/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * 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
* 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.workers.AlignCalcManager;
import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
import jalview.workers.StrucConsensusThread;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
import java.util.Vector;
/**
*/
protected boolean isDataset = false;
- private Hashtable hiddenRepSequences;
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
protected ColumnSelection colSel = new ColumnSelection();
protected ColourSchemeI globalColourScheme = null;
+ /**
+ * gui state - changes to colour scheme propagated to all groups
+ */
+ private boolean colourAppliesToAllGroups;
+
+ /**
+ * @param value
+ * indicating if subsequent colourscheme changes will be propagated
+ * to all groups
+ */
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ /**
+ *
+ *
+ * @return flag indicating if colourchanges propagated to all groups
+ */
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ boolean abovePIDThreshold = false;
+
+ /**
+ * 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;
+ }
+
+ int threshold;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
+ */
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ int increment;
+
+ /**
+ *
+ * @param inc
+ * set the scalar for bleaching colourschemes according to degree of
+ * conservation
+ */
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ /**
+ * GUI State
+ *
+ * @return get scalar for bleaching colourschemes by conservation
+ */
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ boolean conservationColourSelected = false;
+
+ /**
+ * 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;
+ }
+ @Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
+ // TODO: logic refactored from AlignFrame changeColour -
+ // autorecalc stuff should be changed to rely on the worker system
+ // check to see if we should implement a changeColour(cs) method rather than
+ // put th logic in here
+ // - means that caller decides if they want to just modify state and defer
+ // calculation till later or to do all calculations in thread.
+ // via changecolour
globalColourScheme = cs;
+ boolean recalc = false;
+ if (cs != null)
+ {
+ cs.setConservationApplied(recalc = getConservationSelected());
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ recalc = true;
+ cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
+ }
+ else
+ {
+ cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+ }
+ if (recalc)
+ {
+ cs.setConsensus(hconsensus);
+ cs.setConservation(hconservation);
+ }
+ cs.alignmentChanged(alignment, hiddenRepSequences);
+ }
+ if (getColourAppliesToAllGroups())
+ {
+ for (SequenceGroup sg : getAlignment().getGroups())
+ {
+ if (cs == null)
+ {
+ sg.cs = null;
+ continue;
+ }
+ sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.setConsPercGaps(ConsPercGaps);
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
+ recalc = true;
+ }
+ else
+ {
+ sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+
+ if (getConservationSelected())
+ {
+ sg.cs.setConservationApplied(true);
+ recalc = true;
+ }
+ else
+ {
+ sg.cs.setConservation(null);
+ // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+ if (recalc)
+ {
+ sg.recalcConservation();
+ }
+ else
+ {
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
+ }
+ }
+ }
+
}
+ @Override
public ColourSchemeI getGlobalColourScheme()
{
return globalColourScheme;
*/
protected Hashtable[] hStrucConsensus = null;
+ protected Conservation hconservation = null;
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ hconservation = cons;
+ }
+
/**
* 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)
{
{
return;
}
- if (!calculator
- .startRegisteredWorkersOfClass(jalview.workers.ConservationThread.class))
+ if (calculator
+ .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
{
calculator.registerWorker(new jalview.workers.ConservationThread(
this, ap));
{
return;
}
- if (!calculator.startRegisteredWorkersOfClass(ConsensusThread.class))
+ if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
{
calculator.registerWorker(new ConsensusThread(this, ap));
}
if (autoCalculateStrucConsensus && strucConsensus == null
&& alignment.isNucleotide() && alignment.hasRNAStructure())
{
-
+ // secondary structure has been added - so init the consensus line
+ initRNAStructure();
}
// see note in mantis : issue number 8585
{
return;
}
- if (!calculator
- .startRegisteredWorkersOfClass(StrucConsensusThread.class))
+ if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
{
calculator.registerWorker(new StrucConsensusThread(this, ap));
}
return calculator.isWorking();
}
+ @Override
public boolean isCalculationInProgress(
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
+ {
return false;
+ }
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
