JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index f155e51..9228257 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 2.8.2)
- * 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 +20,22 @@
  */
 package jalview.io;
 
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 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 +51,26 @@ 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 +127,9 @@ 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;
@@ -281,7 +311,9 @@ 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 +355,9 @@ public class FileParse
       {
         String suffixLess = extractSuffix(fileStr);
         if (suffixLess != null)
+        {
           is = getClass().getResourceAsStream("/" + suffixLess);
+        }
       }
       if (is != null)
       {
@@ -371,10 +405,25 @@ 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}));
   }
 
+  /**
+   * 
+   * @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;
@@ -471,4 +520,47 @@ 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;
+  }
+
+  /**
+   * 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
+  }
 }