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Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
[jalview.git]
/
src
/
jalview
/
datamodel
/
ContactMatrix.java
diff --git
a/src/jalview/datamodel/ContactMatrix.java
b/src/jalview/datamodel/ContactMatrix.java
index
25aefd3
..
48b6e6b
100644
(file)
--- a/
src/jalview/datamodel/ContactMatrix.java
+++ b/
src/jalview/datamodel/ContactMatrix.java
@@
-1,7
+1,12
@@
package jalview.datamodel;
package jalview.datamodel;
+import java.awt.Color;
+import java.math.BigInteger;
import java.util.ArrayList;
import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
import java.util.List;
import java.util.List;
+import java.util.Spliterator;
import java.util.StringTokenizer;
import jalview.bin.Console;
import java.util.StringTokenizer;
import jalview.bin.Console;
@@
-145,31
+150,27
@@
public abstract class ContactMatrix implements ContactMatrixI
}
@Override
}
@Override
- public boolean hasReferenceSeq()
+ public String getAnnotLabel()
{
{
- // TODO Auto-generated method stub
- return false;
+ return "Contact Matrix";
}
@Override
}
@Override
- public SequenceI getReferenceSeq()
+ public String getAnnotDescr()
{
{
- // TODO Auto-generated method stub
- return null;
+ return "Contact Matrix";
}
}
-
+ GroupSet grps = new GroupSet();
@Override
@Override
- public String getAnnotLabel()
+ public GroupSetI getGroupSet()
{
{
- return "Contact Matrix";
+ return grps;
}
}
-
@Override
@Override
- public String getAnnotDescr()
+ public void setGroupSet(GroupSet makeGroups)
{
{
- return "Contact Matrix";
+ grps = makeGroups;
}
}
-
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
@@
-197,7
+198,6
@@
public abstract class ContactMatrix implements ContactMatrixI
float[][] vals = new float[cols][rows];
StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
int c = 0, r = 0;
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());
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
@@
-209,7
+209,6
@@
public abstract class ContactMatrix implements ContactMatrixI
}
if (c >= vals.length)
{
}
if (c >= vals.length)
{
-
break;
}
}
break;
}
}
@@
-218,7
+217,6
@@
public abstract class ContactMatrix implements ContactMatrixI
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;
}
}
return vals;
}
}