X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FBaseList.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FBaseList.java;h=01ac0b1cee9f411ef6b2047fd68d9d6f8d24c772;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=0000000000000000000000000000000000000000;hpb=056dad85a910551cc95e44d451a61f6b8c4dd35d;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/models/BaseList.java b/srcjar/fr/orsay/lri/varna/models/BaseList.java
new file mode 100644
index 0000000..01ac0b1
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/models/BaseList.java
@@ -0,0 +1,200 @@
+package fr.orsay.lri.varna.models;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+
+public class BaseList {
+	private HashSet<ModeleBase> _bases = new HashSet<ModeleBase>(); 
+	private String _caption;
+
+	public BaseList( BaseList b)
+	{
+		_caption = b._caption;
+		_bases = new HashSet<ModeleBase>(b._bases);
+	}
+
+	
+	public BaseList( String caption)
+	{
+		_caption = caption;
+	}
+	
+	
+	public BaseList( String caption, ModeleBase mb)
+	{
+		this(caption);
+		addBase(mb);
+	}
+
+	public boolean contains(ModeleBase mb)
+	{
+		return _bases.contains(mb);
+	}
+
+	
+	public String getCaption()
+	{
+		return _caption;
+	}
+	
+	public void addBase(ModeleBase b)
+	{
+		_bases.add(b);
+	}
+
+	public void removeBase(ModeleBase b)
+	{
+		_bases.remove(b);
+	}
+
+	
+	public void addBases(Collection<? extends ModeleBase> mbs)
+	{
+		_bases.addAll(mbs);
+	}
+
+	public ArrayList<ModeleBase> getBases()
+	{
+		return new ArrayList<ModeleBase>(_bases);
+	}
+
+	public void clear()
+	{
+		_bases.clear();
+	}
+
+	public static Color getAverageColor(ArrayList<Color> cols)
+	{
+		int r=0,g=0,b=0;
+		for (Color c : cols)
+		{
+			r += c.getRed();
+			g += c.getGreen();
+			b += c.getBlue();
+		}
+		if (cols.size()>0)
+		{ 
+			r /= cols.size();
+			g /= cols.size();
+			b /= cols.size();
+		}
+		return new Color(r,g,b);
+	}
+	
+	public Color getAverageOutlineColor()
+	{
+		ArrayList<Color> cols = new ArrayList<Color>(); 
+		for (ModeleBase mb : _bases)
+		{  cols.add(mb.getStyleBase().getBaseOutlineColor()); }
+		return getAverageColor(cols);
+	}
+
+	public Color getAverageNameColor()
+	{
+		ArrayList<Color> cols = new ArrayList<Color>(); 
+		for (ModeleBase mb : _bases)
+		{  cols.add(mb.getStyleBase().getBaseNameColor()); }
+		return getAverageColor(cols);
+	}
+
+	public Color getAverageNumberColor()
+	{
+		ArrayList<Color> cols = new ArrayList<Color>(); 
+		for (ModeleBase mb : _bases)
+		{  cols.add(mb.getStyleBase().getBaseNumberColor()); }
+		return getAverageColor(cols);
+	}
+
+	public Color getAverageInnerColor()
+	{
+		ArrayList<Color> cols = new ArrayList<Color>(); 
+		for (ModeleBase mb : _bases)
+		{  cols.add(mb.getStyleBase().getBaseInnerColor()); }
+		return getAverageColor(cols);
+	}
+
+	public String getNumbers()
+	{
+		String result = ""; 
+		boolean first = true;
+		for (ModeleBase mb:_bases)
+		{  
+			if (!first)
+			{ result += ","; }
+			else
+			{ first = false; }
+			result += "" + mb.getBaseNumber(); 
+		}
+		result += "";
+		return result;
+	}
+
+	public String getContents()
+	{
+		String result = ""; 
+		boolean first = true;
+		for (ModeleBase mb:_bases)
+		{  
+			if (!first)
+			{ result += ","; }
+			else
+			{ first = false; }
+			result += "" + mb.getContent(); 
+		}
+		result += "";
+		return result;
+	}
+
+	public ArrayList<Integer> getIndices()
+	{
+		ArrayList<Integer> indices = new ArrayList<Integer>();
+		for (ModeleBase mb : _bases)
+		{
+			indices.add(mb.getIndex());
+		}
+		return indices;
+	}
+	
+	/**
+	 * Returns, in a new BaseList, the intersection of the current BaseList and of the argument.
+	 * @param mb The base list to be used for the intersection
+	 * @return The intersection of the current base list and the argument.
+	 */
+	
+	public BaseList retainAll(BaseList mb)
+	{
+		HashSet<ModeleBase> cp = new HashSet<ModeleBase>();
+		cp.addAll(_bases);
+		cp.retainAll(mb._bases);
+		BaseList result = new BaseList("TmpIntersection");
+		result.addBases(cp);
+		return result;
+	}
+
+	/**
+	 * Returns, in a new BaseList, the list consisting of the current BaseList minus the list passed as argument.
+	 * @param mb The base list to be subtracted from the current one
+	 * @return The current base list minus the list passed as argument.
+	 */
+	
+	public BaseList removeAll(BaseList mb)
+	{
+		HashSet<ModeleBase> cp = new HashSet<ModeleBase>();
+		cp.addAll(_bases);
+		cp.removeAll(mb._bases);
+		BaseList result = new BaseList("TmpMinus");
+		result.addBases(cp);
+		return result;
+	}	
+	
+	public int size()
+	{
+		return _bases.size();
+	}
+
+	
+}