* 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;
* @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
*/
+ @Override
public SequenceGroup getSelectionGroup()
{
return selectionGroup;
* - group holding references to sequences in this alignment view
*
*/
+ @Override
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
public void setHiddenColumns(ColumnSelection colsel)
{
this.colSel = colsel;
- if (colSel.getHiddenColumns() != null)
- {
- hasHiddenColumns = true;
- }
}
+ @Override
public ColumnSelection getColumnSelection()
{
return colSel;
}
+ @Override
public void setColumnSelection(ColumnSelection colSel)
{
this.colSel = colSel;
+ if (colSel != null)
+ {
+ updateHiddenColumns();
+ }
}
- public Hashtable getHiddenRepSequences()
+
+ /**
+ *
+ * @return
+ */
+ @Override
+ public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
{
return hiddenRepSequences;
}
- public void setHiddenRepSequences(Hashtable hiddenRepSequences)
+
+ @Override
+ public void setHiddenRepSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
this.hiddenRepSequences = hiddenRepSequences;
}
- protected boolean hasHiddenColumns = false;
+
+ @Override
+ public boolean hasHiddenColumns()
+ {
+ return colSel != null && colSel.hasHiddenColumns();
+ }
public void updateHiddenColumns()
{
- hasHiddenColumns = colSel.getHiddenColumns() != null;
+ // this method doesn't really do anything now. But - it could, since a
+ // column Selection could be in the process of modification
+ // hasHiddenColumns = colSel.hasHiddenColumns();
}
protected boolean hasHiddenRows = false;
+ @Override
public boolean hasHiddenRows()
{
return hasHiddenRows;
sequenceSetID = new String(newid);
}
+ @Override
public String getSequenceSetId()
{
if (sequenceSetID == null)
return false;
}
+ @Override
public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
// / 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;
+ Hashtable sequenceColours;
/**
* Property change listener for changes in alignment
}
// common hide/show column stuff
-
public void hideSelectedColumns()
{
colSel.hideSelectedColumns();
setSelectionGroup(null);
- hasHiddenColumns = true;
}
public void hideColumns(int start, int end)
{
colSel.hideColumns(start, end);
}
-
- hasHiddenColumns = true;
}
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
- if (colSel.getHiddenColumns() == null)
- {
- hasHiddenColumns = false;
- }
+
}
public void showAllHiddenColumns()
{
colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
}
-
// common hide/show seq stuff
public void showAllHiddenSeqs()
{
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- Vector tmp = alignment.getHiddenSequences().showAll(
+ List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
hasHiddenRows = false;
public void showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
+ index,
hiddenRepSequences);
if (tmp.size() > 0)
{
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
// JBPNote: refactor: only update flag if we modified visiblity (used to
// do this regardless)
}
}
-
-
public void hideAllSelectedSeqs()
{
if (selectionGroup == null || selectionGroup.getSize() < 1)
setSelectionGroup(null);
}
-
public void hideSequence(SequenceI[] seq)
{
for (int i = 0; i < seq.length; i++)
{
alignment.getHiddenSequences().hideSequence(seq[i]);
+ setSequenceAnnotationsVisible(seq[i], false);
}
hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
}
+ /**
+ * Set visibility for any annotations for the given sequence.
+ *
+ * @param sequenceI
+ */
+ protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
+ boolean visible)
+ {
+ for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ {
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
+ }
+ }
+
public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
{
int sSize = sg.getSize();
public boolean isHiddenRepSequence(SequenceI seq)
{
- return hiddenRepSequences != null
- && hiddenRepSequences.containsKey(seq);
+ return alignment.getSeqrep()==seq || (hiddenRepSequences != null
+ && hiddenRepSequences.containsKey(seq));
}
public SequenceGroup getRepresentedSequences(SequenceI seq)
: hiddenRepSequences.get(seq));
}
+ @Override
public int adjustForHiddenSeqs(int alignmentIndex)
{
return alignment.getHiddenSequences().adjustForHiddenSeqs(
alignmentIndex);
}
- // Selection manipulation
- /**
- * broadcast selection to any interested parties
- */
+ @Override
public abstract void sendSelection();
-
+ @Override
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
- */
+
+ @Override
public SequenceI[] getSelectionAsNewSequence()
{
SequenceI[] sequences;
// 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)
+ if (selectionGroup == null || selectionGroup.getSize() == 0)
{
sequences = alignment.getSequencesArray();
AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
return sequences;
}
- /**
- * get the currently selected sequence objects or all the sequences in the
- * alignment.
- *
- * @return array of references to sequence objects
- */
+
+ @Override
public SequenceI[] getSequenceSelection()
{
SequenceI[] sequences = null;
}
- /**
- * 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[]
- */
+ @Override
public jalview.datamodel.CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
- return new jalview.datamodel.CigarArray(alignment,
- (hasHiddenColumns ? colSel : null),
+ return new jalview.datamodel.CigarArray(alignment, colSel,
(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
- */
+
+ @Override
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
- */
+
+ @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
return new AlignmentView(alignment, colSel, selectionGroup,
- hasHiddenColumns, selectedOnly, markGroups);
+ colSel != null && colSel.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[]
- */
+ @Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
String[] selection = null;
}
selection = new String[iSize];
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
selection = colSel.getVisibleSequenceStrings(start, end, seqs);
}
return selection;
}
- /**
- * return visible region boundaries within given column range
- *
- * @param min
- * first column (inclusive, from 0)
- * @param max
- * last column (exclusive)
- * @return int[][] range of {start,end} visible positions
- */
+
+ @Override
public int[][] getVisibleRegionBoundaries(int min, int max)
{
Vector regions = new Vector();
do
{
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
if (start == 0)
{
regions.addElement(new int[]
{ start, end });
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
start = colSel.adjustForHiddenColumns(end);
start = colSel.getHiddenBoundaryLeft(start) + 1;
return startEnd;
}
- /**
- * @return the padGaps
- */
+
+ @Override
+ public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+ {
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ AlignmentAnnotation[] aa;
+ if ((aa=alignment.getAlignmentAnnotation())!=null)
+ {
+ for (AlignmentAnnotation annot:aa)
+ {
+ AlignmentAnnotation clone = new AlignmentAnnotation(annot);
+ if (selectedOnly && selectionGroup!=null)
+ {
+ colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
+ } else {
+ colSel.makeVisibleAnnotation(clone);
+ }
+ ala.add(clone);
+ }
+ }
+ return ala;
+ }
+
+
+ @Override
public boolean isPadGaps()
{
return padGaps;
}
- /**
- * @param padGaps
- * the padGaps to set
- */
+
+ @Override
public void setPadGaps(boolean padGaps)
{
this.padGaps = padGaps;
*
* @param ap
*/
+ @Override
public void alignmentChanged(AlignmentViewPanel ap)
{
if (isPadGaps())
// Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
+ List<SequenceGroup> groups = alignment.getGroups();
if (groups != null)
{
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : groups)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
if (sg.getEndRes() > alWidth)
{
sg.setEndRes(alWidth - 1);
// alignment.adjustSequenceAnnotations();
}
-
/**
* reset scope and do calculations for all applied colourschemes on alignment
*/
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(),
- alignment.getWidth());
- }
+ cs.alignmentChanged(alignment, hiddenRepSequences);
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
}
}
- int s, sSize = alignment.getGroups().size();
- for (s = 0; s < sSize; s++)
+ for (SequenceGroup sg : alignment.getGroups())
{
- SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
- if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+ if (sg.cs != null)
{
- ((ClustalxColourScheme) sg.cs).resetClustalX(sg
- .getSequences(hiddenRepSequences), sg.getWidth());
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
}
sg.recalcConservation();
}
{
if (!alignment.isNucleotide())
{
- if (showConservation)
+ initConservation();
+ initQuality();
+ }
+ else
+ {
+ initRNAStructure();
+ }
+ initConsensus();
+ }
+ }
+
+ private void initConsensus()
+ {
+
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+
+ if (showConsensus)
+ {
+ alignment.addAnnotation(consensus);
+ }
+ }
+
+ private void initConservation()
+ {
+ 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);
+ }
+ }
+ }
+
+ private void initQuality()
+ {
+ if (showQuality)
+ {
+ 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);
+ }
+ }
+ }
+
+ private void initRNAStructure()
+ {
+ if (alignment.hasRNAStructure() && strucConsensus == null)
+ {
+ strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ strucConsensus.hasText = true;
+ strucConsensus.autoCalculated = true;
+
+ if (showConsensus)
+ {
+ alignment.addAnnotation(strucConsensus);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.api.AlignViewportI#calcPanelHeight()
+ */
+ @Override
+ public int calcPanelHeight()
+ {
+ // setHeight of panels
+ AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
+ int height = 0;
+ int charHeight = getCharHeight();
+ if (aa != null)
+ {
+ BitSet graphgrp = new BitSet();
