JAL-3541 selectively merged build.gradle and gradle.properties

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

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