X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FClustalFile.java;h=f7a45ded35de59eda6c075784c252adb48536527;hb=b5f2dfda36c463b93f34db95fe5bc5ff2a1516bf;hp=8a1cf0526ad9ae31cbe6de5d0438a57f7da862e4;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 8a1cf05..f7a45de 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,36 +1,34 @@
/*
- * 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
+ * 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 javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
-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.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
public class ClustalFile extends AlignFile
{
@@ -39,28 +37,30 @@ public class ClustalFile extends AlignFile
{
}
- public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public ClustalFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public ClustalFile(FileParse source) throws IOException
{
super(source);
}
+ @Override
public void initData()
{
super.initData();
}
+ @Override
public void parse() throws IOException
{
int i = 0;
boolean flag = false;
- boolean rna=false;
- boolean top=false;
- StringBuffer pssecstr=new StringBuffer(),consstr=new StringBuffer();
+ boolean rna = false;
+ boolean top = false;
+ StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
Vector headers = new Vector();
Hashtable seqhash = new Hashtable();
StringBuffer tempseq;
@@ -71,9 +71,9 @@ public class ClustalFile extends AlignFile
{
while ((line = nextLine()) != null)
{
- if (line.length()==0)
+ if (line.length() == 0)
{
- top=true;
+ top = true;
}
if (line.indexOf(" ") != 0)
{
@@ -110,7 +110,7 @@ public class ClustalFile extends AlignFile
{
tempseq.append(str.nextToken());
}
- top=false;
+ top = false;
}
}
}
@@ -118,13 +118,17 @@ public class ClustalFile extends AlignFile
{
flag = true;
}
- } else {
+ }
+ else
+ {
if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
{
if (top)
{
pssecstr.append(line.trim());
- } else {
+ }
+ else
+ {
consstr.append(line.trim());
}
}
@@ -165,26 +169,33 @@ public class ClustalFile extends AlignFile
+ headers.elementAt(i));
}
}
- AlignmentAnnotation lastssa=null;
- if (pssecstr.length()==maxLength)
+ 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";
+ 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)
+ 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('-', '.')))
+ 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);
}
}
}
}
+
+ @Override
public String print()
{
return print(getSeqsAsArray());
@@ -193,7 +204,7 @@ public class ClustalFile extends AlignFile
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;
@@ -225,7 +236,7 @@ public class ClustalFile extends AlignFile
maxid++;
int len = 60;
- int nochunks = (max / len) + 1;
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
for (i = 0; i < nochunks; i++)
{