/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.awt.*;
import jalview.analysis.*;
-import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.OOMHandlerI;
import jalview.bin.*;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.workers.AlignCalcManager;
+import jalview.workers.ConsensusThread;
+import jalview.workers.ConservationThread;
+import jalview.workers.StrucConsensusThread;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport implements SelectionSource, VamsasSource
+public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
{
private static final int RIGHT_JUSTIFY = 1;
boolean showAnnotation = true;
- boolean colourAppliesToAllGroups = true;
-
- ColourSchemeI globalColourScheme = null;
-
- boolean conservationColourSelected = false;
-
- boolean abovePIDThreshold = false;
-
- SequenceGroup selectionGroup;
-
int charHeight;
int charWidth;
boolean seqNameItalics;
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
-
- int threshold;
-
- int increment;
NJTree currentTree = null;
boolean scaleRightWrapped = true;
- boolean hasHiddenColumns = false;
-
- boolean hasHiddenRows = false;
-
boolean showHiddenMarkers = true;
boolean cursorMode = false;
*/
Hashtable featuresDisplayed = null;
- /** DOCUMENT ME!! */
- public Hashtable[] hconsensus;
-
- public Hashtable[] hStrucConsensus;
-
- AlignmentAnnotation consensus;
-
- AlignmentAnnotation strucConsensus;
-
- AlignmentAnnotation conservation;
-
- AlignmentAnnotation quality;
-
- AlignmentAnnotation[] groupConsensus;
-
- AlignmentAnnotation[] groupConservation;
-
- boolean autoCalculateConsensus = true;
-
- boolean autoCalculateStrucConsensus = true;
-
-
- /** DOCUMENT ME!! */
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- // JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
- this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
- boolean isDataset = false;
-
boolean antiAlias = false;
- boolean padGaps = false;
-
Rectangle explodedPosition;
String viewName;
- String sequenceSetID;
-
boolean gatherViewsHere = false;
Stack historyList = new Stack();
boolean rightAlignIds = false;
- Hashtable hiddenRepSequences;
-
- boolean sortByTree;
-
/**
* Creates a new AlignViewport object.
*
centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
- padGaps = Cache.getDefault("PAD_GAPS", true);
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
{
if (!alignment.isNucleotide())
{
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " + ConsPercGaps
- + "% gaps", new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
- conservation.hasText = true;
- conservation.autoCalculated = true;
-
- if (Cache.getDefault("SHOW_CONSERVATION", true))
- {
- alignment.addAnnotation(conservation);
- }
-
- if (Cache.getDefault("SHOW_QUALITY", true))
- {
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
- quality.hasText = true;
- quality.autoCalculated = true;
-
- alignment.addAnnotation(quality);
- }
+ showConservation=Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality=Cache.getDefault("SHOW_QUALITY", true);
showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
false);
-
- {
-
- }
- }
+ }
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+ normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- // TODO: add menu option action that nulls or creates consensus object
- // depending on if the user wants to see the annotation or not in a
- // specific alignment
+ showConsensus=Cache.getDefault("SHOW_IDENTITY", true);
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
consensus.autoCalculated = true;
-
- //TODO check if this can done accordingly
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- strucConsensus.hasText = true;
- strucConsensus.autoCalculated = true;
-
- if (Cache.getDefault("SHOW_IDENTITY", true))
- {
- alignment.addAnnotation(consensus);
- //TODO: Make own if for structure
- alignment.addAnnotation(strucConsensus);
- }
-
}
-
+ initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,
return showSequenceFeatures;
}
- ConservationThread conservationThread;
-
- 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;
-
/**
* centre columnar annotation labels in displayed alignment annotation TODO:
* add to jalviewXML and annotation display settings
private boolean shownpfeats;
- /**
- * trigger update of conservation annotation
- */
- public void updateConservation(final AlignmentPanel ap)
- {
- // see note in mantis : issue number 8585
- if (alignment.isNucleotide() || conservation == null
- || !autoCalculateConsensus)
- {
- return;
- }
-
- conservationThread = new ConservationThread(this, ap);
- conservationThread.start();
- }
-
- /**
- * trigger update of consensus annotation
- */
- public void updateConsensus(final AlignmentPanel ap)
- {
- // see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
- {
- return;
- }
- 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) ? alignment.getWidth() : -1; // null
- // pointer
- // possibility
- // here.
- if (aWidth <= 0)
- {
- updatingConsensus = false;
- UPDATING_CONSENSUS = false;
- return;
- }
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hconsensus, true);
- updateAnnotation(true);
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
-
- } catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(consensus);
-
- consensus = null;
- hconsensus = null;
- new OOMWarning("calculating consensus", error);
- }
- 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);
- }
- }
- }
-
- //--------START Structure Conservation
- public void updateStrucConsensus(final AlignmentPanel ap)
- {
- // see note in mantis : issue number 8585
- if (strucConsensus == null || !autoCalculateStrucConsensus)
- {
- return;
- }
- strucConsensusThread = new StrucConsensusThread(ap);
- strucConsensusThread.start();
- }
-
- class StrucConsensusThread extends Thread
- {
- AlignmentPanel ap;
-
- public StrucConsensusThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- updatingStrucConsensus = true;
- while (UPDATING_STRUC_CONSENSUS)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_STRUC_CONSENSUS = true;
-
- try
- {
- int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
- // pointer
- // possibility
- // here.
- if (aWidth <= 0)
- {
- updatingStrucConsensus = false;
- UPDATING_STRUC_CONSENSUS = false;
- return;
- }
-
- strucConsensus.annotations = null;
- strucConsensus.annotations = new Annotation[aWidth];
-
- hStrucConsensus = new Hashtable[aWidth];
-
- AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
- AlignmentAnnotation rnaStruc = null;
- for(int i=0; i<aa.length;i++){
- if(aa[i].getRNAStruc() != null){
- rnaStruc=aa[i];
- break;
- }
- }
-
- AlignmentAnnotation rna = ap.av.getAlignment().getAlignmentAnnotation()[0];
- StructureFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hStrucConsensus, true, rnaStruc);
- //TODO AlignmentAnnotation rnaStruc!!!
- updateAnnotation(true);
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hStrucConsensus);
- }
-
- } catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(strucConsensus);
-
- strucConsensus = null;
- hStrucConsensus = null;
- new OOMWarning("calculating structure consensus", error);
- }
- UPDATING_STRUC_CONSENSUS = false;
- updatingStrucConsensus = 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
- || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null))
- {
- StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus, 0,
- hStrucConsensus.length, false,
- showSequenceLogo);
- }
- }
- }
- //--------END Structure Conservation
+ // --------END Structure Conservation
/**
* get the consensus sequence as displayed under the PID consensus annotation
}
/**
- *
- *
- * @return null or the currently selected sequence region
- */
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- /**
- * Set the selection group for this window.
- *
- * @param sg - group holding references to sequences in this alignment view
- *
- */
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
- /**
- * GUI state
- * @return true if conservation based shading is enabled
- */
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- /**
- * GUI state
- * @param b
- * enable conservation based shading
- */
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- /**
- * GUI state
- * @return true if percent identity threshold is applied to shading
- */
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- /**
- * GUI state
- *
- *
- * @param b indicate if percent identity threshold is applied to shading
- */
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
- /**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
/**
* DOCUMENT ME!
*
- * @param cs
- * DOCUMENT ME!
- */
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param res
* DOCUMENT ME!
*/
{
if (alignment != null && alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager(Desktop.instance)
- .removeMappings(alignment.getCodonFrames());
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).removeMappings(alignment.getCodonFrames());
}
this.alignment = align;
- if (alignment.getCodonFrames() != null)
+ if (alignment!=null && alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings(
- alignment.getCodonFrames());
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).addMappings(alignment.getCodonFrames());
}
}
/**
* DOCUMENT ME!
*
- * @param thresh
- * DOCUMENT ME!
- */
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getThreshold()
- {
- return threshold;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param inc
- * DOCUMENT ME!
- */
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getIncrement()
- {
- return increment;
- }
-
- /**
- * DOCUMENT ME!
- *
* @return DOCUMENT ME!
*/
public ColumnSelection getColumnSelection()
/**
* DOCUMENT ME!
*
- * @param b
- * DOCUMENT ME!
- */
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- /**
- * DOCUMENT ME!
- *
* @return DOCUMENT ME!
*/
public boolean getShowJVSuffix()
scaleRightWrapped = b;
}
- /**
- * 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 void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(ap);
- if (globalColourScheme != null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
- }
- }
-
- public boolean getIgnoreGapsConsensus()
- {
- return ignoreGapsInConsensusCalculation;
- }
public void setDataset(boolean b)
{
return isDataset;
}
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- {
- return;
- }
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
- }
-
- 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);
- }
- }
- sg.setSeqrep(repSequence);
- sg.setHidereps(true);
- 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());
- sendSelection();
- hasHiddenRows = false;
- hiddenRepSequences = null;
- }
- }
-
- public void invertColumnSelection()
- {
- colSel.invertColumnSelection(0, alignment.getWidth());
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(
- alignmentIndex);
- }
-
- /**
- * This method returns an array of new SequenceI objects derived from the
- * whole alignment or just the current selection with start and end points
- * adjusted
- *
- * @note if you need references to the actual SequenceI objects in the
- * alignment or currently selected then use getSequenceSelection()
- * @return selection as new sequenceI objects
- */
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- {
- sequences = alignment.getSequencesArray();
- AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
- for (int i = 0; i < sequences.length; i++)
- {
- sequences[i] = new Sequence(sequences[i], annots); // construct new
- // sequence with
- // subset of visible
- // annotation
- }
- }
- 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
- */
- public 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];
- if (hasHiddenColumns)
- {
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
- }
- else
- {
- for (i = 0; i < iSize; i++)
- {
- selection[i] = seqs[i].getSequenceAsString(start, end);
- }
-
- }
- return selection;
- }
-
- public int[][] getVisibleRegionBoundaries(int min, int max)
- {
- Vector regions = new Vector();
- int start = min;
- int end = max;
-
- do
- {
- if (hasHiddenColumns)
- {
- if (start == 0)
- {
- start = colSel.adjustForHiddenColumns(start);
- }
- end = colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = max;
- }
- if (end > max)
- {
- end = max;
- }
- }
-
- regions.addElement(new int[]
- { start, end });
-
- if (hasHiddenColumns)
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < max);
-
- int[][] startEnd = new int[regions.size()][2];
-
- regions.copyInto(startEnd);
-
- return startEnd;
-
- }
public boolean getShowHiddenMarkers()
{
showHiddenMarkers = show;
}
- public String getSequenceSetId()
- {
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
-
- return sequenceSetID;
- }
-
- /**
- * unique viewId for synchronizing state 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)
- {
- if (padGaps)
- {
- alignment.padGaps();
- }
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConservation(ap);
- }
- if (autoCalculateConsensus)
- {
- updateConsensus(ap);
- }
- if(autoCalculateStrucConsensus)
- {
- updateStrucConsensus(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();
-
- // 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())
- {
- Alignment al = (Alignment) alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
- c.calculate();
- c.verdict(false, ConsPercGaps);
-
- cs.setConservation(c);
- }
- }
-
- 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();
- }
- }
-
public Color getSequenceColour(SequenceI seq)
{
if (sequenceColours == null || !sequenceColours.containsKey(seq))
public void updateSequenceIdColours()
{
- Vector groups = alignment.getGroups();
if (sequenceColours == null)
{
sequenceColours = new Hashtable();
}
- for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+ for (SequenceGroup sg:alignment.getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
if (sg.idColour != null)
{
- Vector sqs = sg.getSequences(hiddenRepSequences);
- for (int s = 0, sSize = sqs.size(); s < sSize; s++)
+ for (SequenceI s:sg.getSequences(getHiddenRepSequences()))
{
- sequenceColours.put(sqs.elementAt(s), sg.idColour);
+ sequenceColours.put(s, sg.idColour);
}
}
}
return followSelection;
}
- private long sgrouphash = -1, colselhash = -1;
-
boolean showSeqFeaturesHeight;
- /**
- * checks current SelectionGroup against record of last hash value, and
- * updates record.
- * @param b update the record of last hash value
- *
- * @return true if SelectionGroup changed since last call (when b is true)
- */
- boolean isSelectionGroupChanged(boolean b)
- {
- int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode();
- if (hc!=-1 && hc != sgrouphash)
- {
- if (b) {sgrouphash = hc;}
- return true;
- }
- return false;
- }
-
- /**
- * checks current colsel against record of last hash value, and optionally updates
- * record.
-
- * @param b update the record of last hash value
- * @return true if colsel changed since last call (when b is true)
- */
- boolean isColSelChanged(boolean b)
- {
- int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode();
- if (hc!=-1 && hc != colselhash)
- {
- if (b) {colselhash = hc;}
- return true;
- }
- return false;
- }
-
public void sendSelection()
{
jalview.structure.StructureSelectionManager
return showSeqFeaturesHeight;
}
- boolean showUnconserved = false;
-
- public boolean getShowUnconserved()
- {
- return showUnconserved;
- }
-
- public void setShowUnconserved(boolean showunconserved)
- {
- showUnconserved = showunconserved;
- }
-
/**
* return the alignPanel containing the given viewport. Use this to get the
* components currently handling the given viewport.
}
/**
- * 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 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.
public StructureSelectionManager getStructureSelectionManager()
{
- return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
}
/**
*
* @param pdbEntries
- * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it
+ * @return a series of SequenceI arrays, one for each PDBEntry, listing which
+ * sequence in the alignment holds a reference to it
*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
- for (PDBEntry pdb: pdbEntries) {
- ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
- for (int i = 0; i < alignment.getHeight(); i++)
+ for (PDBEntry pdb : pdbEntries)
{
- Vector pdbs = alignment.getSequenceAt(i)
- .getDatasetSequence().getPDBId();
- if (pdbs == null)
- continue;
- SequenceI sq;
- for (int p = 0; p < pdbs.size(); p++)
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
- if (p1.getId().equals(pdb.getId()))
+ Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+ .getPDBId();
+ if (pdbs == null)
+ continue;
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
{
- if (!seqs.contains(sq=alignment.getSequenceAt(i)))
- seqs.add(sq);
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ seqs.add(sq);
- continue;
+ continue;
+ }
}
}
- }
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
+
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
+ {
+ return validCharWidth;
+ }
}