/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, 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
package jalview.gui;
import java.util.*;
+import java.util.concurrent.ConcurrentHashMap;
import java.awt.*;
import java.awt.event.*;
int charOffset;
- Hashtable featureColours = new Hashtable();
+ Map featureColours = new ConcurrentHashMap();
// A higher level for grouping features of a
// particular type
- Hashtable featureGroups = new Hashtable();
+ Map featureGroups = new ConcurrentHashMap();
// This is actually an Integer held in the hashtable,
// Retrieved using the key feature type
{
String[] renderOrder;
- Hashtable featureGroups;
+ Map featureGroups;
- Hashtable featureColours;
+ Map featureColours;
float transparency;
- Hashtable featureOrder;
+ Map featureOrder;
public FeatureRendererSettings(String[] renderOrder,
Hashtable featureGroups, Hashtable featureColours,
public FeatureRendererSettings(FeatureRenderer fr)
{
renderOrder = null;
- featureGroups = new Hashtable();
- featureColours = new Hashtable();
- featureOrder = new Hashtable();
+ featureGroups = new ConcurrentHashMap();
+ featureColours = new ConcurrentHashMap();
+ featureOrder = new ConcurrentHashMap();
if (fr.renderOrder != null)
{
this.renderOrder = new String[fr.renderOrder.length];
System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
- renderOrder.length);
+ fr.renderOrder.length);
}
if (fr.featureGroups != null)
{
- this.featureGroups = new Hashtable(fr.featureGroups);
+ this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
}
if (fr.featureColours != null)
{
- this.featureColours = new Hashtable(fr.featureColours);
+ this.featureColours = new ConcurrentHashMap(fr.featureColours);
}
- Enumeration en = fr.featureColours.keys();
- while (en.hasMoreElements())
+ Iterator en = fr.featureColours.keySet().iterator();
+ while (en.hasNext())
{
- Object next = en.nextElement();
+ Object next = en.next();
Object val = featureColours.get(next);
if (val instanceof GraduatedColor)
{
this.transparency = fr.transparency;
if (fr.featureOrder != null)
{
- this.featureOrder = new Hashtable(fr.featureOrder);
+ this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
}
}
}
this.featureColours = frs.featureColours;
this.transparency = frs.transparency;
this.featureOrder = frs.featureOrder;
- if (av != null && av!=fr.av)
+ if (av != null && av != fr.av)
{
// copy over the displayed feature settings
if (fr.av != null)
}
}
}
- }
+ }
}
BufferedImage offscreenImage;
* This is used by the Molecule Viewer and Overview to get the accurate
* colourof the rendered sequence
*/
- public synchronized int findFeatureColour(int initialCol, SequenceI seq, int column)
+ public synchronized int findFeatureColour(int initialCol, SequenceI seq,
+ int column)
{
if (!av.showSequenceFeatures)
{
}
currentColour = null;
- // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized.
+ // TODO: non-threadsafe - each rendering thread needs its own instance of
+ // the feature renderer - or this should be synchronized.
offscreenRender = true;
if (offscreenImage != null)
{
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)
.getDatasetSequence().getSequenceFeatures();
if (features == null)
}
- Hashtable featureOrder = null;
+ Map featureOrder = null;
/**
* analogous to colour - store a normalized ordering for all feature types in