git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-845 applet colour by tree; translate as cDNA; pull up history list
[jalview.git]
/
src
/
jalview
/
util
/
MappingUtils.java
diff --git
a/src/jalview/util/MappingUtils.java
b/src/jalview/util/MappingUtils.java
index
6dfebfe
..
1f2e8db
100644
(file)
--- a/
src/jalview/util/MappingUtils.java
+++ b/
src/jalview/util/MappingUtils.java
@@
-16,7
+16,6
@@
import jalview.datamodel.SearchResults.Match;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.ArrayList;
import java.util.HashMap;
@@
-384,8
+383,8
@@
public final class MappingUtils
}
/*
}
/*
- * Have to align the sequences before constructing the OrderCommand - which
- * then realigns them?!?
+ * Have to sort the sequences before constructing the OrderCommand - which
+ * then resorts them?!?
*/
final SequenceI[] mappedOrderArray = mappedOrder
.toArray(new SequenceI[mappedOrder.size()]);
*/
final SequenceI[] mappedOrderArray = mappedOrder
.toArray(new SequenceI[mappedOrder.size()]);
@@
-407,7
+406,7
@@
public final class MappingUtils
* @return
*/
public static ColumnSelection mapColumnSelection(ColumnSelection colsel,
* @return
*/
public static ColumnSelection mapColumnSelection(ColumnSelection colsel,
- AlignViewportI mapFrom, AlignViewport mapTo)
+ AlignViewportI mapFrom, AlignViewportI mapTo)
{
boolean targetIsNucleotide = mapTo.isNucleotide();
AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
{
boolean targetIsNucleotide = mapTo.isNucleotide();
AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
@@
-416,6
+415,12
@@
public final class MappingUtils
ColumnSelection mappedColumns = new ColumnSelection();
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
ColumnSelection mappedColumns = new ColumnSelection();
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
+ // FIXME allow for hidden columns
+
+ /*
+ * For each mapped column, find the range of columns that residues in that
+ * column map to.
+ */
for (Object obj : colsel.getSelected())
{
int col = ((Integer) obj).intValue();
for (Object obj : colsel.getSelected())
{
int col = ((Integer) obj).intValue();
@@
-462,13
+467,15
@@
public final class MappingUtils
// System.out.println(fromSeq.getName() + " mapped to cols "
// + mappedStartCol + ":" + mappedEndCol);
break;
// System.out.println(fromSeq.getName() + " mapped to cols "
// + mappedStartCol + ":" + mappedEndCol);
break;
- // TODO remove break if we ever want to map one to many sequences
+ // note: remove break if we ever want to map one to many sequences
}
}
}
}
/*
}
}
}
}
/*
- * Add mapped columns to mapped selection (converting base 1 to base 0)
+ * Add the range of mapped columns to the mapped selection (converting
+ * base 1 to base 0). Note that this may include intron-only regions which
+ * lie between the start and end ranges of the selection.
*/
for (int i = mappedToMin; i <= mappedToMax; i++)
{
*/
for (int i = mappedToMin; i <= mappedToMax; i++)
{