/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
int startSeq;
int endSeq;
-
boolean cursorMode = false;
boolean showJVSuffix = true;
boolean scaleRightWrapped = true;
// The following vector holds the features which are
- // currently visible, in the correct order or rendering
+ // currently visible, in the correct order or rendering
public Hashtable featuresDisplayed;
boolean hasHiddenColumns = false;
boolean hasHiddenRows = false;
boolean showHiddenMarkers = true;
-
- public Hashtable [] hconsensus;
+ public Hashtable[] hconsensus;
AlignmentAnnotation consensus;
AlignmentAnnotation conservation;
AlignmentAnnotation quality;
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+ PropertyChangeSupport(this);
boolean ignoreGapsInConsensusCalculation = false;
jalview.bin.JalviewLite applet;
+ Hashtable sequenceColours;
+
boolean MAC = false;
+ Stack historyList = new Stack();
+ Stack redoList = new Stack();
+
+ String sequenceSetID;
+
+ Hashtable hiddenRepSequences;
+
public AlignViewport(AlignmentI al, JalviewLite applet)
{
this.applet = applet;
this.endSeq = al.getHeight() - 1;
setFont(font);
- if(System.getProperty("os.name").startsWith("Mac"))
- MAC = true;
-
+ MAC = new jalview.util.Platform().isAMac();
+
if (applet != null)
{
String param = applet.getParameter("showFullId");
param = applet.getParameter("upperCase");
if (param != null)
{
- if(param.equalsIgnoreCase("bold"))
+ if (param.equalsIgnoreCase("bold"))
+ {
upperCasebold = true;
+ }
}
}
- // We must set conservation and consensus before setting colour,
- // as Blosum and Clustal require this to be done
- updateConservation();
- updateConsensus();
-
if (applet != null)
{
String colour = applet.getParameter("defaultColour");
- if(colour == null)
+ if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
- if(colour !=null)
+ if (colour != null)
+ {
colour = "User Defined";
+ }
}
- if(colour != null)
+ if (colour != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
if (globalColourScheme != null)
}
}
- if(applet.getParameter("userDefinedColour")!=null)
+ if (applet.getParameter("userDefinedColour") != null)
{
- ((UserColourScheme)globalColourScheme).parseAppletParameter(
+ ( (UserColourScheme) globalColourScheme).parseAppletParameter(
applet.getParameter("userDefinedColour"));
}
+ }
+ if (hconsensus == null)
+ {
+ if (!alignment.isNucleotide())
+ {
+ conservation = new AlignmentAnnotation("Conservation",
+ "Conservation of total alignment less than " +
+ ConsPercGaps + "% gaps",
+ new Annotation[1], 0f,
+ 11f,
+ AlignmentAnnotation.BAR_GRAPH);
+ conservation.hasText = true;
+ conservation.autoCalculated = true;
+
+ if (showConservation)
+ {
+ alignment.addAnnotation(conservation);
+ }
+
+ if (showQuality)
+ {
+ 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",
+ new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+ if (showConsensus)
+ {
+ alignment.addAnnotation(consensus);
+ }
}
+
}
public void showSequenceFeatures(boolean b)
return showSequenceFeatures;
}
-
- public void updateConservation()
+ class ConservationThread
+ extends Thread
{
- if(alignment.isNucleotide())
- return;
+ AlignmentPanel ap;
+ public ConservationThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0,
- alignment.getWidth() - 1);
- cons.calculate();
- cons.verdict(false, ConsPercGaps);
- cons.findQuality();
- int alWidth = alignment.getWidth();
- Annotation[] annotations = new Annotation[alWidth];
- Annotation[] qannotations = new Annotation[alWidth];
- String sequence = cons.getConsSequence().getSequence();
- float minR, minG, minB, maxR, maxG, maxB;
- minR = 0.3f;
- minG = 0.0f;
- minB = 0f;
- maxR = 1.0f - minR;
- maxG = 0.9f - minG;
