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 4973908..8a1cf05 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
@@ -20,6 +20,15 @@ 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.*;
 
@@ -30,12 +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);
   }
@@ -49,7 +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;
@@ -60,6 +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, " ");
@@ -95,6 +110,7 @@ public class ClustalFile extends AlignFile
                 {
                   tempseq.append(str.nextToken());
                 }
+                top=false;
               }
             }
           }
@@ -102,6 +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)
@@ -139,17 +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;
@@ -189,9 +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;
@@ -209,11 +251,11 @@ public class ClustalFile extends AlignFile
           }
         }
 
-        out.append("\n");
+        out.append(newline);
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();