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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
io
/
StockholmFile.java
diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
eeadcbf
..
72bf86a
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-147,19
+147,20
@@
public class StockholmFile extends AlignFile
+ umcp.getMessage() + ")";
throw new IOException(umcp);
}
+ umcp.getMessage() + ")";
throw new IOException(umcp);
}
- // DEBUG System.out.println("this is the secondary scructure:"
+ // DEBUG jalview.bin.Console.outPrintln("this is the secondary scructure:"
// +result.size());
SequenceI[] seqs = new SequenceI[result.size()];
String id = null;
for (int i = 0; i < result.size(); i++)
{
// +result.size());
SequenceI[] seqs = new SequenceI[result.size()];
String id = null;
for (int i = 0; i < result.size(); i++)
{
- // DEBUG System.err.println("Processing i'th sequence in Stockholm file")
+ // DEBUG jalview.bin.Console.errPrintln("Processing i'th sequence in
+ // Stockholm file")
RNA current = result.get(i);
String seq = current.getSeq();
String rna = current.getStructDBN(true);
RNA current = result.get(i);
String seq = current.getSeq();
String rna = current.getStructDBN(true);
- // DEBUG System.out.println(seq);
- // DEBUG System.err.println(rna);
+ // DEBUG jalview.bin.Console.outPrintln(seq);
+ // DEBUG jalview.bin.Console.errPrintln(rna);
int begin = 0;
int end = seq.length() - 1;
id = safeName(getDataName());
int begin = 0;
int end = seq.length() - 1;
id = safeName(getDataName());
@@
-218,8
+219,9
@@
public class StockholmFile extends AlignFile
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
- throw new IOException(MessageManager
- .getString("exception.stockholm_invalid_format") +" ("+r+")");
+ throw new IOException(
+ MessageManager.getString("exception.stockholm_invalid_format")
+ + " (" + r + ")");
}
else
{
}
else
{
@@
-440,7
+442,7
@@
public class StockholmFile extends AlignFile
}
else if (!r.search(line))
{
}
else if (!r.search(line))
{
- // System.err.println("Found sequence line: " + line);
+ // jalview.bin.Console.errPrintln("Found sequence line: " + line);
// Split sequence in sequence and accession parts
if (!x.search(line))
// Split sequence in sequence and accession parts
if (!x.search(line))
@@
-464,7
+466,8
@@
public class StockholmFile extends AlignFile
String annType = r.stringMatched(1);
String annContent = r.stringMatched(2);
String annType = r.stringMatched(1);
String annContent = r.stringMatched(2);
- // System.err.println("type:" + annType + " content: " + annContent);
+ // jalview.bin.Console.errPrintln("type:" + annType + " content: " +
+ // annContent);
if (annType.equals("GF"))
{
if (annType.equals("GF"))
{
@@
-566,7
+569,8
@@
public class StockholmFile extends AlignFile
else
{
// throw new IOException("Error parsing " + line);
else
{
// throw new IOException("Error parsing " + line);
- System.err.println(">> missing annotation: " + line);
+ jalview.bin.Console
+ .errPrintln(">> missing annotation: " + line);
}
}
else if (annType.equals("GC"))
}
}
else if (annType.equals("GC"))
@@
-684,7
+688,7
@@
public class StockholmFile extends AlignFile
// }
else
{
// }
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning - couldn't parse sequence annotation row line:\n"
+ line);
// throw new IOException("Error parsing " + line);
"Warning - couldn't parse sequence annotation row line:\n"
+ line);
// throw new IOException("Error parsing " + line);
@@
-936,7
+940,7
@@
public class StockholmFile extends AlignFile
annot.annotations.length);
System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
annot.annotations = anns;
annot.annotations.length);
System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
annot.annotations = anns;
- // System.out.println("else: ");
+ // jalview.bin.Console.outPrintln("else: ");
}
return annot;
}
}
return annot;
}
@@
-1052,11
+1056,11
@@
public class StockholmFile extends AlignFile
while (i < slen && (seq = s[i]) != null)
{
while (i < slen && (seq = s[i]) != null)
{
- if (seq.getDescription()!=null)
+ if (seq.getDescription() != null)
{
// out.append("#=GR ");
{
// out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form(
- "#=GS " + printId(seq, jvSuffix) + " DE " + seq.getDescription()));
+ out.append(new Format("%-" + maxid + "s").form("#=GS "
+ + printId(seq, jvSuffix) + " DE " + seq.getDescription()));
out.append(newline);
}
out.append(newline);
}
@@
-1269,7
+1273,7
@@
public class StockholmFile extends AlignFile
{
return (String) typeIds.get(id);
}
{
return (String) typeIds.get(id);
}
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning : Unknown Stockholm annotation type code " + id);
return id;
}
"Warning : Unknown Stockholm annotation type code " + id);
return id;
}
@@
-1291,7
+1295,7
@@
public class StockholmFile extends AlignFile
{
return key;
}
{
return key;
}
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning : Unknown Stockholm annotation type: " + type);
return key;
}
"Warning : Unknown Stockholm annotation type: " + type);
return key;
}