X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=6cec30a2bd7db21e3e06b4c967b466fc7b7bb43a;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=a53a68cf647528fe965bb05a13342d508d12dece;hpb=7d33612534e949fc19d00cd057fd8af9f7cd66eb;p=jalview.git
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a53a68c..6cec30a 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,27 +1,30 @@
/*
- * 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.
- *
- * 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 .
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.api.AlignmentViewPanel;
+import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
@@ -32,7 +35,6 @@ import jalview.datamodel.SequenceCollectionI;
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;
@@ -40,7 +42,9 @@ import jalview.workers.AlignCalcManager;
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;
@@ -49,9 +53,9 @@ import java.util.Vector;
/**
* 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
{
@@ -96,8 +100,8 @@ public abstract class AlignmentViewport implements AlignViewportI
}
/**
- *
- *
+ *
+ *
* @return flag indicating if colourchanges propagated to all groups
*/
public boolean getColourAppliesToAllGroups()
@@ -109,7 +113,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* GUI state
- *
+ *
* @return true if percent identity threshold is applied to shading
*/
public boolean getAbovePIDThreshold()
@@ -119,8 +123,8 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* GUI state
- *
- *
+ *
+ *
* @param b
* indicate if percent identity threshold is applied to shading
*/
@@ -133,7 +137,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* DOCUMENT ME!
- *
+ *
* @param thresh
* DOCUMENT ME!
*/
@@ -144,7 +148,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getThreshold()
@@ -155,7 +159,7 @@ public abstract class AlignmentViewport implements AlignViewportI
int increment;
/**
- *
+ *
* @param inc
* set the scalar for bleaching colourschemes according to degree of
* conservation
@@ -167,7 +171,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* GUI State
- *
+ *
* @return get scalar for bleaching colourschemes by conservation
*/
public int getIncrement()
@@ -179,7 +183,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* GUI state
- *
+ *
* @return true if conservation based shading is enabled
*/
public boolean getConservationSelected()
@@ -189,7 +193,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* GUI state
- *
+ *
* @param b
* enable conservation based shading
*/
@@ -209,6 +213,27 @@ public abstract class AlignmentViewport implements AlignViewportI
// 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())
@@ -218,29 +243,13 @@ public abstract class AlignmentViewport implements AlignViewportI
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
{
@@ -249,20 +258,22 @@ public abstract class AlignmentViewport implements AlignViewportI
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);
}
-
}
}
@@ -297,6 +308,14 @@ public abstract class AlignmentViewport implements AlignViewportI
*/
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
@@ -373,7 +392,7 @@ public abstract class AlignmentViewport implements AlignViewportI
return;
}
if (calculator
- .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class)==null)
+ .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
{
calculator.registerWorker(new jalview.workers.ConservationThread(
this, ap));
@@ -390,7 +409,7 @@ public abstract class AlignmentViewport implements AlignViewportI
{
return;
}
- if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class)==null)
+ if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
{
calculator.registerWorker(new ConsensusThread(this, ap));
}
@@ -402,7 +421,8 @@ public abstract class AlignmentViewport implements AlignViewportI
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
@@ -410,8 +430,7 @@ public abstract class AlignmentViewport implements AlignViewportI
{
return;
}
- if (calculator
- .getRegisteredWorkersOfClass(StrucConsensusThread.class)==null)
+ if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
{
calculator.registerWorker(new StrucConsensusThread(this, ap));
}
@@ -427,7 +446,9 @@ public abstract class AlignmentViewport implements AlignViewportI
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
+ {
return false;
+ }
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
@@ -545,7 +566,7 @@ public abstract class AlignmentViewport implements AlignViewportI
}
/**
- *
+ *
* @return flag to indicate if the consensus histogram should be rendered by
* default
*/
@@ -590,10 +611,11 @@ public abstract class AlignmentViewport implements AlignViewportI
}
/**
- *
- *
+ *
+ *
* @return null or the currently selected sequence region
*/
+ @Override
public SequenceGroup getSelectionGroup()
{
return selectionGroup;
@@ -601,11 +623,12 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* 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;
@@ -614,10 +637,6 @@ public abstract class AlignmentViewport implements AlignViewportI
public void setHiddenColumns(ColumnSelection colsel)
{
this.colSel = colsel;
- if (colSel.getHiddenColumns() != null)
- {
- hasHiddenColumns = true;
- }
}
@Override
@@ -626,13 +645,18 @@ public abstract class AlignmentViewport implements AlignViewportI
return colSel;
}
+ @Override
public void setColumnSelection(ColumnSelection colSel)
{
this.colSel = colSel;
+ if (colSel != null)
+ {
+ updateHiddenColumns();
+ }
}
/**
- *
+ *
* @return
*/
@Override
@@ -648,15 +672,22 @@ public abstract class AlignmentViewport implements AlignViewportI
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;
@@ -674,6 +705,7 @@ public abstract class AlignmentViewport implements AlignViewportI
sequenceSetID = new String(newid);
}
+ @Override
public String getSequenceSetId()
{
if (sequenceSetID == null)
@@ -686,7 +718,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
+ *
*/
protected String viewId = null;
@@ -719,10 +751,10 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* 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)
@@ -743,7 +775,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* 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)
@@ -781,9 +813,11 @@ public abstract class AlignmentViewport implements AlignViewportI
protected boolean showConsensus = true;
+ Hashtable sequenceColours;
+
/**
* Property change listener for changes in alignment
- *
+ *
* @param listener
* DOCUMENT ME!
