/*
* 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!
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;
* @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();
}
11f,
AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
- conservation.autoCalculated = true;
+ conservation.autoCalculated=true;
if (Cache.getDefault("SHOW_CONSERVATION", true))
11f,
AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
- quality.autoCalculated = true;
+ quality.autoCalculated=true;
alignment.addAnnotation(quality);
}
new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
- consensus.autoCalculated = true;
+ consensus.autoCalculated=true;
if (Cache.getDefault("SHOW_IDENTITY", true))
{
if (globalColourScheme instanceof UserColourScheme)
{
globalColourScheme = UserDefinedColours.loadDefaultColours();
- ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
+ ( (UserColourScheme) globalColourScheme).setThreshold(0,
+ getIgnoreGapsConsensus());
}
if (globalColourScheme != null)
return showSequenceFeatures;
}
-
-
- class ConservationThread extends Thread
+ class ConservationThread
+ extends Thread
{
AlignmentPanel ap;
public ConservationThread(AlignmentPanel ap)
{
if (ap != null)
{
- ap.repaint();
+ ap.paintAlignment(false);
}
Thread.sleep(200);
}
int alWidth = alignment.getWidth();
if(alWidth<0)
+ {
return;
+ }
Conservation cons = new jalview.analysis.Conservation("All",
jalview.schemes.ResidueProperties.propHash, 3,
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;
value = ( (Double) cons.quality.get(i)).floatValue();
vprop = value - qmin;
vprop /= qmax;
- quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+ ' ',
value,
new Color(minR + (maxR * vprop),
minG + (maxG * vprop),
if(ap!=null)
{
- ap.repaint();
+ ap.paintAlignment(true);
}
}
public void updateConservation(final AlignmentPanel ap)
{
if (alignment.isNucleotide() || conservation==null)
+ {
return;
+ }
conservationThread = new ConservationThread(ap);
conservationThread.start();
consensusThread.start();
}
-
- class ConsensusThread extends Thread
+ class ConsensusThread
+ extends Thread
{
AlignmentPanel ap;
public ConsensusThread(AlignmentPanel ap)
{
if (ap != null)
{
- ap.repaint();
+ ap.paintAlignment(false);
}
Thread.sleep(200);
{
int aWidth = alignment.getWidth();
if(aWidth<0)
+ {
return;
+ }
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth];
{
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) + " ";
}
mouseOver += ( (int) value + "%");
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+ value);
}
if (globalColourScheme != null)
+ {
globalColourScheme.setConsensus(hconsensus);
+ }
}
catch (OutOfMemoryError error)
if (ap != null)
{
- ap.repaint();
+ 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(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());
+ }
}
/**
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;
}
{
int sSize = sg.getSize();
if(sSize < 2)
+ {
return;
+ }
if(hiddenRepSequences==null)
+ {
hiddenRepSequences = new Hashtable();
+ }
hiddenRepSequences.put(repSequence, sg);
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(alignment.getHiddenSequences().getSize()<1)
+ {
hasHiddenRows = false;
}
+ }
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
if(colSel.getHiddenColumns()==null)
+ {
hasHiddenColumns = false;
}
+ }
public void showAllHiddenColumns()
{
public void invertColumnSelection()
{
- for(int i=0; i<alignment.getWidth(); i++)
- {
- if(colSel.contains(i))
- colSel.removeElement(i);
- else
- {
- if (!hasHiddenColumns || colSel.isVisible(i))
- {
- colSel.addElement(i);
- }
- }
- }
+ 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;
}
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) {
+ if (aligview != null)
+ {
return new AlignmentView(aligview,
- (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
+ (selectedOnly && selectionGroup != null) ?
+ selectionGroup.getStartRes() : 0);
}
return null;
}
}
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].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)
{
{
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();
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