X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFastaFile.java;h=6e5de81d6efd865e0277435d082e35b2cab7b6bb;hb=6a9cf7ddfdb65e38e8caa2d760877725b7f7bae0;hp=d2749dbaaeb2d6b96f2b2fc1436634e4b8f58258;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index d2749db..6e5de81 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,32 +1,27 @@
/*
- * 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 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;
import java.io.*;
-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 jalview.datamodel.*;
/**
@@ -61,18 +56,13 @@ public class FastaFile extends AlignFile
*
* @throws IOException
* DOCUMENT ME!
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
*/
- public FastaFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+ public FastaFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public FastaFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+ public FastaFile(FileParse source) throws IOException
{
super(source);
}
@@ -88,14 +78,14 @@ public class FastaFile extends AlignFile
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line;
+ String line, uline;
Sequence seq = null;
boolean annotation = false;
- while ((line = nextLine()) != null)
+ while ((uline = nextLine()) != null)
{
- line = line.trim();
+ line = uline.trim();
if (line.length() > 0)
{
if (line.charAt(0) == '>')
@@ -104,17 +94,7 @@ public class FastaFile extends AlignFile
{
if (annotation)
{
- Annotation[] anots = new Annotation[sb.length()];
- String anotString = sb.toString();
- for (int i = 0; i < sb.length(); i++)
- {
- anots[i] = new Annotation(anotString.substring(i, i + 1),
- null, ' ', 0);
- }
- AlignmentAnnotation aa = new AlignmentAnnotation(seq
- .getName().substring(2), seq.getDescription(), anots);
-
- annotations.addElement(aa);
+ annotations.addElement(makeAnnotation(seq, sb));
}
}
else
@@ -144,24 +124,14 @@ public class FastaFile extends AlignFile
}
else
{
- sb.append(line);
+ sb.append(annotation ? uline : line);
}
}
}
if (annotation)
{
- Annotation[] anots = new Annotation[sb.length()];
- String anotString = sb.toString();
- for (int i = 0; i < sb.length(); i++)
- {
- anots[i] = new Annotation(anotString.substring(i, i + 1), null,
- ' ', 0);
- }
- AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
- .substring(2), seq.getDescription(), anots);
-
- annotations.addElement(aa);
+ annotations.addElement(makeAnnotation(seq, sb));
}
else if (!firstLine)
@@ -171,6 +141,23 @@ public class FastaFile extends AlignFile
}
}
+ private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
+ {
+ Annotation[] anots = new Annotation[sb.length()];
+ char cb;
+ for (int i = 0; i < anots.length; i++)
+ {
+ char cn = sb.charAt(i);
+ if (cn != ' ')
+ {
+ anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
+ }
+ }
+ AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
+ .substring(2), seq.getDescription(), anots);
+ return aa;
+ }
+
/**
* called by AppletFormatAdapter to generate an annotated alignment, rather
* than bare sequences.