*/
@@ -795,7 +829,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* DOCUMENT ME!
- *
+ *
* @param listener
* DOCUMENT ME!
*/
@@ -807,7 +841,7 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* Property change listener for changes in alignment
- *
+ *
* @param prop
* DOCUMENT ME!
* @param oldvalue
@@ -833,7 +867,6 @@ public abstract class AlignmentViewport implements AlignViewportI
colSel.hideSelectedColumns();
setSelectionGroup(null);
- hasHiddenColumns = true;
}
public void hideColumns(int start, int end)
@@ -846,23 +879,17 @@ public abstract class AlignmentViewport implements AlignViewportI
{
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
@@ -875,11 +902,12 @@ public abstract class AlignmentViewport implements AlignViewportI
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- Vector tmp = alignment.getHiddenSequences().showAll(
+ List 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;
@@ -894,7 +922,8 @@ public abstract class AlignmentViewport implements AlignViewportI
public void showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ List tmp = alignment.getHiddenSequences().showSequence(
+ index,
hiddenRepSequences);
if (tmp.size() > 0)
{
@@ -904,9 +933,10 @@ public abstract class AlignmentViewport implements AlignViewportI
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)
@@ -940,12 +970,30 @@ public abstract class AlignmentViewport implements AlignViewportI
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();
@@ -984,8 +1032,8 @@ public abstract class AlignmentViewport implements AlignViewportI
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)
@@ -994,32 +1042,24 @@ public abstract class AlignmentViewport implements AlignViewportI
: 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;
@@ -1028,7 +1068,7 @@ public abstract class AlignmentViewport implements AlignViewportI
// 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();
@@ -1048,12 +1088,8 @@ public abstract class AlignmentViewport implements AlignViewportI
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;
@@ -1068,63 +1104,35 @@ public abstract class AlignmentViewport implements AlignViewportI
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[]
- */
+
+ @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;
@@ -1146,7 +1154,7 @@ public abstract class AlignmentViewport implements AlignViewportI
}
selection = new String[iSize];
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
selection = colSel.getVisibleSequenceStrings(start, end, seqs);
}
@@ -1161,15 +1169,8 @@ public abstract class AlignmentViewport implements AlignViewportI
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();
@@ -1178,7 +1179,7 @@ public abstract class AlignmentViewport implements AlignViewportI
do
{
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
if (start == 0)
{
@@ -1199,7 +1200,7 @@ public abstract class AlignmentViewport implements AlignViewportI
regions.addElement(new int[]
{ start, end });
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
start = colSel.adjustForHiddenColumns(end);
start = colSel.getHiddenBoundaryLeft(start) + 1;
@@ -1214,18 +1215,37 @@ public abstract class AlignmentViewport implements AlignViewportI
}
- /**
- * @return the padGaps
- */
+ @Override
+ public List getVisibleAlignmentAnnotation(boolean selectedOnly)
+ {
+ ArrayList ala = new ArrayList();
+ 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;
@@ -1234,9 +1254,10 @@ public abstract class AlignmentViewport implements AlignViewportI
/**
* apply any post-edit constraints and trigger any calculations needed after
* an edit has been performed on the alignment
- *
+ *
* @param ap
*/
+ @Override
public void alignmentChanged(AlignmentViewPanel ap)
{
if (isPadGaps())
@@ -1288,7 +1309,7 @@ public abstract class AlignmentViewport implements AlignViewportI
ColourSchemeI cs = globalColourScheme;
if (cs != null)
{
- cs.alignmentChanged(alignment, null);
+ cs.alignmentChanged(alignment, hiddenRepSequences);
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
@@ -1319,75 +1340,95 @@ public abstract class AlignmentViewport implements AlignViewportI
{
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();
+ }
+ }
- consensus = new AlignmentAnnotation("Consensus", "PID",
+ 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);
- 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()
*/
+ @Override
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)
@@ -1401,41 +1442,37 @@ public abstract class AlignmentViewport implements AlignViewportI
}
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;
}
}
@@ -1459,7 +1496,8 @@ public abstract class AlignmentViewport implements AlignViewportI
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;
@@ -1477,8 +1515,7 @@ public abstract class AlignmentViewport implements AlignViewportI
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);
}
}
}
@@ -1514,5 +1551,178 @@ public abstract class AlignmentViewport implements AlignViewportI
}
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;
+ }
+
+ @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;
+ };
+
+ 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;
+ }
}