X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=dc0418fb04d6cae7571d730d65864baeca4ded64;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=690e22ace03ea44a5e5feb45ad67c0f3d7acf09c;hpb=294cc8b0cf3d28310a95e1ffdb2a0f871304b70d;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 690e22a..dc0418f 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -22,6 +22,8 @@ package jalview.io;
 
 import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
 import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
@@ -50,16 +52,26 @@ 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 +81,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-      newline = nl;
+    newline = nl;
   }
 
   public String getNewlineString()
@@ -83,11 +95,11 @@ public class FileParse
    */
   protected String suffix = null;
 
-  protected String type = null;
+  protected DataSourceType dataSourceType = null;
 
   protected BufferedReader dataIn = null;
 
-  protected String errormessage = "UNITIALISED SOURCE";
+  protected String errormessage = "UNINITIALISED SOURCE";
 
   protected boolean error = true;
 
@@ -113,7 +125,9 @@ 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)
     {
@@ -125,7 +139,7 @@ public class FileParse
     suffix = from.suffix;
     errormessage = from.errormessage; // inherit potential error messages
     error = false; // reset any error condition.
-    type = from.type;
+    dataSourceType = from.dataSourceType;
     dataIn = from.dataIn;
     if (dataIn != null)
     {
@@ -228,7 +242,10 @@ 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;
     }
@@ -258,23 +275,47 @@ public class FileParse
   }
 
   /**
+   * not for general use, creates a fileParse object for an existing reader with
+   * configurable values for the origin and the type of the source
+   */
+  public FileParse(BufferedReader source, String originString,
+          DataSourceType sourceType)
+  {
+    dataSourceType = sourceType;
+    error = false;
+    inFile = null;
+    dataName = originString;
+    dataIn = source;
+    try
+    {
+      if (dataIn.markSupported())
+      {
+        dataIn.mark(READAHEAD_LIMIT);
+      }
+    } catch (IOException q)
+    {
+
+    }
+  }
+
+  /**
    * Create a datasource for input to Jalview. See AppletFormatAdapter for the
    * types of sources that are handled.
    * 
    * @param fileStr
    *          - datasource locator/content
-   * @param type
+   * @param sourceType
    *          - protocol of source
    * @throws MalformedURLException
    * @throws IOException
    */
-  public FileParse(String fileStr, String type)
+  public FileParse(String fileStr, DataSourceType sourceType)
           throws MalformedURLException, IOException
   {
-    this.type = type;
+    this.dataSourceType = sourceType;
     error = false;
 
-    if (type.equals(AppletFormatAdapter.FILE))
+    if (sourceType == DataSourceType.FILE)
     {
       if (checkFileSource(fileStr))
       {
@@ -283,16 +324,21 @@ 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 }));
         }
       }
     }
-    else if (type.equals(AppletFormatAdapter.URL))
+    else if (sourceType == DataSourceType.URL)
     {
       try
       {
@@ -300,7 +346,7 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
-           {
+          {
             extractSuffix(fileStr); // URL lref is stored for later reference.
           }
         } catch (IOException e)
@@ -329,13 +375,13 @@ public class FileParse
         error = true;
       }
     }
-    else if (type.equals(AppletFormatAdapter.PASTE))
+    else if (sourceType == DataSourceType.PASTE)
     {
       errormessage = "PASTE INACCESSIBLE!";
       dataIn = new BufferedReader(new StringReader(fileStr));
       dataName = "Paste";
     }
-    else if (type.equals(AppletFormatAdapter.CLASSLOADER))
+    else if (sourceType == DataSourceType.CLASSLOADER)
     {
       errormessage = "RESOURCE CANNOT BE LOCATED";
       java.io.InputStream is = getClass()
@@ -361,13 +407,15 @@ public class FileParse
     else
     {
       errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
-              + (type != null ? type : "null") + "'";
+              + (sourceType != null ? sourceType : "null") + "'";
       error = true;
     }
     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 +435,8 @@ 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 +446,24 @@ 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;
@@ -418,18 +482,28 @@ public class FileParse
   }
 
   /**
-   * rewinds the datasource the beginning.
+   * Rewinds the datasource to the marked point if possible
+   * 
+   * @param bytesRead
    * 
    */
-  public void reset() throws IOException
+  public void reset(int bytesRead) throws IOException
   {
+    if (bytesRead >= READAHEAD_LIMIT)
+    {
+      System.err.println(String.format(
+              "File reset error: read %d bytes but reset limit is %d",
+              bytesRead, READAHEAD_LIMIT));
+    }
     if (dataIn != null && !error)
     {
       dataIn.reset();
     }
     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 +599,35 @@ 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
+  }
+
+  /**
+   * Returns the preferred feature colour configuration if there is one, else
+   * null
+   * 
+   * @return
+   */
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return null;
+  }
+
+  public DataSourceType getDataSourceType()
+  {
+    return dataSourceType;
+  }
 }