X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=34f25dd8be7dc0184d30ab9b4d32ebb3fcb2d12c;hb=refs%2Fheads%2Fbug%2FJAL-1644_Finder-logic-improvement;hp=966689b81f543f3a03aa2f8a8cd44bc294a42215;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 966689b..34f25dd 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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;
@@ -49,7 +52,9 @@ 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 +65,10 @@ 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 +104,7 @@ public class ClustalFile extends AlignFile
{
tempseq.append(str.nextToken());
}
+ top = false;
}
}
}
@@ -103,6 +113,20 @@ 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 +163,41 @@ 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;
@@ -189,9 +237,7 @@ 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 +255,11 @@ public class ClustalFile extends AlignFile
}
}
- out.append("\n");
+ out.append(newline);
j++;
}
- out.append("\n");
+ out.append(newline);
}
return out.toString();