/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.viewmodel;
import java.util.Vector;
/**
- * base class holding visualization and analysis attributes and common logic for an active alignment view displayed in the GUI
+ * base class holding visualization and analysis attributes and common logic for
+ * an active alignment view displayed in the GUI
+ *
* @author jimp
*
*/
protected String sequenceSetID;
/**
- * probably unused indicator that view is of a dataset rather than an alignment
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
*/
protected boolean isDataset = false;
protected ColumnSelection colSel = new ColumnSelection();
-
public boolean autoCalculateConsensus = true;
protected boolean autoCalculateStrucConsensus = true;
protected boolean ignoreGapsInConsensusCalculation = false;
-
protected ColourSchemeI globalColourScheme = null;
globalColourScheme = cs;
}
+ @Override
public ColourSchemeI getGlobalColourScheme()
{
return globalColourScheme;
}
-
protected AlignmentAnnotation consensus;
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation[] groupConservation;
- /**
- * results of alignment consensus analysis for visible portion of view
+ /**
+ * results of alignment consensus analysis for visible portion of view
*/
- protected Hashtable[] hconsensus=null;
+ protected Hashtable[] hconsensus = null;
/**
- * results of secondary structure base pair consensus for visible portion of view
+ * results of secondary structure base pair consensus for visible portion of
+ * view
*/
- protected Hashtable[] hStrucConsensus=null;
+ protected Hashtable[] hStrucConsensus = null;
/**
- * percentage gaps allowed in a column before all amino acid properties should be considered unconserved
+ * percentage gaps allowed in a column before all amino acid properties should
+ * be considered unconserved
*/
int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
+ @Override
public int getConsPercGaps()
{
return ConsPercGaps;
}
+
@Override
public void setSequenceConsensusHash(Hashtable[] hconsensus)
{
- this.hconsensus=hconsensus;
-
+ this.hconsensus = hconsensus;
+
}
@Override
{
return hStrucConsensus;
}
+
@Override
public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
{
- this.hStrucConsensus=hStrucConsensus;
-
+ this.hStrucConsensus = hStrucConsensus;
+
}
+
@Override
public AlignmentAnnotation getAlignmentQualityAnnot()
{
{
return conservation;
}
+
@Override
public AlignmentAnnotation getAlignmentConsensusAnnotation()
{
return consensus;
}
+
@Override
public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
{
return strucConsensus;
}
-
- protected AlignCalcManagerI calculator=new AlignCalcManager();
-
- jalview.workers.ConsensusThread consensusThread;
- StrucConsensusThread strucConsensusThread;
-
-
- private ConservationThread conservationThread;
+ protected AlignCalcManagerI calculator = new AlignCalcManager();
/**
* trigger update of conservation annotation
{
return;
}
-
- calculator.startWorker(conservationThread=new jalview.workers.ConservationThread(this, ap));
+ if (!calculator
+ .startRegisteredWorkersOfClass(jalview.workers.ConservationThread.class))
+ {
+ calculator.registerWorker(new jalview.workers.ConservationThread(
+ this, ap));
+ }
}
/**
{
return;
}
- calculator.startWorker(consensusThread = new ConsensusThread(this, ap));
+ if (!calculator.startRegisteredWorkersOfClass(ConsensusThread.class))
+ {
+ calculator.registerWorker(new ConsensusThread(this, ap));
+ }
}
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
- if (autoCalculateStrucConsensus && strucConsensus==null && alignment.isNucleotide() && alignment.hasRNAStructure())
+ if (autoCalculateStrucConsensus && strucConsensus == null
+ && alignment.isNucleotide() && alignment.hasRNAStructure())
{
-
+
}
// see note in mantis : issue number 8585
{
return;
}
- calculator.startWorker(strucConsensusThread = new StrucConsensusThread(this,ap));
+ if (!calculator
+ .startRegisteredWorkersOfClass(StrucConsensusThread.class))
+ {
+ calculator.registerWorker(new StrucConsensusThread(this, ap));
+ }
}
public boolean isCalcInProgress()
return calculator.isWorking();
}
+ @Override
public boolean isCalculationInProgress(
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
return false;
- if ((calculator.isWorking(consensusThread) && consensus==alignmentAnnotation)
- || (calculator.isWorking(conservationThread) && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
- || (calculator.isWorking(strucConsensusThread) && strucConsensus==alignmentAnnotation)
- )
+ if (calculator.workingInvolvedWith(alignmentAnnotation))
{
+ // System.err.println("grey out ("+alignmentAnnotation.label+")");
return true;
}
return false;
}
+
@Override
public boolean isClosed()
{
- // TODO: check that this isClosed is only true after panel is closed, not before it is fully constructed.
