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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
io
/
TCoffeeScoreFile.java
diff --git
a/src/jalview/io/TCoffeeScoreFile.java
b/src/jalview/io/TCoffeeScoreFile.java
index
648954f
..
52751e9
100644
(file)
--- a/
src/jalview/io/TCoffeeScoreFile.java
+++ b/
src/jalview/io/TCoffeeScoreFile.java
@@
-123,9
+123,10
@@
public class TCoffeeScoreFile extends AlignFile
Integer fWidth;
Integer fWidth;
- public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+ public TCoffeeScoreFile(Object inFile, DataSourceType fileSourceType)
throws IOException
{
throws IOException
{
+ // BH 2018 allows File or String
super(inFile, fileSourceType);
}
super(inFile, fileSourceType);
}
@@
-182,8
+183,9
@@
public class TCoffeeScoreFile extends AlignFile
*/
public String getScoresFor(String id)
{
*/
public String getScoresFor(String id)
{
- return scores != null && scores.containsKey(id) ? scores.get(id)
- .toString() : "";
+ return scores != null && scores.containsKey(id)
+ ? scores.get(id).toString()
+ : "";
}
/**
}
/**
@@
-274,9
+276,9
@@
public class TCoffeeScoreFile extends AlignFile
if (scoreStringBuilder == null)
{
error = true;
if (scoreStringBuilder == null)
{
error = true;
- errormessage = String
- .format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
- entry.getKey());
+ errormessage = String.format(
+ "Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
+ entry.getKey());
return;
}
return;
}
@@
-584,9
+586,9
@@
public class TCoffeeScoreFile extends AlignFile
i++;
if (s == null && i != scores.size() && !id.getKey().equals("cons"))
{
i++;
if (s == null && i != scores.size() && !id.getKey().equals("cons"))
{
- System.err.println("No "
- + (matchids ? "match " : " sequences left ")
- + " for TCoffee score set : " + id.getKey());
+ System.err
+ .println("No " + (matchids ? "match " : " sequences left ")
+ + " for TCoffee score set : " + id.getKey());
continue;
}
int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
continue;
}
int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
@@
-599,16
+601,16
@@
public class TCoffeeScoreFile extends AlignFile
annotations[j] = null;
if (val > 0)
{
annotations[j] = null;
if (val > 0)
{
- System.err
- .println("Warning: non-zero value for positional T-COFFEE score for gap at "
+ jalview.bin.Console.errPrintln(
+ "Warning: non-zero value for positional T-COFFEE score for gap at "
+ j + " in sequence " + s.getName());
}
}
else
{
annotations[j] = new Annotation(s == null ? "" + val : null,
+ j + " in sequence " + s.getName());
}
}
else
{
annotations[j] = new Annotation(s == null ? "" + val : null,
- s == null ? "" + val : null, '\0', val * 1f, val >= 0
- && val < colors.length ? colors[val]
+ s == null ? "" + val : null, '\0', val * 1f,
+ val >= 0 && val < colors.length ? colors[val]
: Color.white);
}
}
: Color.white);
}
}