X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=a9295a3e4665a0fa409c9c81b344b221c7b3f544;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=6a36078ba8f5abd069c8b8ad93454ea42a5a3b0f;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 6a36078..a9295a3 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,27 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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
{
@@ -49,7 +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;
@@ -60,6 +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, " ");
@@ -95,6 +108,7 @@ public class ClustalFile extends AlignFile
{
tempseq.append(str.nextToken());
}
+ top = false;
}
}
}
@@ -103,6 +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)
{
@@ -139,17 +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"+newline+newline);
+ StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
int max = 0;
int maxid = 0;