X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=8f5144b82513b869295806f9a0d4c49563793874;hb=ad1a8c2675db1bda53a09c8acc1c560af9bc8619;hp=b6f94fd53de717b6c5340c70ae93cb2f3261759e;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index b6f94fd..8f5144b 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,21 @@
  */
 package jalview.io;
 
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
 import jalview.util.MessageManager;
 
-import java.io.*;
-import java.net.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
 /**
@@ -39,10 +50,26 @@ public class FileParse
 
   public File inFile = null;
 
-  public int index = 1; // sequence counter for FileParse object created from
+  /**
+   * a viewport associated with the current file operation. May be null. May
+   * move to different object.
+   */
+  private AlignViewportI viewport;
 
-  // same data source
+  /**
+   * specific settings for exporting data from the current context
+   */
+  private AlignExportSettingI exportSettings;
 
+  /**
+   * sequence counter for FileParse object created from same data source
+   */
+  public int index = 1;
+
+  /**
+   * separator for extracting specific 'frame' of a datasource for formats that
+   * support multiple records (e.g. BLC, Stockholm, etc)
+   */
   protected char suffixSeparator = '#';
 
   /**
@@ -99,7 +126,9 @@ public class FileParse
       throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
+    {
       return;
+    }
     index = ++from.index;
     inFile = from.inFile;
     suffixSeparator = from.suffixSeparator;
@@ -157,7 +186,7 @@ public class FileParse
         {
           warningMessage = "Failed  to resolve as a GZ stream ("
                   + x.getMessage() + ")";
-          x.printStackTrace();
+          // x.printStackTrace();
         }
         ;
       }
@@ -281,7 +310,9 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
+           {
             extractSuffix(fileStr); // URL lref is stored for later reference.
+          }
         } catch (IOException e)
         {
           String suffixLess = extractSuffix(fileStr);
@@ -323,7 +354,9 @@ public class FileParse
       {
         String suffixLess = extractSuffix(fileStr);
         if (suffixLess != null)
+        {
           is = getClass().getResourceAsStream("/" + suffixLess);
+        }
       }
       if (is != null)
       {
@@ -371,7 +404,9 @@ public class FileParse
   public String nextLine() throws IOException
   {
     if (!error)
+    {
       return dataIn.readLine();
+    }
     throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
   }
 
@@ -471,4 +506,33 @@ public class FileParse
     }
     return null;
   }
+
+  public AlignViewportI getViewport()
+  {
+    return viewport;
+  }
+
+  public void setViewport(AlignViewportI viewport)
+  {
+    this.viewport = viewport;
+  }
+
+  /**
+   * @return the currently configured exportSettings for writing data.
+   */
+  public AlignExportSettingI getExportSettings()
+  {
+    return exportSettings;
+  }
+
+  /**
+   * Set configuration for export of data.
+   * 
+   * @param exportSettings
+   *          the exportSettings to set
+   */
+  public void setExportSettings(AlignExportSettingI exportSettings)
+  {
+    this.exportSettings = exportSettings;
+  }
 }