X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FMSFfile.java;h=f62ad81f999e5ba713fc471f2d88aaf4d7d379a0;hb=64b79e3758bd98db1664c47205f6570b2d689ba9;hp=161634c3cb56041d1704c358b8e2d29f8d6fe84c;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 161634c..f62ad81 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,36 +1,33 @@
/*
- * 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.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;
/**
* DOCUMENT ME!
@@ -58,31 +55,21 @@ public class MSFfile extends AlignFile
*
* @throws IOException
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
*/
- public MSFfile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public MSFfile(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public MSFfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public MSFfile(FileParse source) throws IOException
{
super(source);
}
- {
- // TODO Auto-generated constructor stub
- }
-
/**
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
int i = 0;
@@ -233,7 +220,7 @@ public class MSFfile extends AlignFile
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
+ "_MULTIPLE_ALIGNMENT 1.0");
- // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+ // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
out.append(newline);
out.append(newline);
int max = 0;
@@ -244,7 +231,7 @@ public class MSFfile extends AlignFile
{
// Replace all internal gaps with . and external spaces with ~
s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
- .replace('-', '.'), seqs[i].getStart(),seqs[i].getEnd());
+ .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
StringBuffer sb = new StringBuffer();
sb.append(s[i].getSequence());
@@ -317,7 +304,7 @@ public class MSFfile extends AlignFile
idBlock[i] = new String("Len: "
+ maxLenpad.form(s[i].getSequence().length) + " Check: "
- + maxChkpad.form(checksums[i]) + " Weight: 1.00"+newline);
+ + maxChkpad.form(checksums[i]) + " Weight: 1.00" + newline);
if (s[i].getName().length() > maxid)
{
@@ -351,17 +338,13 @@ public class MSFfile extends AlignFile
maxid++;
out.append(newline);
- out.append(newline);out.append("//");
+ out.append(newline);
+ out.append("//");
out.append(newline);
out.append(newline);
int len = 50;
- int nochunks = (max / len) + 1;
-
- if ((max % len) == 0)
- {
- nochunks--;
- }
+ int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
for (i = 0; i < nochunks; i++)
{
@@ -423,6 +406,7 @@ public class MSFfile extends AlignFile
*
* @return DOCUMENT ME!
*/
+ @Override
public String print()
{
return print(getSeqsAsArray());