package jalview.datamodel;
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+
+import jalview.util.ColorUtils;
+import jalview.ws.datamodel.MappableContactMatrixI;
+
public interface ContactMatrixI
{
float getMax();
- boolean hasReferenceSeq();
-
- SequenceI getReferenceSeq();
-
String getAnnotDescr();
String getAnnotLabel();
/**
- * string indicating how the contactMatrix should be rendered - stored in calcId
- * @return
+ * string indicating how the contactMatrix should be rendered - stored in
+ * calcId
+ *
+ * @return
*/
String getType();
int getWidth();
int getHeight();
+ public GroupSetI getGroupSet();
+
+ /// proxy methods to simplify use of the interface
+ /// Mappable contact matrices can override these to perform mapping
+
+ default public boolean hasGroupSet()
+ {
+ return getGroupSet() != null;
+ }
+ default boolean hasGroups()
+ {
+ return hasGroupSet() && getGroupSet().hasGroups();
+ }
+
+ default BitSet getGroupsFor(int column)
+ {
+ if (!hasGroupSet())
+ {
+ BitSet colbitset = new BitSet();
+ colbitset.set(column);
+ return colbitset;
+ }
+ return getGroupSet().getGroupsFor(column);
+ }
+
+ default List<BitSet> getGroups()
+ {
+ if (!hasGroupSet())
+ {
+ return Arrays.asList();
+ }
+ return getGroupSet().getGroups();
+ }
+
+ default boolean hasTree()
+ {
+ return hasGroupSet() ? getGroupSet().hasTree() : false;
+ }
+
+ /**
+ * Newick representation of clustered matrix
+ *
+ * @return null unless hasTree is true
+ */
+ default String getNewick()
+ {
+ return hasGroupSet() ? getGroupSet().getNewick() : null;
+ }
+
+ default String getTreeMethod()
+ {
+ return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
+ }
+
+ default boolean hasCutHeight()
+ {
+ return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
+ }
+
+ default double getCutHeight()
+ {
+ return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
+ }
+
+ default void updateGroups(List<BitSet> colGroups)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().updateGroups(colGroups);
+ }
+ }
+
+ default void setColorForGroup(BitSet bs, Color color)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().setColorForGroup(bs, color);
+ }
+ }
+
+ default Color getColourForGroup(BitSet bs)
+ {
+ if (hasGroupSet())
+ {
+ return getGroupSet().getColourForGroup(bs);
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+
+ void setGroupSet(GroupSet makeGroups);
+
+ default void randomlyReColourGroups() {
+ if (hasGroupSet())
+ {
+ GroupSetI groups = getGroupSet();
+ for (BitSet group:groups.getGroups())
+ {
+ groups.setColorForGroup(group, ColorUtils.getARandomColor());
+ }
+ }
+ }
+
+ default void transferGroupColorsTo(AlignmentAnnotation aa)
+ {
+ if (hasGroupSet())
+ {
+ GroupSetI groups = getGroupSet();
+ // stash colors in linked annotation row.
+ // doesn't work yet. TESTS!
+ int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+ : 0;
+ Annotation ae;
+ Color gpcol = null;
+ int[] seqpos = null;
+ for (BitSet gp : groups.getGroups())
+ {
+ gpcol = groups.getColourForGroup(gp);
+ for (int p = gp.nextSetBit(0); p >= 0
+ && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+ {
+ if (this instanceof MappableContactMatrixI)
+ {
+ MappableContactMatrixI mcm = (MappableContactMatrixI) this;
+ seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+ if (seqpos == null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ ae = aa.getAnnotationForPosition(seqpos[0]);
+ }
+ else
+ {
+ ae = aa.getAnnotationForPosition(p + sstart);
+ }
+ if (ae != null)
+ {
+ ae.colour = gpcol.brighter().darker();
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * look up the colour for a column in the associated contact matrix
+ * @return Color.white or assigned colour
+ */
+ default Color getGroupColorForPosition(int column)
+ {
+ if (hasGroupSet())
+ {
+ GroupSetI groups = getGroupSet();
+ for (BitSet gp:groups.getGroups())
+ {
+ if (gp.get(column))
+ {
+ return groups.getColourForGroup(gp);
+ }
+ }
+ }
+ return Color.white;
+ }
+
}