/*
* 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
*/
package jalview.gui;
+import java.util.*;
+
+import java.awt.*;
+
import jalview.analysis.*;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
-
-import java.awt.*;
-
-import java.util.*;
-
+import jalview.structure.StructureSelectionManager;
/**
* DOCUMENT ME!
boolean renderGaps = true;
boolean showSequenceFeatures = false;
boolean showAnnotation = true;
- boolean showConservation = true;
- boolean showQuality = true;
- boolean showIdentity = true;
boolean colourAppliesToAllGroups = true;
ColourSchemeI globalColourScheme = null;
boolean conservationColourSelected = false;
boolean validCharWidth;
int wrappedWidth;
Font font;
+ boolean seqNameItalics;
AlignmentI alignment;
ColumnSelection colSel = new ColumnSelection();
int threshold;
/** DOCUMENT ME!! */
- public Vector vconsensus;
+ public Hashtable [] hconsensus;
AlignmentAnnotation consensus;
AlignmentAnnotation conservation;
AlignmentAnnotation quality;
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
// JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+ PropertyChangeSupport(this);
boolean ignoreGapsInConsensusCalculation = false;
boolean gatherViewsHere = false;
+ Stack historyList = new Stack();
+ Stack redoList = new Stack();
+
+ Hashtable sequenceColours;
+
+ int thresholdTextColour = 0;
+ Color textColour = Color.black;
+ Color textColour2 = Color.white;
+
+ boolean rightAlignIds = false;
+
+ Hashtable hiddenRepSequences;
+
- public AlignViewport(AlignmentI al, boolean dataset)
- {
- isDataset = dataset;
- setAlignment(al);
- init();
- }
/**
* Creates a new AlignViewport object.
*
* @param al AlignmentI
* @param hiddenColumns ColumnSelection
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ {
setAlignment(al);
- if (hiddenColumns!=null) {
+ if (hiddenColumns != null)
+ {
this.colSel = hiddenColumns;
if (hiddenColumns.getHiddenColumns() != null)
+ {
hasHiddenColumns = true;
}
+ }
init();
}
showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
- showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
- showQuality = Cache.getDefault("SHOW_QUALITY", true);
- showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
+ rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
- padGaps = Cache.getDefault("PAD_GAPS", false);
+ padGaps = Cache.getDefault("PAD_GAPS", true);
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
String fontSize = Cache.getDefault("FONT_SIZE", "10");
+ seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
int style = 0;
if (fontStyle.equals("bold"))
setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
-
alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
- if(vconsensus==null && !isDataset)
+ if(hconsensus==null && !isDataset)
{
- updateConservation();
- updateConsensus();
+ 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 (Cache.getDefault("SHOW_CONSERVATION", true))
+ {
+ alignment.addAnnotation(conservation);
+ }
+
+ if (Cache.getDefault("SHOW_QUALITY", true))
+ {
+ 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 (Cache.getDefault("SHOW_IDENTITY", true))
+ {
+ alignment.addAnnotation(consensus);
+ }
}
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
if (globalColourScheme instanceof UserColourScheme)
{
globalColourScheme = UserDefinedColours.loadDefaultColours();
- ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
+ ( (UserColourScheme) globalColourScheme).setThreshold(0,
+ getIgnoreGapsConsensus());
}
if (globalColourScheme != null)
{
- globalColourScheme.setConsensus(vconsensus);
+ globalColourScheme.setConsensus(hconsensus);
}
}
+
+ wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
}
return showSequenceFeatures;
}
- /**
- * DOCUMENT ME!
- */
- public void updateConservation()
+ class ConservationThread
+ extends Thread
{
- if(alignment.isNucleotide())
- return;
-
- try{
- 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();
+ AlignmentPanel ap;
+ public ConservationThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
- int alWidth = alignment.getWidth();
- Annotation[] annotations = new Annotation[alWidth];
- Annotation[] qannotations = new Annotation[alWidth];
- String 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 = cons.qualityRange[0].floatValue();
- float qmax = cons.qualityRange[1].floatValue();
-
- for (int i = 0; i < alWidth; i++)
+ public void run()
+ {
+ try
{
- float value = 0;
+ updatingConservation = true;
- try
+ while (UPDATING_CONSERVATION)
{
- value = Integer.parseInt(sequence.charAt(i) + "");
- }
- catch (Exception ex)
- {
- if (sequence.charAt(i) == '*')
+ try
{
- value = 11;
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+ Thread.sleep(200);
}
-
- if (sequence.charAt(i) == '+')
+ catch (Exception ex)
{
- value = 10;
+ ex.printStackTrace();
}
}
- float vprop = value - min;
- vprop /= max;
- annotations[i] = new Annotation(sequence.charAt(i) + "",
- String.valueOf(value), ' ', value,
- new Color(minR + (maxR * vprop),
- minG + (maxG * vprop),
- minB + (maxB * vprop)));
-
- // Quality calc
- value = ( (Double) cons.quality.get(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)));
- }
+ UPDATING_CONSERVATION = true;
+
- if (conservation == null)
+ int alWidth = alignment.getWidth();
+ if(alWidth<0)
{
- 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)
+ return;
+ }
+
+ 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)
{
- alignment.addAnnotation(conservation);
+ quality.graphMax = cons.qualityRange[1].floatValue();
+ quality.annotations = new Annotation[alWidth];
+ qmin = cons.qualityRange[0].floatValue();
+ qmax = cons.qualityRange[1].floatValue();
}
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- qannotations,
- cons.qualityRange[0].floatValue(),
- cons.qualityRange[1].floatValue(),
- AlignmentAnnotation.BAR_GRAPH);
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+
+ c = sequence[i];
- if (showQuality)
+ if (Character.isDigit(c))
{
- alignment.addAnnotation(quality);
+ 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.get(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)));
+ }
}
}
- else
- {
- conservation.annotations = annotations;
- quality.annotations = qannotations;
- quality.graphMax = cons.qualityRange[1].floatValue();
- }
- }
- catch (OutOfMemoryError error)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ catch (OutOfMemoryError error)
{
- public void run()
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating conservation!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
- System.out.println("Conservation calculation: " + error);
- System.gc();
+
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory calculating conservation!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
+ conservation = null;
+ quality = null;
+
+ System.out.println("Conservation calculation: " + error);
+ System.gc();
+
+ }
+
+ UPDATING_CONSERVATION = false;
+ updatingConservation = false;
+
+ if(ap!=null)
+ {
+ ap.paintAlignment(true);
+ }
}
}
+
+ 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)
+ {
+ return;
+ }
+
+ conservationThread = new ConservationThread(ap);
+ conservationThread.start();
+ }
+
/**
* DOCUMENT ME!
*/
- public void updateConsensus()
+ public void updateConsensus(final AlignmentPanel ap)
{
- try{
- Annotation[] annotations = new Annotation[alignment.getWidth()];
+ consensusThread = new ConsensusThread(ap);
+ consensusThread.start();
+ }
- // this routine prevents vconsensus becoming a new object each time
- // consenus is calculated. Important for speed of Blosum62
- // and PID colouring of alignment
- if (vconsensus == null)
- {
- vconsensus = alignment.getAAFrequency();
- }
- else
+ class ConsensusThread
+ extends Thread
+ {
+ AlignmentPanel ap;
+ public ConsensusThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+ public void run()
+ {
+ updatingConsensus = true;
+ while (UPDATING_CONSENSUS)
{
- Vector temp = alignment.getAAFrequency();
- vconsensus.clear();
-
- Enumeration e = temp.elements();
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
- while (e.hasMoreElements())
+ Thread.sleep(200);
+ }
+ catch (Exception ex)
{
- vconsensus.add(e.nextElement());
+ ex.printStackTrace();
}
}
- Hashtable hash = null;
- for (int i = 0; i < alignment.getWidth(); i++)
+ UPDATING_CONSENSUS = true;
+
+ try
+ {
+ int aWidth = alignment.getWidth();
+ if(aWidth<0)
{
- hash = (Hashtable) vconsensus.elementAt(i);
+ return;
+ }
+
+ consensus.annotations = null;
+ consensus.annotations = new Annotation[aWidth];
- float value = 0;
- if (ignoreGapsInConsensusCalculation)
- value = ( (Float) hash.get("pid_nogaps")).floatValue();
- else
- value = ( (Float) hash.get("pid_gaps")).floatValue();
- String maxRes = hash.get("maxResidue").toString();
- String mouseOver = hash.get("maxResidue") + " ";
+ hconsensus = new Hashtable[aWidth];
+ AAFrequency.calculate(alignment.getSequencesArray(),
+ 0,
+ alignment.getWidth(),
+ hconsensus);
- if (maxRes.length() > 1)
