X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FSimpleBlastFile.java;h=f4dc5a2a89a3383384d452a21b9e63b05a464f66;hb=19f8ee5562523508666b4472ad624b9e549a3cea;hp=42b593e2fc341aea25c7d0123080ab7956fa09fc;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git
diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index 42b593e..f4dc5a2 100644
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -1,35 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
-
-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 jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* parse a simple blast report. Attempt to cope with query anchored and pairwise
@@ -54,12 +51,12 @@ public class SimpleBlastFile extends AlignFile
{
}
- public SimpleBlastFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+ public SimpleBlastFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public SimpleBlastFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+ public SimpleBlastFile(FileParse source) throws IOException
{
super(source);
}
@@ -203,9 +200,8 @@ public class SimpleBlastFile extends AlignFile
if (seqentry == null)
{
padseq = true; // prepend gaps to new sequences in this block
- seqentry = new Object[]
- { new StringBuffer(), new long[]
- { rstart, rend } };
+ seqentry = new Object[] { new StringBuffer(),
+ new long[] { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);