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JAL-2574 preparation for Sequence.findFeatures(col1, col2)
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 31 May 2017 09:59:58 +0000
(10:59 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 31 May 2017 09:59:58 +0000
(10:59 +0100)
src/jalview/analysis/AlignmentSorter.java
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src/jalview/controller/AlignViewController.java
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src/jalview/gui/AlignmentPanel.java
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src/jalview/renderer/seqfeatures/FeatureRenderer.java
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src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
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diff --git
a/src/jalview/analysis/AlignmentSorter.java
b/src/jalview/analysis/AlignmentSorter.java
index
e7733e9
..
bddf6e3
100755
(executable)
--- a/
src/jalview/analysis/AlignmentSorter.java
+++ b/
src/jalview/analysis/AlignmentSorter.java
@@
-760,8
+760,8
@@
public class AlignmentSorter
int endResidue = seqs[i].findPosition(endCol);
String[] types = featureTypes == null ? null : featureTypes
.toArray(new String[featureTypes.size()]);
int endResidue = seqs[i].findPosition(endCol);
String[] types = featureTypes == null ? null : featureTypes
.toArray(new String[featureTypes.size()]);
- List<SequenceFeature> sfs = seqs[i].getFeatures().findFeatures(
- startResidue, endResidue, types);
+ List<SequenceFeature> sfs = seqs[i].findFeatures(startResidue,
+ endResidue, types);
seqScores[i] = 0;
scores[i] = 0.0;
seqScores[i] = 0;
scores[i] = 0.0;
diff --git
a/src/jalview/controller/AlignViewController.java
b/src/jalview/controller/AlignViewController.java
index
d1d61d2
..
33683fd
100644
(file)
--- a/
src/jalview/controller/AlignViewController.java
+++ b/
src/jalview/controller/AlignViewController.java
@@
-242,8
+242,7
@@
public class AlignViewController implements AlignViewControllerI
{
int ist = sq.findPosition(sqcol.getStartRes());
int iend = sq.findPosition(sqcol.getEndRes()); // see JAL-2526
{
int ist = sq.findPosition(sqcol.getStartRes());
int iend = sq.findPosition(sqcol.getEndRes()); // see JAL-2526
- List<SequenceFeature> sfs = sq.getFeatures().findFeatures(ist,
- iend, featureType);
+ List<SequenceFeature> sfs = sq.findFeatures(ist, iend, featureType);
boolean overlap = false;
for (SequenceFeature sf : sfs)
{
boolean overlap = false;
for (SequenceFeature sf : sfs)
{
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
f3e2733
..
f32dd7b
100644
(file)
--- a/
src/jalview/gui/AlignmentPanel.java
+++ b/
src/jalview/gui/AlignmentPanel.java
@@
-1507,8
+1507,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
}
if (!Comparison.isGap(seq.getCharAt(res)))
{
}
if (!Comparison.isGap(seq.getCharAt(res)))
{
- List<SequenceFeature> features = seq.getFeatures()
- .findFeatures(seqPos, seqPos);
+ List<SequenceFeature> features = seq.findFeatures(seqPos,
+ seqPos);
for (SequenceFeature sf : features)
{
if (sf.isContactFeature())
for (SequenceFeature sf : features)
{
if (sf.isContactFeature())
diff --git
a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index
5dce2b8
..
950d0cd
100644
(file)
--- a/
src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/
src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@
-302,23
+302,23
@@
public class FeatureRenderer extends FeatureRendererModel
List<SequenceFeature> overlaps = seq.findFeatures(seqRange.start,
seqRange.end, type);
List<SequenceFeature> overlaps = seq.findFeatures(seqRange.start,
seqRange.end, type);
- for (SequenceFeature sequenceFeature : overlaps)
+ for (SequenceFeature sf : overlaps)
{
/*
* a feature type may be flagged as shown but the group
* an instance of it belongs to may be hidden
*/
{
/*
* a feature type may be flagged as shown but the group
* an instance of it belongs to may be hidden
*/
- if (featureGroupNotShown(sequenceFeature))
+ if (featureGroupNotShown(sf))
{
continue;
}
{
continue;
}
- Color featureColour = getColour(sequenceFeature);
- boolean isContactFeature = sequenceFeature.isContactFeature();
+ Color featureColour = getColour(sf);
+ boolean isContactFeature = sf.isContactFeature();
- // todo overload findIndex using Location data
- int featureStartCol = seq.findIndex(sequenceFeature.begin);
- int featureEndCol = seq.findIndex(sequenceFeature.end);
+ int featureStartCol = seq.findIndex(sf.begin);
+ int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
+ .findIndex(sf.end);
if (isContactFeature)
{
boolean drawn = renderFeature(g, seq,
if (isContactFeature)
{
boolean drawn = renderFeature(g, seq,
@@
-334,7
+334,7
@@
public class FeatureRenderer extends FeatureRendererModel
drawnColour = featureColour;
}
}
drawnColour = featureColour;
}
}
- else if (showFeature(sequenceFeature))
+ else if (showFeature(sf))
{
/*
* showing feature score by height of colour
{
/*
* showing feature score by height of colour
diff --git
a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index
a8e8989
..
eb47a80
100644
(file)
--- a/
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@
-280,8
+280,8
@@
public abstract class FeatureRendererModel implements
* include features at the position provided their feature type is
* displayed, and feature group is null or marked for display
*/
* include features at the position provided their feature type is
* displayed, and feature group is null or marked for display
*/
- List<SequenceFeature> features = sequence.getFeatures().findFeatures(
- res, res, visibleTypes);
+ List<SequenceFeature> features = sequence.findFeatures(res, res,
+ visibleTypes);
for (SequenceFeature sf : features)
{
for (SequenceFeature sf : features)
{