JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 3cd7bc1..f7a45de 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,35 +1,34 @@
 /*
- * 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 jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
 
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 public class ClustalFile extends AlignFile
 {
@@ -38,28 +37,30 @@ public class ClustalFile extends AlignFile
   {
   }
 
-  public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public ClustalFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public ClustalFile(FileParse source) throws IOException
   {
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
   }
 
+  @Override
   public void parse() throws IOException
   {
     int i = 0;
     boolean flag = false;
-    boolean rna=false;
-    boolean top=false;
-    StringBuffer pssecstr=new StringBuffer(),consstr=new StringBuffer();
+    boolean rna = false;
+    boolean top = false;
+    StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
     Vector headers = new Vector();
     Hashtable seqhash = new Hashtable();
     StringBuffer tempseq;
@@ -70,9 +71,9 @@ public class ClustalFile extends AlignFile
     {
       while ((line = nextLine()) != null)
       {
-        if (line.length()==0)
+        if (line.length() == 0)
         {
-          top=true;
+          top = true;
         }
         if (line.indexOf(" ") != 0)
         {
@@ -109,7 +110,7 @@ public class ClustalFile extends AlignFile
                 {
                   tempseq.append(str.nextToken());
                 }
-                top=false;
+                top = false;
               }
             }
           }
@@ -117,13 +118,17 @@ public class ClustalFile extends AlignFile
           {
             flag = true;
           }
-        } else {
+        }
+        else
+        {
           if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
           {
             if (top)
             {
               pssecstr.append(line.trim());
-            } else {
+            }
+            else
+            {
               consstr.append(line.trim());
             }
           }
@@ -164,26 +169,33 @@ public class ClustalFile extends AlignFile
                           + headers.elementAt(i));
         }
       }
-      AlignmentAnnotation lastssa=null;
-      if (pssecstr.length()==maxLength)
+      AlignmentAnnotation lastssa = null;
+      if (pssecstr.length() == maxLength)
       {
-        Vector ss=new Vector();
-        AlignmentAnnotation ssa=lastssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", pssecstr.toString());
-        ssa.label="Secondary Structure";
+        Vector ss = new Vector();
+        AlignmentAnnotation ssa = lastssa = StockholmFile
+                .parseAnnotationRow(ss, "secondary structure",
+                        pssecstr.toString());
+        ssa.label = "Secondary Structure";
         annotations.addElement(ssa);
       }
-      if (consstr.length()==maxLength)
+      if (consstr.length() == maxLength)
       {
-        Vector ss=new Vector();
-        AlignmentAnnotation ssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", consstr.toString());
-        ssa.label="Consensus Secondary Structure";
-        if (lastssa==null || !lastssa.getRNAStruc().equals(ssa.getRNAStruc().replace('-', '.')))
+        Vector ss = new Vector();
+        AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
+                "secondary structure", consstr.toString());
+        ssa.label = "Consensus Secondary Structure";
+        if (lastssa == null
+                || !lastssa.getRNAStruc().equals(
+                        ssa.getRNAStruc().replace('-', '.')))
         {
           annotations.addElement(ssa);
         }
       }
     }
   }
+
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
@@ -192,7 +204,7 @@ public class ClustalFile extends AlignFile
 
   public String print(SequenceI[] s)
   {
-    StringBuffer out = new StringBuffer("CLUSTAL"+newline+newline);
+    StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
 
     int max = 0;
     int maxid = 0;
@@ -224,7 +236,7 @@ public class ClustalFile extends AlignFile
     maxid++;
 
     int len = 60;
-    int nochunks = (max / len) + 1;
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {