X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=7117d0fcf537a5ae211577c0e290a59d8404af84;hb=c860648463c56ba9f75e9d239e2f56edea8e31e7;hp=8f5144b82513b869295806f9a0d4c49563793874;hpb=ad1a8c2675db1bda53a09c8acc1c560af9bc8619;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 8f5144b..7117d0f 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;
@@ -43,6 +45,10 @@ import java.util.zip.GZIPInputStream;
  */
 public class FileParse
 {
+  protected static final String SPACE = " ";
+
+  protected static final String TAB = "\t";
+
   /**
    * text specifying source of data. usually filename or url.
    */
@@ -79,7 +85,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-      newline = nl;
+    newline = nl;
   }
 
   public String getNewlineString()
@@ -93,11 +99,11 @@ 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;
 
@@ -123,7 +129,8 @@ 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)
     {
@@ -135,7 +142,7 @@ 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)
     {
@@ -200,16 +207,16 @@ public class FileParse
   private BufferedReader tryAsGzipSource(InputStream inputStream)
           throws Exception
   {
-    BufferedReader inData = new BufferedReader(new InputStreamReader(
-            new GZIPInputStream(inputStream)));
+    BufferedReader inData = new BufferedReader(
+            new InputStreamReader(new GZIPInputStream(inputStream)));
     inData.mark(2048);
     inData.read();
     inData.reset();
     return inData;
   }
 
-  private boolean checkURLSource(String fileStr) throws IOException,
-          MalformedURLException
+  private boolean checkURLSource(String fileStr)
+          throws IOException, MalformedURLException
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
@@ -238,7 +245,8 @@ 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;
     }
@@ -268,23 +276,47 @@ 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))
       {
@@ -293,16 +325,21 @@ 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
       {
@@ -310,7 +347,7 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
-           {
+          {
             extractSuffix(fileStr); // URL lref is stored for later reference.
           }
         } catch (IOException e)
@@ -339,13 +376,13 @@ 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()
@@ -371,13 +408,15 @@ 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);
@@ -397,7 +436,8 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
+      throw new IOException(
+              MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
@@ -407,9 +447,24 @@ 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;
@@ -428,18 +483,27 @@ 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"));
     }
   }
 
@@ -535,4 +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;
+  }
 }