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Merge remote-tracking branch 'origin/bug/JAL-3239monospacedEps' into develop
[jalview.git]
/
src
/
jalview
/
io
/
PfamFile.java
diff --git
a/src/jalview/io/PfamFile.java
b/src/jalview/io/PfamFile.java
index
e71bb4b
..
6b9dc3f
100755
(executable)
--- a/
src/jalview/io/PfamFile.java
+++ b/
src/jalview/io/PfamFile.java
@@
-36,9
+36,10
@@
public class PfamFile extends AlignFile
{
}
{
}
- public PfamFile(String inFile, String type) throws IOException
+ public PfamFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public PfamFile(FileParse source) throws IOException
}
public PfamFile(FileParse source) throws IOException
@@
-116,8
+117,8
@@
public class PfamFile extends AlignFile
if (noSeqs < 1)
{
if (noSeqs < 1)
{
- throw new IOException(
- MessageManager.getString("exception.pfam_no_sequences_found"));
+ throw new IOException(MessageManager
+ .getString("exception.pfam_no_sequences_found"));
}
for (i = 0; i < headers.size(); i++)
}
for (i = 0; i < headers.size(); i++)
@@
-130,8
+131,8
@@
public class PfamFile extends AlignFile
}
Sequence newSeq = parseId(headers.get(i).toString());
}
Sequence newSeq = parseId(headers.get(i).toString());
- newSeq.setSequence(seqhash.get(headers.get(i).toString())
- .toString());
+ newSeq.setSequence(
+ seqhash.get(headers.get(i).toString()).toString());
seqs.addElement(newSeq);
}
else
seqs.addElement(newSeq);
}
else
@@
-142,7
+143,8
@@
public class PfamFile extends AlignFile
}
}
}
}
- public String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("");
{
StringBuffer out = new StringBuffer("");
@@
-153,12
+155,9
@@
public class PfamFile extends AlignFile
while ((i < s.length) && (s[i] != null))
{
while ((i < s.length) && (s[i] != null))
{
- String tmp = printId(s[i]);
+ String tmp = printId(s[i], jvsuffix);
- if (s[i].getSequence().length > max)
- {
- max = s[i].getSequence().length;
- }
+ max = Math.max(max, s[i].getLength());
if (tmp.length() > maxid)
{
if (tmp.length() > maxid)
{
@@
-177,7
+176,8
@@
public class PfamFile extends AlignFile
while ((j < s.length) && (s[j] != null))
{
while ((j < s.length) && (s[j] != null))
{
- out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[j], jvsuffix) + " "));
out.append(s[j].getSequenceAsString());
out.append(newline);
out.append(s[j].getSequenceAsString());
out.append(newline);
@@
-188,10
+188,4
@@
public class PfamFile extends AlignFile
return out.toString();
}
return out.toString();
}
-
- @Override
- public String print()
- {
- return print(getSeqsAsArray());
- }
}
}