/*
* 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.
*
featureGroups = fr.featureGroups;
featureColours = fr.featureColours;
transparency = fr.transparency;
- if (av!=null && fr.av!=null && fr.av!=av)
+ if (av != null && fr.av != null && fr.av != av)
{
- if (fr.av.featuresDisplayed!=null)
+ if (fr.av.featuresDisplayed != null)
{
- if (av.featuresDisplayed==null)
+ if (av.featuresDisplayed == null)
{
av.featuresDisplayed = new Hashtable();
- } else {
+ }
+ else
+ {
av.featuresDisplayed.clear();
}
- Enumeration en=fr.av.featuresDisplayed.keys();
+ Enumeration en = fr.av.featuresDisplayed.keys();
while (en.hasMoreElements())
{
av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
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)
}
}
- ArrayList<String> hiddenGroups=new ArrayList<String>();
+ ArrayList<String> hiddenGroups = new ArrayList<String>();
+
/**
* analyse alignment for groups and hash tables (used to be embedded in
* FeatureSettings.setTableData)
{
featureGroups = new Hashtable();
}
- hiddenGroups =new ArrayList<String>();
+ hiddenGroups = new ArrayList<String>();
hiddenGroups.addAll(featureGroups.keySet());
ArrayList allFeatures = new ArrayList();
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;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
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;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{