-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class AlignViewport
-{
- int startRes;
- int endRes;
-
- int startSeq;
- int endSeq;
-
-
- boolean cursorMode = false;
-
- boolean showJVSuffix = true;
- boolean showText = true;
- boolean showColourText = false;
- boolean showBoxes = true;
- boolean wrapAlignment = false;
- boolean renderGaps = true;
- boolean showSequenceFeatures = false;
- boolean showAnnotation = true;
- boolean showConservation = true;
- boolean showQuality = true;
- boolean showConsensus = true;
- boolean upperCasebold = false;
-
- boolean colourAppliesToAllGroups = true;
- ColourSchemeI globalColourScheme = null;
- boolean conservationColourSelected = false;
- boolean abovePIDThreshold = false;
-
- SequenceGroup selectionGroup;
-
- int charHeight;
- int charWidth;
- int wrappedWidth;
-
- Font font = new Font("SansSerif", Font.PLAIN, 10);
- boolean validCharWidth = true;
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
-
- int threshold;
- int increment;
-
- NJTree currentTree = null;
-
- boolean scaleAboveWrapped = true;
- boolean scaleLeftWrapped = true;
- boolean scaleRightWrapped = true;
-
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
- public Hashtable featuresDisplayed;
-
- boolean hasHiddenColumns = false;
- boolean hasHiddenRows = false;
- boolean showHiddenMarkers = true;
-
-
- public Hashtable [] hconsensus;
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- AlignmentAnnotation quality;
-
- boolean autocalculateConsensus = true;
-
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
- jalview.bin.JalviewLite applet;
-
- boolean MAC = false;
-
- public AlignViewport(AlignmentI al, JalviewLite applet)
- {
- this.applet = applet;
- setAlignment(al);
- this.startRes = 0;
- this.endRes = al.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = al.getHeight() - 1;
- setFont(font);
-
- if(System.getProperty("os.name").startsWith("Mac"))
- MAC = true;
-
- if (applet != null)
- {
- String param = applet.getParameter("showFullId");
- if (param != null)
- {
- showJVSuffix = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showAnnotation");
- if (param != null)
- {
- showAnnotation = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showConservation");
- if (param != null)
- {
- showConservation = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showQuality");
- if (param != null)
- {
- showQuality = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showConsensus");
- if (param != null)
- {
- showConsensus = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("upperCase");
- if (param != null)
- {
- 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)
- {
- colour = applet.getParameter("userDefinedColour");
- if(colour !=null)
- colour = "User Defined";
- }
-
- if(colour != null)
- {
- globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
- }
-
- if(applet.getParameter("userDefinedColour")!=null)
- {
- ((UserColourScheme)globalColourScheme).parseAppletParameter(
- applet.getParameter("userDefinedColour"));
- }
-
-
- }
- }
-
- public void showSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
-
-
- public void updateConservation()
- {
- if(alignment.isNucleotide())
- return;
-
- 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++)
- {
- float value = 0;
- try
- {
- value = Integer.parseInt(sequence.charAt(i) + "");
- }
- catch (Exception ex)
- {
- if (sequence.charAt(i) == '*')
- {
- value = 11;
- }
- if (sequence.charAt(i) == '+')
- {
- value = 10;
- }
- }
- 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)
- {
- alignment.addAnnotation(conservation);
- }
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- qannotations,
- cons.qualityRange[0].floatValue(),
- cons.qualityRange[1].floatValue(),
- AlignmentAnnotation.BAR_GRAPH);
- if (showQuality)
- {
- alignment.addAnnotation(quality);
- }
- }
- else
- {
- conservation.annotations = annotations;
- quality.annotations = qannotations;
- quality.graphMax = cons.qualityRange[1].floatValue();
- }
-
- }
-
- public void updateConsensus()
- {
- // 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);
-
- 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 = maxRes;
- if (maxRes.length() > 1)
- {
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
- }
-
-
- mouseOver += (int) value + "%";
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-
- }
-
- if (consensus == null)
- {
- consensus = new AlignmentAnnotation("Consensus",
- "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- if (showConsensus)
- {
- alignment.addAnnotation(consensus);
- }
- }
- else
- {
- consensus.annotations = annotations;
- }
-
- if(globalColourScheme!=null)
- globalColourScheme.setConsensus(hconsensus);
-
- }
- /**
- * 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)
- return 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" : ""));
- return sq;
- }
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
- public int getStartRes()
- {
- return startRes;
- }
-
- public int getEndRes()
- {
- return endRes;
- }
-
- public int getStartSeq()
- {
- return startSeq;
- }
-
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- public void setEndRes(int res)
- {
- if (res > alignment.getWidth() - 1)
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
- if (res < 0)
- {
- res = 0;
- }
- this.endRes = res;
- }
-
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
-
- public int getEndSeq()
- {
- return endSeq;
- }
-
- java.awt.Frame nullFrame;
- public void setFont(Font f)
- {
- font = f;
- if(nullFrame == null)
- {
- nullFrame = new java.awt.Frame();
- nullFrame.addNotify();
- }
-
- java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
- setCharHeight(fm.getHeight());
- charWidth = fm.charWidth('M');
-
- if(upperCasebold)
- {
- Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
- fm = nullFrame.getGraphics().getFontMetrics(f2);
- charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
- }
- }
-
- public Font getFont()
- {
- return font;
- }
-
- public int getCharWidth()
- {
- return charWidth;
- }
-
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
-
- public int getCharHeight()
- {
- return charHeight;
- }
-
- public void setWrappedWidth(int w)
- {
- this.wrappedWidth = w;
- }
-
- public int getwrappedWidth()
- {
- return wrappedWidth;
- }
-
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- public void setAlignment(AlignmentI align)
- {
- this.alignment = align;
- }
-
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- public boolean getColourText()
- {
- return showColourText;
- }
-
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- public boolean getShowText()
- {
- return showText;
- }
-
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- public char getGapCharacter()
- {
- return getAlignment().getGapCharacter();
- }
-
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
- {
- getAlignment().setGapCharacter(gap);
- }
- }
-
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- public int getThreshold()
- {
- return threshold;
- }
-
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- public int getIncrement()
- {
- return increment;
- }
-
- public void setHiddenColumns(ColumnSelection colsel)
- {
- this.colSel = colsel;
- if(colSel.getHiddenColumns()!=null)
- hasHiddenColumns = true;
- }
-
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- public void resetSeqLimits(int height)
- {
- setEndSeq(height / getCharHeight());
- }
-
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- public void setIgnoreGapsConsensus(boolean b)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus();
- if (globalColourScheme!=null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
-
- }
- }
-
- /**
- * Property change listener for changes in alignment
- *
- * @param listener DOCUMENT ME!
