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JAL-1705 Javadoc / debug output tweaks
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 28 Mar 2016 09:12:36 +0000
(10:12 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 28 Mar 2016 09:12:36 +0000
(10:12 +0100)
src/jalview/datamodel/AlignedCodonFrame.java
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src/jalview/datamodel/SequenceFeature.java
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src/jalview/datamodel/xdb/embl/EmblEntry.java
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src/jalview/ws/SequenceFetcher.java
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diff --git
a/src/jalview/datamodel/AlignedCodonFrame.java
b/src/jalview/datamodel/AlignedCodonFrame.java
index
3fc8c28
..
179f5cc
100644
(file)
--- a/
src/jalview/datamodel/AlignedCodonFrame.java
+++ b/
src/jalview/datamodel/AlignedCodonFrame.java
@@
-638,4
+638,13
@@
public class AlignedCodonFrame
{
return mappings.isEmpty();
}
{
return mappings.isEmpty();
}
+
+ /**
+ * Method for debug / inspection purposes only, may change in future
+ */
+ @Override
+ public String toString()
+ {
+ return mappings == null ? "null" : mappings.toString();
+ }
}
}
diff --git
a/src/jalview/datamodel/SequenceFeature.java
b/src/jalview/datamodel/SequenceFeature.java
index
8146400
..
4a7706f
100755
(executable)
--- a/
src/jalview/datamodel/SequenceFeature.java
+++ b/
src/jalview/datamodel/SequenceFeature.java
@@
-423,6
+423,12
@@
public class SequenceFeature
return strand;
}
return strand;
}
+ /**
+ * Set the value of strand
+ *
+ * @param strand
+ * should be "+" for forward, or "-" for reverse
+ */
public void setStrand(String strand)
{
setValue(STRAND, strand);
public void setStrand(String strand)
{
setValue(STRAND, strand);
diff --git
a/src/jalview/datamodel/xdb/embl/EmblEntry.java
b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index
d830130
..
fda042e
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-708,9
+708,9
@@
public class EmblEntry
sxpos = x;
if (cdslength != cdspos)
{
sxpos = x;
if (cdslength != cdspos)
{
- System.err
- .println("Truncating final exon interval on region by "
- + (cdspos - cdslength));
+ // System.err
+ // .println("Truncating final exon interval on region by "
+ // + (cdspos - cdslength));
}
// locate the new end boundary of final exon as endxon
endxon = exon[x + 1] - cdspos + cdslength;
}
// locate the new end boundary of final exon as endxon
endxon = exon[x + 1] - cdspos + cdslength;
diff --git
a/src/jalview/ws/SequenceFetcher.java
b/src/jalview/ws/SequenceFetcher.java
index
902ce27
..
1f8c28a
100644
(file)
--- a/
src/jalview/ws/SequenceFetcher.java
+++ b/
src/jalview/ws/SequenceFetcher.java
@@
-39,9
+39,7
@@
import java.util.ArrayList;
import java.util.List;
/**
import java.util.List;
/**
- * This is the the concrete implementation of the sequence retrieval interface
- * and abstract class in jalview.ws.seqfetcher. This implements the run-time
- * discovery of sequence database clientss.
+ * This implements the run-time discovery of sequence database clients.
*
*/
public class SequenceFetcher extends ASequenceFetcher
*
*/
public class SequenceFetcher extends ASequenceFetcher