From d545553b53ac1bd1e29eb72250cdb29745f7292f Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 7 Sep 2006 11:39:36 +0000 Subject: [PATCH] added copy consensus sequence to consensus annotation popup menu --- src/jalview/appletgui/AlignViewport.java | 2095 ++++++++++---------- src/jalview/appletgui/AnnotationLabels.java | 447 +++-- src/jalview/datamodel/ColumnSelection.java | 1399 ++++++------- src/jalview/gui/AlignViewport.java | 2842 +++++++++++++-------------- src/jalview/gui/AnnotationLabels.java | 1145 ++++++----- 5 files changed, 4044 insertions(+), 3884 deletions(-) diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 0013bc0..eb832f2 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,1035 +1,1060 @@ -/* - * 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 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 - Hashtable featuresDisplayed; - - boolean hasHiddenColumns = false; - boolean hasHiddenRows = false; - boolean showHiddenMarkers = true; - - - public Vector vconsensus; - 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(); - } - } - // 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(vconsensus); - } - } - - 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() - { - Annotation[] annotations = new Annotation[alignment.getWidth()]; - - // 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 - { - Vector temp = alignment.getAAFrequency(); - vconsensus.removeAllElements(); - Enumeration e = temp.elements(); - while (e.hasMoreElements()) - { - vconsensus.addElement(e.nextElement()); - } - } - Hashtable hash = null; - for (int i = 0; i < alignment.getWidth(); i++) - { - hash = (Hashtable) vconsensus.elementAt(i); - 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") + " "; - 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(vconsensus); - - } - - 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'); - } - - 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 hideSequence(SequenceI seq) - { - if(seq!=null) - { - alignment.getHiddenSequences().hideSequence(seq); - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); - } - } - - public void hideAllSelectedSeqs() - { - if (selectionGroup == null) - return; - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - for (int i = 0; i < seqs.length; i++) - { - alignment.getHiddenSequences().hideSequence(seqs[i]); - } - firePropertyChange("alignment", null, alignment.getSequences()); - hasHiddenRows = true; - setSelectionGroup(null); - } - - 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