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
- float min = 0f;
- float max = 11f;
- float qmin = cons.qualityRange[0].floatValue();
- float qmax = cons.qualityRange[1].floatValue();
-
- for (int i = 0; i < alWidth; i++)
+ public void run()
{
- float value = 0;
try
{
- value = Integer.parseInt(sequence.charAt(i) + "");
- }
- catch (Exception ex)
- {
- if (sequence.charAt(i) == '*')
+ updatingConservation = true;
+
+ while (UPDATING_CONSERVATION)
{
- value = 11;
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+ Thread.sleep(200);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
}
- if (sequence.charAt(i) == '+')
+
+ UPDATING_CONSERVATION = true;
+
+ int alWidth = alignment.getWidth();
+ if (alWidth < 0)
{
- value = 10;
+ return;
}
- }
- float vprop = value - min;
- vprop /= max;
-
- annotations[i] = new Annotation(sequence.charAt(i) + "",
- "", ' ', value,
- new Color(minR + maxR * vprop,
- minG + maxG * vprop,
- minB + maxB * vprop));
- // Quality calc
- value = ( (Double) cons.quality.elementAt(i)).floatValue();
- vprop = value - qmin;
- vprop /= qmax;
- qannotations[i] = new Annotation(" ",
- String.valueOf(value), ' ', value,
- new
- Color(minR + maxR * vprop,
- minG + maxG * vprop,
- minB + maxB * vprop));
- }
- if (conservation == null)
- {
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " +
- ConsPercGaps + "% gaps",
- annotations,
- 0f, // cons.qualityRange[0].floatValue(),
- 11f, // cons.qualityRange[1].floatValue()
- AlignmentAnnotation.BAR_GRAPH);
- if (showConservation)
+ Conservation cons = new jalview.analysis.Conservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth - 1);
+
+ cons.calculate();
+ cons.verdict(false, ConsPercGaps);
+
+ if (quality != null)
+ {
+ cons.findQuality();
+ }
+
+ char[] sequence = cons.getConsSequence().getSequence();
+ float minR;
+ float minG;
+ float minB;
+ float maxR;
+ float maxG;
+ float maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ char c;
+
+ conservation.annotations = new Annotation[alWidth];
+
+ if (quality != null)
+ {
+ quality.graphMax = cons.qualityRange[1].floatValue();
+ quality.annotations = new Annotation[alWidth];
+ qmin = cons.qualityRange[0].floatValue();
+ qmax = cons.qualityRange[1].floatValue();
+ }
+
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+
+ c = sequence[i];
+
+ if (Character.isDigit(c))
+ {
+ value = (int) (c - '0');
+ }
+ else if (c == '*')
+ {
+ value = 11;
+ }
+ else if (c == '+')
+ {
+ value = 10;
+ }
+
+ float vprop = value - min;
+ vprop /= max;
+ conservation.annotations[i] =
+ new Annotation(String.valueOf(c),
+ String.valueOf(value), ' ', value,
+ new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop),
+ minB + (maxB * vprop)));
+
+ // Quality calc
+ if (quality != null)
+ {
+ value = ( (Double) cons.quality.elementAt(i)).floatValue();
+ vprop = value - qmin;
+ vprop /= qmax;
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+ ' ',
+ value,
+ new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop),
+ minB + (maxB * vprop)));
+ }
+ }
+ }
+ catch (OutOfMemoryError error)
{
- alignment.addAnnotation(conservation);
+ System.out.println("Out of memory calculating conservation!!");
+ conservation = null;
+ quality = null;
+ System.gc();
}
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- qannotations,
- cons.qualityRange[0].floatValue(),
- cons.qualityRange[1].floatValue(),
- AlignmentAnnotation.BAR_GRAPH);
- if (showQuality)
+
+ UPDATING_CONSERVATION = false;
+ updatingConservation = false;
+
+ if (ap != null)
{
- alignment.addAnnotation(quality);
+ ap.paintAlignment(true);
}
+
}
- else
+ }
+
+ ConservationThread conservationThread;
+
+ ConsensusThread consensusThread;
