From a6afc82877599e6ad2c52f01249c36338f251983 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 25 Jul 2006 09:36:57 +0000
Subject: [PATCH] PDB format added

---
 src/jalview/io/AppletFormatAdapter.java |   76 +++++++++++++++++--------------
 src/jalview/io/DBRefFetcher.java        |    4 +-
 src/jalview/io/FileLoader.java          |    1 -
 src/jalview/io/IdentifyFile.java        |   21 ++++++---
 4 files changed, 58 insertions(+), 44 deletions(-)

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5f228fb..8d2d796 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -48,6 +48,7 @@
             formats.addElement("PileUp");
             formats.addElement("PIR");
             formats.addElement("PFAM");
+            formats.addElement("PDB");
         }
 
 
@@ -57,6 +58,7 @@
         public static String CLASSLOADER = "ClassLoader";
 
         AlignFile afile = null;
+        String inFile;
 
         /**
          * DOCUMENT ME!
@@ -70,46 +72,52 @@
         public SequenceI[] readFile(String inFile, String type, String format)
             throws java.io.IOException
         {
+            this.inFile = inFile;
             try
             {
-                if (format.equals("FASTA"))
-                {
-                    afile = new FastaFile(inFile, type);
-                }
-                else if (format.equals("MSF"))
-                {
-                    afile = new MSFfile(inFile, type);
-                }
-                else if (format.equals("PileUp"))
-                {
-                    afile = new PileUpfile(inFile, type);
-                }
-                else if (format.equals("CLUSTAL"))
-                {
-                    afile = new ClustalFile(inFile, type);
-                }
-                else if (format.equals("BLC"))
-                {
-                    afile = new BLCFile(inFile, type);
-                }
-                else if (format.equals("PIR"))
-                {
-                    afile = new PIRFile(inFile, type);
-                }
-                else if (format.equals("PFAM"))
-                {
-                    afile = new PfamFile(inFile, type);
-                }
-                else if (format.equals("JnetFile"))
-                {
-                  afile = new JPredFile(inFile, type);
-                  ((JPredFile)afile).removeNonSequences();
-                }
+              if (format.equals("FASTA"))
+              {
+                afile = new FastaFile(inFile, type);
+              }
+              else if (format.equals("MSF"))
+              {
+                afile = new MSFfile(inFile, type);
+              }
+              else if (format.equals("PileUp"))
+              {
+                afile = new PileUpfile(inFile, type);
+              }
+              else if (format.equals("CLUSTAL"))
+              {
+                afile = new ClustalFile(inFile, type);
+              }
+              else if (format.equals("BLC"))
+              {
+                afile = new BLCFile(inFile, type);
+              }
+              else if (format.equals("PIR"))
+              {
+                afile = new PIRFile(inFile, type);
+              }
+              else if (format.equals("PFAM"))
+              {
+                afile = new PfamFile(inFile, type);
+              }
+              else if (format.equals("JnetFile"))
+              {
+                afile = new JPredFile(inFile, type);
+                ( (JPredFile) afile).removeNonSequences();
+              }
+              else if (format.equals("PDB"))
+              {
+                afile = new MCview.PDBfile(inFile, type);
+              }
 
-                return afile.getSeqsAsArray();
+              return afile.getSeqsAsArray();
             }
             catch (Exception e)
             {
+              e.printStackTrace();
               System.err.println("Failed to read alignment using the '" + format +
                                  "' reader.\n"+e);
 
diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 8490a68..92e7e4b 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -284,7 +284,7 @@ public class DBRefFetcher implements Runnable
 
 
       sequence.addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
-                                       "1.0",
+                                       "0",
                                        entry.getAccession().elementAt(0).toString()));
 
       System.out.println("Adding dbref to "+sequence.getName()+" : "+
@@ -342,7 +342,7 @@ public class DBRefFetcher implements Runnable
           continue;
 
         sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,
-                                       "1.0",
+                                       "0",
                                        pdb.getId()));
 
         onlyPdbEntries.addElement(pdb);
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 67c72c2..77f2a79 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -175,7 +175,6 @@ public class FileLoader
             {
             }
           }
-
         }
         else
         {
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 6b32fe1..348b085 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -125,13 +125,19 @@ public class IdentifyFile
                     }
 
                     break;
-                }
-                else if (data.indexOf(":")<data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
-                {
-                  // file looks like a concise JNet file
-                  reply="JnetFile";
-                  break;
-                }
+                  }
+                  else if (data.indexOf("HEADER") > -1 ||
+                           data.indexOf("ATOM") > -1)
+                  {
+                    reply = "PDB";
+                    break;
+                  }
+                  else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+                  {
+                    // file looks like a concise JNet file
+                    reply = "JnetFile";
+                    break;
+                  }
             }
 
             reader.close();
@@ -141,6 +147,7 @@ public class IdentifyFile
             System.err.println("File Identification failed!\n" + ex);
             return error;
         }
+
         return reply;
     }
 }
-- 
1.7.10.2