import jalview.schemes.*;
import jalview.structure.SelectionSource;
import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
import jalview.workers.ConservationThread;
+import jalview.workers.ConsensusThread;
public class AlignViewport extends AlignmentViewport implements AlignViewportI, SelectionSource, VamsasSource
{
boolean colourAppliesToAllGroups = true;
- ColourSchemeI globalColourScheme = null;
-
boolean conservationColourSelected = false;
boolean abovePIDThreshold = false;
- SequenceGroup selectionGroup;
-
int charHeight;
int charWidth;
boolean validCharWidth = true;
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
-
int threshold;
int increment;
// currently visible, in the correct order or rendering
public Hashtable featuresDisplayed;
- boolean hasHiddenColumns = false;
-
- boolean hasHiddenRows = false;
boolean showHiddenMarkers = true;
- public Hashtable[] hconsensus;
-
- AlignmentAnnotation consensus;
-
- AlignmentAnnotation conservation;
-
- AlignmentAnnotation quality;
-
- AlignmentAnnotation[] groupConsensus;
-
- AlignmentAnnotation[] groupConservation;
-
- boolean autocalculateConsensus = true;
-
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
- this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
public jalview.bin.JalviewLite applet;
Hashtable sequenceColours;
Stack historyList = new Stack();
Stack redoList = new Stack();
-
- String sequenceSetID;
-
- Hashtable hiddenRepSequences;
-
- AlignCalcManagerI calculator=new jalview.workers.AlignCalcManager();
-
+
public void finalize() {
applet=null;
quality=null;
public AlignViewport(AlignmentI al, JalviewLite applet)
{
+ calculator = new jalview.workers.AlignCalcManager();
this.applet = applet;
setAlignment(al);
+ // we always pad gaps
+ this.setPadGaps(true);
this.startRes = 0;
this.endRes = al.getWidth() - 1;
this.startSeq = 0;
}
- ConsensusThread consensusThread;
-
-// StrucConsensusThread strucConsensusThread;
-
-
- boolean consUpdateNeeded = false;
-
- static boolean UPDATING_CONSENSUS = false;
-
- static boolean UPDATING_STRUC_CONSENSUS = false;
-
- static boolean UPDATING_CONSERVATION = false;
-
- boolean updatingConsensus = false;
-
- boolean updatingStrucConsensus = false;
-
- boolean updatingConservation = false;
-
- /**
- * DOCUMENT ME!
- */
- public void updateConservation(final AlignmentPanel ap)
- {
- if (alignment.isNucleotide() || conservation == null)
- {
- return;
- }
-
- calculator.startWorker(new ConservationThread(this, ap));
- }
-
- /**
- * DOCUMENT ME!
- */
- public void updateConsensus(final AlignmentPanel ap)
- {
- consensusThread = new ConsensusThread(ap);
- consensusThread.start();
- }
-
- class ConsensusThread extends Thread
- {
- AlignmentPanel ap;
-
- public ConsensusThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- updatingConsensus = true;
- while (UPDATING_CONSENSUS)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSENSUS = true;
-
- try
- {
- int aWidth = alignment==null ? -1 : alignment.getWidth();
- if (aWidth < 0)
- {
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
- return;
- }
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hconsensus, true); // always calculate the
- // full profile
- updateAnnotation(true);
- //AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
- // ignoreGapsInConsensusCalculation,
- // true);
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
-
- } catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(consensus);
-
- consensus = null;
- hconsensus = null;
- System.out.println("Out of memory calculating consensus!!");
- System.gc();
- }
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
-
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- }
-
- /**
- * update the consensus annotation from the sequence profile data using
- * current visualization settings.
- */
- public void updateAnnotation()
- {
- updateAnnotation(false);
- }
-
- protected void updateAnnotation(boolean immediate)
- {
- // TODO: make calls thread-safe, so if another thread calls this method,
- // it will either return or wait until one calculation is finished.
- if (immediate
- || (!updatingConsensus && consensus != null && hconsensus != null))
- {
- AAFrequency.completeConsensus(consensus, hconsensus, 0,
- hconsensus.length, ignoreGapsInConsensusCalculation,
- showSequenceLogo);
- }
- }
- }
-
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
return sq;
}
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
public boolean getConservationSelected()
{
return conservationColourSelected;
return startSeq;
}
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
public void setStartRes(int res)
{
this.startRes = res;
return increment;
}
- public void setHiddenColumns(ColumnSelection colsel)
- {
- this.colSel = colsel;
- if (colSel.getHiddenColumns() != null)
- {
- hasHiddenColumns = true;
- }
- }
-
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
}
}
- /**
- * Property change listener for changes in alignment
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
- /**
- * DOCUMENT ME!
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
+
- /**
- * Property change listener for changes in alignment
- *
- * @param prop
- * DOCUMENT ME!
- * @param oldvalue
- * DOCUMENT ME!
- * @param newvalue
- * DOCUMENT ME!
- */
- public void firePropertyChange(String prop, Object oldvalue,
- Object newvalue)
- {
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
- }
-
- public boolean getIgnoreGapsConsensus()
- {
- return ignoreGapsInConsensusCalculation;
- }
-
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- {
- return;
- }
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
- }
-
- public void invertColumnSelection()
- {
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- if (colSel.contains(i))
- {
- colSel.removeElement(i);
- }
- else
- {
- if (!hasHiddenColumns || colSel.isVisible(i))
- {
- colSel.addElement(i);
- }
- }
- }
- }
-
- public void hideColumns(int start, int end)
- {
- if (start == end)
- {
- colSel.hideColumns(start);
- }
- else
- {
- colSel.hideColumns(start, end);
- }
-
- hasHiddenColumns = true;
- }
-
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
- {
- int sSize = sg.getSize();
- if (sSize < 2)
- {
- return;
- }
-
- if (hiddenRepSequences == null)
- {
- hiddenRepSequences = new Hashtable();
- }
-
- hiddenRepSequences.put(repSequence, sg);
-
- // Hide all sequences except the repSequence
- SequenceI[] seqs = new SequenceI[sSize - 1];
- int index = 0;
- for (int i = 0; i < sSize; i++)
- {
- if (sg.getSequenceAt(i) != repSequence)
- {
- if (index == sSize - 1)
- {
- return;
- }
-
- seqs[index++] = sg.getSequenceAt(i);
- }
- }
-
- hideSequence(seqs);
-
- }
-
- public void hideAllSelectedSeqs()
- {
- if (selectionGroup == null || selectionGroup.getSize() < 1)
- {
- return;
- }
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
- }
-
- public void hideSequence(SequenceI[] seq)
- {
- if (seq != null)
- {
- for (int i = 0; i < seq.length; i++)
- {
- alignment.getHiddenSequences().hideSequence(seq[i]);
- }
-
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
- }
- public void showSequence(int index)
- {
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
- hiddenRepSequences);
- if (tmp.size() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth() - 1);
- }
-
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- sendSelection();
- }
-
- if (alignment.getHiddenSequences().getSize() < 1)
- {
- hasHiddenRows = false;
- }
- }
- public void showColumn(int col)
- {
- colSel.revealHiddenColumns(col);
- if (colSel.getHiddenColumns() == null)
- {
- hasHiddenColumns = false;
- }
- }
-
- public void showAllHiddenColumns()
- {
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenSeqs()
- {
- if (alignment.getHiddenSequences().getSize() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth() - 1);
- }
- Vector tmp = alignment.getHiddenSequences().showAll(
- hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- hasHiddenRows = false;
- hiddenRepSequences = null;
- sendSelection();
- }
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(
- alignmentIndex);
- }
-
- /**
- * This method returns the a new SequenceI [] with the selection sequence and
- * start and end points adjusted
- *
- * @return String[]
- */
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- {
- sequences = alignment.getSequencesArray();
- }
- else
- {
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
- }
-
- return sequences;
- }
-
- /**
- * get the currently selected sequence objects or all the sequences in the
- * alignment.
- *
- * @return array of references to sequence objects
- */
- public SequenceI[] getSequenceSelection()
- {
- SequenceI[] sequences = null;
- if (selectionGroup != null)
- {
- sequences = selectionGroup.getSequencesInOrder(alignment);
- }
- if (sequences == null)
- {
- sequences = alignment.getSequencesArray();
- }
- return sequences;
- }
-
- /**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
- public jalview.datamodel.CigarArray getViewAsCigars(
- boolean selectedRegionOnly)
- {
- return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
- }
-
- /**
- * return a compact representation of the current alignment selection to pass
- * to an analysis function
- *
- * @param selectedOnly
- * boolean true to just return the selected view
- * @return AlignmentView
- */
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
- {
- return getAlignmentView(selectedOnly, false);
- }
-
- /**
- * return a compact representation of the current alignment selection to pass
- * to an analysis function
- *
- * @param selectedOnly
- * boolean true to just return the selected view
- * @param markGroups
- * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true)
- * @return AlignmentView
- */
- public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
- {
- return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
- }
- /**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
- public String[] getViewAsString(boolean selectedRegionOnly)
- {
- String[] selection = null;
- SequenceI[] seqs = null;
- int i, iSize;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
- }
-
- selection = new String[iSize];
-
- for (i = 0; i < iSize; i++)
- {
- if (hasHiddenColumns)
- {
- StringBuffer visibleSeq = new StringBuffer();
- Vector regions = colSel.getHiddenColumns();
-
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
-
- if (end > blockStart)
- {
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
- }
-
- selection[i] = visibleSeq.toString();
- }
- else
- {
- selection[i] = seqs[i].getSequenceAsString(start, end);
- }
- }
-
- return selection;
- }
public boolean getShowHiddenMarkers()
{
}
}
- public String getSequenceSetId()
- {
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
-
- return sequenceSetID;
- }
- /**
- * unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
- */
- private String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
- }
- return viewId;
- }
-
- public void alignmentChanged(AlignmentPanel ap)
- {
- alignment.padGaps();
-
- if (hconsensus != null && autocalculateConsensus)
- {
- updateConsensus(ap);
- updateConservation(ap);
- }
-
- // Reset endRes of groups if beyond alignment width
- int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
- if (groups != null)
- {
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (sg.getEndRes() > alWidth)
- {
- sg.setEndRes(alWidth - 1);
- }
- }
- }
-
- if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
- {
- selectionGroup.setEndRes(alWidth - 1);
- }
-
- resetAllColourSchemes();
-
- // AW alignment.adjustSequenceAnnotations();
- }
-
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = globalColourScheme;
- if (cs != null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
- alignment.getWidth());
- }
-
- cs.setConsensus(hconsensus);
- if (cs.conservationApplied())
- {
- cs.setConservation(Conservation.calculateConservation("All",
- ResidueProperties.propHash, 3, alignment.getSequences(), 0,
- alignment.getWidth(), false, getConsPercGaps(), false));
- }
- }
-
- int s, sSize = alignment.getGroups().size();
- for (s = 0; s < sSize; s++)
- {
- SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
- if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) sg.cs).resetClustalX(
- sg.getSequences(hiddenRepSequences), sg.getWidth());
- }
- sg.recalcConservation();
- }
- }
-
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
if (sg.idColour != null)
{
- Vector sqs = sg.getSequences(hiddenRepSequences);
+ Vector sqs = sg.getSequences(getHiddenRepSequences());
for (int s = 0, sSize = sqs.size(); s < sSize; s++)
{
this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
{
return followSelection;
}
-
- private long sgrouphash = -1, colselhash = -1;
-
- /**
- * checks current SelectionGroup against record of last hash value, and
- * updates record.
- *
- * @return true if SelectionGroup changed since last call
- */
- boolean isSelectionGroupChanged()
- {
- int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode();
- if (hc != sgrouphash)
- {
- sgrouphash = hc;
- return true;
- }
- return false;
- }
-
- /**
- * checks current colsel against record of last hash value, and updates
- * record.
