JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 8f5144b..2221312 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -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;
@@ -268,6 +269,30 @@ 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,
+          String typeString)
+  {
+    type = typeString;
+    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.
    * 
@@ -410,6 +435,19 @@ public class FileParse
     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;
@@ -535,4 +573,18 @@ 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
+  }
 }