X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FBaseList.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2FBaseList.java;h=0000000000000000000000000000000000000000;hb=d27359893c99db0e749a59d8a7ab73ea751da09e;hp=01ac0b1cee9f411ef6b2047fd68d9d6f8d24c772;hpb=9f55415c9f8005e9dcd8243453883ff853fd5b76;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/models/BaseList.java b/src2/fr/orsay/lri/varna/models/BaseList.java
deleted file mode 100644
index 01ac0b1..0000000
--- a/src2/fr/orsay/lri/varna/models/BaseList.java
+++ /dev/null
@@ -1,200 +0,0 @@
-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();
-	}
-
-	
-}