- *
- * @return true if colsel changed since last call
- */
- boolean isColSelChanged()
- {
- int hc = (colSel == null) ? -1 : colSel.hashCode();
- if (hc != colselhash)
- {
- colselhash = hc;
- return true;
- }
- return false;
- }
public void sendSelection()
{
jalview.structure.StructureSelectionManager
/**
- * show non-conserved residues only
- */
- public boolean showUnconserved = false;
-
- /**
- * when set, alignment should be reordered according to a newly opened tree
- */
- public boolean sortByTree = false;
-
- /**
- * @return the showUnconserved
- */
- public boolean getShowunconserved()
- {
- return showUnconserved;
- }
-
- /**
- * @param showNonconserved
- * the showUnconserved to set
- */
- public void setShowunconserved(boolean displayNonconserved)
- {
- this.showUnconserved = displayNonconserved;
- }
-
- /**
- * should conservation rows be shown for groups
- */
- boolean showGroupConservation = false;
-
- /**
- * should consensus rows be shown for groups
- */
- boolean showGroupConsensus = false;
-
- /**
- * should consensus profile be rendered by default
- */
- public boolean showSequenceLogo = false;
- /**
- * should consensus profile be rendered normalised to row height
- */
- public boolean normaliseSequenceLogo = false;
-
- /**
- * should consensus histograms be rendered by default
- */
- public boolean showConsensusHistogram = true;
-
- /**
- * @return the showConsensusProfile
- */
- public boolean isShowSequenceLogo()
- {
- return showSequenceLogo;
- }
-
- /**
- * @param showSequenceLogo
- * the new value
- */
- public void setShowSequenceLogo(boolean showSequenceLogo)
- {
- if (showSequenceLogo != this.showSequenceLogo)
- {
- // TODO: decouple settings setting from calculation when refactoring
- // annotation update method from alignframe to viewport
- this.showSequenceLogo = showSequenceLogo;
- if (consensusThread != null)
- {
- consensusThread.updateAnnotation();
- }
- }
- this.showSequenceLogo = showSequenceLogo;
- }
-
- /**
- * @param showConsensusHistogram
- * the showConsensusHistogram to set
- */
- public void setShowConsensusHistogram(boolean showConsensusHistogram)
- {
- this.showConsensusHistogram = showConsensusHistogram;
- }
-
- /**
- * @return the showGroupConservation
- */
- public boolean isShowGroupConservation()
- {
- return showGroupConservation;
- }
-
- /**
- * @param showGroupConservation
- * the showGroupConservation to set
- */
- public void setShowGroupConservation(boolean showGroupConservation)
- {
- this.showGroupConservation = showGroupConservation;
- }
-
- /**
- * @return the showGroupConsensus
- */
- public boolean isShowGroupConsensus()
- {
- return showGroupConsensus;
- }
-
- /**
- * @param showGroupConsensus
- * the showGroupConsensus to set
- */
- public void setShowGroupConsensus(boolean showGroupConsensus)
- {
- this.showGroupConsensus = showGroupConsensus;
- }
-
- /**
- *
- * @return flag to indicate if the consensus histogram should be rendered by
- * default
- */
- public boolean isShowConsensusHistogram()
- {
- return this.showConsensusHistogram;
- }
-
- /**
* synthesize a column selection if none exists so it covers the given
* selection group. if wholewidth is false, no column selection is made if the
* selection group covers the whole alignment width.
normaliseSequenceLogo = state;
}
- public boolean isCalcInProgress()
- {
- // TODO generalise to iterate over all calculators associated with av
- return updatingConsensus || updatingConservation || updatingStrucConsensus;
- }
-
- public boolean isCalculationInProgress(
- AlignmentAnnotation alignmentAnnotation)
- {
- if (!alignmentAnnotation.autoCalculated)
- return false;
- if ((updatingConsensus && consensus==alignmentAnnotation)
- || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
- // || (updatingStrucConsensus && strucConsensus==alignmentAnnotation)
- )
- {
- return true;
- }
- return false;
- }
-
/**
*
* @return true if alignment characters should be displayed
return validCharWidth;
}
- @Override
- public Hashtable[] getSequenceConsensusHash()
- {
- return hconsensus;
- }
-
- @Override
- public Hashtable[] getRnaStructureConsensusHash()
- {
- return null; // TODO: JAL-891 port to jvlite : refactor and introduce hStrucConsensus;
- }
-
- @Override
- public AlignmentAnnotation getAlignmentQualityAnnot()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public AlignmentAnnotation getAlignmentConservationAnnotation()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public boolean isClosed()
- {
- System.err.println("Alignment is "+alignment==null ? "closed" : "open");
- return alignment==null;
- }
-
- @Override
- public AlignCalcManagerI getCalcManager()
- {
- // TODO Auto-generated method stub
- return null;
- }
}