X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8f615aa55480e4eda1d6155f2e371d13e0b0dcd7;hb=ca2d191924169cd2fa37a9eafcb7d4de41b28c53;hp=a135620ea8c3c7353b57f7159470f665acfdd539;hpb=ebb52a433edbbdbd31ab82cbb1c59fc116a72b1d;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index a135620..8f615aa --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,537 +1,1413 @@ -package jalview.gui; - -import java.awt.*; -import jalview.analysis.*; -import jalview.analysis.NJTree; -import jalview.datamodel.*; -import jalview.schemes.*; -import java.util.*; -import jalview.bin.Cache; - -public class AlignViewport -{ - int startRes; - int endRes; - - int startSeq; - int endSeq; - - boolean showFullId = false; - 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 showIdentity = true; - - boolean colourAppliesToAllGroups = true; - ColourSchemeI globalColourScheme = null; - boolean conservationColourSelected = false; - boolean abovePIDThreshold = false; - - SequenceGroup selectionGroup = new SequenceGroup(); - - RendererI renderer = new SequenceRenderer(this); - - int charHeight; - int charWidth; - int chunkWidth; - int chunkHeight; - - Font font = new Font("SansSerif",Font.PLAIN,10); - AlignmentI alignment; - - ColumnSelection colSel = new ColumnSelection(); - - int threshold; - int increment; - - NJTree currentTree = null; - - boolean scaleAboveWrapped = false; - boolean scaleLeftWrapped = true; - boolean scaleRightWrapped = true; - - - public AlignViewport(AlignmentI al) - { - setAlignment(al); - this.startRes = 0; - this.endRes = al.getWidth()-1; - this.startSeq = 0; - this.endSeq = al.getHeight()-1; - - updateFromPreferences(); - - } - - public void updateFromPreferences() - { - String string = Cache.getProperty("SHOW_FULL_ID"); - if(string!=null) - showFullId = Boolean.valueOf(string).booleanValue(); - - string = Cache.getProperty("SHOW_ANNOTATIONS"); - if(string!=null) - showAnnotation = Boolean.valueOf(string).booleanValue(); - - string = Cache.getProperty("SHOW_CONSERVATION"); - if(string!=null) - showConservation = Boolean.valueOf(string).booleanValue(); - string = Cache.getProperty("SHOW_QUALITY"); - if(string!=null) - showQuality = Boolean.valueOf(string).booleanValue(); - string = Cache.getProperty("SHOW_IDENTITY"); - if(string!=null) - showIdentity = Boolean.valueOf(string).booleanValue(); - - string = Cache.getProperty("SHOW_FULL_ID"); - if(string!=null) - showFullId = Boolean.valueOf(string).booleanValue(); - - String fontName = Cache.getProperty("FONT_NAME"); - String fontStyle= Cache.getProperty("FONT_STYLE"); - String fontSize = Cache.getProperty("FONT_SIZE"); - if(fontName!=null && fontStyle!=null && fontSize!=null) - setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) ); - else - setFont( font ); - - string = Cache.getProperty("GAP_SYMBOL"); - if(string!=null) - alignment.setGapCharacter( string.charAt(0) ); - - - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - updateConservation(); - updateConsensus(); - string = Cache.getProperty("DEFAULT_COLOUR"); - if(string!=null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, string); - if(globalColourScheme!=null) - globalColourScheme.setConsensus( vconsensus ); - } - - } - - public void showSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } - - public Vector vconsensus; - AlignmentAnnotation consensus; - AlignmentAnnotation conservation; - AlignmentAnnotation quality; - - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - - public void updateConservation() - { - 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) + "", - "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop)); - // Quality calc - value = ((Double) cons.quality.get(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() - 1); - if(showConservation) - alignment.addAnnotation(conservation); - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), - 1); - 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.clear(); - Enumeration e = temp.elements(); - while(e.hasMoreElements()) - { - vconsensus.add(e.nextElement()); - } - } - Hashtable hash = null; - for (int i = 0; i2) - { - mouseOver = "["+maxRes+"] "; - maxRes = "+ "; - } - - mouseOver += (int)value+"%"; - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - - } - - if(consensus==null) - { - consensus = new AlignmentAnnotation("% Identity", - "PID", annotations, 0f, 100f, 1); - if(showIdentity) - alignment.addAnnotation(consensus); - } - else - consensus.annotations = annotations; - - } - - - 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) { - 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; - javax.swing.JFrame temp = new javax.swing.JFrame(); - 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 setChunkWidth(int w) { - this.chunkWidth = w; - } - public int getChunkWidth() { - return chunkWidth; - } - public void setChunkHeight(int h) { - this.chunkHeight = h; - } - public int getChunkHeight() { - return chunkHeight; - } - 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; - if(renderer instanceof SequenceRenderer) - { - SequenceRenderer sr = (SequenceRenderer)renderer; - sr.