+
+ boolean consUpdateNeeded = false;
+
+ static boolean UPDATING_CONSENSUS = false;
+
+ static boolean UPDATING_CONSERVATION = false;
+
+ boolean updatingConsensus = false;
+
+ boolean updatingConservation = false;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateConservation(final AlignmentPanel ap)
+ {
+ if (alignment.isNucleotide() || conservation == null)
{
- conservation.annotations = annotations;
- quality.annotations = qannotations;
- quality.graphMax = cons.qualityRange[1].floatValue();
+ return;
}
+ conservationThread = new ConservationThread(ap);
+ conservationThread.start();
}
- public void updateConsensus()
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateConsensus(final AlignmentPanel ap)
{
- // this routine prevents vconsensus becoming a new object each time
- // consenus is calculated. Important for speed of Blosum62
- // and PID colouring of alignment
- int aWidth = alignment.getWidth();
-
- Annotation[] annotations = new Annotation[aWidth];
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(),
- 0, aWidth,
- hconsensus);
+ consensusThread = new ConsensusThread(ap);
+ consensusThread.start();
+ }
- for (int i = 0; i < aWidth; i++)
+ class ConsensusThread
+ extends Thread
+ {
+ AlignmentPanel ap;
+ public ConsensusThread(AlignmentPanel ap)
{
- float value = 0;
- if(ignoreGapsInConsensusCalculation)
- value = ((Float)hconsensus[i].get("pid_nogaps")).floatValue();
- else
- value = ((Float)hconsensus[i].get("pid_gaps")).floatValue();
+ this.ap = ap;
+ }
- String maxRes = hconsensus[i].get("maxResidue").toString();
- String mouseOver = hconsensus[i].get("maxResidue") + " ";
- if (maxRes.length() > 1)
+ public void run()
+ {
+ updatingConsensus = true;
+ while (UPDATING_CONSENSUS)
{
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
}
+ UPDATING_CONSENSUS = true;
- mouseOver += (int) value + "%";
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+ try
+ {
+ int aWidth = alignment.getWidth();
+ if (aWidth < 0)
+ {
+ return;
+ }
- }
+ consensus.annotations = null;
+ consensus.annotations = new Annotation[aWidth];
- if (consensus == null)
- {
- consensus = new AlignmentAnnotation("Consensus",
- "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- if (showConsensus)
- {
- alignment.addAnnotation(consensus);
- }
- }
- else
- {
- consensus.annotations = annotations;
- }
+ hconsensus = new Hashtable[aWidth];
+ AAFrequency.calculate(alignment.getSequencesArray(),
+ 0,
+ alignment.getWidth(),
+ hconsensus);
+
+ for (int i = 0; i < aWidth; i++)
+ {
+ float value = 0;
+ if (ignoreGapsInConsensusCalculation)
+ {
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
+ floatValue();
+ }
+ else
+ {
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
+ floatValue();
+ }
+
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+
+ if (maxRes.length() > 1)
+ {
+ mouseOver = "[" + maxRes + "] ";
+ maxRes = "+";
+ }
+
+ mouseOver += ( (int) value + "%");
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+ value);
+ }
- if(globalColourScheme!=null)
+ if (globalColourScheme != null)
+ {
globalColourScheme.setConsensus(hconsensus);
+ }
+
+ }
+ catch (OutOfMemoryError error)
+ {
+ alignment.deleteAnnotation(consensus);
+ consensus = null;
+ hconsensus = null;
+ System.out.println("Out of memory calculating consensus!!");
+ System.gc();
+ }
+ UPDATING_CONSENSUS = false;
+ updatingConsensus = false;
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
+ }
}
+
/**
* get the consensus sequence as displayed under the PID consensus annotation row.
* @return consensus sequence as a new sequence object
* get the consensus sequence as displayed under the PID consensus annotation row.
