From 6366cf9dcc083ef36aa9fe822bf49fbc18100dca Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 17 Apr 2007 17:05:41 +0000 Subject: [PATCH] bugfix for jalviewApplet run from command line. --- src/jalview/appletgui/AlignViewport.java | 2896 +++++++++++++++--------------- 1 file changed, 1448 insertions(+), 1448 deletions(-) diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 43831a2..e5551e2 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,1448 +1,1448 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * 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 - * 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; - - Hashtable sequenceColours; - - boolean MAC = false; - - Stack historyList = new Stack(); - Stack redoList = new Stack(); - - String sequenceSetID; - - Hashtable hiddenRepSequences; - - public AlignViewport(AlignmentI al, JalviewLite applet) - { - this.applet = applet; - 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; - } - } - - } - - 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")); - } - - if (hconsensus == null) - { - if (!alignment.isNucleotide()) - { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", - new Annotation[1], 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); - conservation.hasText = true; - conservation.autoCalculated = true; - - if (showConservation) - { - alignment.addAnnotation(conservation); - } - - if (showQuality) - { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], - 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - quality.autoCalculated = true; - - alignment.addAnnotation(quality); - } - } - - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; - - if (showConsensus) - { - alignment.addAnnotation(consensus); - } - } - } - } - - public void showSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } - - public boolean getShowSequenceFeatures() - { - return showSequenceFeatures; - } - - class ConservationThread - extends Thread - { - AlignmentPanel ap; - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - try - { - updatingConservation = true; - - while (UPDATING_CONSERVATION) - { - try - { - if (ap != null) - { - ap.paintAlignment(true); - } - Thread.sleep(200); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSERVATION = true; - - int alWidth = alignment.getWidth(); - if (alWidth < 0) - { - 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) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - quality.annotations = new Annotation[alWidth]; - qmin = cons.qualityRange[0].floatValue(); - qmax = cons.qualityRange[1].floatValue(); - } - - for (int i = 0; i < alWidth; i++) - { - float value = 0; - - c = sequence[i]; - - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') - { - value = 11; - } - else if (c == '+') - { - value = 10; - } - - float vprop = value - min; - vprop /= max; - conservation.annotations[i] = - new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - - // Quality calc - if (quality != null) - { - value = ( (Double) cons.quality.elementAt(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String.valueOf(value), - ' ', - value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - } - } - } - catch (OutOfMemoryError error) - { - System.out.println("Out of memory calculating conservation!!"); - conservation = null; - quality = null; - 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(final AlignmentPanel ap) - { - consensusThread = new ConsensusThread(ap); - consensusThread.start(); - } - - class ConsensusThread - extends Thread - { - AlignmentPanel ap; - public ConsensusThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - updatingConsensus = true; - while (UPDATING_CONSENSUS) - { - try - { - if (ap != null) - { - ap.paintAlignment(true); - } - - Thread.sleep(200); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSENSUS = true; - - try - { - int aWidth = alignment.getWidth(); - if (aWidth < 0) - { - return; - } - - consensus.annotations = null; - consensus.annotations = new Annotation[aWidth]; - - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - { - value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)). - floatValue(); - } - else - { - value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)). - floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ( (int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } - - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - - } - catch (OutOfMemoryError error) - { - alignment.deleteAnnotation(consensus); - - consensus = null; - hconsensus = null; - System.out.println("Out of memory calculating consensus!!"); - System.gc(); - } - UPDATING_CONSENSUS = false; - updatingConsensus = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - } - } - - /** - * get the consensus sequence as displayed under the PID consensus annotation row. - * @return consensus sequence as a new sequence object - */ - /** - * get the consensus sequence as displayed under the PID consensus annotation row. - * @return consensus sequence as a new sequence object - */ - public SequenceI getConsensusSeq() - { - if (consensus == null) - { - 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(null); - 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() - { - for (int i = 0; i < alignment.getWidth(); i++) - { - if (colSel.contains(i)) - { - colSel.removeElement(i); - } - else - { - if (!hasHiddenColumns || colSel.isVisible(i)) - { - colSel.addElement(i); - } - } - } - } - - 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 || selectionGroup.getSize()<1) - { - 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(hiddenRepSequences); - for (int t = 0; t < tmp.size(); t++) - { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); - } - firePropertyChange("alignment", null, alignment.getSequences()); - hasHiddenRows = false; - hiddenRepSequences = null; - } - } - - 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(); - 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(); - 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].getSequenceAsString(start, end); - } - } - - return selection; - } - - public boolean getShowHiddenMarkers() - { - return showHiddenMarkers; - } - - public void setShowHiddenMarkers(boolean show) - { - showHiddenMarkers = show; - } - - public Color getSequenceColour(SequenceI seq) - { - if (sequenceColours == null || !sequenceColours.containsKey(seq)) - { - return Color.white; - } - else - { - return (Color) sequenceColours.get(seq); - } - } - - public void setSequenceColour(SequenceI seq, Color col) - { - if (sequenceColours == null) - { - sequenceColours = new Hashtable(); - } - - if (col == null) - { - sequenceColours.remove(seq); - } - else - { - sequenceColours.put(seq, col); - } - } - - public String getSequenceSetId() - { - if (sequenceSetID == null) - { - sequenceSetID = alignment.hashCode() + ""; - } - - return sequenceSetID; - } - - public void alignmentChanged(AlignmentPanel ap) - { - alignment.padGaps(); - - if (hconsensus != null && autocalculateConsensus) - { - updateConsensus(ap); - updateConservation(ap); - } - - //Reset endRes of groups if beyond alignment width - int alWidth = alignment.getWidth(); - Vector groups = alignment.getGroups(); - if (groups != null) - { - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (sg.getEndRes() > alWidth) - { - sg.setEndRes(alWidth - 1); - } - } - } - - if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) - { - selectionGroup.setEndRes(alWidth - 1); - } - - resetAllColourSchemes(); - - //AW alignment.adjustSequenceAnnotations(); - } - - void resetAllColourSchemes() - { - ColourSchemeI cs = globalColourScheme; - if (cs != null) - { - if (cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) cs). - resetClustalX(alignment.getSequences(), - alignment.getWidth()); - } - - cs.setConsensus(hconsensus); - if (cs.conservationApplied()) - { - Alignment al = (Alignment) alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); - c.calculate(); - c.verdict(false, ConsPercGaps); - - cs.setConservation(c); - } - } - - int s, sSize = alignment.getGroups().size(); - for (s = 0; s < sSize; s++) - { - SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); - if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) sg.cs).resetClustalX( - sg.getSequences(hiddenRepSequences), sg.getWidth()); - } - sg.recalcConservation(); - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * 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 + * 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; + + Hashtable sequenceColours; + + boolean MAC = false; + + Stack historyList = new Stack(); + Stack redoList = new Stack(); + + String sequenceSetID; + + Hashtable hiddenRepSequences; + + public AlignViewport(AlignmentI al, JalviewLite applet) + { + this.applet = applet; + 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; + } + } + + } + + 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")); + } + } + if (hconsensus == null) + { + if (!alignment.isNucleotide()) + { + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + + ConsPercGaps + "% gaps", + new Annotation[1], 0f, + 11f, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + conservation.autoCalculated = true; + + if (showConservation) + { + alignment.addAnnotation(conservation); + } + + if (showQuality) + { + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], + 0f, + 11f, + AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; + + alignment.addAnnotation(quality); + } + } + + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + + if (showConsensus) + { + alignment.addAnnotation(consensus); + } + } + + } + + public void showSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + + public boolean getShowSequenceFeatures() + { + return showSequenceFeatures; + } + + class ConservationThread + extends Thread + { + AlignmentPanel ap; + public ConservationThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + try + { + updatingConservation = true; + + while (UPDATING_CONSERVATION) + { + try + { + if (ap != null) + { + ap.paintAlignment(true); + } + Thread.sleep(200); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_CONSERVATION = true; + + int alWidth = alignment.getWidth(); + if (alWidth < 0) + { + 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) + { + quality.graphMax = cons.qualityRange[1].floatValue(); + quality.annotations = new Annotation[alWidth]; + qmin = cons.qualityRange[0].floatValue(); + qmax = cons.qualityRange[1].floatValue(); + } + + for (int i = 0; i < alWidth; i++) + { + float value = 0; + + c = sequence[i]; + + if (Character.isDigit(c)) + { + value = (int) (c - '0'); + } + else if (c == '*') + { + value = 11; + } + else if (c == '+') + { + value = 10; + } + + float vprop = value - min; + vprop /= max; + conservation.annotations[i] = + new Annotation(String.valueOf(c), + String.valueOf(value), ' ', value, + new Color(minR + (maxR * vprop), + minG + (maxG * vprop), + minB + (maxB * vprop))); + + // Quality calc + if (quality != null) + { + value = ( (Double) cons.quality.elementAt(i)).floatValue(); + vprop = value - qmin; + vprop /= qmax; + quality.annotations[i] = new Annotation(" ", String.valueOf(value), + ' ', + value, + new