PDB format added

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5f228fb..8d2d796 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -48,6 +48,7 @@
             formats.addElement("PileUp");\r
             formats.addElement("PIR");\r
             formats.addElement("PFAM");\r
+            formats.addElement("PDB");\r
         }\r
 \r
 \r
@@ -57,6 +58,7 @@
         public static String CLASSLOADER = "ClassLoader";\r
 \r
         AlignFile afile = null;\r
+        String inFile;\r
 \r
         /**\r
          * DOCUMENT ME!\r
@@ -70,46 +72,52 @@
         public SequenceI[] readFile(String inFile, String type, String format)\r
             throws java.io.IOException\r
         {\r
+            this.inFile = inFile;\r
             try\r
             {\r
-                if (format.equals("FASTA"))\r
-                {\r
-                    afile = new FastaFile(inFile, type);\r
-                }\r
-                else if (format.equals("MSF"))\r
-                {\r
-                    afile = new MSFfile(inFile, type);\r
-                }\r
-                else if (format.equals("PileUp"))\r
-                {\r
-                    afile = new PileUpfile(inFile, type);\r
-                }\r
-                else if (format.equals("CLUSTAL"))\r
-                {\r
-                    afile = new ClustalFile(inFile, type);\r
-                }\r
-                else if (format.equals("BLC"))\r
-                {\r
-                    afile = new BLCFile(inFile, type);\r
-                }\r
-                else if (format.equals("PIR"))\r
-                {\r
-                    afile = new PIRFile(inFile, type);\r
-                }\r
-                else if (format.equals("PFAM"))\r
-                {\r
-                    afile = new PfamFile(inFile, type);\r
-                }\r
-                else if (format.equals("JnetFile"))\r
-                {\r
-                  afile = new JPredFile(inFile, type);\r
-                  ((JPredFile)afile).removeNonSequences();\r
-                }\r
+              if (format.equals("FASTA"))\r
+              {\r
+                afile = new FastaFile(inFile, type);\r
+              }\r
+              else if (format.equals("MSF"))\r
+              {\r
+                afile = new MSFfile(inFile, type);\r
+              }\r
+              else if (format.equals("PileUp"))\r
+              {\r
+                afile = new PileUpfile(inFile, type);\r
+              }\r
+              else if (format.equals("CLUSTAL"))\r
+              {\r
+                afile = new ClustalFile(inFile, type);\r
+              }\r
+              else if (format.equals("BLC"))\r
+              {\r
+                afile = new BLCFile(inFile, type);\r
+              }\r
+              else if (format.equals("PIR"))\r
+              {\r
+                afile = new PIRFile(inFile, type);\r
+              }\r
+              else if (format.equals("PFAM"))\r
+              {\r
+                afile = new PfamFile(inFile, type);\r
+              }\r
+              else if (format.equals("JnetFile"))\r
+              {\r
+                afile = new JPredFile(inFile, type);\r
+                ( (JPredFile) afile).removeNonSequences();\r
+              }\r
+              else if (format.equals("PDB"))\r
+              {\r
+                afile = new MCview.PDBfile(inFile, type);\r
+              }\r
 \r
-                return afile.getSeqsAsArray();\r
+              return afile.getSeqsAsArray();\r
             }\r
             catch (Exception e)\r
             {\r
+              e.printStackTrace();\r
               System.err.println("Failed to read alignment using the '" + format +\r
                                  "' reader.\n"+e);\r
 \r

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 8490a68..92e7e4b 100644 (file)
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -284,7 +284,7 @@ public class DBRefFetcher implements Runnable
 \r
 \r
       sequence.addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
-                                       "1.0",\r
+                                       "0",\r
                                        entry.getAccession().elementAt(0).toString()));\r
 \r
       System.out.println("Adding dbref to "+sequence.getName()+" : "+\r
@@ -342,7 +342,7 @@ public class DBRefFetcher implements Runnable
           continue;\r
 \r
         sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,\r
-                                       "1.0",\r
+                                       "0",\r
                                        pdb.getId()));\r
 \r
         onlyPdbEntries.addElement(pdb);\r

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 67c72c2..77f2a79 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -175,7 +175,6 @@ public class FileLoader
             {\r
             }\r
           }\r
-\r
         }\r
         else\r
         {\r

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 6b32fe1..348b085 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -125,13 +125,19 @@ public class IdentifyFile
                     }\r
 \r
                     break;\r
-                }\r
-                else if (data.indexOf(":")<data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
-                {\r
-                  // file looks like a concise JNet file\r
-                  reply="JnetFile";\r
-                  break;\r
-                }\r
+                  }\r
+                  else if (data.indexOf("HEADER") > -1 ||\r
+                           data.indexOf("ATOM") > -1)\r
+                  {\r
+                    reply = "PDB";\r
+                    break;\r
+                  }\r
+                  else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
+                  {\r
+                    // file looks like a concise JNet file\r
+                    reply = "JnetFile";\r
+                    break;\r
+                  }\r
             }\r
 \r
             reader.close();\r
@@ -141,6 +147,7 @@ public class IdentifyFile
             System.err.println("File Identification failed!\n" + ex);\r
             return error;\r
         }\r
+\r
         return reply;\r
     }\r
 }\r