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-958 flag indicating if visualization settings for new group annotation should...
[jalview.git]
/
src
/
jalview
/
appletgui
/
FeatureRenderer.java
diff --git
a/src/jalview/appletgui/FeatureRenderer.java
b/src/jalview/appletgui/FeatureRenderer.java
index
03f15d3
..
259030f
100755
(executable)
--- a/
src/jalview/appletgui/FeatureRenderer.java
+++ b/
src/jalview/appletgui/FeatureRenderer.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-786,10
+786,10
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
minmax = new Hashtable();
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
minmax = new Hashtable();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment=av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
{
- SequenceFeature[] features = av.alignment.getSequenceAt(i)
+ SequenceFeature[] features = alignment.getSequenceAt(i)
.getSequenceFeatures();
if (features == null)
.getSequenceFeatures();
if (features == null)
@@
-1110,16
+1110,17
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment=av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
int index = 0;
while (index < tmpfeatures.length)
{
@@
-1175,16
+1176,17
@@
public class FeatureRenderer implements jalview.api.FeatureRenderer
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment=av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
int index = 0;
while (index < tmpfeatures.length)
{