X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=4c69ce0fcdee5134761e15ae69893617c3cb4de3;hb=f49e86c9f8e7c0301f2b8824d0c033a3df291e6a;hp=f4f765c63f3ab1866da1d00981827e078b8cae54;hpb=1233e68299e9a3c8b2a075f18e5179d8480e2aee;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index f4f765c..4c69ce0 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -27,6 +27,7 @@ import java.net.*;
 public class FileParse
 {
   public File inFile=null;
+  public int index = 1; // sequence counter for FileParse object created from same data source
   protected char suffixSeparator = '#';
   /**
    * '#' separated string tagged on to end of filename 
@@ -46,6 +47,34 @@ public class FileParse
   {
   }
   /**
+   * Create a new FileParse instance reading from the same datasource starting at the current position.
+   * WARNING! Subsequent reads from either object will affect the read position of the other, but not
+   * the error state.
+   * 
+   * @param from
+   */
+  public FileParse(FileParse from) throws IOException
+  {
+    if (from==null)
+    {
+      throw new Error("Implementation error. Null FileParse in copy constructor");
+    }
+    if (from==this)
+      return;
+    index = ++from.index;
+    inFile = from.inFile;
+    suffixSeparator = from.suffixSeparator;
+    suffix = from.suffix;
+    errormessage = from.errormessage; // inherit potential error messages
+    error = false; // reset any error condition.
+    type = from.type;
+    dataIn = from.dataIn;
+    if (dataIn!=null)
+    {
+      mark();
+    }
+  }
+  /**
    * Attempt to open a file as a datasource.
    * Sets error and errormessage if fileStr was invalid.
    * @param fileStr
@@ -128,6 +157,7 @@ public class FileParse
     else if (type.equals(AppletFormatAdapter.URL))
     {
       try {
+      try {
         checkURLSource(fileStr);
         if (suffixSeparator=='#')
           extractSuffix(fileStr); // URL lref is stored for later reference.
@@ -146,6 +176,12 @@ public class FileParse
           }
         }
       }
+      }
+      catch (Exception e)
+      {
+        errormessage = "CANNOT ACCESS DATA AT URL '"+fileStr+"' ("+e.getMessage()+")";
+        error=true;
+      }
     }
     else if (type.equals(AppletFormatAdapter.PASTE))
     {
@@ -168,9 +204,28 @@ public class FileParse
         error = true;
       }
     }
+    if (dataIn==null)
+    {
+      // pass up the reason why we have no source to read from
+      throw new IOException("Failed to read data from source:\n"+errormessage);
+    }
     error=false;
     dataIn.mark(READAHEAD_LIMIT);
   }
+  /**
+   * mark the current position in the source as start
+   * for the purposes of it being analysed by IdentifyFile().identify
+   * @throws IOException
+   */
+  public void mark() throws IOException
+  {
+    if (dataIn!=null)
+    {
+      dataIn.mark(READAHEAD_LIMIT);
+    } else {
+      throw new IOException("Unitialised Source Stream");
+    }
+  }
   public String nextLine()
       throws IOException
   {
@@ -221,4 +276,15 @@ public class FileParse
   public String getWarningMessage() {
     return warningMessage;
   }
+  public String getInFile()
+  {
+    if (inFile!=null)
+    {
+      return inFile.getAbsolutePath()+" ("+index+")";
+    }
+    else
+    {
+      return "From Paste + ("+index+")";
+    }
+  }
 }