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Merge branch 'develop' into releases/Release_2_11_3_Branch
[jalview.git]
/
src
/
jalview
/
io
/
FastaFile.java
diff --git
a/src/jalview/io/FastaFile.java
b/src/jalview/io/FastaFile.java
index
2db0ded
..
c698a31
100755
(executable)
--- a/
src/jalview/io/FastaFile.java
+++ b/
src/jalview/io/FastaFile.java
@@
-1,27
+1,32
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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
*
* 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.
*
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
+import java.io.IOException;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-50,20
+55,31
@@
public class FastaFile extends AlignFile
*
* @param inFile
* DOCUMENT ME!
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param sourceType
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
- public FastaFile(String inFile, String type) throws IOException
+ public FastaFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public FastaFile(FileParse source) throws IOException
{
}
public FastaFile(FileParse source) throws IOException
{
- super(source);
+ this(source, true);
+ }
+
+ public FastaFile(FileParse source, boolean closeData) throws IOException
+ {
+ super(true, source, closeData);
+ }
+
+ public FastaFile(SequenceI[] seqs)
+ {
+ super(seqs);
}
/**
}
/**
@@
-72,12
+88,13
@@
public class FastaFile extends AlignFile
* @throws IOException
* DOCUMENT ME!
*/
* @throws IOException
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line,uline;
+ String line, uline;
Sequence seq = null;
boolean annotation = false;
Sequence seq = null;
boolean annotation = false;
@@
-139,23
+156,24
@@
public class FastaFile extends AlignFile
seqs.addElement(seq);
}
}
seqs.addElement(seq);
}
}
+
private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
{
Annotation[] anots = new Annotation[sb.length()];
char cb;
private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
{
Annotation[] anots = new Annotation[sb.length()];
char cb;
- for (int i=0;i<anots.length;i++)
+ for (int i = 0; i < anots.length; i++)
{
char cn = sb.charAt(i);
if (cn != ' ')
{
{
char cn = sb.charAt(i);
if (cn != ' ')
{
- anots[i] = new Annotation(""+cn, null,
- ' ', Float.NaN);
+ anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
}
}
}
}
- AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
- .substring(2), seq.getDescription(), anots);
+ AlignmentAnnotation aa = new AlignmentAnnotation(
+ seq.getName().substring(2), seq.getDescription(), anots);
return aa;
}
return aa;
}
+
/**
* called by AppletFormatAdapter to generate an annotated alignment, rather
* than bare sequences.
/**
* called by AppletFormatAdapter to generate an annotated alignment, rather
* than bare sequences.
@@
-167,35
+185,21
@@
public class FastaFile extends AlignFile
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotations
- .elementAt(i);
+ AlignmentAnnotation aa = annotations.elementAt(i);
aa.setPadGaps(true, al.getGapCharacter());
al.addAnnotation(aa);
}
}
aa.setPadGaps(true, al.getGapCharacter());
al.addAnnotation(aa);
}
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- * @param len
- * DOCUMENT ME!
- * @param gaps
- * DOCUMENT ME!
- * @param displayId
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
out = new StringBuffer();
int i = 0;
while ((i < s.length) && (s[i] != null))
{
{
out = new StringBuffer();
int i = 0;
while ((i < s.length) && (s[i] != null))
{
- out.append(">" + printId(s[i]));
+ out.append(">" + printId(s[i], jvsuffix));
if (s[i].getDescription() != null)
{
out.append(" " + s[i].getDescription());
if (s[i].getDescription() != null)
{
out.append(" " + s[i].getDescription());
@@
-203,7
+207,8
@@
public class FastaFile extends AlignFile
out.append(newline);
out.append(newline);
- int nochunks = (s[i].getLength() / len) + 1;
+ int nochunks = (s[i].getLength() / len)
+ + (s[i].getLength() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{
for (int j = 0; j < nochunks; j++)
{
@@
-226,14
+231,4
@@
public class FastaFile extends AlignFile
return out.toString();
}
return out.toString();
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String print()
- {
- return print(getSeqsAsArray());
- }
}
}