X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;fp=src%2Fjalview%2Fio%2FAlignFile.java;h=c5d44edab913e4720eb8602080d1df54e0db16bb;hb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;hp=3ef721003a82c83babb5a951563de6ff79ff3c2a;hpb=54b98888f691a29c2bdeedcfc120036e921e73d6;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3ef7210..c5d44ed 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -27,6 +27,14 @@ import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
 
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+
 /**
  * DOCUMENT ME!
  * 
@@ -65,6 +73,8 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile()
   {
+	  // Shouldn't we init data structures
+	  initData();
   }
 
   /**
@@ -74,8 +84,13 @@ public abstract class AlignFile extends FileParse
    *          Filename to read from.
    * @param type
    *          What type of file to read from (File, URL)
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
    */
-  public AlignFile(String inFile, String type) throws IOException
+  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     super(inFile, type);
     initData();
@@ -92,8 +107,13 @@ public abstract class AlignFile extends FileParse
    * 
    * @param source
    * @throws IOException
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
    */
-  public AlignFile(FileParse source) throws IOException
+  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
   {
     super(source);
     initData();
@@ -237,8 +257,13 @@ public abstract class AlignFile extends FileParse
 
   /**
    * This method must be implemented to parse the contents of the file.
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
    */
-  public abstract void parse() throws IOException;
+  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.