JAL-2909 JAL-3894 hack in support to import regions of an unindexed SAM file.

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

diff --git a/src/jalview/io/AlignmentFileReaderI.java b/src/jalview/io/AlignmentFileReaderI.java
index c3e148d..507ae4c 100644 (file)
--- a/src/jalview/io/AlignmentFileReaderI.java
+++ b/src/jalview/io/AlignmentFileReaderI.java
@@ -26,6 +26,8 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
+import java.io.IOException;
+
 public interface AlignmentFileReaderI
 {
 
@@ -47,4 +49,13 @@ public interface AlignmentFileReaderI
 
   FeatureSettingsModelI getFeatureColourScheme();
 
+  /**
+   * Get a string array resulting from preprocessing the file
+   * 
+   * @return preprocess result
+   */
+  Object[] preprocess();
+
+  public abstract void parse() throws IOException;
+
 }