Color(minR + (maxR * vprop), + minG + (maxG * vprop), + minB + (maxB * vprop))); + } + } + } + catch (OutOfMemoryError error) + { + System.out.println("Out of memory calculating conservation!!"); + conservation = null; + quality = null; + 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(final AlignmentPanel ap) + { + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + } + + class ConsensusThread + extends Thread + { + AlignmentPanel ap; + public ConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + updatingConsensus = true; + while (UPDATING_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(true); + } + + Thread.sleep(200); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_CONSENSUS = true; + + try + { + int aWidth = alignment.getWidth(); + if (aWidth < 0) + { + return; + } + + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; + + hconsensus = new Hashtable[aWidth]; + AAFrequency.calculate(alignment.getSequencesArray(), + 0, + alignment.getWidth(), + hconsensus); + + for (int i = 0; i < aWidth; i++) + { + float value = 0; + if (ignoreGapsInConsensusCalculation) + { + value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)). + floatValue(); + } + else + { + value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)). + floatValue(); + } + + String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); + String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + + if (maxRes.length() > 1) + { + mouseOver = "[" + maxRes + "] "; + maxRes = "+"; + } + + mouseOver += ( (int) value + "%"); + consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', + value); + } + + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + + } + catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(consensus); + + consensus = null; + hconsensus = null; + System.out.println("Out of memory calculating consensus!!"); + System.gc(); + } + UPDATING_CONSENSUS = false; + updatingConsensus = false; + + if (ap != null) + { + ap.paintAlignment(true); + } + } + } + + /** + * get the consensus sequence as displayed under the PID consensus annotation row. + * @return consensus sequence as a new sequence object + */ + /** + * get the consensus sequence as displayed under the PID consensus annotation row. + * @return consensus sequence as a new sequence object + */ + public SequenceI getConsensusSeq() + { + if (consensus == null) + { + 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(null); + 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() + { + for (int i = 0; i < alignment.getWidth(); i++) + { + if (colSel.contains(i)) + { + colSel.removeElement(i); + } + else + { + if (!hasHiddenColumns || colSel.isVisible(i)) + { + colSel.addElement(i); + } + } + } + } + + 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 || selectionGroup.getSize()<1) + { + 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(hiddenRepSequences); + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence( + (SequenceI) tmp.elementAt(t), false + ); + } + firePropertyChange("alignment", null, alignment.getSequences()); + hasHiddenRows = false; + hiddenRepSequences = null; + } + } + + 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(); + 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(); + 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].getSequenceAsString(start, end); + } + } + + return selection; + } + + public boolean getShowHiddenMarkers() + { + return showHiddenMarkers; + } + + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; + } + + public Color getSequenceColour(SequenceI seq) + { + if (sequenceColours == null || !sequenceColours.containsKey(seq)) + { + return Color.white; + } + else + { + return (Color) sequenceColours.get(seq); + } + } + + public void setSequenceColour(SequenceI seq, Color col) + { + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + + if (col == null) + { + sequenceColours.remove(seq); + } + else + { + sequenceColours.put(seq, col); + } + } + + public String getSequenceSetId() + { + if (sequenceSetID == null) + { + sequenceSetID = alignment.hashCode() + ""; + } + + return sequenceSetID; + } + + public void alignmentChanged(AlignmentPanel ap) + { + alignment.padGaps(); + + if (hconsensus != null && autocalculateConsensus) + { + updateConsensus(ap); + updateConservation(ap); + } + + //Reset endRes of groups if beyond alignment width + int alWidth = alignment.getWidth(); + Vector groups = alignment.getGroups(); + if (groups != null) + { + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if (sg.getEndRes() > alWidth) + { + sg.setEndRes(alWidth - 1); + } + } + } + + if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) + { + selectionGroup.setEndRes(alWidth - 1); + } + + resetAllColourSchemes(); + + //AW alignment.adjustSequenceAnnotations(); + } + + void resetAllColourSchemes() + { + ColourSchemeI cs = globalColourScheme; + if (cs != null) + { + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) cs). + resetClustalX(alignment.getSequences(), + alignment.getWidth()); + } + + cs.setConsensus(hconsensus); + if (cs.conservationApplied()) + { + Alignment al = (Alignment) alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); + c.calculate(); + c.verdict(false, ConsPercGaps); + + cs.setConservation(c); + } + } + + int s, sSize = alignment.getGroups().size(); + for (s = 0; s < sSize; s++) + { + SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); + if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) sg.cs).resetClustalX( + sg.getSequences(hiddenRepSequences), sg.getWidth()); + } + sg.recalcConservation(); + } + } + +} -- 1.7.10.2