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JAL-4366 avoid corrupting map when no complete mapping available for chain to sequence
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
GffHelperBase.java
diff --git
a/src/jalview/io/gff/GffHelperBase.java
b/src/jalview/io/gff/GffHelperBase.java
index
3db1755
..
0097343
100644
(file)
--- a/
src/jalview/io/gff/GffHelperBase.java
+++ b/
src/jalview/io/gff/GffHelperBase.java
@@
-114,8
+114,9
@@
public abstract class GffHelperBase implements GffHelperI
*/
if (!trimMapping(from, to, fromRatio, toRatio))
{
*/
if (!trimMapping(from, to, fromRatio, toRatio))
{
- System.err.println("Ignoring mapping from " + Arrays.toString(from)
- + " to " + Arrays.toString(to) + " as counts don't match!");
+ jalview.bin.Console.errPrintln(
+ "Ignoring mapping from " + Arrays.toString(from) + " to "
+ + Arrays.toString(to) + " as counts don't match!");
return null;
}
return null;
}
@@
-166,7
+167,7
@@
public abstract class GffHelperBase implements GffHelperI
{
from[1] += fromOverlap / toRatio;
}
{
from[1] += fromOverlap / toRatio;
}
- System.err.println(Arrays.toString(from));
+ jalview.bin.Console.errPrintln(Arrays.toString(from));
return true;
}
else if (fromOverlap < 0 && fromOverlap % fromRatio == 0)
return true;
}
else if (fromOverlap < 0 && fromOverlap % fromRatio == 0)
@@
-185,7
+186,7
@@
public abstract class GffHelperBase implements GffHelperI
{
to[1] += fromOverlap / fromRatio;
}
{
to[1] += fromOverlap / fromRatio;
}
- System.err.println(Arrays.toString(to));
+ jalview.bin.Console.errPrintln(Arrays.toString(to));
return true;
}
return true;
}
@@
-381,7
+382,8
@@
public abstract class GffHelperBase implements GffHelperI
* @return
*/
protected SequenceFeature buildSequenceFeature(String[] gff,
* @return
*/
protected SequenceFeature buildSequenceFeature(String[] gff,
- int typeColumn, String group, Map<String, List<String>> attributes)
+ int typeColumn, String group,
+ Map<String, List<String>> attributes)
{
try
{
{
try
{
@@
-443,7
+445,8
@@
public abstract class GffHelperBase implements GffHelperI
return sf;
} catch (NumberFormatException nfe)
{
return sf;
} catch (NumberFormatException nfe)
{
- System.err.println("Invalid number in gff: " + nfe.getMessage());
+ jalview.bin.Console
+ .errPrintln("Invalid number in gff: " + nfe.getMessage());
return null;
}
}
return null;
}
}
@@
-503,7
+506,7
@@
public abstract class GffHelperBase implements GffHelperI
if (!valid)
{
if (!valid)
{
- System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+ jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
return map;
}
return map;
}
@@
-525,7
+528,7
@@
public abstract class GffHelperBase implements GffHelperI
theKey = theKey.trim();
if (theKey.isEmpty())
{
theKey = theKey.trim();
if (theKey.isEmpty())
{
- System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+ jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
map.clear();
return map;
}
map.clear();
return map;
}