* @return consensus sequence as a new sequence object
*/
- public SequenceI getConsensusSeq() {
- if (consensus==null)
- updateConsensus();
- if (consensus==null)
+ public SequenceI getConsensusSeq()
+ {
+ if (consensus == null)
+ {
return null;
- StringBuffer seqs=new StringBuffer();
- for (int i=0; i<consensus.annotations.length; i++) {
- if (consensus.annotations[i]!=null) {
+ }
+ StringBuffer seqs = new StringBuffer();
+ for (int i = 0; i < consensus.annotations.length; i++)
+ {
+ if (consensus.annotations[i] != null)
+ {
if (consensus.annotations[i].description.charAt(0) == '[')
+ {
seqs.append(consensus.annotations[i].description.charAt(1));
+ }
else
+ {
seqs.append(consensus.annotations[i].displayCharacter);
+ }
}
}
SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+ sq.setDescription("Percentage Identity Consensus " +
+ ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
+ ""));
return sq;
}
+
public SequenceGroup getSelectionGroup()
{
return selectionGroup;
}
java.awt.Frame nullFrame;
+ protected FeatureSettings featureSettings=null;
public void setFont(Font f)
{
font = f;
- if(nullFrame == null)
+ if (nullFrame == null)
{
nullFrame = new java.awt.Frame();
nullFrame.addNotify();
setCharHeight(fm.getHeight());
charWidth = fm.charWidth('M');
- if(upperCasebold)
+ if (upperCasebold)
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
fm = nullFrame.getGraphics().getFontMetrics(f2);
public void setHiddenColumns(ColumnSelection colsel)
{
this.colSel = colsel;
- if(colSel.getHiddenColumns()!=null)
+ if (colSel.getHiddenColumns() != null)
+ {
hasHiddenColumns = true;
+ }
}
public ColumnSelection getColumnSelection()
public void setIgnoreGapsConsensus(boolean b)
{
ignoreGapsInConsensusCalculation = b;
- updateConsensus();
- if (globalColourScheme!=null)
+ updateConsensus(null);
+ if (globalColourScheme != null)
{
globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensusCalculation);
}
}
public void addPropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
- changeSupport.addPropertyChangeListener(listener);
+ changeSupport.addPropertyChangeListener(listener);
}
/**
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
- changeSupport.removePropertyChangeListener(listener);
+ changeSupport.removePropertyChangeListener(listener);
}
/**
*/
public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
{
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);
}
-
-
public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
}
+
public void hideSelectedColumns()
{
if (colSel.size() < 1)
+ {
return;
+ }
colSel.hideSelectedColumns();
setSelectionGroup(null);
public void invertColumnSelection()
{
- int column;
for (int i = 0; i < alignment.getWidth(); i++)
{
- column = i;
-
- if (colSel.contains(column))
- colSel.removeElement(column);
+ if (colSel.contains(i))
+ {
+ colSel.removeElement(i);
+ }
else
- colSel.addElement(column);
-
+ {
+ if (!hasHiddenColumns || colSel.isVisible(i))
+ {
+ colSel.addElement(i);
+ }
+ }
}
}
-
public void hideColumns(int start, int end)
{
- if(start==end)
+ if (start == end)
+ {
colSel.hideColumns(start);
+ }
else
+ {
colSel.hideColumns(start, end);
+ }
hasHiddenColumns = true;
}
+ public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+ {
+ int sSize = sg.getSize();
+ if (sSize < 2)
+ {
+ return;
+ }
+
+ if (hiddenRepSequences == null)
+ {
+ hiddenRepSequences = new Hashtable();
+ }
+
+ hiddenRepSequences.put(repSequence, sg);
+
+ //Hide all sequences except the repSequence
+ SequenceI[] seqs = new SequenceI[sSize - 1];
+ int index = 0;
+ for (int i = 0; i < sSize; i++)
+ {
+ if (sg.getSequenceAt(i) != repSequence)
+ {
+ if (index == sSize - 1)
+ {
+ return;
+ }
+
+ seqs[index++] = sg.getSequenceAt(i);
+ }
+ }
+
+ hideSequence(seqs);
+
+ }
+
public void hideAllSelectedSeqs()
{
- if (selectionGroup == null)
+ if (selectionGroup == null || selectionGroup.getSize()<1)
+ {
return;
+ }
SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
setSelectionGroup(null);
}
- public void hideSequence(SequenceI [] seq)
+ public void hideSequence(SequenceI[] seq)
{
- if(seq!=null)
+ if (seq != null)
{
for (int i = 0; i < seq.length; i++)
+ {
alignment.getHiddenSequences().hideSequence(seq[i]);
+ }
hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
- if(colSel.getHiddenColumns()==null)
+ if (colSel.getHiddenColumns() == null)
+ {
hasHiddenColumns = false;
+ }
}
public void showAllHiddenColumns()
public void showAllHiddenSeqs()
{
- if(alignment.getHiddenSequences().getSize()>0)
+ if (alignment.getHiddenSequences().getSize() > 0)
{
- if(selectionGroup==null)
+ if (selectionGroup == null)
{
selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
+ selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- Vector tmp = alignment.getHiddenSequences().showAll();
- for(int t=0; t<tmp.size(); t++)
+ Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
+ for (int t = 0; t < tmp.size(); t++)
{
selectionGroup.addSequence(
- (SequenceI)tmp.elementAt(t), false
+ (SequenceI) tmp.elementAt(t), false
);
}
firePropertyChange("alignment", null, alignment.getSequences());
hasHiddenRows = false;
+ hiddenRepSequences = null;
}
}
SequenceI[] sequences;
if (selectionGroup == null)
+ {
sequences = alignment.getSequencesArray();
+ }
else
+ {
sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+ }
return sequences;
}
* which contain hidden columns.
