apollo.gui.genomemap
Class DrawableTierManager

java.lang.Object
  apollo.gui.TierManager
      apollo.gui.genomemap.DrawableTierManager

All Implemented Interfaces:

ControlledObjectI, DrawableTierManagerI, TierManagerI, java.io.Serializable

Direct Known Subclasses:

FeatureTierManager

public class DrawableTierManager
extends TierManager
implements DrawableTierManagerI

See Also:

Serialized Form

Field Summary

protected java.util.Vector	drawables
protected static org.apache.log4j.Logger	logger
protected java.util.Hashtable	tierhash
protected Transformer	transformer

Fields inherited from class apollo.gui.TierManager

aggregateSizeChange, charHeight, controller, offsetPixelHeight, tierManagerListeners, tiers, view, viewHeight, visibleLimits

Fields inherited from interface apollo.gui.TierManagerI

Y_PIXELS_PER_FEATURE

Constructor Summary

DrawableTierManager()

Method Summary

void	clearFeatures() Clears features from tiers, and clear tiers
void	fillTiers()
java.util.Vector	getVisibleDrawables(int[] limits) int[] limits is an array of 2 ints corresponding to low and high limits Returns a Vector of Vectors, each Vector within the outer Vector contains DrawableSeqFeatures that are the visible Features for a given tier Each DrawableSeqFeature is assigned a tier index corresponding to vertical placement.
protected void	populateTier(Drawable dsf) Add a Feature to a tier with which it has no overlaps.
protected void	setDrawables(java.util.Vector drawables)
void	setTierData(java.lang.Object data)
void	setTransformer(Transformer transformer) This is needed so that the features (in DNA coord space) can be transformed into pixel space by the tiers to determing how much horizontal real estate they need

Methods inherited from class apollo.gui.TierManager

addTierManagerListener, decrementTierHeight, doLayoutTiers, fireTierManagerEvent, fireTierManagerEvent, getAggregateSizeChange, getController, getControllerWindow, getLowestVisible, getMaximumVisibleTransformCoord, getMaxTierUserHeight, getMaxUserCoord, getMaxVisibleTierNumber, getMinimumVisibleTransformCoord, getNumTiers, getNumVisible, getTier, getTierLabel, getTiers, getTotalHeight, getView, getViewHeight, getVisibleUserCoord, getYRange, ignoreScoreThresholds, incrementTierHeight, needsAutoRemoval, setAggregateSizeChange, setCharHeight, setController, setIgnoreScoreThresholds, setLowestVisible, setOffsetHeight, setView, setViewHeight, toTier, toUser, updateUserCoordBoundaries

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface apollo.gui.TierManagerI

decrementTierHeight, doLayoutTiers, fireTierManagerEvent, getAggregateSizeChange, getLowestVisible, getMaxTierUserHeight, getMaxUserCoord, getMaxVisibleTierNumber, getMinimumVisibleTransformCoord, getNumTiers, getNumVisible, getTier, getTiers, getTotalHeight, getView, getVisibleUserCoord, getYRange, incrementTierHeight, setAggregateSizeChange, setCharHeight, setIgnoreScoreThresholds, setLowestVisible, setView, setViewHeight, toTier, toUser

Methods inherited from interface apollo.gui.ControlledObjectI

getController, getControllerWindow, needsAutoRemoval, setController

Field Detail

logger

protected static final org.apache.log4j.Logger logger

drawables

protected java.util.Vector drawables

tierhash

protected java.util.Hashtable tierhash

transformer

protected Transformer transformer

Constructor Detail

DrawableTierManager

public DrawableTierManager()

Method Detail

setTransformer

public void setTransformer(Transformer transformer)

This is needed so that the features (in DNA coord space) can be transformed into pixel space by the tiers to determing how much horizontal real estate they need

setTierData

public void setTierData(java.lang.Object data)

Specified by:

setTierData in interface TierManagerI

Specified by:

setTierData in class TierManager

fillTiers

public void fillTiers()

Specified by:

fillTiers in class TierManager

setDrawables

protected void setDrawables(java.util.Vector drawables)

populateTier

protected void populateTier(Drawable dsf)

Add a Feature to a tier with which it has no overlaps. This routine is called recursively with each of the tiers that this Feature can be be added to. If no non-overlapping tier is found a new tier is created and added to the newTiers Vector, and the Feature is added to this newly created tier. NOTE: This routine requires that the Features are delivered in sorted order on low. Put in call to Drawable.setTierIndex to set its tier and keep drawables in synch with tiers - this did not work - not sure why - so im using FeatureTierManager.synchDrawablesWithTiers to do the same task instead. This should be reexamined. This should be the place where the assignment happens but obviously I'm missing something.

clearFeatures

public void clearFeatures()

Clears features from tiers, and clear tiers

getVisibleDrawables

public java.util.Vector getVisibleDrawables(int[] limits)

int[] limits is an array of 2 ints corresponding to low and high limits Returns a Vector of Vectors, each Vector within the outer Vector contains DrawableSeqFeatures that are the visible Features for a given tier Each DrawableSeqFeature is assigned a tier index corresponding to vertical placement. All the DrawableSeqFeatures at the same vertical level have the same tier index. The tier indices can go higher than the total number of tiers. This happens when a given tier is hidden it obviously is not added to the returned Vector of visible features, but the number it wouldve been assigned is skipped and not reused for the next tier. The following note: NOTE: This routine requires that the features are in sorted order in the tiers (which they are in FeatureTiers). is once again true. There was an optimization that assumed the DSFs were sorted from low to high, so when it hit a DSF that was above the bounds (>limits[1]) it would stop looking at the rest of the DSFs in that "tier". There are 2 problems with the sorting assumption. 1) The reverse strand is sorted high to low (when expanded) This could be solved by reversing the order for reverse strand but more killer is: 2) When collapsed all the "subtiers" get jammed together sequentially and there is no ordering for a whole collapsed row. this could be solved by doing a sort of the collapsed row but it probably isnt worth it. So now it looks at all the features from a "subtier" It turns out there was just a sorting bug for collapsed tiers that is now fixed so the optimization can once again assume sorting and is reinstated.

Specified by:

getVisibleDrawables in interface DrawableTierManagerI