apollo.gui.genomemap
Class ScaleView

java.lang.Object
  apollo.gui.genomemap.LinearView
      apollo.gui.genomemap.ScrollAdjustedView
          apollo.gui.genomemap.ScaleView

All Implemented Interfaces:

PickViewI, PopupViewI, ViewI

public class ScaleView
extends ScrollAdjustedView
implements PopupViewI, PickViewI

Draw a scale line, BUT also draws sequence, and allows dragging of hairpins. I think it would be easier if pixels were used instead of user coords in the vertical direction

Field Summary

static int	FEATURES
protected static org.apache.log4j.Logger	logger
static int	SPLICE

Fields inherited from class apollo.gui.genomemap.ScrollAdjustedView

prefHeight, reverseComplement, scroller

Fields inherited from class apollo.gui.genomemap.LinearView

apollo_panel, backgroundColour, debug, foregroundColour, graphics, limitsSet, transformer, transparent, viewBounds, visibilityListeners, visible

Fields inherited from interface apollo.gui.genomemap.ViewI

LEFTSIDE, NONE, RIGHTSIDE

Constructor Summary

ScaleView(javax.swing.JComponent ap, java.lang.String name)

Method Summary

void	addCutSites(java.util.Vector forward_sites, java.util.Vector reverse_sites, java.awt.Color site_color)
void	clear()
void	clearCutSites()
protected void	drawSpliceBases(java.awt.Graphics graphics, Transformer transformer, int startCoord, int endCoord, java.lang.String seq, int offset, int viewY, int strand)
protected void	drawSpliceLines(java.awt.Graphics graphics, Transformer transformer, int startCoord, int endCoord, java.lang.String seq, int strand)
Selection	findFeaturesForSelection(java.awt.Point p, boolean selectParents) Find features for selection.
Selection	findFeaturesForSelection(java.awt.Rectangle rect) Triggered by rubberbanding.
javax.swing.Action	getColouringAction()
java.awt.Rectangle	getSelectedRectangle()
protected java.awt.Color	getSpliceColor(java.awt.Graphics graphics, int i, int startCoord, int endCoord, java.lang.String seq, int strand, java.awt.Color prior_color)
void	paintView() paintView draws a cross in the centre of the View and a small cross in the upper left quadrant
void	select(Selection selection)
void	setCurationSet(CurationSet set) This gets set to null by szap.getClearData to clear out old cur set on loads.
void	setMinorTicks(boolean state)
void	setSelectedRange(int startBase, int endBase, int strand)
void	showPopupMenu(java.awt.event.MouseEvent evt)

Methods inherited from class apollo.gui.genomemap.ScrollAdjustedView

featureContains, getPreferredSize, setDrawBounds, setScrollFlag, setScrollSpace, setXOrientation

Methods inherited from class apollo.gui.genomemap.LinearView

addViewListener, addVisibilityListener, areLimitsSet, fireViewEvent, getBackgroundColour, getBounds, getCentre, getComponent, getDrawBounds, getForegroundColour, getGraphics, getLimits, getMaximum, getMinimum, getName, getSelectionRectangle, getStrand, getTransform, getVisibleRange, init, isInvalid, isTransparent, isVisible, setBackgroundColour, setBounds, setCentre, setComponent, setDebug, setForegroundColour, setGraphics, setInvalidity, setLimits, setLimitsSet, setMaximum, setMinimum, setName, setStrand, setTransform, setTransparent, setVisible, setVisible, setZoomFactor

Methods inherited from class java.lang.Object

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

Methods inherited from interface apollo.gui.genomemap.ViewI

addViewListener, areLimitsSet, getBounds, getCentre, getComponent, getLimits, getMaximum, getMinimum, getName, getPreferredSize, getTransform, getVisibleRange, isInvalid, isTransparent, isVisible, setBounds, setCentre, setComponent, setGraphics, setInvalidity, setLimits, setLimitsSet, setMaximum, setMinimum, setName, setTransparent, setVisible, setZoomFactor

Field Detail

logger

protected static final org.apache.log4j.Logger logger

SPLICE

public static final int SPLICE

See Also:

Constant Field Values

FEATURES

public static final int FEATURES

See Also:

Constant Field Values

Constructor Detail

ScaleView

public ScaleView(javax.swing.JComponent ap,
                 java.lang.String name)

Method Detail

setCurationSet

public void setCurationSet(CurationSet set)

This gets set to null by szap.getClearData to clear out old cur set on loads. All drawing access to curation set has to check for null curation set on every use of curation set, because they are on 2 different threads, curation set could be nulled at anytime during draw. An alternative would be to have this spin if in the middle of the draw but the funny thing there is you are then delaying the load in order to draw the scale view of the old cur set you dont care about anymore - so the null checks dont delay the load

setMinorTicks

public void setMinorTicks(boolean state)

setSelectedRange

public void setSelectedRange(int startBase,
                             int endBase,
                             int strand)

clear

public void clear()

Specified by:

clear in interface ViewI

Overrides:

clear in class LinearView

getSelectedRectangle

public java.awt.Rectangle getSelectedRectangle()

paintView

public void paintView()

Description copied from class: LinearView

paintView draws a cross in the centre of the View and a small cross in the upper left quadrant

Specified by:

paintView in interface ViewI

Overrides:

paintView in class LinearView

clearCutSites

public void clearCutSites()

addCutSites

public void addCutSites(java.util.Vector forward_sites,
                        java.util.Vector reverse_sites,
                        java.awt.Color site_color)

drawSpliceBases

protected void drawSpliceBases(java.awt.Graphics graphics,
                               Transformer transformer,
                               int startCoord,
                               int endCoord,
                               java.lang.String seq,
                               int offset,
                               int viewY,
                               int strand)

drawSpliceLines

protected void drawSpliceLines(java.awt.Graphics graphics,
                               Transformer transformer,
                               int startCoord,
                               int endCoord,
                               java.lang.String seq,
                               int strand)

getSpliceColor

protected java.awt.Color getSpliceColor(java.awt.Graphics graphics,
                                        int i,
                                        int startCoord,
                                        int endCoord,
                                        java.lang.String seq,
                                        int strand,
                                        java.awt.Color prior_color)

select

public void select(Selection selection)

showPopupMenu

public void showPopupMenu(java.awt.event.MouseEvent evt)

Specified by:

showPopupMenu in interface PopupViewI

getColouringAction

public javax.swing.Action getColouringAction()

findFeaturesForSelection

public Selection findFeaturesForSelection(java.awt.Rectangle rect)

Triggered by rubberbanding. Find and remember region that was selected by rubberbanding at the axis. This shouldn't trigger when we rubberband in some other view, yet it is.

Specified by:

findFeaturesForSelection in interface PickViewI

findFeaturesForSelection

public Selection findFeaturesForSelection(java.awt.Point p,
                                          boolean selectParents)

Description copied from interface: PickViewI

Find features for selection. Returns selection with SelectionItems that have model as data and drawables as listeners. This replaces findFeatures that only returned model, the problem there being we then would hafta refind the drawables later on which was awkward and inefficient. If selectParents is true then return the parents of the features under the point.

Specified by:

findFeaturesForSelection in interface PickViewI