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jalview::appletgui::AlignViewport Class Reference

Inheritance diagram for jalview::appletgui::AlignViewport:
Inheritance graph
Collaboration diagram for jalview::appletgui::AlignViewport:
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List of all members.


class  ConsensusThread
class  ConservationThread

Public Member Functions

void addPropertyChangeListener (java.beans.PropertyChangeListener listener)
int adjustForHiddenSeqs (int alignmentIndex)
void alignmentChanged (AlignmentPanel ap)
 AlignViewport (AlignmentI al, JalviewLite applet)
void expandColSelection (SequenceGroup sg, boolean wholewidth)
void finalize ()
void firePropertyChange (String prop, Object oldvalue, Object newvalue)
boolean getAbovePIDThreshold ()
AlignmentI getAlignment ()
jalview.datamodel.AlignmentView getAlignmentView (boolean selectedOnly, boolean markGroups)
boolean getCentreColumnLabels ()
int getCharHeight ()
int getCharWidth ()
boolean getColourAppliesToAllGroups ()
boolean getColourText ()
ColumnSelection getColumnSelection ()
SequenceI getConsensusSeq ()
boolean getConservationSelected ()
NJTree getCurrentTree ()
int getEndRes ()
int getEndSeq ()
boolean getFollowHighlight ()
boolean getFollowSelection ()
Font getFont ()
char getGapCharacter ()
ColourSchemeI getGlobalColourScheme ()
boolean getIgnoreGapsConsensus ()
int getIncrement ()
boolean getScaleAboveWrapped ()
boolean getScaleLeftWrapped ()
boolean getScaleRightWrapped ()
SequenceI[] getSelectionAsNewSequence ()
SequenceGroup getSelectionGroup ()
Color getSequenceColour (SequenceI seq)
SequenceI[] getSequenceSelection ()
String getSequenceSetId ()
boolean getShowAnnotation ()
boolean getShowBoxes ()
boolean getShowHiddenMarkers ()
boolean getShowJVSuffix ()
boolean getShowSequenceFeatures ()
boolean getShowText ()
boolean getShowunconserved ()
int getStartRes ()
int getStartSeq ()
int getThreshold ()
jalview.datamodel.CigarArray getViewAsCigars (boolean selectedRegionOnly)
String[] getViewAsString (boolean selectedRegionOnly)
String getViewId ()
boolean getWrapAlignment ()
int getwrappedWidth ()
void hideAllSelectedSeqs ()
void hideColumns (int start, int end)
void hideRepSequences (SequenceI repSequence, SequenceGroup sg)
void hideSelectedColumns ()
void hideSequence (SequenceI[] seq)
void invertColumnSelection ()
boolean isShowConsensusHistogram ()
boolean isShowGroupConsensus ()
boolean isShowGroupConservation ()
boolean isShowSequenceLogo ()
void removePropertyChangeListener (java.beans.PropertyChangeListener listener)
void resetSeqLimits (int height)
void sendSelection ()
void setAbovePIDThreshold (boolean b)
void setAlignment (AlignmentI align)
void setCharHeight (int h)
void setColourAppliesToAllGroups (boolean b)
void setColourText (boolean state)
void setConservationSelected (boolean b)
void setCurrentTree (NJTree tree)
void setEndRes (int res)
void setEndSeq (int seq)
void setFont (Font f)
void setGapCharacter (char gap)
void setGlobalColourScheme (ColourSchemeI cs)
void setHiddenColumns (ColumnSelection colsel)
void setIgnoreGapsConsensus (boolean b)
void setIncrement (int inc)
void setRenderGaps (boolean state)
void setScaleAboveWrapped (boolean b)
void setScaleLeftWrapped (boolean b)
void setScaleRightWrapped (boolean b)
void setSelectionGroup (SequenceGroup sg)
void setSequenceColour (SequenceI seq, Color col)
void setShowAnnotation (boolean b)
void setShowBoxes (boolean state)
void setShowConsensusHistogram (boolean showConsensusHistogram)
void setShowGroupConsensus (boolean showGroupConsensus)
void setShowGroupConservation (boolean showGroupConservation)
void setShowHiddenMarkers (boolean show)
void setShowJVSuffix (boolean b)
void setShowSequenceLogo (boolean showSequenceLogo)
void setShowText (boolean state)
void setShowunconserved (boolean displayNonconserved)
void setStartRes (int res)
void setStartSeq (int seq)
void setThreshold (int thresh)
void setWrapAlignment (boolean state)
void setWrappedWidth (int w)
void showAllHiddenColumns ()
void showAllHiddenSeqs ()
void showColumn (int col)
void showSequence (int index)
void showSequenceFeatures (boolean b)
void updateConsensus (final AlignmentPanel ap)
void updateConservation (final AlignmentPanel ap)
void updateSequenceIdColours ()

Public Attributes

jalview.bin.JalviewLite applet
int ConsPercGaps = 25
Hashtable featuresDisplayed
boolean followHighlight = true
boolean followSelection = true
Hashtable[] hconsensus
boolean showConsensusHistogram = true
boolean showSequenceLogo = false
boolean showUnconserved = false
boolean sortByTree = false

Protected Attributes

FeatureSettings featureSettings = null

Package Functions

jalview.datamodel.AlignmentView getAlignmentView (boolean selectedOnly)
boolean isColSelChanged ()
boolean isSelectionGroupChanged ()
void resetAllColourSchemes ()

Package Attributes

boolean abovePIDThreshold = false
AlignmentI alignment
boolean autocalculateConsensus = true
boolean centreColumnLabels
int charHeight
int charWidth
boolean colourAppliesToAllGroups = true
ColumnSelection colSel = new ColumnSelection()
long colselhash = -1
AlignmentAnnotation consensus
ConsensusThread consensusThread
AlignmentAnnotation conservation
boolean conservationColourSelected = false
ConservationThread conservationThread
boolean consUpdateNeeded = false
NJTree currentTree = null
boolean cursorMode = false
int endRes
int endSeq
Font font = new Font("SansSerif", Font.PLAIN, 10)
ColourSchemeI globalColourScheme = null
AlignmentAnnotation[] groupConsensus
AlignmentAnnotation[] groupConservation
boolean hasHiddenColumns = false
boolean hasHiddenRows = false
Hashtable hiddenRepSequences
Stack historyList = new Stack()
boolean ignoreGapsInConsensusCalculation = false
int increment
boolean MAC = false
java.awt.Frame nullFrame
AlignmentAnnotation quality
Stack redoList = new Stack()
boolean renderGaps = true
boolean scaleAboveWrapped = true
boolean scaleLeftWrapped = true
boolean scaleRightWrapped = true
SequenceGroup selectionGroup
Hashtable sequenceColours
String sequenceSetID
boolean showAnnotation = true
boolean showBoxes = true
boolean showColourText = false
boolean showConsensus = true
boolean showConservation = true
boolean showGroupConsensus = false
boolean showGroupConservation = false
boolean showHiddenMarkers = true
boolean showJVSuffix = true
boolean showQuality = true
boolean showSequenceFeatures = false
boolean showText = true
int startRes
int startSeq
int threshold
boolean updatingConsensus = false
boolean updatingConservation = false
boolean upperCasebold = false
boolean validCharWidth = true
float widthScale = 1
boolean wrapAlignment = false
int wrappedWidth

Static Package Attributes

static boolean UPDATING_CONSENSUS = false
static boolean UPDATING_CONSERVATION = false

Private Attributes

java.beans.PropertyChangeSupport changeSupport
float heightScale = 1
long sgrouphash = -1
String viewId = null

Detailed Description

Definition at line 32 of file AlignViewport.java.

The documentation for this class was generated from the following file:

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