/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * 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
+ * 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
* 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.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.workers.ConsensusThread;
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;
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
- *
+ *
* @author jimp
- *
+ *
*/
public abstract class AlignmentViewport implements AlignViewportI
{
}
/**
- *
- *
+ *
+ *
* @return flag indicating if colourchanges propagated to all groups
*/
public boolean getColourAppliesToAllGroups()
/**
* GUI state
- *
+ *
* @return true if percent identity threshold is applied to shading
*/
public boolean getAbovePIDThreshold()
/**
* GUI state
- *
- *
+ *
+ *
* @param b
* indicate if percent identity threshold is applied to shading
*/
/**
* DOCUMENT ME!
- *
+ *
* @param thresh
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getThreshold()
int increment;
/**
- *
+ *
* @param inc
* set the scalar for bleaching colourschemes according to degree of
* conservation
/**
* GUI State
- *
+ *
* @return get scalar for bleaching colourschemes by conservation
*/
public int getIncrement()
/**
* GUI state
- *
+ *
* @return true if conservation based shading is enabled
*/
public boolean getConservationSelected()
/**
* GUI state
- *
+ *
* @param b
* enable conservation based shading
*/
// 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())
sg.cs = null;
continue;
}
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(sg, getHiddenRepSequences());
- }
- else
- {
- try
- {
- sg.cs = cs.getClass().newInstance();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- sg.cs = cs;
- }
- }
-
+ sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.setConsPercGaps(ConsPercGaps);
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(getHiddenRepSequences()), 0,
- sg.getWidth()));
+ recalc = true;
}
else
{
if (getConservationSelected())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(getHiddenRepSequences()), 0,
- getAlignment().getWidth() - 1);
- c.calculate();
- c.verdict(false, getConsPercGaps());
- sg.cs.setConservation(c);
+ sg.cs.setConservationApplied(true);
+ recalc = true;
}
else
{
sg.cs.setConservation(null);
- sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+ if (recalc)
+ {
+ sg.recalcConservation();
+ }
+ else
+ {
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
}
-
}
}
*/
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
return;
}
if (calculator
- .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class)==null)
+ .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
{
calculator.registerWorker(new jalview.workers.ConservationThread(
this, ap));
{
return;
}
- if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class)==null)
+ 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
- .getRegisteredWorkersOfClass(StrucConsensusThread.class)==null)
+ if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
{
calculator.registerWorker(new StrucConsensusThread(this, ap));
}
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
+ {
return false;
+ }
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
}
/**
- *
+ *
* @return flag to indicate if the consensus histogram should be rendered by
* default
*/
}
/**
- *
- *
+ *
+ *
* @return null or the currently selected sequence region
*/
+ @Override
public SequenceGroup getSelectionGroup()
{
return selectionGroup;
/**
* Set the selection group for this window.
- *
+ *
* @param sg
* - group holding references to sequences in this alignment view
- *
+ *
*/
+ @Override
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
}
/**
- *
+ *
* @return
*/
@Override
/**
* unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
+ *
*/
protected String viewId = null;
/**
* 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)
protected boolean showConsensus = true;
+ Hashtable sequenceColours;
+
/**
* 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
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)
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();
* 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
// 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 || selectionGroup.getSize()==0)
+ if (selectionGroup == null || selectionGroup.getSize() == 0)
{
sequences = alignment.getSequencesArray();
AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
/**
* 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;
* 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 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 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
* is true)
* @return AlignmentView
*/
+ @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
* 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;
/**
* return visible region boundaries within given column range
- *
+ *
* @param min
* first column (inclusive, from 0)
* @param max
}
+ @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;
+ }
+
/**
* @return the padGaps
*/
/**
* 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)
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
- cs.alignmentChanged(alignment, null);
+ cs.alignmentChanged(alignment, hiddenRepSequences);
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
if (!alignment.isNucleotide())
{
- 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 (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);
- }
- }
+ initConservation();
+ initQuality();
}
else
{
- if (alignment.hasRNAStructure())
- {
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
- strucConsensus.hasText = true;
- strucConsensus.autoCalculated = true;
- }
+ 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);
}
+ }
+ }
- consensus = new AlignmentAnnotation("Consensus", "PID",
+ private void initRNAStructure()
+ {
+ if (alignment.hasRNAStructure() && strucConsensus == null)
+ {
+ strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+ strucConsensus.hasText = true;
+ strucConsensus.autoCalculated = true;
if (showConsensus)
{
- alignment.addAnnotation(consensus);
- if (strucConsensus != null)
- {
- alignment.addAnnotation(strucConsensus);
- }
+ alignment.addAnnotation(strucConsensus);
}
}
}
/*
* (non-Javadoc)
+ *
* @see jalview.api.AlignViewportI#calcPanelHeight()
*/
public int calcPanelHeight()
// setHeight of panels
AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
int height = 0;
- int charHeight=getCharHeight();
+ int charHeight = getCharHeight();
if (aa != null)
{
- boolean graphgrp[] = null;
+ BitSet graphgrp = new BitSet();
for (int i = 0; i < aa.length; i++)
{
if (aa[i] == null)
}
if (aa[i].graphGroup > -1)
{
- if (graphgrp == null)
- {
- graphgrp = new boolean[aa.length];
- }
- if (graphgrp[aa[i].graphGroup])
+ if (graphgrp.get(aa[i].graphGroup))
{
continue;
}
else
{
- graphgrp[aa[i].graphGroup] = true;
+ 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;
}
}
boolean normLogo = isNormaliseSequenceLogo();
/**
- * TODO reorder the annotation rows according to group/sequence ordering on alignment
+ * TODO reorder the annotation rows according to group/sequence ordering on
+ * alignment
*/
boolean sortg = true;
if (aan[an].autoCalculated && aan[an].groupRef != null)
{
oldrfs.add(aan[an].groupRef);
- alignment.deleteAnnotation(aan[an]);
- aan[an] = null;
+ alignment.deleteAnnotation(aan[an], false);
}
}
}
oldrfs.clear();
}
+ @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;
+ }
+
+ @Override
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+
+ 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)
+ {
+ for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+ {
+ sequenceColours.put(s, sg.idColour);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void clearSequenceColours()
+ {
+ sequenceColours = null;
+ };
}
git://source.jalview.org / jalview.git / blobdiff