Merge branch 'develop' into menard

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 6c1a343..1d6b76b 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -27,6 +27,15 @@ 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;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+
 /**
  * DOCUMENT ME!
  * 
@@ -65,6 +74,8 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile()
   {
+         // Shouldn't we init data structures
+         initData();
   }
 
   /**
@@ -74,8 +85,15 @@ 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 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public AlignFile(String inFile, String type) throws IOException
+  public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, type);
     initData();
@@ -93,8 +111,15 @@ public abstract class AlignFile extends FileParse
    * 
    * @param source
    * @throws IOException
+ * @throws SAXException 
+ * @throws ParserConfigurationException 
+ * @throws ExceptionFileFormatOrSyntax 
+ * @throws ExceptionLoadingFailed 
+ * @throws ExceptionPermissionDenied 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public AlignFile(FileParse source) throws IOException
+  public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
     initData();
@@ -239,8 +264,15 @@ 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 
+ * @throws InterruptedException 
+ * @throws ExceptionUnmatchedClosingParentheses 
    */
-  public abstract void parse() throws IOException;
+  public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.