+ for (int i = 0; i < aWidth; i++)
+ {
+ float value = 0;
+ if (ignoreGapsInConsensusCalculation)
+ {
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
+ floatValue();
+ }
+ else
{
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
+ floatValue();
}
- mouseOver += ( (int) value + "%");
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
- }
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
- if (consensus == null)
- {
- consensus = new AlignmentAnnotation("Consensus", "PID",
- annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
+ if (maxRes.length() > 1)
+ {
+ mouseOver = "[" + maxRes + "] ";
+ maxRes = "+";
+ }
- if (showIdentity)
- {
- alignment.addAnnotation(consensus);
+ mouseOver += ( (int) value + "%");
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+ value);
}
- }
- else
+
+
+ if (globalColourScheme != null)
{
- consensus.annotations = annotations;
+ globalColourScheme.setConsensus(hconsensus);
}
- if (globalColourScheme != null)
- globalColourScheme.setConsensus(vconsensus);
-
- }catch(OutOfMemoryError error)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ }
+ catch (OutOfMemoryError error)
{
- public void run()
+ alignment.deleteAnnotation(consensus);
+
+ consensus = null;
+ hconsensus = null;
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating consensus!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory calculating consensus!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ System.out.println("Consensus calculation: " + error);
+ System.gc();
+ }
+ UPDATING_CONSENSUS = false;
+ updatingConsensus = false;
- System.out.println("Consensus calculation: " + error);
- System.gc();
+ 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
*/
- public SequenceI getConsensusSeq() {
+ public SequenceI getConsensusSeq()
+ {
if (consensus==null)
- updateConsensus();
+ {
+ updateConsensus(null);
+ }
if (consensus==null)
+ {
return null;
+ }
StringBuffer seqs=new StringBuffer();
- for (int i=0; i<consensus.annotations.length; i++) {
- if (consensus.annotations[i]!=null) {
+ 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 void setAlignment(AlignmentI align)
{
+ if (alignment!=null && alignment.getCodonFrames()!=null)
+ {
+ StructureSelectionManager.getStructureSelectionManager().removeMappings(alignment.getCodonFrames());
+ }
this.alignment = align;
+ if (alignment.getCodonFrames()!=null)
+ {
+ StructureSelectionManager.getStructureSelectionManager().addMappings(alignment.getCodonFrames());
+ }
}
/**
changeSupport.firePropertyChange(prop, oldvalue, newvalue);
}
- public void setIgnoreGapsConsensus(boolean b)
+ public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
{
ignoreGapsInConsensusCalculation = b;
- updateConsensus();
+ updateConsensus(ap);
if(globalColourScheme!=null)
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ ignoreGapsInConsensusCalculation);
}
}
public void hideSelectedColumns()
{
if (colSel.size() < 1)
+ {
return;
+ }
colSel.hideSelectedColumns();
setSelectionGroup(null);
public void hideColumns(int start, int 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);
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 showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index);
+ Vector tmp = alignment.getHiddenSequences().showSequence(index
+ , hiddenRepSequences);
if(tmp.size()>0)
{
if(selectionGroup==null)
}
if(alignment.getHiddenSequences().getSize()<1)
+ {
hasHiddenRows = false;
}
+ }
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
if(colSel.getHiddenColumns()==null)
+ {
hasHiddenColumns = false;
}
+ }
public void showAllHiddenColumns()
{
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth()-1);
}
- Vector tmp = alignment.getHiddenSequences().showAll();
+ Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
for(int t=0; t<tmp.size(); t++)
{
selectionGroup.addSequence(
}
firePropertyChange("alignment", null, alignment.getSequences());
hasHiddenRows = false;
+ hiddenRepSequences = null;
}
}
- public void invertColumnSelection()
- {
- int column;
- for(int i=0; i<alignment.getWidth(); i++)
- {
- column = i;
-
- if(colSel.contains(column))
- colSel.removeElement(column);
- else
- colSel.addElement(column);
- }
+ public void invertColumnSelection()
+ {
+ colSel.invertColumnSelection(0,alignment.getWidth());
}
public int adjustForHiddenSeqs(int alignmentIndex)
}
/**
- * This method returns the a new SequenceI [] with
- * the selection sequence and start and end points adjusted
- * @return String[]
+ * This method returns an array of new SequenceI objects
+ * derived from the whole alignment or just the current
+ * selection with start and end points adjusted
+ * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
+ * @return selection as new sequenceI objects
*/
public SequenceI[] getSelectionAsNewSequence()
{
SequenceI[] sequences;
if (selectionGroup == null)
+ {
sequences = alignment.getSequencesArray();
+ AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+ for (int i=0; i<sequences.length; i++)
+ {
+ sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
+ }
+ }
else
+ {
sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+ }
return sequences;
}
-
+
+ /**
+ * get the currently selected sequence objects or all the sequences in the alignment.
+ * @return array of references to sequence objects
+ */
+ public SequenceI[] getSequenceSelection()
+ {
+ SequenceI[] sequences;
+ if (selectionGroup==null)
+ {
+ sequences = alignment.getSequencesArray();
+ }
+ else
+ {
+ sequences = selectionGroup.getSequencesInOrder(alignment);
+ }
+ return sequences;
+ }
/**
* 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 jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+ public jalview.datamodel.CigarArray getViewAsCigars(boolean
+ selectedRegionOnly)
{
CigarArray selection=null;
SequenceI [] seqs= null;
int start = 0, end = 0;
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
}
selection=new CigarArray(selseqs);
// now construct the CigarArray operations
- if (hasHiddenColumns) {
+ if (hasHiddenColumns)
+ {
Vector regions = colSel.getHiddenColumns();
int [] region;
int hideStart, hideEnd;
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)
+ {
break;
+ }
if (hideEnd>end)
+ {
hideEnd=end;
+ }
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;
}
// Final match if necessary.
if (last<end)
+ {
selection.addOperation(CigarArray.M, end-last+1);
- } else {
+ }
+ }
+ else
+ {
selection.addOperation(CigarArray.M, end-start+1);
}
return selection;
* @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);
+ if (aligview != null)
+ {
+ return new AlignmentView(aligview,
+ (selectedOnly && selectionGroup != null) ?
+ selectionGroup.getStartRes() : 0);
+ }
return null;
}
/**
int start = 0, end = 0;
if(selectedRegionOnly && selectionGroup!=null)
{
- iSize = selectionGroup.getSize(false);
+ iSize = selectionGroup.getSize();
seqs = selectionGroup.getSequencesInOrder(alignment);
start = selectionGroup.getStartRes();
end = selectionGroup.getEndRes()+1;
}
selection = new String[iSize];
- if (hasHiddenColumns) {
+ if (hasHiddenColumns)
+ {
selection = colSel.getVisibleSequenceStrings(start, end, seqs);
- } else {
+ }
+ else
+ {
for(i=0; i<iSize; i++)
{
- selection[i] = seqs[i].getSequence(start, end);
+ selection[i] = seqs[i].getSequenceAsString(start, end);
}
}
return selection;
}
+ public int [][] getVisibleRegionBoundaries(int min, int max)
+ {
+ Vector regions = new Vector();
+ int start = min;
+ int end = max;
+
+ do
+ {
+ if (hasHiddenColumns)
+ {
+ if (start == 0)
+ {
+ start = colSel.adjustForHiddenColumns(start);
+ }
+
+ end = colSel.getHiddenBoundaryRight(start);
+ if (start == end)
+ {
+ end = max;
+ }
+ if (end > max)
+ {
+ end = max;
+ }
+ }
+
+ regions.addElement(new int[]
+ {start, end});
+
+ if (hasHiddenColumns)
+ {
+ start = colSel.adjustForHiddenColumns(end);
+ start = colSel.getHiddenBoundaryLeft(start) + 1;
+ }
+ }
+ while (end < max);
+
+ int[][] startEnd = new int[regions.size()][2];
+
+ regions.copyInto(startEnd);
+
+ return startEnd;
+
+ }
+
public boolean getShowHiddenMarkers()
{
return showHiddenMarkers;
public String getSequenceSetId()
{
if(sequenceSetID==null)
+ {
sequenceSetID = alignment.hashCode()+"";
+ }
return sequenceSetID;
}
+ public void alignmentChanged(AlignmentPanel ap)
+ {
+ if (padGaps)
+ {
+ 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();
+
+ // 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();
+ }
+ }
+
+
+ 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);
+ }
+ }
+ /**
+ * returns the visible column regions of the alignment
+ * @param selectedRegionOnly true to just return the contigs intersecting with the selected area
+ * @return
+ */
+ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) {
+ int[] viscontigs=null;
+ int start = 0, end = 0;
+ if(selectedRegionOnly && selectionGroup!=null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes()+1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ viscontigs = colSel.getVisibleContigs(start, end);
+ return viscontigs;
+ }
+ /**
+ * get hash of undo and redo list for the alignment
+ * @return long[] { historyList.hashCode, redoList.hashCode };
+ */
+ public long[] getUndoRedoHash()
+ {
+ if (historyList==null || redoList==null)
+ return new long[] { -1, -1};
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
+ }
+ /**
+ * test if a particular set of hashcodes are different to the hashcodes for the undo and redo list.
+ * @param undoredo the stored set of hashcodes as returned by getUndoRedoHash
+ * @return true if the hashcodes differ (ie the alignment has been edited) or the stored hashcode array differs in size
+ */
+ public boolean isUndoRedoHashModified(long[] undoredo)
+ {
+ if (undoredo==null)
+ {
+ return true;
+ }
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length!=undoredo.length)
+ { return true; }
+
+ for (int i=0; i<cstate.length; i++)
+ {
+ if (cstate[i]!=undoredo[i])
+ {
+ return true;
+ }
+ }
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff