returning src2 -> srcjar

[jalview.git] / src2 / fr / orsay / lri / varna / models / BaseList.java

diff --git a/src2/fr/orsay/lri/varna/models/BaseList.java b/src2/fr/orsay/lri/varna/models/BaseList.java
deleted file mode 100644 (file)
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();
-       }
-
-       
-}