* @return String[]
*/
- public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+ public jalview.datamodel.CigarArray getViewAsCigars(boolean
+ selectedRegionOnly)
{
- CigarArray selection=null;
- SequenceI [] seqs= null;
+ CigarArray selection = null;
+ SequenceI[] seqs = null;
int i, iSize;
int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
+ if (selectedRegionOnly && selectionGroup != null)
{
- iSize = selectionGroup.getSize(false);
+ iSize = selectionGroup.getSize();
seqs = selectionGroup.getSequencesInOrder(alignment);
start = selectionGroup.getStartRes();
end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
{
iSize = alignment.getHeight();
seqs = alignment.getSequencesArray();
- end = alignment.getWidth()-1;
+ end = alignment.getWidth() - 1;
}
SeqCigar[] selseqs = new SeqCigar[iSize];
- for(i=0; i<iSize; i++)
+ for (i = 0; i < iSize; i++)
{
selseqs[i] = new SeqCigar(seqs[i], start, end);
}
- selection=new CigarArray(selseqs);
+ selection = new CigarArray(selseqs);
// now construct the CigarArray operations
- if (hasHiddenColumns) {
+ if (hasHiddenColumns)
+ {
Vector regions = colSel.getHiddenColumns();
- int [] region;
+ int[] region;
int hideStart, hideEnd;
- int last=start;
- for (int j = 0; last<end & j < regions.size(); j++)
+ int last = start;
+ for (int j = 0; last < end & j < regions.size(); j++)
{
region = (int[]) regions.elementAt(j);
hideStart = region[0];
hideEnd = region[1];
// edit hidden regions to selection range
- if(hideStart<last) {
+ if (hideStart < last)
+ {
if (hideEnd > last)
{
hideStart = last;
- } else
+ }
+ else
+ {
continue;
+ }
}
- if (hideStart>end)
+ if (hideStart > end)
+ {
break;
+ }
- if (hideEnd>end)
- hideEnd=end;
+ if (hideEnd > end)
+ {
+ hideEnd = end;
+ }
- if (hideStart>hideEnd)
+ if (hideStart > hideEnd)
+ {
break;
+ }
/**
* form operations...
*/
- if (last<hideStart)
- selection.addOperation(CigarArray.M, hideStart-last);
- selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
- last = hideEnd+1;
+ if (last < hideStart)
+ {
+ selection.addOperation(CigarArray.M, hideStart - last);
+ }
+ selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
+ last = hideEnd + 1;
}
// Final match if necessary.
- if (last<end)
- selection.addOperation(CigarArray.M, end-last+1);
- } else {
- selection.addOperation(CigarArray.M, end-start+1);
+ if (last < end)
+ {
+ selection.addOperation(CigarArray.M, end - last + 1);
+ }
+ }
+ else
+ {
+ selection.addOperation(CigarArray.M, end - start + 1);
}
return selection;
}
+
/**
* 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
*/
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
+ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ {
// JBPNote:
// this is here because the AlignmentView constructor modifies the CigarArray
// object. Refactoring of Cigar and alignment view representation should
// be done to remove redundancy.
CigarArray aligview = getViewAsCigars(selectedOnly);
- if (aligview!=null) {
- return new AlignmentView(aligview,
- (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
+ if (aligview != null)
+ {
+ return new AlignmentView(aligview,
+ (selectedOnly && selectionGroup != null) ?
+ selectionGroup.getStartRes() : 0);
}
return null;
}
+
/**
* This method returns the visible alignment as text, as
* seen on the GUI, ie if columns are hidden they will not
* which contain hidden columns.