- return alignment==null;
+ // TODO: check that this isClosed is only true after panel is closed, not
+ // before it is fully constructed.
+ return alignment == null;
}
@Override
* should consensus profile be rendered by default
*/
protected boolean showSequenceLogo = false;
+
/**
* should consensus profile be rendered normalised to row height
*/
protected boolean normaliseSequenceLogo = false;
+
/**
* should consensus histograms be rendered by default
*/
/**
* @return the showConsensusProfile
*/
+ @Override
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
// TODO: decouple settings setting from calculation when refactoring
// annotation update method from alignframe to viewport
this.showSequenceLogo = showSequenceLogo;
- if (consensusThread != null)
- {
- consensusThread.updateAnnotation();
- }
- if (strucConsensusThread != null)
- {
- strucConsensusThread.updateAnnotation();
- }
+ calculator.updateAnnotationFor(ConsensusThread.class);
+ calculator.updateAnnotationFor(StrucConsensusThread.class);
}
this.showSequenceLogo = showSequenceLogo;
}
}
/**
- *
+ *
* @return flag to indicate if the consensus histogram should be rendered by
* default
*/
+ @Override
public boolean isShowConsensusHistogram()
{
return this.showConsensusHistogram;
*/
protected boolean showUnconserved = false;
-
/**
* when set, updateAlignment will always ensure sequences are of equal length
*/
}
/**
- *
- *
+ *
+ *
* @return null or the currently selected sequence region
*/
public SequenceGroup getSelectionGroup()
/**
* Set the selection group for this window.
- *
+ *
* @param sg
* - group holding references to sequences in this alignment view
- *
+ *
*/
public void setSelectionGroup(SequenceGroup sg)
{
}
}
+ @Override
public ColumnSelection getColumnSelection()
{
return colSel;
}
+
public void setColumnSelection(ColumnSelection colSel)
{
- this.colSel=colSel;
+ this.colSel = colSel;
}
public Hashtable getHiddenRepSequences()
{
public void updateHiddenColumns()
{
- hasHiddenColumns = colSel.getHiddenColumns() != null;
+ hasHiddenColumns = colSel.getHiddenColumns() != null;
}
-
+
protected boolean hasHiddenRows = false;
-
- public boolean hasHiddenRows() {
+
+ public boolean hasHiddenRows()
+ {
return hasHiddenRows;
}
public void setSequenceSetId(String newid)
{
- if (sequenceSetID!=null)
+ if (sequenceSetID != null)
{
- System.err.println("Warning - overwriting a sequenceSetId for a viewport!");
+ System.err
+ .println("Warning - overwriting a sequenceSetId for a viewport!");
}
- sequenceSetID=new String(newid);
+ sequenceSetID = new String(newid);
}
+
public String getSequenceSetId()
{
if (sequenceSetID == null)
return sequenceSetID;
}
+
/**
* unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
+ *
*/
protected String viewId = null;
}
return viewId;
}
+
public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
{
ignoreGapsInConsensusCalculation = b;
- if (ap!=null) {updateConsensus(ap);
- if (globalColourScheme != null)
+ if (ap != null)
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
- }}
-
+ updateConsensus(ap);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+ }
+ }
+
}
+
private long sgrouphash = -1, colselhash = -1;
/**
* 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)
*/
public boolean isSelectionGroupChanged(boolean b)
/**
* 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)
return false;
}
+ @Override
public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
}
- /// property change stuff
+ // / property change stuff
// JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
this);
protected boolean showConservation = true;
protected boolean showConsensus = true;
-
/**
* Property change listener for changes in alignment
- *
+ *
* @param listener
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param listener
* DOCUMENT ME!
*/
/**
* Property change listener for changes in alignment
- *
+ *
* @param prop
* DOCUMENT ME!
