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package jalview.datamodel; |
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import java.awt.Color; |
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import java.util.Arrays; |
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import java.util.BitSet; |
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import java.util.List; |
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import jalview.util.ColorUtils; |
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import jalview.ws.datamodel.MappableContactMatrixI; |
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| 30.1% |
Uncovered Elements: 72 (103) |
Complexity: 35 |
Complexity Density: 0.7 |
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public interface ContactMatrixI |
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{ |
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ContactListI getContactList(int column); |
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float getMin(); |
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float getMax(); |
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String getAnnotDescr(); |
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String getAnnotLabel(); |
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@return |
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String getType(); |
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int getWidth(); |
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int getHeight(); |
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public GroupSetI getGroupSet(); |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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7857 |
default public boolean hasGroupSet()... |
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{ |
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7857 |
return getGroupSet() != null; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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5 |
default boolean hasGroups()... |
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{ |
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return hasGroupSet() && getGroupSet().hasGroups(); |
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} |
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| 42.9% |
Uncovered Elements: 4 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
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3913 |
default BitSet getGroupsFor(int column)... |
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{ |
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if (!hasGroupSet()) |
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{ |
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BitSet colbitset = new BitSet(); |
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colbitset.set(column); |
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return colbitset; |
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} |
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return getGroupSet().getGroupsFor(column); |
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} |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
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default List<BitSet> getGroups()... |
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{ |
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if (!hasGroupSet()) |
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{ |
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return Arrays.asList(); |
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} |
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return getGroupSet().getGroups(); |
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} |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
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5 |
default boolean hasTree()... |
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{ |
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return hasGroupSet() ? getGroupSet().hasTree() : false; |
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} |
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@return |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
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default String getNewick()... |
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{ |
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return hasGroupSet() ? getGroupSet().getNewick() : null; |
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} |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
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3 |
default String getTreeMethod()... |
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{ |
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return hasGroupSet() ? getGroupSet().getTreeMethod() : null; |
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} |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
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3 |
default boolean hasCutHeight()... |
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{ |
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return hasGroupSet() ? getGroupSet().hasCutHeight() : false; |
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} |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
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default double getCutHeight()... |
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{ |
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return hasGroupSet() ? getGroupSet().getCutHeight() : 0; |
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} |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
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default void updateGroups(List<BitSet> colGroups)... |
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{ |
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if (hasGroupSet()) |
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{ |
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getGroupSet().updateGroups(colGroups); |
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} |
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} |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
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default void setColorForGroup(BitSet bs, Color color)... |
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{ |
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if (hasGroupSet()) |
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getGroupSet().setColorForGroup(bs, color); |
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} |
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} |
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| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
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3913 |
default Color getColourForGroup(BitSet bs)... |
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3913 |
if (hasGroupSet()) |
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3913 |
return getGroupSet().getColourForGroup(bs); |
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} |
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else |
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return Color.white; |
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} |
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} |
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void setGroupSet(GroupSet makeGroups); |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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default void randomlyReColourGroups()... |
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if (hasGroupSet()) |
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GroupSetI groups = getGroupSet(); |
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for (BitSet group : groups.getGroups()) |
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groups.setColorForGroup(group, ColorUtils.getARandomColor()); |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 30 (30) |
Complexity: 8 |
Complexity Density: 0.44 |
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default void transferGroupColorsTo(AlignmentAnnotation aa)... |
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{ |
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if (hasGroupSet()) |
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{ |
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GroupSetI groups = getGroupSet(); |
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int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1 |
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: 0; |
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Annotation ae; |
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Color gpcol = null; |
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int[] seqpos = null; |
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for (BitSet gp : groups.getGroups()) |
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{ |
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gpcol = groups.getColourForGroup(gp); |
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for (int p = gp.nextSetBit(0); p >= 0 |
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&& p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1)) |
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{ |
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if (this instanceof MappableContactMatrixI) |
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{ |
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MappableContactMatrixI mcm = (MappableContactMatrixI) this; |
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seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p); |
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if (seqpos == null) |
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{ |
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continue; |
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} |
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ae = aa.getAnnotationForPosition(seqpos[0]); |
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} |
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else |
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{ |
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ae = aa.getAnnotationForPosition(p + sstart); |
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} |
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if (ae != null) |
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{ |
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ae.colour = gpcol.brighter().darker(); |
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} |
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} |
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} |
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} |
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} |
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@return |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
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0 |
default Color getGroupColorForPosition(int column)... |
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{ |
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if (hasGroupSet()) |
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{ |
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GroupSetI groups = getGroupSet(); |
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for (BitSet gp : groups.getGroups()) |
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if (gp.get(column)) |
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return groups.getColourForGroup(gp); |
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} |
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} |
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} |
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return Color.white; |
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} |
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@param |
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@param |
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@return |
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double getElementAt(int column, int row); |
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} |