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fixed after refactoring of SequenceFeature[] seq.getSequenceFeatures
author
jprocter
<Jim Procter>
Wed, 1 Mar 2006 16:23:15 +0000
(16:23 +0000)
committer
jprocter
<Jim Procter>
Wed, 1 Mar 2006 16:23:15 +0000
(16:23 +0000)
src/jalview/analysis/SeqsetUtils.java
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diff --git
a/src/jalview/analysis/SeqsetUtils.java
b/src/jalview/analysis/SeqsetUtils.java
index
61f10b5
..
691b905
100755
(executable)
--- a/
src/jalview/analysis/SeqsetUtils.java
+++ b/
src/jalview/analysis/SeqsetUtils.java
@@
-49,7
+49,13
@@
public class SeqsetUtils
sqinfo.put("Name", seq.getName());
\r
sqinfo.put("Start", new Integer(seq.getStart()));
\r
sqinfo.put("End", new Integer(seq.getEnd()));
\r
sqinfo.put("Name", seq.getName());
\r
sqinfo.put("Start", new Integer(seq.getStart()));
\r
sqinfo.put("End", new Integer(seq.getEnd()));
\r
- sqinfo.put("SeqFeatures", (seq.getSequenceFeatures() !=null) ? seq.getSequenceFeatures() : null);
\r
+ Vector sfeat = new Vector();
\r
+ jalview.datamodel.SequenceFeature[] sfarray=seq.getSequenceFeatures();
\r
+ if (sfarray!=null && sfarray.length>0) {
\r
+ for (int i=0;i<sfarray.length;i++)
\r
+ sfeat.add(sfarray[i]);
\r
+ }
\r
+ sqinfo.put("SeqFeatures", sfeat);
\r
sqinfo.put("PdbId",
\r
(seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
\r
sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));
\r
sqinfo.put("PdbId",
\r
(seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
\r
sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));
\r
@@
-61,7
+67,7
@@
public class SeqsetUtils
* TODO: replace these methods with something more elegant.
\r
* @param sq SequenceI
\r
* @param sqinfo Hashtable
\r
* TODO: replace these methods with something more elegant.
\r
* @param sq SequenceI
\r
* @param sqinfo Hashtable
\r
- * @return boolean
\r
+ * @return boolean true if name was not updated from sqinfo Name entry
\r
*/
\r
public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
\r
{
\r
*/
\r
public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
\r
{
\r
@@
-71,7
+77,7
@@
public class SeqsetUtils
String oldname = (String) sqinfo.get("Name");
\r
Integer start = (Integer) sqinfo.get("Start");
\r
Integer end = (Integer) sqinfo.get("End");
\r
String oldname = (String) sqinfo.get("Name");
\r
Integer start = (Integer) sqinfo.get("Start");
\r
Integer end = (Integer) sqinfo.get("End");
\r
- SequenceFeature [] sfeatures = (SequenceFeature[]) sqinfo.get(
\r
+ Vector sfeatures = (Vector) sqinfo.get(
\r
"SeqFeatures");
\r
Vector pdbid = (Vector) sqinfo.get("PdbId");
\r
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
\r
"SeqFeatures");
\r
Vector pdbid = (Vector) sqinfo.get("PdbId");
\r
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
\r
@@
-94,10
+100,12
@@
public class SeqsetUtils
sq.setEnd(end.intValue());
\r
}
\r
\r
sq.setEnd(end.intValue());
\r
}
\r
\r
- if ((sfeatures != null) && (sfeatures.length>0))
\r
+ if ((sfeatures != null) && (sfeatures.size()>0))
\r
{
\r
{
\r
- sq.setSequenceFeatures(sfeatures);
\r
+ SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
\r
+ sq.setSequenceFeatures(sfarray);
\r
}
\r
}
\r
+
\r
if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {
\r
sq.setDatasetSequence(seqds);
\r
}
\r
if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {
\r
sq.setDatasetSequence(seqds);
\r
}
\r