X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=42aae94691bf77acabbdf864283a4394ca6f2f77;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=8c6c7d26f4dc176ceac0eaa90bc243824526400f;hpb=25716aeeb932199c0b16221ed20e501fc2e448a1;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java old mode 100755 new mode 100644 index 8c6c7d2..42aae94 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,708 +1,665 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 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 = new SequenceGroup(); - - int charHeight; - int charWidth; - int wrappedWidth; - - Font font = new Font("SansSerif", Font.PLAIN, 10); - 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 = null; - - - public Vector vconsensus; - AlignmentAnnotation consensus; - AlignmentAnnotation conservation; - AlignmentAnnotation quality; - - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this); - - boolean ignoreGapsInConsensusCalculation = false; - - public AlignViewport(AlignmentI al, JalviewLite applet) - { - setAlignment(al); - this.startRes = 0; - this.endRes = al.getWidth() - 1; - this.startSeq = 0; - this.endSeq = al.getHeight() - 1; - setFont(font); - - 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 && applet.getParameter("defaultColour") != null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - applet.getParameter("defaultColour")); - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(vconsensus); - } - } - } - - public void showSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } - - - 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; - } - - public void setFont(Font f) - { - font = f; - java.awt.Frame temp = new java.awt.Frame(); - temp.addNotify(); - java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - } - - public Font getFont() - { - return font; - } - - public void setCharWidth(int w) - { - this.charWidth = w; - } - - 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 int getIndex(int y) - { - int y1 = 0; - int starty = getStartSeq(); - int endy = getEndSeq(); - - for (int i = starty; i <= endy; i++) - { - if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) - { - int y2 = y1 + getCharHeight(); - - if (y >= y1 && y <= y2) - { - return i; - } - y1 = y2; - } - else - { - return -1; - } - } - return -1; - } - - 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; - } - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.appletgui; + +import java.util.*; + +import java.awt.*; + +import jalview.analysis.*; +import jalview.api.AlignViewportI; +import jalview.bin.*; +import jalview.datamodel.*; +import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.VamsasSource; +import jalview.viewmodel.AlignmentViewport; + +public class AlignViewport extends AlignmentViewport implements + AlignViewportI, SelectionSource, VamsasSource +{ + 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 upperCasebold = false; + + int charHeight; + + int charWidth; + + int wrappedWidth; + + Font font = new Font("SansSerif", Font.PLAIN, 10); + + boolean validCharWidth = true; + + 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 showHiddenMarkers = true; + + public jalview.bin.JalviewLite applet; + + boolean MAC = false; + + Stack historyList = new Stack(); + + Stack redoList = new Stack(); + + public void finalize() + { + applet = null; + quality = null; + alignment = null; + colSel = null; + } + + public AlignViewport(AlignmentI al, JalviewLite applet) + { + calculator = new jalview.workers.AlignCalcManager(); + this.applet = applet; + setAlignment(al); + // we always pad gaps + this.setPadGaps(true); + this.startRes = 0; + this.endRes = al.getWidth() - 1; + this.startSeq = 0; + this.endSeq = al.getHeight() - 1; + if (applet != null) + { + // get the width and height scaling factors if they were specified + String param = applet.getParameter("widthScale"); + if (param != null) + { + try + { + widthScale = new Float(param).floatValue(); + } catch (Exception e) + { + } + if (widthScale <= 1.0) + { + System.err + .println("Invalid alignment character width scaling factor (" + + widthScale + "). Ignoring."); + widthScale = 1; + } + if (applet.debug) + { + System.err + .println("Alignment character width scaling factor is now " + + widthScale); + } + } + param = applet.getParameter("heightScale"); + if (param != null) + { + try + { + heightScale = new Float(param).floatValue(); + } catch (Exception e) + { + } + if (heightScale <= 1.0) + { + System.err + .println("Invalid alignment character height scaling factor (" + + heightScale + "). Ignoring."); + heightScale = 1; + } + if (applet.debug) + { + System.err + .println("Alignment character height scaling factor is now " + + heightScale); + } + } + } + setFont(font); + + MAC = new jalview.util.Platform().isAMac(); + + if (applet != null) + { + showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix); + + showAnnotation = applet.getDefaultParameter("showAnnotation", + showAnnotation); + + showConservation = applet.getDefaultParameter("showConservation", + showConservation); + + showQuality = applet.getDefaultParameter("showQuality", showQuality); + + showConsensus = applet.getDefaultParameter("showConsensus", + showConsensus); + + showUnconserved = applet.getDefaultParameter("showUnconserved", + showUnconserved); + + String param = applet.getParameter("upperCase"); + if (param != null) + { + if (param.equalsIgnoreCase("bold")) + { + upperCasebold = true; + } + } + sortByTree = applet.getDefaultParameter("sortByTree", sortByTree); + + followHighlight = applet.getDefaultParameter("automaticScrolling", + followHighlight); + followSelection = followHighlight; + + showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", + showSequenceLogo); + + normaliseSequenceLogo = applet.getDefaultParameter( + "normaliseSequenceLogo", applet.getDefaultParameter( + "normaliseLogo", normaliseSequenceLogo)); + + showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", + showGroupConsensus); + + showGroupConservation = applet.getDefaultParameter( + "showGroupConservation", showGroupConservation); + + showConsensusHistogram = applet.getDefaultParameter( + "showConsensusHistogram", showConsensusHistogram); + + } + + 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")); + } + } + initAutoAnnotation(); + + } + + public void showSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + + public boolean getShowSequenceFeatures() + { + return showSequenceFeatures; + } + + /** + * 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(null); + } + 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 int getStartRes() + { + return startRes; + } + + public int getEndRes() + { + return endRes; + } + + public int getStartSeq() + { + return startSeq; + } + + 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; + + protected FeatureSettings featureSettings = null; + + private float heightScale = 1, widthScale = 1; + + 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((int) (heightScale * fm.getHeight())); + charWidth = (int) (widthScale * fm.charWidth('M')); + + if (upperCasebold) + { + Font f2 = new Font(f.getName(), Font.BOLD, f.getSize()); + fm = nullFrame.getGraphics().getFontMetrics(f2); + charWidth = (int) (widthScale * (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 resetSeqLimits(int height) + { + setEndSeq(height / getCharHeight()); + } + + public void setCurrentTree(NJTree tree) + { + currentTree = tree; + } + + public NJTree getCurrentTree() + { + return currentTree; + } + + 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); + + } + } + + public boolean getShowHiddenMarkers() + { + return showHiddenMarkers; + } + + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; + } + + boolean centreColumnLabels; + + public boolean getCentreColumnLabels() + { + return centreColumnLabels; + } + + public boolean followHighlight = true; + + public boolean getFollowHighlight() + { + return followHighlight; + } + + public boolean followSelection = true; + + /** + * @return true if view selection should always follow the selections + * broadcast by other selection sources + */ + public boolean getFollowSelection() + { + return followSelection; + } + + public void sendSelection() + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(applet).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + /** + * synthesize a column selection if none exists so it covers the given + * selection group. if wholewidth is false, no column selection is made if the + * selection group covers the whole alignment width. + * + * @param sg + * @param wholewidth + */ + public void expandColSelection(SequenceGroup sg, boolean wholewidth) + { + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } + } + + @Override + public boolean hasHiddenColumns() + { + return hasHiddenColumns; + } + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + + /** + * + * @return true if alignment characters should be displayed + */ + public boolean isValidCharWidth() + { + return validCharWidth; + } + +}