/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
import java.awt.event.*;
-import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
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();
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceFeature[] features = alignment.getSequenceAt(i)
}
}
- 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;
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
if (alignment.getSequenceAt(i).getSequenceFeatures() == null)