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Formatting changes
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
04ddff3
..
d22dc12
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-25,7
+25,14
@@
import java.io.*;
import java.util.*;
\r
\r
\r
import java.util.*;
\r
\r
\r
-public abstract class AlignFile extends FileParse {
\r
+/**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @author $author$
\r
+ * @version $Revision$
\r
+ */
\r
+public abstract class AlignFile extends FileParse
\r
+{
\r
int noSeqs = 0;
\r
int maxLength = 0;
\r
Vector seqs;
\r
int noSeqs = 0;
\r
int maxLength = 0;
\r
Vector seqs;
\r
@@
-33,16
+40,29
@@
public abstract class AlignFile extends FileParse {
long start;
\r
long end;
\r
\r
long start;
\r
long end;
\r
\r
- public AlignFile() {
\r
+ /**
\r
+ * Creates a new AlignFile object.
\r
+ */
\r
+ public AlignFile()
\r
+ {
\r
}
\r
\r
}
\r
\r
- public AlignFile(String inStr) {
\r
+ /**
\r
+ * Creates a new AlignFile object.
\r
+ *
\r
+ * @param inStr DOCUMENT ME!
\r
+ */
\r
+ public AlignFile(String inStr)
\r
+ {
\r
initData();
\r
System.out.println("is this ever called??");
\r
\r
initData();
\r
System.out.println("is this ever called??");
\r
\r
- try {
\r
+ try
\r
+ {
\r
parse();
\r
parse();
\r
- } catch (Exception ex) {
\r
+ }
\r
+ catch (Exception ex)
\r
+ {
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
@@
-51,7
+71,8
@@
public abstract class AlignFile extends FileParse {
* @param inFile Filename to read from.
\r
* @param type What type of file to read from (File, URL)
\r
*/
\r
* @param inFile Filename to read from.
\r
* @param type What type of file to read from (File, URL)
\r
*/
\r
- public AlignFile(String inFile, String type) throws IOException {
\r
+ public AlignFile(String inFile, String type) throws IOException
\r
+ {
\r
super(inFile, type);
\r
\r
initData();
\r
super(inFile, type);
\r
\r
initData();
\r
@@
-62,17
+83,20
@@
public abstract class AlignFile extends FileParse {
/**
\r
* Return the seqs Vector
\r
*/
\r
/**
\r
* Return the seqs Vector
\r
*/
\r
- public Vector getSeqs() {
\r
+ public Vector getSeqs()
\r
+ {
\r
return seqs;
\r
}
\r
\r
/**
\r
* Return the Sequences in the seqs Vector as an array of Sequences
\r
*/
\r
return seqs;
\r
}
\r
\r
/**
\r
* Return the Sequences in the seqs Vector as an array of Sequences
\r
*/
\r
- public SequenceI[] getSeqsAsArray() {
\r
+ public SequenceI[] getSeqsAsArray()
\r
+ {
\r
SequenceI[] s = new SequenceI[seqs.size()];
\r
\r
SequenceI[] s = new SequenceI[seqs.size()];
\r
\r
- for (int i = 0; i < seqs.size(); i++) {
\r
+ for (int i = 0; i < seqs.size(); i++)
\r
+ {
\r
s[i] = (SequenceI) seqs.elementAt(i);
\r
}
\r
\r
s[i] = (SequenceI) seqs.elementAt(i);
\r
}
\r
\r
@@
-82,24
+106,34
@@
public abstract class AlignFile extends FileParse {
/**
\r
* Initialise objects to store sequence data in.
\r
*/
\r
/**
\r
* Initialise objects to store sequence data in.
\r
*/
\r
- protected void initData() {
\r
+ protected void initData()
\r
+ {
\r
seqs = new Vector();
\r
headers = new Vector();
\r
}
\r
\r
seqs = new Vector();
\r
headers = new Vector();
\r
}
\r
\r
- protected void setSeqs(SequenceI[] s) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param s DOCUMENT ME!
\r
+ */
\r
+ protected void setSeqs(SequenceI[] s)
\r
+ {
\r
seqs = new Vector();
\r
\r
seqs = new Vector();
\r
\r
- for (int i = 0; i < s.length; i++) {
\r
+ for (int i = 0; i < s.length; i++)
\r
+ {
\r
seqs.addElement(s[i]);
\r
}
\r
}
\r
\r
// Checks whether sequence is valid aa characters
\r
seqs.addElement(s[i]);
\r
}
\r
}
\r
\r
// Checks whether sequence is valid aa characters
\r
- protected boolean isValidProteinSequence(String sequence) {
\r
+ protected boolean isValidProteinSequence(String sequence)
\r
+ {
\r
for (int i = 0; i < sequence.length(); i++)
\r
if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
\r
for (int i = 0; i < sequence.length(); i++)
\r
if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
\r
- String.valueOf(sequence.charAt(i)))) {
\r
+ String.valueOf(sequence.charAt(i))))
\r
+ {
\r
return false;
\r
}
\r
\r
return false;
\r
}
\r
\r