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i] == null)
{
- 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);
- }
+ System.err.println("Null annotation row: ignoring.");
+ continue;
}
- if (showQuality)
+ if (!aa[i].visible)
{
- if (quality == null)
+ continue;
+ }
+ if (aa[i].graphGroup > -1)
+ {
+ if (graphgrp.get(aa[i].graphGroup))
{
- 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);
+ continue;
}
+ else
+ {
+ graphgrp.set(aa[i].graphGroup);
+ }
+ }
+ aa[i].height = 0;
+
+ if (aa[i].hasText)
+ {
+ aa[i].height += charHeight;
+ }
+
+ if (aa[i].hasIcons)
+ {
+ aa[i].height += 16;
+ }
+
+ if (aa[i].graph > 0)
+ {
+ aa[i].height += aa[i].graphHeight;
+ }
+
+ if (aa[i].height == 0)
+ {
+ aa[i].height = 20;
}
+
+ height += aa[i].height;
}
- else
+ }
+ if (height == 0)
+ {
+ // set minimum
+ height = 20;
+ }
+ return height;
+ }
+
+ @Override
+ public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ boolean updateCalcs = false;
+ boolean conv = isShowGroupConservation();
+ boolean cons = isShowGroupConsensus();
+ boolean showprf = isShowSequenceLogo();
+ boolean showConsHist = isShowConsensusHistogram();
+ boolean normLogo = isNormaliseSequenceLogo();
+
+ /**
+ * TODO reorder the annotation rows according to group/sequence ordering on
+ * alignment
+ */
+ boolean sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
+ List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
{
- if (alignment.hasRNAStructure())
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
{
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
- strucConsensus.hasText = true;
- strucConsensus.autoCalculated = true;
+ oldrfs.add(aan[an].groupRef);
+ alignment.deleteAnnotation(aan[an], false);
}
}
+ }
+ if (alignment.getGroups() != null)
+ {
+ for (SequenceGroup sg : alignment.getGroups())
+ {
+ updateCalcs = false;
+ if (applyGlobalSettings
+ || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ sg.setNormaliseSequenceLogo(normLogo);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ }
+ /**
+ * show the reference sequence in the alignment view
+ */
+ private boolean displayReferenceSeq=false;
+ /**
+ * colour according to the reference sequence defined on the alignment
+ */
+ private boolean colourByReferenceSeq=false;
+
+ @Override
+ public boolean isDisplayReferenceSeq()
+ {
+ return alignment.hasSeqrep() && displayReferenceSeq;
+ }
+
+ @Override
+ public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+ {
+ this.displayReferenceSeq = displayReferenceSeq;
+ }
+
+ public boolean isColourByReferenceSeq()
+ {
+ return alignment.hasSeqrep() && colourByReferenceSeq;
+ }
+
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ {
+ this.colourByReferenceSeq = colourByReferenceSeq;
+ }
+
+ @Override
+ public Color getSequenceColour(SequenceI seq)
+ {
+ Color sqc = Color.white;
+ if (sequenceColours != null)
+ {
+ sqc = (Color) sequenceColours.get(seq);
+ if (sqc == null)
+ {
+ sqc = Color.white;
+ }
+ }
+ return sqc;
+ }
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+ @Override
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
- if (showConsensus)
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ @Override
+ public void updateSequenceIdColours()
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+ for (SequenceGroup sg : alignment.getGroups())
+ {
+ if (sg.idColour != null)
{
- alignment.addAnnotation(consensus);
- if (strucConsensus != null)
+ for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
{
- alignment.addAnnotation(strucConsensus);
+ sequenceColours.put(s, sg.idColour);
}
}
}
}
+ @Override
+ public void clearSequenceColours()
+ {
+ sequenceColours = null;
+ };
+
+ FeaturesDisplayedI featuresDisplayed = null;
+
+ @Override
+ public FeaturesDisplayedI getFeaturesDisplayed()
+ {
+ return featuresDisplayed;
+ }
+
+ @Override
+ public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
+ {
+ featuresDisplayed = featuresDisplayedI;
+ }
+
+ @Override
+ public boolean areFeaturesDisplayed()
+ {
+ return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+ }
+
+ /**
+ * display setting for showing/hiding sequence features on alignment view
+ */
+ boolean showSequenceFeatures = false;
+
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ @Override
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+ @Override
+ public boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ boolean showSeqFeaturesHeight;
+
+ @Override
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+ }
+
+ @Override
+ public boolean isShowSequenceFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+
+ private boolean showAnnotation = true;
+
+ private boolean rightAlignIds = false;
+
+
+ @Override
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ @Override
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ @Override
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ @Override
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff