Add support RNAML format

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 8f6a12f..2827191 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
  * \r
  * This file is part of Jalview.\r
  * \r
@@ -23,7 +23,15 @@ package jalview.io;
 import java.io.*;\r
 import java.util.*;\r
 \r
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
 import com.stevesoft.pat.*;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
 import jalview.datamodel.*;\r
 import jalview.analysis.Rna;\r
 \r
@@ -49,12 +57,12 @@ public class StockholmFile extends AlignFile
   {\r
   }\r
 \r
-  public StockholmFile(String inFile, String type) throws IOException\r
+  public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed\r
   {\r
     super(inFile, type);\r
   }\r
 \r
-  public StockholmFile(FileParse source) throws IOException\r
+  public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed\r
   {\r
     super(source);\r
   }\r
@@ -521,7 +529,7 @@ public class StockholmFile extends AlignFile
     }\r
   }\r
 \r
-  private AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
+  protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
           String label, String annots)\r
   {\r
     String convert1, convert2 = null;\r
@@ -640,7 +648,7 @@ public class StockholmFile extends AlignFile
     }\r
   }\r
 \r
-  private String id2type(String id)\r
+  protected static String id2type(String id)\r
   {\r
     if (typeIds.containsKey(id))\r
     {\r