last version stay many bugs ..

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 702715f..8a1cf05 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,26 +1,34 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * 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.
  * 
- * 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
+ * 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/>.
  */
 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.*;
 import jalview.util.*;
 
@@ -31,12 +39,12 @@ public class ClustalFile extends AlignFile
   {
   }
 
-  public ClustalFile(String inFile, String type) throws IOException
+  public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, type);
   }
 
-  public ClustalFile(FileParse source) throws IOException
+  public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
   }
@@ -50,7 +58,9 @@ 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 +71,10 @@ 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 +110,7 @@ public class ClustalFile extends AlignFile
                 {
                   tempseq.append(str.nextToken());
                 }
+                top=false;
               }
             }
           }
@@ -103,6 +118,16 @@ 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 +165,35 @@ 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 +233,7 @@ 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 +251,11 @@ public class ClustalFile extends AlignFile
           }
         }
 
-        out.append("\n");
+        out.append(newline);
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();