\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
-              else\r
-                entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
 \r
               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
             }\r