JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index 03f76ea..502eced 100644 (file)
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -1,20 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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;
 
@@ -22,7 +22,6 @@ import java.io.*;
 import java.util.*;
 
 import jalview.datamodel.*;
-import jalview.util.*;
 
 /**
  * parse a simple blast report. Attempt to cope with query anchored and pairwise
@@ -37,10 +36,12 @@ public class SimpleBlastFile extends AlignFile
    * header and footer info goes into alignment annotation.
    */
   StringBuffer headerLines, footerLines;
+
   /**
    * hold sequence ids in order of appearance in file
    */
   Vector seqids;
+
   public SimpleBlastFile()
   {
   }
@@ -87,6 +88,8 @@ public class SimpleBlastFile extends AlignFile
             continue;
           }
           // parse out the sequences
+          // query anchored means that we use the query sequence as the
+          // alignment ruler
           if (line.indexOf("Query") == 0)
           {
             padding = -1;
@@ -104,7 +107,7 @@ public class SimpleBlastFile extends AlignFile
                 {
                   numcol = p;
                 }
-                else if (aligcol!=-1 && lastcol == -1)
+                else if (aligcol != -1 && lastcol == -1)
                 {
                   lastcol = p;
                 }
@@ -133,7 +136,8 @@ public class SimpleBlastFile extends AlignFile
               padding = aligcol;
             }
           }
-          if (line.indexOf("Database:")>-1 || (aligcol == -1 || numcol == -1 || lastcol == -1)
+          if (line.indexOf("Database:") > -1
+                  || (aligcol == -1 || numcol == -1 || lastcol == -1)
                   || line.length() < lastcol)
           {
             inAlignments = false;
@@ -153,7 +157,8 @@ 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
             }
@@ -162,12 +167,30 @@ 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
             }
-            Object[] seqentry = (Object[]) seqhash.get(sqid);
+            Vector seqentries = (Vector) seqhash.get(sqid);
+            if (seqentries == null)
+            {
+              seqentries = new Vector();
+              seqhash.put(sqid, seqentries);
+              seqids.addElement(sqid);
+            }
+
+            Object[] seqentry = null;
+            Enumeration sqent = seqentries.elements();
+            while (seqentry == null && sqent.hasMoreElements())
+            {
+              seqentry = (Object[]) sqent.nextElement();
+              if (((long[]) seqentry[1])[1] + 1 != rstart)
+              {
+                seqentry = null;
+              }
+            }
             padseq = false;
             if (seqentry == null)
             {
@@ -175,9 +198,9 @@ public class SimpleBlastFile extends AlignFile
               seqentry = new Object[]
               { new StringBuffer(), new long[]
               { rstart, rend } };
+              seqentries.addElement(seqentry);
               seqhash.put(sqid, seqentry);
-              seqids.addElement(sqid);
-              
+
             }
             if (sqid.equals("Query"))
             {