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JAL-2110 additional tests for setDatasetSequence, javadoc for isProtein
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
29d114d
..
68c8c50
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-22,6
+22,7
@@
package jalview.datamodel;
import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
+import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
@@
-1013,12
+1014,12
@@
public class Sequence extends ASequence implements SequenceI
{
if (seq == this)
{
{
if (seq == this)
{
- throw new Error(
+ throw new IllegalArgumentException(
"Implementation Error: self reference passed to SequenceI.setDatasetSequence");
}
if (seq != null && seq.getDatasetSequence() != null)
{
"Implementation Error: self reference passed to SequenceI.setDatasetSequence");
}
if (seq != null && seq.getDatasetSequence() != null)
{
- throw new Error(
+ throw new IllegalArgumentException(
"Implementation error: cascading dataset sequences are not allowed.");
}
datasetSequence = seq;
"Implementation error: cascading dataset sequences are not allowed.");
}
datasetSequence = seq;
@@
-1117,6
+1118,10
@@
public class Sequence extends ASequence implements SequenceI
private long _seqhash = 0;
private long _seqhash = 0;
+ /**
+ * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+ * true
+ */
@Override
public boolean isProtein()
{
@Override
public boolean isProtein()
{
@@
-1127,7
+1132,7
@@
public class Sequence extends ASequence implements SequenceI
if (_seqhash != sequence.hashCode())
{
_seqhash = sequence.hashCode();
if (_seqhash != sequence.hashCode())
{
_seqhash = sequence.hashCode();
- _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+ _isNa = Comparison.isNucleotide(this);
}
return !_isNa;
};
}
return !_isNa;
};