* @param oldvalue
}
// common hide/show column stuff
-
public void hideSelectedColumns()
{
hasHiddenColumns = false;
}
-
// common hide/show seq stuff
public void showAllHiddenSeqs()
{
hiddenRepSequences = null;
firePropertyChange("alignment", null, alignment.getSequences());
- // used to set hasHiddenRows/hiddenRepSequences here, after the property changed event
+ // used to set hasHiddenRows/hiddenRepSequences here, after the property
+ // changed event
sendSelection();
}
}
{
selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
}
- // JBPNote: refactor: only update flag if we modified visiblity (used to do this regardless)
+ // JBPNote: refactor: only update flag if we modified visiblity (used to
+ // do this regardless)
if (alignment.getHiddenSequences().getSize() < 1)
{
hasHiddenRows = false;
}
}
-
-
public void hideAllSelectedSeqs()
{
if (selectionGroup == null || selectionGroup.getSize() < 1)
setSelectionGroup(null);
}
-
public void hideSequence(SequenceI[] seq)
{
seqs[index++] = sg.getSequenceAt(i);
}
}
- sg.setSeqrep(repSequence); // note: not done in 2.7applet
+ sg.setSeqrep(repSequence); // note: not done in 2.7applet
sg.setHidereps(true); // note: not done in 2.7applet
hideSequence(seqs);
public boolean isHiddenRepSequence(SequenceI seq)
{
return hiddenRepSequences != null
- && hiddenRepSequences.containsKey(seq);
+ && hiddenRepSequences.containsKey(seq);
}
+
public SequenceGroup getRepresentedSequences(SequenceI seq)
{
- return (SequenceGroup) (hiddenRepSequences == null ? null : hiddenRepSequences.get(seq));
+ return (SequenceGroup) (hiddenRepSequences == null ? null
+ : hiddenRepSequences.get(seq));
}
public int adjustForHiddenSeqs(int alignmentIndex)
* broadcast selection to any interested parties
*/
public abstract void sendSelection();
-
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth());
}
-
/**
* 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;
- // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - this was the only caller in the applet for this method
- // JBPNote: in applet, this method returned references to the alignment sequences, and it did not honour the presence/absence of annotation attached to the alignment (probably!)
+ // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
+ // this was the only caller in the applet for this method
+ // JBPNote: in applet, this method returned references to the alignment
+ // sequences, and it did not honour the presence/absence of annotation
+ // attached to the alignment (probably!)
if (selectionGroup == null)
{
sequences = alignment.getSequencesArray();
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()
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(
/**
* 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
/**
* 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
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)
return selection;
}
-
/**
* return visible region boundaries within given column range
- * @param min first column (inclusive, from 0)
- * @param max last column (exclusive)
+ *
+ * @param min
+ * first column (inclusive, from 0)
+ * @param max
+ * last column (exclusive)
* @return int[][] range of {start,end} visible positions
*/
public int[][] getVisibleRegionBoundaries(int min, int max)
return startEnd;
}
+
/**
* @return the padGaps
*/
{
return padGaps;
}
+
/**
- * @param padGaps the padGaps to set
+ * @param padGaps
+ * the padGaps to set
*/
public void setPadGaps(boolean padGaps)
{
this.padGaps = padGaps;
}
+
/**
- * apply any post-edit constraints and trigger any calculations needed after an edit has been performed on the alignment
+ * apply any post-edit constraints and trigger any calculations needed after
+ * an edit has been performed on the alignment
+ *
* @param ap
*/
public void alignmentChanged(AlignmentViewPanel ap)
}
resetAllColourSchemes();
-
+ calculator.restartWorkers();
// alignment.adjustSequenceAnnotations();
}
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
+ cs.alignmentChanged(alignment);
+ // TODO: fold all recalc events for clustalX into alignmentChanged
if (cs instanceof ClustalxColourScheme)
{
((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
{
if (showConservation)
{
- if (conservation==null)
- {
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " + getConsPercGaps()
- + "% gaps", new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
- conservation.hasText = true;
- conservation.autoCalculated = true;
- alignment.addAnnotation(conservation);
- }
+ if (conservation == null)
+ {
+ conservation = new AlignmentAnnotation("Conservation",
+ "Conservation of total alignment less than "
+ + getConsPercGaps() + "% gaps",
+ new Annotation[1], 0f, 11f,
+ AlignmentAnnotation.BAR_GRAPH);
+ conservation.hasText = true;
+ conservation.autoCalculated = true;
+ alignment.addAnnotation(conservation);
+ }
}
if (showQuality)
{
- if (quality==null)
+ if (quality == null)
{
- 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);
- }
+ 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);
+ }
}
- } else {
+ }
+ else
+ {
if (alignment.hasRNAStructure())
{
strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
}
}
-
+
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
consensus.autoCalculated = true;
-
+
if (showConsensus)
{
alignment.addAnnotation(consensus);
- if (strucConsensus!=null)
+ if (strucConsensus != null)
{
alignment.addAnnotation(strucConsensus);
}
git://source.jalview.org / jalview.git / blobdiff