Merge branch 'documentation/JAL-2325_release2101' into develop

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 8711354..fddb565 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -23,6 +23,7 @@ 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;
@@ -274,6 +275,30 @@ 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.
    * 
@@ -589,4 +614,15 @@ public class FileParse
     }
     // could also set export/import settings
   }
+
+  /**
+   * Returns the preferred feature colour configuration if there is one, else
+   * null
+   * 
+   * @return
+   */
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return null;
+  }
 }