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Merge branch 'develop' into imp/JAL-2775
[jalview.git]
/
src
/
jalview
/
analysis
/
Dna.java
diff --git
a/src/jalview/analysis/Dna.java
b/src/jalview/analysis/Dna.java
index
0128624
..
a10b037
100644
(file)
--- a/
src/jalview/analysis/Dna.java
+++ b/
src/jalview/analysis/Dna.java
@@
-45,7
+45,6
@@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
-import java.util.Map;
public class Dna
{
public class Dna
{
@@
-120,8
+119,7
@@
public class Dna
* @param ac2
* @return
*/
* @param ac2
* @return
*/
- public static final int compareCodonPos(AlignedCodon ac1,
- AlignedCodon ac2)
+ public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
{
return comparator.compare(ac1, ac2);
// return jalview_2_8_2compare(ac1, ac2);
{
return comparator.compare(ac1, ac2);
// return jalview_2_8_2compare(ac1, ac2);
@@
-689,7
+687,7
@@
public class Dna
*/
MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
*/
MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
- transferCodedFeatures(selection, newseq, map, null, null);
+ transferCodedFeatures(selection, newseq, map);
/*
* Construct a dataset sequence for our new peptide.
/*
* Construct a dataset sequence for our new peptide.
@@
-758,25
+756,15
@@
public class Dna
/**
* Given a peptide newly translated from a dna sequence, copy over and set any
/**
* Given a peptide newly translated from a dna sequence, copy over and set any
- * features on the peptide from the DNA. If featureTypes is null, all features
- * on the dna sequence are searched (rather than just the displayed ones), and
- * similarly for featureGroups.
+ * features on the peptide from the DNA.
*
* @param dna
* @param pep
* @param map
*
* @param dna
* @param pep
* @param map
- * @param featureTypes
- * hash whose keys are the displayed feature type strings
- * @param featureGroups
- * hash where keys are feature groups and values are Boolean objects
- * indicating if they are displayed.
*/
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
*/
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
- MapList map, Map<String, Object> featureTypes,
- Map<String, Boolean> featureGroups)
+ MapList map)
{
{
- SequenceFeature[] sfs = dna.getSequenceFeatures();
- Boolean fgstate;
DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
DBRefSource.DNACODINGDBS);
if (dnarefs != null)
DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
DBRefSource.DNACODINGDBS);
if (dnarefs != null)
@@
-790,24
+778,15
@@
public class Dna
}
}
}
}
}
}
- if (sfs != null)
+ for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
{
{
- for (SequenceFeature sf : sfs)
- {
- fgstate = (featureGroups == null) ? null
- : featureGroups.get(sf.featureGroup);
- if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
- && (fgstate == null || fgstate.booleanValue()))
+ if (FeatureProperties.isCodingFeature(null, sf.getType()))
{
{
- if (FeatureProperties.isCodingFeature(null, sf.getType()))
+ // if (map.intersectsFrom(sf[f].begin, sf[f].end))
{
{
- // if (map.intersectsFrom(sf[f].begin, sf[f].end))
- {
- }
}
}
}
}
- }
}
}
}
}