JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index 5c2b2f3..ba6b2f3 100644 (file)
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -1,36 +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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 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 fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+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
@@ -55,16 +51,18 @@ public class SimpleBlastFile extends AlignFile
   {
   }
 
-  public SimpleBlastFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public SimpleBlastFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
-  public SimpleBlastFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public SimpleBlastFile(FileParse source) throws IOException
   {
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
@@ -73,6 +71,7 @@ public class SimpleBlastFile extends AlignFile
     seqids = new Vector();
   }
 
+  @Override
   public void parse() throws IOException
   {
     String line;
@@ -166,8 +165,8 @@ public class SimpleBlastFile extends AlignFile
               rstart = Long.parseLong(stindx);
             } catch (Exception e)
             {
-              System.err.println("Couldn't parse '" + stindx
-                      + "' as start of row");
+              System.err.println(
+                      "Couldn't parse '" + stindx + "' as start of row");
               // inAlignments = false;
               // warn for this line
             }
@@ -176,8 +175,8 @@ public class SimpleBlastFile extends AlignFile
               rend = Long.parseLong(endindx);
             } catch (Exception e)
             {
-              System.err.println("Couldn't parse '" + endindx
-                      + "' as end of row");
+              System.err.println(
+                      "Couldn't parse '" + endindx + "' as end of row");
               // inAlignments = false;
 
               // warn for this line
@@ -204,9 +203,9 @@ 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);
 
@@ -260,7 +259,7 @@ public class SimpleBlastFile extends AlignFile
         {
           Sequence newseq = new Sequence(idstring,
 
-          ((StringBuffer) seqentry[0]).toString(),
+                  ((StringBuffer) seqentry[0]).toString(),
                   (int) ((long[]) seqentry[1])[0],
                   (int) ((long[]) seqentry[1])[1]);
           if (newseq.getEnd() == 0)
@@ -291,13 +290,9 @@ public class SimpleBlastFile extends AlignFile
     }
   }
 
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     return new String("Not Implemented.");
   }
-
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }