JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 690e22a..4526eba 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,7 @@ package jalview.io;
 
 import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
@@ -50,16 +51,26 @@ public class FileParse
 
   public File inFile = null;
 
+  /**
+   * a viewport associated with the current file operation. May be null. May
+   * move to different object.
+   */
   private AlignViewportI viewport;
 
-  public int index = 1; // sequence counter for FileParse object created from
   /**
    * specific settings for exporting data from the current context
    */
   private AlignExportSettingI exportSettings;
 
-  // same data source
+  /**
+   * 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 = '#';
 
   /**
@@ -69,7 +80,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-      newline = nl;
+    newline = nl;
   }
 
   public String getNewlineString()
@@ -87,7 +98,7 @@ public class FileParse
 
   protected BufferedReader dataIn = null;
 
-  protected String errormessage = "UNITIALISED SOURCE";
+  protected String errormessage = "UNINITIALISED SOURCE";
 
   protected boolean error = true;
 
@@ -113,7 +124,9 @@ public class FileParse
   {
     if (from == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
     {
@@ -228,7 +241,10 @@ public class FileParse
     {
       if (e != null)
       {
-        throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
+        throw new IOException(
+                MessageManager
+                        .getString("exception.failed_to_resolve_gzip_stream"),
+                e);
       }
       throw q;
     }
@@ -283,12 +299,17 @@ public class FileParse
         {
           if (checkFileSource(suffixLess))
           {
-            throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
+            throw new IOException(MessageManager.formatMessage(
+                    "exception.problem_opening_file_also_tried",
+                    new String[] { inFile.getName(), suffixLess,
+                        errormessage }));
           }
         }
         else
         {
-          throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
+          throw new IOException(MessageManager.formatMessage(
+                  "exception.problem_opening_file",
+                  new String[] { inFile.getName(), errormessage }));
         }
       }
     }
@@ -300,7 +321,7 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
-           {
+          {
             extractSuffix(fileStr); // URL lref is stored for later reference.
           }
         } catch (IOException e)
@@ -367,7 +388,9 @@ public class FileParse
     if (dataIn == null || error)
     {
       // pass up the reason why we have no source to read from
-      throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
+      throw new IOException(MessageManager.formatMessage(
+              "exception.failed_to_read_data_from_source",
+              new String[] { errormessage }));
     }
     error = false;
     dataIn.mark(READAHEAD_LIMIT);
@@ -387,7 +410,8 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
+      throw new IOException(
+              MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
@@ -397,9 +421,24 @@ public class FileParse
     {
       return dataIn.readLine();
     }
-    throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
+    throw new IOException(MessageManager.formatMessage(
+            "exception.invalid_source_stream",
+            new String[] { errormessage }));
+  }
+
+  /**
+   * 
+   * @return true if this FileParse is configured for Export only
+   */
+  public boolean isExporting()
+  {
+    return !error && dataIn == null;
   }
 
+  /**
+   * 
+   * @return true if the data source is valid
+   */
   public boolean isValid()
   {
     return !error;
@@ -429,7 +468,9 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
+      throw new IOException(
+              MessageManager
+                      .getString("error.implementation_error_reset_called_for_invalid_source"));
     }
   }
 
@@ -525,4 +566,19 @@ public class FileParse
   {
     this.exportSettings = exportSettings;
   }
+
+  /**
+   * method overridden by complex file exporter/importers which support
+   * exporting visualisation and layout settings for a view
+   * 
+   * @param avpanel
+   */
+  public void configureForView(AlignmentViewPanel avpanel)
+  {
+    if (avpanel != null)
+    {
+      setViewport(avpanel.getAlignViewport());
+    }
+    // could also set export/import settings
+  }
 }