JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index f46e3ad..5dd0e40 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,28 +1,34 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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
+ * 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 jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
 
-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
 {
@@ -50,7 +56,9 @@ public class ClustalFile extends AlignFile
   {
     int i = 0;
     boolean flag = false;
-
+    boolean rna = false;
+    boolean top = false;
+    StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
     Vector headers = new Vector();
     Hashtable seqhash = new Hashtable();
     StringBuffer tempseq;
@@ -61,6 +69,10 @@ public class ClustalFile extends AlignFile
     {
       while ((line = nextLine()) != null)
       {
+        if (line.length() == 0)
+        {
+          top = true;
+        }
         if (line.indexOf(" ") != 0)
         {
           str = new StringTokenizer(line, " ");
@@ -96,6 +108,7 @@ public class ClustalFile extends AlignFile
                 {
                   tempseq.append(str.nextToken());
                 }
+                top = false;
               }
             }
           }
@@ -104,6 +117,20 @@ public class ClustalFile extends AlignFile
             flag = true;
           }
         }
+        else
+        {
+          if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
+          {
+            if (top)
+            {
+              pssecstr.append(line.trim());
+            }
+            else
+            {
+              consstr.append(line.trim());
+            }
+          }
+        }
       }
     } catch (IOException e)
     {
@@ -140,17 +167,41 @@ public class ClustalFile extends AlignFile
                           + headers.elementAt(i));
         }
       }
+      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";
+        annotations.addElement(ssa);
+      }
+      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('-', '.')))
+        {
+          annotations.addElement(ssa);
+        }
+      }
     }
   }
 
   public String print()
   {
     return print(getSeqsAsArray());
+    // TODO: locaRNA style aln output
   }
 
   public String print(SequenceI[] s)
   {
-    StringBuffer out = new StringBuffer("CLUSTAL\n\n");
+    StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
 
     int max = 0;
     int maxid = 0;
@@ -190,9 +241,7 @@ public class ClustalFile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        out
-                .append(new Format("%-" + maxid + "s").form(printId(s[j])
-                        + " "));
+        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
 
         int start = i * len;
         int end = start + len;
@@ -210,11 +259,11 @@ public class ClustalFile extends AlignFile
           }
         }
 
-        out.append("\n");
+        out.append(newline);
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();