Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

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

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 1b1889e..8434b4a 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,12 +1,10 @@
 package jalview.datamodel;
 
 import java.awt.Color;
-import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Spliterator;
 import java.util.StringTokenizer;
 
 import jalview.bin.Console;
@@ -174,27 +172,33 @@ public abstract class ContactMatrix implements ContactMatrixI
   {
     return "Contact Matrix";
   }
-  List<BitSet> groups=null;
+
+  List<BitSet> groups = null;
+
   @Override
   public void updateGroups(List<BitSet> colGroups)
   {
     groups = colGroups;
-    colorMap=new HashMap<>();
+    colorMap = new HashMap<>();
   }
+
   @Override
   public boolean hasGroups()
   {
-    return groups!=null && groups.size()>0;
+    return groups != null && groups.size() > 0;
   }
+
   @Override
   public List<BitSet> getGroups()
   {
     return groups;
   }
+
   @Override
   public BitSet getGroupsFor(int column)
   {
-    for (BitSet gp:groups) {
+    for (BitSet gp : groups)
+    {
       if (gp.get(column))
       {
         return gp;
@@ -202,39 +206,46 @@ public abstract class ContactMatrix implements ContactMatrixI
     }
     return ContactMatrixI.super.getGroupsFor(column);
   }
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
+
+  HashMap<BitSet, Color> colorMap = new HashMap<>();
+
+  @Override
   public Color getColourForGroup(BitSet bs)
   {
-    if (bs==null) {
+    if (bs == null)
+    {
       return Color.white;
     }
-    Color groupCol=colorMap.get(bs);
-    if (groupCol==null)
+    Color groupCol = colorMap.get(bs);
+    if (groupCol == null)
     {
       return Color.white;
     }
     return groupCol;
   }
-  @Override 
-  public void setColorForGroup(BitSet bs,Color color)
+
+  @Override
+  public void setColorForGroup(BitSet bs, Color color)
   {
-    colorMap.put(bs,color);
+    colorMap.put(bs, color);
   }
+
   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 +255,30 @@ 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;
   }
 }