Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / datamodel / ContactMatrix.java

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 1b1889e..48b6e6b 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -150,20 +150,6 @@ public abstract class ContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public boolean hasReferenceSeq()
-  {
-    // TODO Auto-generated method stub
-    return false;
-  }
-
-  @Override
-  public SequenceI getReferenceSeq()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
   public String getAnnotLabel()
   {
     return "Contact Matrix";
@@ -174,67 +160,33 @@ public abstract class ContactMatrix implements ContactMatrixI
   {
     return "Contact Matrix";
   }
-  List<BitSet> groups=null;
-  @Override
-  public void updateGroups(List<BitSet> colGroups)
-  {
-    groups = colGroups;
-    colorMap=new HashMap<>();
-  }
-  @Override
-  public boolean hasGroups()
-  {
-    return groups!=null && groups.size()>0;
-  }
+  GroupSet grps = new GroupSet();
   @Override
-  public List<BitSet> getGroups()
+  public GroupSetI getGroupSet()
   {
-    return groups;
+    return grps;
   }
   @Override
-  public BitSet getGroupsFor(int column)
+  public void setGroupSet(GroupSet makeGroups)
   {
-    for (BitSet gp:groups) {
-      if (gp.get(column))
-      {
-        return gp;
-      }
-    }
-    return ContactMatrixI.super.getGroupsFor(column);
-  }
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
-  public Color getColourForGroup(BitSet bs)
-  {
-    if (bs==null) {
-      return Color.white;
-    }
-    Color groupCol=colorMap.get(bs);
-    if (groupCol==null)
-    {
-      return Color.white;
-    }
-    return groupCol;
-  }
-  @Override 
-  public void setColorForGroup(BitSet bs,Color color)
-  {
-    colorMap.put(bs,color);
+    grps = makeGroups;
   }
   public static String contactToFloatString(ContactMatrixI cm)
   {
     StringBuilder sb = new StringBuilder();
-    for (int c=0;c<cm.getWidth();c++)
+    for (int c = 0; c < cm.getWidth(); c++)
     {
-      ContactListI cl=cm.getContactList(c);
-      if (cl!=null) {
-      for (int h=0;h<=cl.getContactHeight();h++)
+      ContactListI cl = cm.getContactList(c);
+      if (cl != null)
       {
-        if (sb.length()>0) {
-          sb.append('\t');
+        for (int h = 0; h <= cl.getContactHeight(); h++)
+        {
+          if (sb.length() > 0)
+          {
+            sb.append('\t');
+          }
+          sb.append(cl.getContactAt(h));
         }
-        sb.append(cl.getContactAt(h));
-      }
       }
     }
     return sb.toString();
@@ -244,29 +196,27 @@ public abstract class ContactMatrix implements ContactMatrixI
           int rows)
   {
     float[][] vals = new float[cols][rows];
-    StringTokenizer tabsep = new StringTokenizer(values,""+'\t');
-    int c=0,r=0;
-    
+    StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+    int c = 0, r = 0;
     while (tabsep.hasMoreTokens())
     {
       double elem = Double.valueOf(tabsep.nextToken());
-      vals[c][r++]=(float) elem;
-      if (r>=vals[c].length)
+      vals[c][r++] = (float) elem;
+      if (r >= vals[c].length)
       {
-        r=0;
+        r = 0;
         c++;
       }
-      if (c>=vals.length)
+      if (c >= vals.length)
       {
-        
         break;
       }
     }
     if (tabsep.hasMoreElements())
     {
-      Console.warn("Ignoring additional elements for Float string to contact matrix parsing.");
+      Console.warn(
+              "Ignoring additional elements for Float string to contact matrix parsing.");
     }
-      
     return vals;
   }
 }