X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=635c80175fcc3a574f3a0abb4fe8ec106016b90a;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=5301ab6fef6e47ffa96999e863f508949a4035ba;hpb=75963e12376e3dbfc94e6324461024baea68178f;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5301ab6..635c801 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -18,6 +18,7 @@
 package jalview.io;
 
 import java.io.File;
+import java.io.InputStream;
 
 import jalview.datamodel.*;
 
@@ -65,18 +66,22 @@ public class AppletFormatAdapter
    * corresponding to READABLE_FNAMES
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", "sto" }; // ,
-                                                                             // ".blast"
-                                                                             // };
+  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+      "sto" }; // ,
+
+  // ".blast"
+  // };
 
   /**
    * List of readable formats by application in order corresponding to
    * READABLE_EXTENSIONS
    */
   public static final String[] READABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", "Stockholm" };// ,
-                                                                         // "SimpleBLAST"
-                                                                         // };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+      "Stockholm" };// ,
+
+  // "SimpleBLAST"
+  // };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
@@ -112,7 +117,18 @@ public class AppletFormatAdapter
   AlignFile afile = null;
 
   String inFile;
-
+  /**
+   * character used to write newlines 
+   */
+  protected String newline = System.getProperty("line.separator");
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+  public String getNewlineString()
+  {
+    return newline;
+  }
   /**
    * check that this format is valid for reading
    * 
@@ -436,7 +452,7 @@ public class AppletFormatAdapter
         throw new Exception(
                 "Implementation error: Unknown file format string");
       }
-
+      afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
 
       afile.setSeqs(alignment.getSequencesArray());
@@ -458,6 +474,17 @@ public class AppletFormatAdapter
     return null;
   }
 
+  public static String checkProtocol(String file)
+  {
+    String protocol = FILE;
+    String ft = file.toLowerCase().trim();
+    if (ft.indexOf("http:") ==0 || ft.indexOf("https:") ==0 || ft.indexOf("file:") == 0)
+    {
+      protocol = URL;
+    }
+    return protocol;
+  }
+
   public static void main(String[] args)
   {
     int i = 0;
@@ -474,8 +501,8 @@ public class AppletFormatAdapter
           System.gc();
           long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
-          Alignment al = afa.readFile(args[i], FILE, new IdentifyFile()
-                  .Identify(args[i], FILE));
+          Alignment al = afa.readFile(args[i], FILE,
+                  new IdentifyFile().Identify(args[i], FILE));
           t1 += System.currentTimeMillis();
           System.gc();
           memf += r.totalMemory() - r.freeMemory();
@@ -516,6 +543,176 @@ public class AppletFormatAdapter
       }
       i++;
     }
+  }
+
+  /**
+   * try to discover how to access the given file as a valid datasource that
+   * will be identified as the given type.
+   * 
+   * @param file
+   * @param format
+   * @return protocol that yields the data parsable as the given type
+   */
+  public static String resolveProtocol(String file, String format)
+  {
+    return resolveProtocol(file, format, false);
+  }
+
+  public static String resolveProtocol(String file, String format,
+          boolean debug)
+  {
+    // TODO: test thoroughly!
+    String protocol = null;
+    if (debug)
+    {
+      System.out.println("resolving datasource started with:\n>>file\n"
+              + file + ">>endfile");
+    }
+
+    // This might throw a security exception in certain browsers
+    // Netscape Communicator for instance.
+    try
+    {
+      boolean rtn = false;
+      InputStream is = System.getSecurityManager().getClass()
+              .getResourceAsStream("/" + file);
+      if (is != null)
+      {
+        rtn = true;
+        is.close();
+      }
+      if (debug)
+      {
+        System.err.println("Resource '" + file + "' was "
+                + (rtn ? "" : "not") + " located by classloader.");
+      }
+      ;
+      if (rtn)
+      {
+        protocol = AppletFormatAdapter.CLASSLOADER;
+      }
+
+    } catch (Exception ex)
+    {
+      System.err
+              .println("Exception checking resources: " + file + " " + ex);
+    }
 
+    if (file.indexOf("://") > -1)
+    {
+      protocol = AppletFormatAdapter.URL;
+    }
+    else
+    {
+      // skipping codebase prepend check.
+      protocol = AppletFormatAdapter.FILE;
+    }
+    FileParse fp = null;
+    try
+    {
+      if (debug)
+      {
+        System.out.println("Trying to get contents of resource as "
+                + protocol + ":");
+      }
+      fp = new FileParse(file, protocol);
+      if (!fp.isValid())
+      {
+        fp = null;
+      }
+      else
+      {
+        if (debug)
+        {
+          System.out.println("Successful.");
+        }
+      }
+    } catch (Exception e)
+    {
+      if (debug)
+      {
+        System.err.println("Exception when accessing content: " + e);
+      }
+      fp = null;
+    }
+    if (fp == null)
+    {
+      if (debug)
+      {
+        System.out.println("Accessing as paste.");
+      }
+      protocol = AppletFormatAdapter.PASTE;
+      fp = null;
+      try
+      {
+        fp = new FileParse(file, protocol);
+        if (!fp.isValid())
+        {
+          fp = null;
+        }
+      } catch (Exception e)
+      {
+        System.err.println("Failed to access content as paste!");
+        e.printStackTrace();
+        fp = null;
+      }
+    }
+    if (fp == null)
+    {
+      return null;
+    }
+    if (format == null || format.length() == 0)
+    {
+      return protocol;
+    }
+    else
+    {
+      try
+      {
+        String idformat = new jalview.io.IdentifyFile().Identify(file,
+                protocol);
+        if (idformat == null)
+        {
+          if (debug)
+          {
+            System.out.println("Format not identified. Inaccessible file.");
+          }
+          return null;
+        }
+        if (debug)
+        {
+          System.out.println("Format identified as " + idformat
+                  + "and expected as " + format);
+        }
+        if (idformat.equals(format))
+        {
+          if (debug)
+          {
+            System.out.println("Protocol identified as " + protocol);
+          }
+          return protocol;
+        }
+        else
+        {
+          if (debug)
+          {
+            System.out
+                    .println("File deemed not accessible via " + protocol);
+          }
+          fp.close();
+          return null;
+        }
+      } catch (Exception e)
+      {
+        if (debug)
+        {
+          System.err.println("File deemed not accessible via " + protocol);
+          e.printStackTrace();
+        }
+        ;
+
+      }
+    }
+    return null;
   }
 }