- */
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param listener DOCUMENT ME!
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
-
- /**
- * Property change listener for changes in alignment
- *
- * @param prop DOCUMENT ME!
- * @param oldvalue DOCUMENT ME!
- * @param newvalue DOCUMENT ME!
- */
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
- {
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
- }
-
-
-
- public boolean getIgnoreGapsConsensus()
- {
- return ignoreGapsInConsensusCalculation;
- }
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- return;
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
- }
-
- 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 hideColumns(int start, int end)
- {
- if(start==end)
- colSel.hideColumns(start);
- else
- colSel.hideColumns(start, end);
-
- hasHiddenColumns = true;
- }
-
- public void hideAllSelectedSeqs()
- {
- if (selectionGroup == null)
- return;
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
- }
-
- public void hideSequence(SequenceI [] seq)
- {
- 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)
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenColumns()
- {
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenSeqs()
- {
- if(alignment.getHiddenSequences().getSize()>0)
- {
- if(selectionGroup==null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
- }
- Vector tmp = alignment.getHiddenSequences().showAll();
- for(int t=0; t<tmp.size(); t++)
- {
- selectionGroup.addSequence(
- (SequenceI)tmp.elementAt(t), false
- );
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- hasHiddenRows = false;
- }
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
- }
-
- /**
- * This method returns the a new SequenceI [] with
- * the selection sequence and start and end points adjusted
- * @return String[]
- */
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- sequences = alignment.getSequencesArray();
- else
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
-
- 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[]
- */
- public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
- {
- CigarArray selection=null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
- {
- iSize = selectionGroup.getSize(false);
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth()-1;
- }
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for(i=0; i<iSize; i++)
- {
- selseqs[i] = new SeqCigar(seqs[i], start, end);
- }
- selection=new CigarArray(selseqs);
- // now construct the CigarArray operations
- if (hasHiddenColumns) {
- Vector regions = colSel.getHiddenColumns();
- int [] region;
- int hideStart, hideEnd;
- 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 (hideEnd > last)
- {
- hideStart = last;
- } 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 {
- 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) {
- // 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);
- }
- return null;
- }
- /**
- * 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[]
- */
- public String [] getViewAsString(boolean selectedRegionOnly)
- {
- String [] selection = null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
- {
- iSize = selectionGroup.getSize(false);
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes()+1;
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
- }
-
- selection = new String[iSize];
-
-
- 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;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if(hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd+1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if(blockStart>blockEnd)
- {
- break;
- }
-
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd+1;
- blockEnd = end;
- }
-
- if(end>blockStart)
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
-
- selection[i] = visibleSeq.toString();
- }
- else
- {
- selection[i] = seqs[i].getSequence(start, end);
- }
- }
-
- return selection;
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+\r
+package jalview.appletgui;\r
+\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.bin.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+\r
+public class AlignViewport\r
+{\r
+ int startRes;\r
+ int endRes;\r
+\r
+ int startSeq;\r
+ int endSeq;\r
+\r
+ boolean cursorMode = false;\r
+\r
+ boolean showJVSuffix = true;\r
+ boolean showText = true;\r
+ boolean showColourText = false;\r
+ boolean showBoxes = true;\r
+ boolean wrapAlignment = false;\r
+ boolean renderGaps = true;\r
+ boolean showSequenceFeatures = false;\r
+ boolean showAnnotation = true;\r
+ boolean showConservation = true;\r
+ boolean showQuality = true;\r
+ boolean showConsensus = true;\r
+ boolean upperCasebold = false;\r
+\r
+ boolean colourAppliesToAllGroups = true;\r
+ ColourSchemeI globalColourScheme = null;\r
+ boolean conservationColourSelected = false;\r
+ boolean abovePIDThreshold = false;\r
+\r
+ SequenceGroup selectionGroup;\r
+\r
+ int charHeight;\r
+ int charWidth;\r
+ int wrappedWidth;\r
+\r
+ Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ boolean validCharWidth = true;\r
+ AlignmentI alignment;\r
+\r
+ ColumnSelection colSel = new ColumnSelection();\r
+\r
+ int threshold;\r
+ int increment;\r
+\r
+ NJTree currentTree = null;\r
+\r
+ boolean scaleAboveWrapped = true;\r
+ boolean scaleLeftWrapped = true;\r
+ boolean scaleRightWrapped = true;\r
+\r
+ // The following vector holds the features which are\r
+ // currently visible, in the correct order or rendering\r
+ public Hashtable featuresDisplayed;\r
+\r
+ boolean hasHiddenColumns = false;\r
+ boolean hasHiddenRows = false;\r
+ boolean showHiddenMarkers = true;\r
+\r
+ public Hashtable[] hconsensus;\r
+ AlignmentAnnotation consensus;\r
+ AlignmentAnnotation conservation;\r
+ AlignmentAnnotation quality;\r
+\r
+ boolean autocalculateConsensus = true;\r
+\r
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+\r
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.\r
+ PropertyChangeSupport(this);\r
+\r
+ boolean ignoreGapsInConsensusCalculation = false;\r
+\r
+ jalview.bin.JalviewLite applet;\r
+\r
+ Hashtable sequenceColours;\r
+\r
+ boolean MAC = false;\r
+\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
+\r
+ String sequenceSetID;\r
+\r
+ Hashtable hiddenRepSequences;\r
+\r
+ public AlignViewport(AlignmentI al, JalviewLite applet)\r
+ {\r
+ this.applet = applet;\r
+ setAlignment(al);\r
+ this.startRes = 0;\r
+ this.endRes = al.getWidth() - 1;\r
+ this.startSeq = 0;\r
+ this.endSeq = al.getHeight() - 1;\r
+ setFont(font);\r
+\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
+ MAC = true;\r
+ }\r
+\r
+ if (applet != null)\r
+ {\r
+ String param = applet.getParameter("showFullId");\r
+ if (param != null)\r
+ {\r
+ showJVSuffix = Boolean.valueOf(param).booleanValue();\r
+ }\r
+\r
+ param = applet.getParameter("showAnnotation");\r
+ if (param != null)\r
+ {\r
+ showAnnotation = Boolean.valueOf(param).booleanValue();\r
+ }\r
+\r
+ param = applet.getParameter("showConservation");\r
+ if (param != null)\r
+ {\r
+ showConservation = Boolean.valueOf(param).booleanValue();\r
+ }\r
+\r
+ param = applet.getParameter("showQuality");\r
+ if (param != null)\r
+ {\r
+ showQuality = Boolean.valueOf(param).booleanValue();\r
+ }\r
+\r
+ param = applet.getParameter("showConsensus");\r
+ if (param != null)\r
+ {\r
+ showConsensus = Boolean.valueOf(param).booleanValue();\r
+ }\r
+\r
+ param = applet.getParameter("upperCase");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("bold"))\r
+ {\r
+ upperCasebold = true;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ if (applet != null)\r
+ {\r
+ String colour = applet.getParameter("defaultColour");\r
+\r
+ if (colour == null)\r
+ {\r
+ colour = applet.getParameter("userDefinedColour");\r
+ if (colour != null)\r
+ {\r
+ colour = "User Defined";\r
+ }\r
+ }\r
+\r
+ if (colour != null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(hconsensus);\r
+ }\r
+ }\r
+\r
+ if (applet.getParameter("userDefinedColour") != null)\r
+ {\r
+ ( (UserColourScheme) globalColourScheme).parseAppletParameter(\r
+ applet.getParameter("userDefinedColour"));\r
+ }\r
+\r
+ if (hconsensus == null)\r
+ {\r
+ if (!alignment.isNucleotide())\r
+ {\r
+ conservation = new AlignmentAnnotation("Conservation",\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
+ new Annotation[1], 0f,\r
+ 11f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ conservation.hasText = true;\r
+ conservation.autoCalculated = true;\r
+\r
+ if (showConservation)\r
+ {\r
+ alignment.addAnnotation(conservation);\r
+ }\r
+\r
+ if (showQuality)\r
+ {\r
+ quality = new AlignmentAnnotation("Quality",\r
+ "Alignment Quality based on Blosum62 scores",\r
+ new Annotation[1],\r
+ 0f,\r
+ 11f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ quality.hasText = true;\r
+ quality.autoCalculated = true;\r
+\r
+ alignment.addAnnotation(quality);\r
+ }\r
+ }\r
+\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ new Annotation[1], 0f, 100f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ consensus.hasText = true;\r
+ consensus.autoCalculated = true;\r
+\r
+ if (showConsensus)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public void showSequenceFeatures(boolean b)\r
+ {\r
+ showSequenceFeatures = b;\r
+ }\r
+\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
+ return showSequenceFeatures;\r
+ }\r
+\r
+ class ConservationThread\r
+ extends Thread\r
+ {\r
+ AlignmentPanel ap;\r
+ public ConservationThread(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ updatingConservation = true;\r
+\r
+ while (UPDATING_CONSERVATION)\r
+ {\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ UPDATING_CONSERVATION = true;\r
+\r
+ int alWidth = alignment.getWidth();\r
+ if (alWidth < 0)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Conservation cons = new jalview.analysis.Conservation("All",\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
+ alignment.getSequences(), 0, alWidth - 1);\r
+\r
+ cons.calculate();\r
+ cons.verdict(false, ConsPercGaps);\r
+\r
+ if (quality != null)\r
+ {\r
+ cons.findQuality();\r
+ }\r
+\r
+ char[] sequence = cons.getConsSequence().getSequence();\r
+ float minR;\r
+ float minG;\r
+ float minB;\r
+ float maxR;\r
+ float maxG;\r
+ float maxB;\r
+ minR = 0.3f;\r
+ minG = 0.0f;\r
+ minB = 0f;\r
+ maxR = 1.0f - minR;\r
+ maxG = 0.9f - minG;\r
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
+\r
+ float min = 0f;\r
+ float max = 11f;\r
+ float qmin = 0f;\r
+ float qmax = 0f;\r
+\r
+ char c;\r
+\r
+ conservation.annotations = new Annotation[alWidth];\r
+\r
+ if (quality != null)\r
+ {\r
+ quality.graphMax = cons.qualityRange[1].floatValue();\r
+ quality.annotations = new Annotation[alWidth];\r
+ qmin = cons.qualityRange[0].floatValue();\r
+ qmax = cons.qualityRange[1].floatValue();\r
+ }\r
+\r
+ for (int i = 0; i < alWidth; i++)\r
+ {\r
+ float value = 0;\r
+\r
+ c = sequence[i];\r
+\r
+ if (Character.isDigit(c))\r
+ {\r
+ value = (int) (c - '0');\r
+ }\r
+ else if (c == '*')\r
+ {\r
+ value = 11;\r
+ }\r
+ else if (c == '+')\r
+ {\r
+ value = 10;\r
+ }\r
+\r
+ float vprop = value - min;\r
+ vprop /= max;\r
+ conservation.annotations[i] =\r
+ new Annotation(String.valueOf(c),\r
+ String.valueOf(value), ' ', value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+\r
+ // Quality calc\r
+ if (quality != null)\r
+ {\r
+ value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
+ vprop = value - qmin;\r
+ vprop /= qmax;\r
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value),\r
+ ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+ }\r
+ }\r
+ }\r
+ catch (OutOfMemoryError error)\r
+ {\r
+ System.out.println("Out of memory calculating conservation!!");\r
+ conservation = null;\r
+ quality = null;\r
+ System.gc();\r
+ }\r
+\r
+ UPDATING_CONSERVATION = false;\r
+ updatingConservation = false;\r
+\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ ConservationThread conservationThread;\r
+\r
+ ConsensusThread consensusThread;\r
+\r
+ boolean consUpdateNeeded = false;\r
+\r
+ static boolean UPDATING_CONSENSUS = false;\r
+\r
+ static boolean UPDATING_CONSERVATION = false;\r
+\r
+ boolean updatingConsensus = false;\r
+\r
+ boolean updatingConservation = false;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConservation(final AlignmentPanel ap)\r
+ {\r
+ if (alignment.isNucleotide() || conservation == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ conservationThread = new ConservationThread(ap);\r
+ conservationThread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConsensus(final AlignmentPanel ap)\r
+ {\r
+ consensusThread = new ConsensusThread(ap);\r
+ consensusThread.start();\r
+ }\r
+\r
+ class ConsensusThread\r
+ extends Thread\r
+ {\r
+ AlignmentPanel ap;\r
+ public ConsensusThread(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ updatingConsensus = true;\r
+ while (UPDATING_CONSENSUS)\r
+ {\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ UPDATING_CONSENSUS = true;\r
+\r
+ try\r
+ {\r
+ int aWidth = alignment.getWidth();\r
+ if (aWidth < 0)\r
+ {\r
+ return;\r
+ }\r
+\r
+ consensus.annotations = null;\r
+ consensus.annotations = new Annotation[aWidth];\r
+\r
+ hconsensus = new Hashtable[aWidth];\r
+ AAFrequency.calculate(alignment.getSequencesArray(),\r
+ 0,\r
+ alignment.getWidth(),\r
+ hconsensus);\r
+\r
+ for (int i = 0; i < aWidth; i++)\r
+ {\r
+ float value = 0;\r
+ if (ignoreGapsInConsensusCalculation)\r
+ {\r
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).\r
+ floatValue();\r
+ }\r
+ else\r
+ {\r
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).\r
+ floatValue();\r
+ }\r
+\r
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";\r
+\r
+ if (maxRes.length() > 1)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+";\r
+ }\r
+\r
+ mouseOver += ( (int) value + "%");\r
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',\r
+ value);\r
+ }\r
+\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(hconsensus);\r
+ }\r
+\r
+ }\r
+ catch (OutOfMemoryError error)\r
+ {\r
+ alignment.deleteAnnotation(consensus);\r
+\r
+ consensus = null;\r
+ hconsensus = null;\r
+ System.out.println("Out of memory calculating consensus!!");\r
+ System.gc();\r
+ }\r
+ UPDATING_CONSENSUS = false;\r
+ updatingConsensus = false;\r
+\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * get the consensus sequence as displayed under the PID consensus annotation row.\r
+ * @return consensus sequence as a new sequence object\r
+ */\r
+ /**\r
+ * get the consensus sequence as displayed under the PID consensus annotation row.\r
+ * @return consensus sequence as a new sequence object\r
+ */\r
+ public SequenceI getConsensusSeq()\r
+ {\r
+ if (consensus == null)\r
+ {\r
+ return null;\r
+ }\r
+ StringBuffer seqs = new StringBuffer();\r
+ for (int i = 0; i < consensus.annotations.length; i++)\r
+ {\r
+ if (consensus.annotations[i] != null)\r
+ {\r
+ if (consensus.annotations[i].description.charAt(0) == '[')\r
+ {\r
+ seqs.append(consensus.annotations[i].description.charAt(1));\r
+ }\r
+ else\r
+ {\r
+ seqs.append(consensus.annotations[i].displayCharacter);\r
+ }\r
+ }\r
+ }\r
+ SequenceI sq = new Sequence("Consensus", seqs.toString());\r
+ sq.setDescription("Percentage Identity Consensus " +\r
+ ( (ignoreGapsInConsensusCalculation) ? " without gaps" :\r
+ ""));\r
+ return sq;\r
+ }\r
+\r
+ public SequenceGroup getSelectionGroup()\r
+ {\r
+ return selectionGroup;\r
+ }\r
+\r
+ public void setSelectionGroup(SequenceGroup sg)\r
+ {\r
+ selectionGroup = sg;\r
+ }\r
+\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
+\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
+\r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+ return abovePIDThreshold;\r
+ }\r
+\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+ abovePIDThreshold = b;\r
+ }\r
+\r
+ public int getStartRes()\r
+ {\r
+ return startRes;\r
+ }\r
+\r
+ public int getEndRes()\r
+ {\r
+ return endRes;\r
+ }\r
+\r
+ public int getStartSeq()\r
+ {\r
+ return startSeq;\r
+ }\r
+\r
+ public void setGlobalColourScheme(ColourSchemeI cs)\r
+ {\r
+ globalColourScheme = cs;\r
+ }\r
+\r
+ public ColourSchemeI getGlobalColourScheme()\r
+ {\r
+ return globalColourScheme;\r
+ }\r
+\r
+ public void setStartRes(int res)\r
+ {\r
+ this.startRes = res;\r
+ }\r
+\r
+ public void setStartSeq(int seq)\r
+ {\r
+ this.startSeq = seq;\r
+ }\r
+\r
+ public void setEndRes(int res)\r
+ {\r
+ if (res > alignment.getWidth() - 1)\r
+ {\r
+ // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
+ res = alignment.getWidth() - 1;\r
+ }\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
+ this.endRes = res;\r
+ }\r
+\r
+ public void setEndSeq(int seq)\r
+ {\r
+ if (seq > alignment.getHeight())\r
+ {\r
+ seq = alignment.getHeight();\r
+ }\r
+ if (seq < 0)\r
+ {\r
+ seq = 0;\r
+ }\r
+ this.endSeq = seq;\r
+ }\r
+\r
+ public int getEndSeq()\r
+ {\r
+ return endSeq;\r
+ }\r
+\r
+ java.awt.Frame nullFrame;\r
+ public void setFont(Font f)\r
+ {\r
+ font = f;\r
+ if (nullFrame == null)\r
+ {\r
+ nullFrame = new java.awt.Frame();\r
+ nullFrame.addNotify();\r
+ }\r
+\r
+ java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);\r
+ setCharHeight(fm.getHeight());\r
+ charWidth = fm.charWidth('M');\r
+\r
+ if (upperCasebold)\r
+ {\r
+ Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());\r
+ fm = nullFrame.getGraphics().getFontMetrics(f2);\r
+ charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;\r
+ }\r
+ }\r
+\r
+ public Font getFont()\r
+ {\r
+ return font;\r
+ }\r
+\r
+ public int getCharWidth()\r
+ {\r
+ return charWidth;\r
+ }\r
+\r
+ public void setCharHeight(int h)\r
+ {\r
+ this.charHeight = h;\r
+ }\r
+\r
+ public int getCharHeight()\r
+ {\r
+ return charHeight;\r
+ }\r
+\r
+ public void setWrappedWidth(int w)\r
+ {\r
+ this.wrappedWidth = w;\r
+ }\r
+\r
+ public int getwrappedWidth()\r
+ {\r
+ return wrappedWidth;\r
+ }\r
+\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return alignment;\r
+ }\r
+\r
+ public void setAlignment(AlignmentI align)\r
+ {\r
+ this.alignment = align;\r
+ }\r
+\r
+ public void setWrapAlignment(boolean state)\r
+ {\r
+ wrapAlignment = state;\r
+ }\r
+\r
+ public void setShowText(boolean state)\r
+ {\r
+ showText = state;\r
+ }\r
+\r
+ public void setRenderGaps(boolean state)\r
+ {\r
+ renderGaps = state;\r
+ }\r
+\r
+ public boolean getColourText()\r
+ {\r
+ return showColourText;\r
+ }\r
+\r
+ public void setColourText(boolean state)\r
+ {\r
+ showColourText = state;\r
+ }\r
+\r
+ public void setShowBoxes(boolean state)\r
+ {\r
+ showBoxes = state;\r
+ }\r
+\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return wrapAlignment;\r
+ }\r
+\r
+ public boolean getShowText()\r
+ {\r
+ return showText;\r
+ }\r
+\r
+ public boolean getShowBoxes()\r
+ {\r
+ return showBoxes;\r
+ }\r
+\r
+ public char getGapCharacter()\r
+ {\r
+ return getAlignment().getGapCharacter();\r
+ }\r
+\r
+ public void setGapCharacter(char gap)\r
+ {\r
+ if (getAlignment() != null)\r
+ {\r
+ getAlignment().setGapCharacter(gap);\r
+ }\r
+ }\r
+\r
+ public void setThreshold(int thresh)\r
+ {\r
+ threshold = thresh;\r
+ }\r
+\r
+ public int getThreshold()\r
+ {\r
+ return threshold;\r
+ }\r
+\r
+ public void setIncrement(int inc)\r
+ {\r
+ increment = inc;\r
+ }\r
+\r
+ public int getIncrement()\r
+ {\r
+ return increment;\r
+ }\r
+\r
+ public void setHiddenColumns(ColumnSelection colsel)\r
+ {\r
+ this.colSel = colsel;\r
+ if (colSel.getHiddenColumns() != null)\r
+ {\r
+ hasHiddenColumns = true;\r
+ }\r
+ }\r
+\r
+ public ColumnSelection getColumnSelection()\r
+ {\r
+ return colSel;\r
+ }\r
+\r
+ public void resetSeqLimits(int height)\r
+ {\r
+ setEndSeq(height / getCharHeight());\r
+ }\r
+\r
+ public void setCurrentTree(NJTree tree)\r
+ {\r
+ currentTree = tree;\r
+ }\r
+\r
+ public NJTree getCurrentTree()\r
+ {\r
+ return currentTree;\r
+ }\r
+\r
+ public void setColourAppliesToAllGroups(boolean b)\r
+ {\r
+ colourAppliesToAllGroups = b;\r
+ }\r
+\r
+ public boolean getColourAppliesToAllGroups()\r
+ {\r
+ return colourAppliesToAllGroups;\r
+ }\r
+\r
+ public boolean getShowJVSuffix()\r
+ {\r
+ return showJVSuffix;\r
+ }\r
+\r
+ public void setShowJVSuffix(boolean b)\r
+ {\r
+ showJVSuffix = b;\r
+ }\r
+\r
+ public boolean getShowAnnotation()\r
+ {\r
+ return showAnnotation;\r
+ }\r
+\r
+ public void setShowAnnotation(boolean b)\r
+ {\r
+ showAnnotation = b;\r
+ }\r
+\r
+ public boolean getScaleAboveWrapped()\r
+ {\r
+ return scaleAboveWrapped;\r
+ }\r
+\r
+ public boolean getScaleLeftWrapped()\r
+ {\r
+ return scaleLeftWrapped;\r
+ }\r
+\r
+ public boolean getScaleRightWrapped()\r
+ {\r
+ return scaleRightWrapped;\r
+ }\r
+\r
+ public void setScaleAboveWrapped(boolean b)\r
+ {\r
+ scaleAboveWrapped = b;\r
+ }\r
+\r
+ public void setScaleLeftWrapped(boolean b)\r
+ {\r
+ scaleLeftWrapped = b;\r
+ }\r
+\r
+ public void setScaleRightWrapped(boolean b)\r
+ {\r
+ scaleRightWrapped = b;\r
+ }\r
+\r
+ public void setIgnoreGapsConsensus(boolean b)\r
+ {\r
+ ignoreGapsInConsensusCalculation = b;\r
+ updateConsensus(null);\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),\r
+ ignoreGapsInConsensusCalculation);\r
+\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Property change listener for changes in alignment\r
+ *\r
+ * @param listener DOCUMENT ME!\r
+ */\r
+ public void addPropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
+ changeSupport.addPropertyChangeListener(listener);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param listener DOCUMENT ME!\r
+ */\r
+ public void removePropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
+ changeSupport.removePropertyChangeListener(listener);\r
+ }\r
+\r
+ /**\r
+ * Property change listener for changes in alignment\r
+ *\r
+ * @param prop DOCUMENT ME!\r
+ * @param oldvalue DOCUMENT ME!\r
+ * @param newvalue DOCUMENT ME!\r
+ */\r
+ public void firePropertyChange(String prop, Object oldvalue, Object newvalue)\r
+ {\r
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
+ }\r
+\r
+ public boolean getIgnoreGapsConsensus()\r
+ {\r
+ return ignoreGapsInConsensusCalculation;\r
+ }\r
+\r
+ public void hideSelectedColumns()\r
+ {\r
+ if (colSel.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ colSel.hideSelectedColumns();\r
+ setSelectionGroup(null);\r
+\r
+ hasHiddenColumns = true;\r
+ }\r
+\r
+ public void invertColumnSelection()\r
+ {\r
+ for (int i = 0; i < alignment.getWidth(); i++)\r
+ {\r
+ if (colSel.contains(i))\r
+ {\r
+ colSel.removeElement(i);\r
+ }\r
+ else\r
+ {\r
+ if (!hasHiddenColumns || colSel.isVisible(i))\r
+ {\r
+ colSel.addElement(i);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public void hideColumns(int start, int end)\r
+ {\r
+ if (start == end)\r
+ {\r
+ colSel.hideColumns(start);\r
+ }\r
+ else\r
+ {\r
+ colSel.hideColumns(start, end);\r
+ }\r
+\r
+ hasHiddenColumns = true;\r
+ }\r
+\r
+ public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)\r
+ {\r
+ int sSize = sg.getSize();\r
+ if (sSize < 2)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (hiddenRepSequences == null)\r
+ {\r
+ hiddenRepSequences = new Hashtable();\r
+ }\r
+\r
+ hiddenRepSequences.put(repSequence, sg);\r
+\r
+ //Hide all sequences except the repSequence\r
+ SequenceI[] seqs = new SequenceI[sSize - 1];\r
+ int index = 0;\r
+ for (int i = 0; i < sSize; i++)\r
+ {\r
+ if (sg.getSequenceAt(i) != repSequence)\r
+ {\r
+ if (index == sSize - 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ seqs[index++] = sg.getSequenceAt(i);\r
+ }\r
+ }\r
+\r
+ hideSequence(seqs);\r
+\r
+ }\r
+\r
+ public void hideAllSelectedSeqs()\r
+ {\r
+ if (selectionGroup == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);\r
+\r
+ hideSequence(seqs);\r
+\r
+ setSelectionGroup(null);\r
+ }\r
+\r
+ public void hideSequence(SequenceI[] seq)\r
+ {\r
+ if (seq != null)\r
+ {\r
+ for (int i = 0; i < seq.length; i++)\r
+ {\r
+ alignment.getHiddenSequences().hideSequence(seq[i]);\r
+ }\r
+\r
+ hasHiddenRows = true;\r
+ firePropertyChange("alignment", null, alignment.getSequences());\r
+ }\r
+ }\r
+\r
+ public void showColumn(int col)\r
+ {\r
+ colSel.revealHiddenColumns(col);\r
+ if (colSel.getHiddenColumns() == null)\r
+ {\r
+ hasHiddenColumns = false;\r
+ }\r
+ }\r
+\r
+ public void showAllHiddenColumns()\r
+ {\r
+ colSel.revealAllHiddenColumns();\r
+ hasHiddenColumns = false;\r
+ }\r
+\r
+ public void showAllHiddenSeqs()\r
+ {\r
+ if (alignment.getHiddenSequences().getSize() > 0)\r
+ {\r
+ if (selectionGroup == null)\r
+ {\r
+ selectionGroup = new SequenceGroup();\r
+ selectionGroup.setEndRes(alignment.getWidth() - 1);\r
+ }\r
+ Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);\r
+ for (int t = 0; t < tmp.size(); t++)\r
+ {\r
+ selectionGroup.addSequence(\r
+ (SequenceI) tmp.elementAt(t), false\r
+ );\r
+ }\r
+ firePropertyChange("alignment", null, alignment.getSequences());\r
+ hasHiddenRows = false;\r
+ hiddenRepSequences = null;\r
+ }\r
+ }\r
+\r
+ public int adjustForHiddenSeqs(int alignmentIndex)\r
+ {\r
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
+ }\r
+\r
+ /**\r
+ * This method returns the a new SequenceI [] with\r
+ * the selection sequence and start and end points adjusted\r
+ * @return String[]\r
+ */\r
+ public SequenceI[] getSelectionAsNewSequence()\r
+ {\r
+ SequenceI[] sequences;\r
+\r
+ if (selectionGroup == null)\r
+ {\r
+ sequences = alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ sequences = selectionGroup.getSelectionAsNewSequences(alignment);\r
+ }\r
+\r
+ return sequences;\r
+ }\r
+\r
+ /**\r
+ * This method returns the visible alignment as text, as\r
+ * seen on the GUI, ie if columns are hidden they will not\r
+ * be returned in the result.\r
+ * Use this for calculating trees, PCA, redundancy etc on views\r
+ * which contain hidden columns.\r
+ * @return String[]\r
+ */\r
+ public jalview.datamodel.CigarArray getViewAsCigars(boolean\r
+ selectedRegionOnly)\r
+ {\r
+ CigarArray selection = null;\r
+ SequenceI[] seqs = null;\r
+ int i, iSize;\r
+ int start = 0, end = 0;\r
+ if (selectedRegionOnly && selectionGroup != null)\r
+ {\r
+ iSize = selectionGroup.getSize();\r
+ seqs = selectionGroup.getSequencesInOrder(alignment);\r
+ start = selectionGroup.getStartRes();\r
+ end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor\r
+ }\r
+ else\r
+ {\r
+ iSize = alignment.getHeight();\r
+ seqs = alignment.getSequencesArray();\r
+ end = alignment.getWidth() - 1;\r
+ }\r
+ SeqCigar[] selseqs = new SeqCigar[iSize];\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ selseqs[i] = new SeqCigar(seqs[i], start, end);\r
+ }\r
+ selection = new CigarArray(selseqs);\r
+ // now construct the CigarArray operations\r
+ if (hasHiddenColumns)\r
+ {\r
+ Vector regions = colSel.getHiddenColumns();\r
+ int[] region;\r
+ int hideStart, hideEnd;\r
+ int last = start;\r
+ for (int j = 0; last < end & j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+ // edit hidden regions to selection range\r
+ if (hideStart < last)\r
+ {\r
+ if (hideEnd > last)\r
+ {\r
+ hideStart = last;\r
+ }\r
+ else\r
+ {\r
+ continue;\r
+ }\r
+ }\r
+\r
+ if (hideStart > end)\r
+ {\r
+ break;\r
+ }\r
+\r
+ if (hideEnd > end)\r
+ {\r
+ hideEnd = end;\r
+ }\r
+\r
+ if (hideStart > hideEnd)\r
+ {\r
+ break;\r
+ }\r
+ /**\r
+ * form operations...\r
+ */\r
+ if (last < hideStart)\r
+ {\r
+ selection.addOperation(CigarArray.M, hideStart - last);\r
+ }\r
+ selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);\r
+ last = hideEnd + 1;\r
+ }\r
+ // Final match if necessary.\r
+ if (last < end)\r
+ {\r
+ selection.addOperation(CigarArray.M, end - last + 1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ selection.addOperation(CigarArray.M, end - start + 1);\r
+ }\r
+ return selection;\r
+ }\r
+\r
+ /**\r
+ * return a compact representation of the current alignment selection to\r
+ * pass to an analysis function\r
+ * @param selectedOnly boolean true to just return the selected view\r
+ * @return AlignmentView\r
+ */\r
+ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)\r
+ {\r
+ // JBPNote:\r
+ // this is here because the AlignmentView constructor modifies the CigarArray\r
+ // object. Refactoring of Cigar and alignment view representation should\r
+ // be done to remove redundancy.\r
+ CigarArray aligview = getViewAsCigars(selectedOnly);\r
+ if (aligview != null)\r
+ {\r
+ return new AlignmentView(aligview,\r
+ (selectedOnly && selectionGroup != null) ?\r
+ selectionGroup.getStartRes() : 0);\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * This method returns the visible alignment as text, as\r
+ * seen on the GUI, ie if columns are hidden they will not\r
+ * be returned in the result.\r
+ * Use this for calculating trees, PCA, redundancy etc on views\r
+ * which contain hidden columns.\r
+ * @return String[]\r
+ */\r
+ public String[] getViewAsString(boolean selectedRegionOnly)\r
+ {\r
+ String[] selection = null;\r
+ SequenceI[] seqs = null;\r
+ int i, iSize;\r
+ int start = 0, end = 0;\r
+ if (selectedRegionOnly && selectionGroup != null)\r
+ {\r
+ iSize = selectionGroup.getSize();\r
+ seqs = selectionGroup.getSequencesInOrder(alignment);\r
+ start = selectionGroup.getStartRes();\r
+ end = selectionGroup.getEndRes() + 1;\r
+ }\r
+ else\r
+ {\r
+ iSize = alignment.getHeight();\r
+ seqs = alignment.getSequencesArray();\r
+ end = alignment.getWidth();\r
+ }\r
+\r
+ selection = new String[iSize];\r
+\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (hasHiddenColumns)\r
+ {\r
+ StringBuffer visibleSeq = new StringBuffer();\r
+ Vector regions = colSel.getHiddenColumns();\r
+\r
+ int blockStart = start, blockEnd = end;\r
+ int[] region;\r
+ int hideStart, hideEnd;\r
+\r
+ for (int j = 0; j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+\r
+ if (hideStart < start)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ blockStart = Math.min(blockStart, hideEnd + 1);\r
+ blockEnd = Math.min(blockEnd, hideStart);\r
+\r
+ if (blockStart > blockEnd)\r
+ {\r
+ break;\r
+ }\r
+\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));\r
+\r
+ blockStart = hideEnd + 1;\r
+ blockEnd = end;\r
+ }\r
+\r
+ if (end > blockStart)\r
+ {\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));\r
+ }\r
+\r
+ selection[i] = visibleSeq.toString();\r
+ }\r
+ else\r
+ {\r
+ selection[i] = seqs[i].getSequenceAsString(start, end);\r
+ }\r
+ }\r
+\r
+ return selection;\r
+ }\r
+\r
+ public boolean getShowHiddenMarkers()\r
+ {\r
+ return showHiddenMarkers;\r
+ }\r
+\r
+ public void setShowHiddenMarkers(boolean show)\r
+ {\r
+ showHiddenMarkers = show;\r
+ }\r
+\r
+ public Color getSequenceColour(SequenceI seq)\r
+ {\r
+ if (sequenceColours == null || !sequenceColours.containsKey(seq))\r
+ {\r
+ return Color.white;\r
+ }\r
+ else\r
+ {\r
+ return (Color) sequenceColours.get(seq);\r
+ }\r
+ }\r
+\r
+ public void setSequenceColour(SequenceI seq, Color col)\r
+ {\r
+ if (sequenceColours == null)\r
+ {\r
+ sequenceColours = new Hashtable();\r
+ }\r
+\r
+ if (col == null)\r
+ {\r
+ sequenceColours.remove(seq);\r
+ }\r
+ else\r
+ {\r
+ sequenceColours.put(seq, col);\r
+ }\r
+ }\r
+\r
+ public String getSequenceSetId()\r
+ {\r
+ if (sequenceSetID == null)\r
+ {\r
+ sequenceSetID = alignment.hashCode() + "";\r
+ }\r
+\r
+ return sequenceSetID;\r
+ }\r
+\r
+ public void alignmentChanged(AlignmentPanel ap)\r
+ {\r
+ alignment.padGaps();\r
+\r
+ if (hconsensus != null && autocalculateConsensus)\r
+ {\r
+ updateConsensus(ap);\r
+ updateConservation(ap);\r
+ }\r
+\r
+ //Reset endRes of groups if beyond alignment width\r
+ int alWidth = alignment.getWidth();\r
+ Vector groups = alignment.getGroups();\r
+ if (groups != null)\r
+ {\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+ if (sg.getEndRes() > alWidth)\r
+ {\r
+ sg.setEndRes(alWidth - 1);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)\r
+ {\r
+ selectionGroup.setEndRes(alWidth - 1);\r
+ }\r
+\r
+ resetAllColourSchemes();\r
+\r
+ //AW alignment.adjustSequenceAnnotations();\r
+ }\r
+\r
+ void resetAllColourSchemes()\r
+ {\r
+ ColourSchemeI cs = globalColourScheme;\r
+ if (cs != null)\r
+ {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).\r
+ resetClustalX(alignment.getSequences(),\r
+ alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(hconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
+ int s, sSize = alignment.getGroups().size();\r
+ for (s = 0; s < sSize; s++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);\r
+ if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) sg.cs).resetClustalX(\r
+ sg.getSequences(hiddenRepSequences), sg.getWidth());\r
+ }\r
+ sg.recalcConservation();\r
+ }\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff