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jalview::gui::AlignViewport Class Reference

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


class  ConsensusThread

Public Member Functions

void addPropertyChangeListener (java.beans.PropertyChangeListener listener)
int adjustForHiddenSeqs (int alignmentIndex)
void alignmentChanged (AlignmentPanel ap)
 AlignViewport (AlignmentI al, String seqsetid)
 AlignViewport (AlignmentI al, ColumnSelection hiddenColumns)
 AlignViewport (AlignmentI al)
 AlignViewport (AlignmentI al, ColumnSelection hiddenColumns, String seqsetid)
 AlignViewport (AlignmentI al, String seqsetid, String viewid)
 AlignViewport (AlignmentI al, ColumnSelection hiddenColumns, String seqsetid, String viewid)
SequenceI[][] collateForPDB (PDBEntry[] pdbEntries)
void expandColSelection (SequenceGroup sg, boolean wholewidth)
void firePropertyChange (String prop, Object oldvalue, Object newvalue)
boolean getAbovePIDThreshold ()
AlignmentI getAlignment ()
jalview.datamodel.AlignmentView getAlignmentView (boolean selectedOnly)
jalview.datamodel.AlignmentView getAlignmentView (boolean selectedOnly, boolean markGroups)
AlignmentPanel getAlignPanel ()
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 getShowSequenceFeaturesHeight ()
boolean getShowText ()
boolean getShowUnconserved ()
boolean getSortByTree ()
int getStartRes ()
int getStartSeq ()
StructureSelectionManager getStructureSelectionManager ()
int getThreshold ()
long[] getUndoRedoHash ()
jalview.datamodel.CigarArray getViewAsCigars (boolean selectedRegionOnly)
String[] getViewAsString (boolean selectedRegionOnly)
int[] getViewAsVisibleContigs (boolean selectedRegionOnly)
String getViewId ()
int[][] getVisibleRegionBoundaries (int min, int max)
boolean getWrapAlignment ()
int getWrappedWidth ()
boolean hasHiddenColumns ()
boolean hasHiddenRows ()
void hideAllSelectedSeqs ()
void hideColumns (int start, int end)
void hideRepSequences (SequenceI repSequence, SequenceGroup sg)
void hideSelectedColumns ()
void hideSequence (SequenceI[] seq)
void invertColumnSelection ()
boolean isDataset ()
boolean isShowConsensusHistogram ()
boolean isShowDbRefs ()
boolean isShowGroupConsensus ()
boolean isShowGroupConservation ()
boolean isShowNpFeats ()
boolean isShowSequenceLogo ()
boolean isUndoRedoHashModified (long[] undoredo)
void removePropertyChangeListener (java.beans.PropertyChangeListener listener)
void sendSelection ()
void setAbovePIDThreshold (boolean b)
void setAlignment (AlignmentI align)
void setCentreColumnLabels (boolean centrecolumnlabels)
void setCharHeight (int h)
void setCharWidth (int w)
void setColourAppliesToAllGroups (boolean b)
void setColourText (boolean state)
void setConservationSelected (boolean b)
void setCurrentTree (NJTree tree)
void setDataset (boolean b)
void setEndRes (int res)
void setEndSeq (int seq)
void setFont (Font f)
void setGapCharacter (char gap)
void setGlobalColourScheme (ColourSchemeI cs)
void setIgnoreGapsConsensus (boolean b, AlignmentPanel ap)
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 setShowDbRefs (boolean show)
void setShowGroupConsensus (boolean showGroupConsensus)
void setShowGroupConservation (boolean showGroupConservation)
void setShowHiddenMarkers (boolean show)
void setShowJVSuffix (boolean b)
void setShowNpFeats (boolean show)
void setShowSequenceFeatures (boolean b)
void setShowSequenceFeaturesHeight (boolean selected)
void setShowSequenceLogo (boolean showSequenceLogo)
void setShowText (boolean state)
void setShowUnconserved (boolean showunconserved)
void setSortByTree (boolean sort)
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 updateConsensus (final AlignmentPanel ap)
void updateConservation (final AlignmentPanel ap)
void updateSequenceIdColours ()

Public Attributes

int ConsPercGaps = 25
boolean followHighlight = true
boolean followSelection = true
Hashtable[] hconsensus
boolean showConsensusHistogram = true
boolean showSequenceLogo = false

Package Functions

void init ()
boolean isColSelChanged (boolean b)
boolean isSelectionGroupChanged (boolean b)
void resetAllColourSchemes ()

Package Attributes

boolean abovePIDThreshold = false
AlignmentI alignment
boolean antiAlias = false
boolean autoCalculateConsensus = true
boolean centreColumnLabels = false
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
Rectangle explodedPosition
Hashtable featuresDisplayed = null
Font font
boolean gatherViewsHere = false
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 isDataset = false
boolean padGaps = false
AlignmentAnnotation quality
Stack redoList = new Stack()
boolean renderGaps = true
boolean rightAlignIds = false
boolean scaleAboveWrapped = false
boolean scaleLeftWrapped = true
boolean scaleRightWrapped = true
SequenceGroup selectionGroup
boolean seqNameItalics
Hashtable sequenceColours
String sequenceSetID
boolean showAnnotation = true
boolean showBoxes = true
boolean showColourText = false
boolean showGroupConsensus = false
boolean showGroupConservation = false
boolean showHiddenMarkers = true
boolean showJVSuffix = true
boolean showSeqFeaturesHeight
boolean showSequenceFeatures = false
boolean showText = true
boolean showUnconserved = false
boolean sortByTree
int startRes
int startSeq
Color textColour = Color.black
Color textColour2 = Color.white
int threshold
int thresholdTextColour = 0
boolean updatingConsensus = false
boolean updatingConservation = false
boolean validCharWidth
String viewName
boolean wrapAlignment = false
int wrappedWidth

Static Package Attributes

static boolean UPDATING_CONSENSUS = false
static boolean UPDATING_CONSERVATION = false

Private Attributes

java.beans.PropertyChangeSupport changeSupport
long sgrouphash = -1
boolean showdbrefs
boolean shownpfeats
String viewId = null

Static Private Attributes

static final int RIGHT_JUSTIFY = 1

Detailed Description



Definition at line 60 of file AlignViewport.java.

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

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