X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=5d58d423cd8b73ef0edab08c0761ee139cc3d120;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=c789139489b41cc698ccc98b26e3f9327e6aa586;hpb=1a8f953dd71a9e319e910261927f269d69b4692c;p=jalview.git
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index c789139..5d58d42 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 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 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.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
public class ClustalFile extends AlignFile
{
@@ -39,21 +37,24 @@ public class ClustalFile extends AlignFile
{
}
- public ClustalFile(String inFile, String type) throws Exception
+ public ClustalFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
- public ClustalFile(FileParse source) throws Exception
+ public ClustalFile(FileParse source) throws IOException
{
super(source);
}
+ @Override
public void initData()
{
super.initData();
}
+ @Override
public void parse() throws IOException
{
int i = 0;
@@ -195,13 +196,8 @@ public class ClustalFile extends AlignFile
}
}
- public String print()
- {
- return print(getSeqsAsArray());
- // TODO: locaRNA style aln output
- }
-
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
@@ -212,7 +208,7 @@ public class ClustalFile extends AlignFile
while ((i < s.length) && (s[i] != null))
{
- String tmp = printId(s[i]);
+ String tmp = printId(s[i], jvsuffix);
if (s[i].getSequence().length > max)
{
@@ -235,7 +231,7 @@ 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++)
{
@@ -243,7 +239,8 @@ 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],
+ jvsuffix) + " "));
int start = i * len;
int end = start + len;