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AnnotationId is hashcode of object
[jalview.git]
/
src
/
jalview
/
io
/
BLCFile.java
diff --git
a/src/jalview/io/BLCFile.java
b/src/jalview/io/BLCFile.java
index
ceeac64
..
04867a2
100755
(executable)
--- a/
src/jalview/io/BLCFile.java
+++ b/
src/jalview/io/BLCFile.java
@@
-71,10
+71,7
@@
public class BLCFile extends AlignFile
public void parse() throws IOException
\r
{
\r
boolean idsFound = false;
\r
public void parse() throws IOException
\r
{
\r
boolean idsFound = false;
\r
- Vector ids = new Vector();
\r
StringBuffer[] seqstrings;
\r
StringBuffer[] seqstrings;
\r
- Vector starts = new Vector();
\r
- Vector ends = new Vector();
\r
\r
String line = null;
\r
\r
\r
String line = null;
\r
\r
@@
-94,27
+91,18
@@
public class BLCFile extends AlignFile
\r
if (abracket > -1)
\r
{
\r
\r
if (abracket > -1)
\r
{
\r
- if (line.indexOf(" ") > -1) //
\r
- {
\r
- line = line.substring(abracket + 1,
\r
- line.indexOf(" ", abracket + 1));
\r
- }
\r
- else
\r
- line = line.substring(abracket+1);
\r
-
\r
+ line = line.substring(abracket+1);
\r
\r
Sequence seq = parseId(line);
\r
\r
Sequence seq = parseId(line);
\r
- ids.addElement(seq.getName());
\r
- starts.addElement(seq.getStart() + "");
\r
- ends.addElement(seq.getEnd() + "");
\r
+ seqs.addElement(seq);
\r
}
\r
}
\r
while (!idsFound);
\r
\r
int starCol = line.indexOf("*");
\r
}
\r
}
\r
while (!idsFound);
\r
\r
int starCol = line.indexOf("*");
\r
- seqstrings = new StringBuffer[ids.size()];
\r
+ seqstrings = new StringBuffer[seqs.size()];
\r
\r
\r
- for (int i = 0; i < ids.size(); i++)
\r
+ for (int i = 0; i < seqs.size(); i++)
\r
{
\r
if (seqstrings[i] == null)
\r
{
\r
{
\r
if (seqstrings[i] == null)
\r
{
\r
@@
-124,7
+112,7
@@
public class BLCFile extends AlignFile
\r
while ((line = nextLine()).indexOf("*") == -1)
\r
{
\r
\r
while ((line = nextLine()).indexOf("*") == -1)
\r
{
\r
- for (int i = 0; i < ids.size(); i++)
\r
+ for (int i = 0; i < seqs.size(); i++)
\r
{
\r
if (line.length() > (i + starCol))
\r
{
\r
{
\r
if (line.length() > (i + starCol))
\r
{
\r
@@
-133,23
+121,18
@@
public class BLCFile extends AlignFile
}
\r
}
\r
\r
}
\r
}
\r
\r
- for (int i = 0; i < ids.size(); i++)
\r
+ for (int i = 0; i < seqs.size(); i++)
\r
{
\r
{
\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
\r
- seqstrings[i].toString(),
\r
- Integer.parseInt(starts.elementAt(i).
\r
- toString()),
\r
- Integer.parseInt(ends.elementAt(i).toString()));
\r
+ Sequence newSeq = (Sequence) seqs.elementAt(i);
\r
\r
if (!isValidProteinSequence(newSeq.getSequence()))
\r
{
\r
throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
\r
+" : "+ newSeq.getName()
\r
+" : "+invalidCharacter);
\r
\r
if (!isValidProteinSequence(newSeq.getSequence()))
\r
{
\r
throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
\r
+" : "+ newSeq.getName()
\r
+" : "+invalidCharacter);
\r
-
\r
}
\r
\r
}
\r
\r
- seqs.addElement(newSeq);
\r
+ newSeq.setSequence(seqstrings[i].toString());
\r
}
\r
\r
}
\r
}
\r
\r
}
\r
@@
-186,11
+169,15
@@
public class BLCFile extends AlignFile
\r
while ((i < s.length) && (s[i] != null))
\r
{
\r
\r
while ((i < s.length) && (s[i] != null))
\r
{
\r
- out.append(">" + printId(s[i]) +"\n");
\r
+ out.append(">" + printId(s[i]));
\r
+ if(s[i].getDescription()!=null)
\r
+ out.append(" "+s[i].getDescription());
\r
+
\r
+ out.append("\n");
\r
\r
\r
- if (s[i].getSequence().length() > max)
\r
+ if (s[i].getSequence().length > max)
\r
{
\r
{
\r
- max = s[i].getSequence().length();
\r
+ max = s[i].getSequence().length;
\r
}
\r
\r
i++;
\r
}
\r
\r
i++;
\r
@@
-204,9
+191,9
@@
public class BLCFile extends AlignFile
\r
while ((i < s.length) && (s[i] != null))
\r
{
\r
\r
while ((i < s.length) && (s[i] != null))
\r
{
\r
- if (s[i].getSequence().length() > j)
\r
+ if (s[i].getSequence().length > j)
\r
{
\r
{
\r
- out.append(s[i].getSequence().substring(j, j + 1));
\r
+ out.append(s[i].getSequenceAsString(j, j + 1));
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r