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;
}
@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";
{
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;
- }
-
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- @Override
- public BitSet getGroupsFor(int column)
- {
- for (BitSet gp : groups)
- {
- if (gp.get(column))
- {
- return gp;
- }
- }
- return ContactMatrixI.super.getGroupsFor(column);
- }
-
- HashMap<BitSet, Color> colorMap = new HashMap<>();
-
+ GroupSet grps = new GroupSet();
@Override
- public Color getColourForGroup(BitSet bs)
+ public GroupSetI getGroupSet()
{
- if (bs == null)
- {
- return Color.white;
- }
- Color groupCol = colorMap.get(bs);
- if (groupCol == null)
- {
- return Color.white;
- }
- return groupCol;
+ return grps;
}
-
@Override
- public void setColorForGroup(BitSet bs, Color color)
+ public void setGroupSet(GroupSet makeGroups)
{
- colorMap.put(bs, color);
+ grps = makeGroups;
}
-
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
float[][] vals = new float[cols][rows];
StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
int c = 0, r = 0;
-
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
}
if (c >= vals.length)
{
-
break;
}
}
Console.warn(
"Ignoring additional elements for Float string to contact matrix parsing.");
}
-
return vals;
}
}