update author list in license for (JAL-826)

[jalview.git] / src / jalview / io / FileParse.java

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index cca8ace..05a7212 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.io;
 
@@ -27,13 +26,30 @@ import java.net.*;
  */
 public class FileParse
 {
+  /**
+   * text specifying source of data. usually filename or url.
+   */
+  private String dataName = "unknown source";
+
   public File inFile = null;
 
   public int index = 1; // sequence counter for FileParse object created from
-                        // same data source
 
-  protected char suffixSeparator = '#';
+  // same data source
 
+  protected char suffixSeparator = '#';
+  /**
+   * character used to write newlines 
+   */
+  protected String newline = System.getProperty("line.separator");
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+  public String getNewlineString()
+  {
+    return newline;
+  }
   /**
    * '#' separated string tagged on to end of filename or url that was clipped
    * off to resolve to valid filename
@@ -87,6 +103,7 @@ public class FileParse
     {
       mark();
     }
+    dataName = from.dataName;
   }
 
   /**
@@ -121,6 +138,7 @@ public class FileParse
     if (!error)
     {
       dataIn = new BufferedReader(new FileReader(fileStr));
+      dataName = fileStr;
     }
     return error;
   }
@@ -131,6 +149,8 @@ public class FileParse
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
     dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    // record URL as name of datasource.
+    dataName = fileStr;
     return false;
   }
 
@@ -158,10 +178,10 @@ public class FileParse
    * Create a datasource for input to Jalview. See AppletFormatAdapter for the
    * types of sources that are handled.
    * 
-   * @param fileStr -
-   *                datasource locator/content
-   * @param type -
-   *                protocol of source
+   * @param fileStr
+   *          - datasource locator/content
+   * @param type
+   *          - protocol of source
    * @throws MalformedURLException
    * @throws IOException
    */
@@ -230,6 +250,7 @@ public class FileParse
     {
       errormessage = "PASTE INACCESSIBLE!";
       dataIn = new BufferedReader(new StringReader(fileStr));
+      dataName = "Paste";
     }
     else if (type.equals(AppletFormatAdapter.CLASSLOADER))
     {
@@ -245,6 +266,7 @@ public class FileParse
       if (is != null)
       {
         dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+        dataName = fileStr;
       }
       else
       {
@@ -356,9 +378,30 @@ public class FileParse
     }
   }
 
-  public Reader getReader() throws IOException
+  /**
+   * @return the dataName
+   */
+  public String getDataName()
+  {
+    return dataName;
+  }
+  /**
+   * set the (human readable) name or URI for this datasource
+   * @param dataname
+   */
+  protected void setDataName(String dataname) {
+    dataName = dataname;
+  }
+  
+
+  /**
+   * get the underlying bufferedReader for this data source.
+   * @return null if no reader available
+   * @throws IOException
+   */
+  public Reader getReader()
   {
-    if (dataIn != null && dataIn.ready())
+    if (dataIn != null) // Probably don't need to test for readiness && dataIn.ready())
     {
       return dataIn;
     }