* @return String[]
*/
- public String [] getViewAsString(boolean selectedRegionOnly)
+ public String[] getViewAsString(boolean selectedRegionOnly)
{
- String [] selection = null;
- SequenceI [] seqs= null;
+ String[] selection = null;
+ SequenceI[] seqs = null;
int i, iSize;
int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
+ if (selectedRegionOnly && selectionGroup != null)
{
- iSize = selectionGroup.getSize(false);
+ iSize = selectionGroup.getSize();
seqs = selectionGroup.getSequencesInOrder(alignment);
start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes()+1;
+ end = selectionGroup.getEndRes() + 1;
}
else
{
selection = new String[iSize];
-
- for(i=0; i<iSize; i++)
+ for (i = 0; i < iSize; i++)
{
if (hasHiddenColumns)
{
- StringBuffer visibleSeq = new StringBuffer();
- Vector regions = colSel.getHiddenColumns();
-
- int blockStart = start, blockEnd=end;
- int [] region;
- int hideStart, hideEnd;
+ StringBuffer visibleSeq = new StringBuffer();
+ Vector regions = colSel.getHiddenColumns();
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
+ int blockStart = start, blockEnd = end;
+ int[] region;
+ int hideStart, hideEnd;
- if(hideStart < start)
- {
- continue;
- }
+ for (int j = 0; j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
- blockStart = Math.min(blockStart, hideEnd+1);
- blockEnd = Math.min(blockEnd, hideStart);
+ if (hideStart < start)
+ {
+ continue;
+ }
- if(blockStart>blockEnd)
- {
- break;
- }
+ blockStart = Math.min(blockStart, hideEnd + 1);
+ blockEnd = Math.min(blockEnd, hideStart);
+ if (blockStart > blockEnd)
+ {
+ break;
+ }
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
- blockStart = hideEnd+1;
- blockEnd = end;
- }
+ blockStart = hideEnd + 1;
+ blockEnd = end;
+ }
- if(end>blockStart)
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
+ if (end > blockStart)
+ {
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));
+ }
- selection[i] = visibleSeq.toString();
+ selection[i] = visibleSeq.toString();
}
else
{
- selection[i] = seqs[i].getSequence(start, end);
+ selection[i] = seqs[i].getSequenceAsString(start, end);
}
}
showHiddenMarkers = show;
}
+ public Color getSequenceColour(SequenceI seq)
+ {
+ if (sequenceColours == null || !sequenceColours.containsKey(seq))
+ {
+ return Color.white;
+ }
+ else
+ {
+ return (Color) sequenceColours.get(seq);
+ }
+ }
+
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ public String getSequenceSetId()
+ {
+ if (sequenceSetID == null)
+ {
+ sequenceSetID = alignment.hashCode() + "";
+ }
+
+ return sequenceSetID;
+ }
+
+ public void alignmentChanged(AlignmentPanel ap)
+ {
+ alignment.padGaps();
+
+ if (hconsensus != null && autocalculateConsensus)
+ {
+ updateConsensus(ap);
+ updateConservation(ap);
+ }
+
+ //Reset endRes of groups if beyond alignment width
+ int alWidth = alignment.getWidth();
+ Vector groups = alignment.getGroups();
+ if (groups != null)
+ {
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ if (sg.getEndRes() > alWidth)
+ {
+ sg.setEndRes(alWidth - 1);
+ }
+ }
+ }
+
+ if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
+ {
+ selectionGroup.setEndRes(alWidth - 1);
+ }
+
+ resetAllColourSchemes();
+
+ //AW alignment.adjustSequenceAnnotations();
+ }
+
+ void resetAllColourSchemes()
+ {
+ ColourSchemeI cs = globalColourScheme;
+ if (cs != null)
+ {
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ( (ClustalxColourScheme) cs).
+ resetClustalX(alignment.getSequences(),
+ alignment.getWidth());
+ }
+
+ cs.setConsensus(hconsensus);
+ if (cs.conservationApplied())
+ {
+ Alignment al = (Alignment) alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3,
+ al.getSequences(), 0,
+ al.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, ConsPercGaps);
+
+ cs.setConservation(c);
+ }
+ }
+
+ int s, sSize = alignment.getGroups().size();
+ for (s = 0; s < sSize; s++)
+ {
+ SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+ if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+ {
+ ( (ClustalxColourScheme) sg.cs).resetClustalX(
+ sg.getSequences(hiddenRepSequences), sg.getWidth());
+ }
+ sg.recalcConservation();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff