java.lang.Object
apollo.gui.TierManager
apollo.gui.genomemap.FeatureTierManager
apollo.gui.genomemap.CollapsedFeatureTierManager
apollo.gui.genomemap.FlexibleFeatureTierManager
- All Implemented Interfaces:
- apollo.gui.ControlledObjectI, java.util.EventListener, java.io.Serializable, apollo.gui.event.TypesChangedListener
- public class FlexibleFeatureTierManager
- extends CollapsedFeatureTierManager
- implements apollo.gui.event.TypesChangedListener
A FeatureTierManager which arranges its tiers in the expanded
way (no overlapping featuresets). It may seem odd that this class
extends CollapsedFeatureTierManager, but the tiers are in basically the
same arrangement (tiers ordered by type), it is just that in the expanded
view overlaps are not allowed whereas in the collapsed view they are.
CollapsedFeatureTierManager actually does the sorting of the DrawableSeqFeatures
within the tiers.
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Method Summary |
protected void |
_add(apollo.gui.drawable.DrawableSeqFeature dsf,
int tierInd,
java.util.Vector newTiers)
Add a Feature to a tier with which it has no overlaps. |
protected int |
_addWithAvoidance(apollo.gui.drawable.DrawableSeqFeature dsf,
int tierInd,
java.util.Vector newTiers)
|
boolean |
areAnyTiersLabeled()
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boolean |
checkTiers()
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void |
collapseTier(java.lang.String tier_label)
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void |
expandAll(boolean state)
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void |
expandTier(java.lang.String type)
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java.util.Vector |
getHiddenTiers()
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int |
getIndexForType(java.lang.String type)
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protected java.util.Vector |
getNextOverlap(java.util.Vector typeTiers,
int typeTiersSize,
int[] startInds,
java.util.Vector[] typeTiersFeatures,
int[] typeTiersSizes,
java.util.Vector overlapEnds)
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int |
getTextEnd(apollo.gui.drawable.DrawableSeqFeature dsf,
int start)
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int |
getTextStart(apollo.gui.drawable.DrawableSeqFeature dsf)
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boolean |
handleTiersChangedEvent(apollo.gui.event.TypesChangedEvent evt)
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boolean |
isAvoidingTextOverlaps()
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boolean |
isExpanded(java.lang.String type)
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boolean |
isVisible(java.lang.String type)
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void |
layoutTiers()
First calls super.layoutTiers() which is CollapsedFeatureTierManager.layoutTiers()
CollapsedFeatureTierManager adds all the DSFs to tiers with sorting. |
protected java.util.Vector |
removeTextOverlapsFromSorted(java.util.Vector sortedTiers,
apollo.gui.schemes.TierProperty tp,
int[] overlapEnds)
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void |
setAllVisible(boolean state)
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void |
setTextAvoidance(apollo.gui.Transformer trans,
java.awt.FontMetrics fm)
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void |
setVisible(java.lang.String type,
boolean state)
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protected void |
sortOverlap(java.util.Vector newTiers,
java.util.Vector overlap)
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protected java.util.Vector |
sortTierByScore(java.util.Vector oldTiers,
apollo.gui.schemes.TierProperty tp,
java.util.Vector overlapEnds)
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java.lang.String |
toString()
Convert this Object to a human-readable String. |
void |
unsetTextAvoidance()
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| Methods inherited from class apollo.gui.genomemap.FeatureTierManager |
getAllFeatures, getCopyOfOrder, getDebug, getPropertyScheme, getTierLabel, getVisibleFeatures, setDebug, setFeatureSet, setTierData, setup, synchDrawablesWithTiers |
| Methods inherited from class apollo.gui.TierManager |
addTierManagerListener, decrementTierHeight, doLayoutTiers, fireTierManagerEvent, fireTierManagerEvent, getAggregateSizeChange, getController, getControllerWindow, getLowestVisible, getMaximumVisibleTransformCoord, getMaxTierUserHeight, getMaxUserCoord, getMaxVisibleTierNumber, getMinimumVisibleTransformCoord, getNumTiers, getNumVisible, getTier, getTiers, getTotalHeight, getView, getVisibleUserCoord, getYRange, incrementTierHeight, needsAutoRemoval, setAggregateSizeChange, setCharHeight, setController, setLowestVisible, setOffsetHeight, setView, setViewHeight, toTier, toUser, updateUserCoordBoundaries |
maxOverlapping
static int maxOverlapping
feats
static apollo.gui.drawable.DrawableSeqFeature[] feats
scores
static double[] scores
textTransform
protected apollo.gui.Transformer textTransform
fm
protected java.awt.FontMetrics fm
textAvoidance
protected boolean textAvoidance
FlexibleFeatureTierManager
public FlexibleFeatureTierManager()
FlexibleFeatureTierManager
public FlexibleFeatureTierManager(apollo.gui.drawable.DrawableFeatureSet fset)
handleTiersChangedEvent
public boolean handleTiersChangedEvent(apollo.gui.event.TypesChangedEvent evt)
- Specified by:
handleTiersChangedEvent in interface apollo.gui.event.TypesChangedListener- Overrides:
handleTiersChangedEvent in class CollapsedFeatureTierManager
isExpanded
public boolean isExpanded(java.lang.String type)
isVisible
public boolean isVisible(java.lang.String type)
getIndexForType
public int getIndexForType(java.lang.String type)
collapseTier
public void collapseTier(java.lang.String tier_label)
expandTier
public void expandTier(java.lang.String type)
setVisible
public void setVisible(java.lang.String type,
boolean state)
getHiddenTiers
public java.util.Vector getHiddenTiers()
setAllVisible
public void setAllVisible(boolean state)
expandAll
public void expandAll(boolean state)
areAnyTiersLabeled
public boolean areAnyTiersLabeled()
layoutTiers
public void layoutTiers()
- First calls super.layoutTiers() which is CollapsedFeatureTierManager.layoutTiers()
CollapsedFeatureTierManager adds all the DSFs to tiers with sorting.
FlexibleFeatureTierManager deals with expanding the tiers
- Overrides:
layoutTiers in class CollapsedFeatureTierManager
checkTiers
public boolean checkTiers()
toString
public java.lang.String toString()
- Description copied from class:
java.lang.Object
- Convert this Object to a human-readable String.
There are no limits placed on how long this String
should be or what it should contain. We suggest you
make it as intuitive as possible to be able to place
it into System.out.println() 55
and such.
It is typical, but not required, to ensure that this method
never completes abruptly with a java.lang.RuntimeException.
This method will be called when performing string
concatenation with this object. If the result is
null, string concatenation will instead
use "null".
The default implementation returns
getClass().getName() + "@" +
Integer.toHexString(hashCode()).
_add
protected void _add(apollo.gui.drawable.DrawableSeqFeature dsf,
int tierInd,
java.util.Vector newTiers)
- 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 DrawableSeqFeature.setYindex 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.
sortTierByScore
protected java.util.Vector sortTierByScore(java.util.Vector oldTiers,
apollo.gui.schemes.TierProperty tp,
java.util.Vector overlapEnds)
getNextOverlap
protected java.util.Vector getNextOverlap(java.util.Vector typeTiers,
int typeTiersSize,
int[] startInds,
java.util.Vector[] typeTiersFeatures,
int[] typeTiersSizes,
java.util.Vector overlapEnds)
sortOverlap
protected void sortOverlap(java.util.Vector newTiers,
java.util.Vector overlap)
setTextAvoidance
public void setTextAvoidance(apollo.gui.Transformer trans,
java.awt.FontMetrics fm)
unsetTextAvoidance
public void unsetTextAvoidance()
isAvoidingTextOverlaps
public boolean isAvoidingTextOverlaps()
getTextStart
public int getTextStart(apollo.gui.drawable.DrawableSeqFeature dsf)
getTextEnd
public int getTextEnd(apollo.gui.drawable.DrawableSeqFeature dsf,
int start)
removeTextOverlapsFromSorted
protected java.util.Vector removeTextOverlapsFromSorted(java.util.Vector sortedTiers,
apollo.gui.schemes.TierProperty tp,
int[] overlapEnds)
_addWithAvoidance
protected int _addWithAvoidance(apollo.gui.drawable.DrawableSeqFeature dsf,
int tierInd,
java.util.Vector newTiers)
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