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 setRenderer(RendererI rend) { - this.renderer = rend; - } - - public RendererI getRenderer() { - return renderer; - } - - public void setColourAppliesToAllGroups(boolean b) - { colourAppliesToAllGroups = b; } - - public boolean getColourAppliesToAllGroups() - {return colourAppliesToAllGroups; } - - public boolean getShowFullId() - { - return showFullId; - } - - public void setShowFullId(boolean b) - { - showFullId = 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; } - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ +/* + * 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.gui; + +import java.util.*; + +import java.awt.*; + +import jalview.analysis.*; +import jalview.api.AlignCalcManagerI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.OOMHandlerI; + +import jalview.bin.*; + +import jalview.datamodel.*; + +import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.viewmodel.AlignmentViewport; +import jalview.workers.AlignCalcManager; +import jalview.workers.ConsensusThread; +import jalview.workers.ConservationThread; +import jalview.workers.StrucConsensusThread; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision: 1.141 $ + */ +public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI +{ + private static final int RIGHT_JUSTIFY = 1; + + 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 colourAppliesToAllGroups = true; + + boolean conservationColourSelected = false; + + boolean abovePIDThreshold = false; + + int charHeight; + + int charWidth; + + boolean validCharWidth; + + int wrappedWidth; + + Font font; + + boolean seqNameItalics; + + int threshold; + + int increment; + + NJTree currentTree = null; + + boolean scaleAboveWrapped = false; + + boolean scaleLeftWrapped = true; + + boolean scaleRightWrapped = true; + + boolean showHiddenMarkers = true; + + boolean cursorMode = false; + + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ + Hashtable featuresDisplayed = null; + + boolean antiAlias = false; + + Rectangle explodedPosition; + + String viewName; + + boolean gatherViewsHere = false; + + Stack historyList = new Stack(); + + Stack redoList = new Stack(); + + Hashtable sequenceColours; + + int thresholdTextColour = 0; + + Color textColour = Color.black; + + Color textColour2 = Color.white; + + boolean rightAlignIds = false; + + /** + * Creates a new AlignViewport object. + * + * @param al + * alignment to view + */ + public AlignViewport(AlignmentI al) + { + setAlignment(al); + init(); + } + + /** + * Create a new AlignViewport object with a specific sequence set ID + * + * @param al + * @param seqsetid + * (may be null - but potential for ambiguous constructor exception) + */ + public AlignViewport(AlignmentI al, String seqsetid) + { + this(al, seqsetid, null); + } + + public AlignViewport(AlignmentI al, String seqsetid, String viewid) + { + sequenceSetID = seqsetid; + viewId = viewid; + // TODO remove these once 2.4.VAMSAS release finished + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + init(); + } + + /** + * Create a new AlignViewport with hidden regions + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + { + setAlignment(al); + if (hiddenColumns != null) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } + } + init(); + } + + /** + * New viewport with hidden columns and an existing sequence set id + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid) + { + this(al, hiddenColumns, seqsetid, null); + } + + /** + * New viewport with hidden columns and an existing sequence set id and viewid + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + * @param viewid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid, String viewid) + { + sequenceSetID = seqsetid; + viewId = viewid; + // TODO remove these once 2.4.VAMSAS release finished + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + if (hiddenColumns != null) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } + } + init(); + } + + void init() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; + + antiAlias = Cache.getDefault("ANTI_ALIAS", false); + + showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); + showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); + + rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); + centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); + autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + + setPadGaps(Cache.getDefault("PAD_GAPS", true)); + shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); + showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); + + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); + String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); + String fontSize = Cache.getDefault("FONT_SIZE", "10"); + + seqNameItalics = Cache.getDefault("ID_ITALICS", true); + + int style = 0; + + if (fontStyle.equals("bold")) + { + style = 1; + } + else if (fontStyle.equals("italic")) + { + style = 2; + } + + setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + + alignment + .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + + // We must set conservation and consensus before setting colour, + // as Blosum and Clustal require this to be done + if (hconsensus == null && !isDataset) + { + if (!alignment.isNucleotide()) + { + showConservation=Cache.getDefault("SHOW_CONSERVATION", true); + showQuality=Cache.getDefault("SHOW_QUALITY", true); + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); + } + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); + showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false); + showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); + showConsensus=Cache.getDefault("SHOW_IDENTITY", true); + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + } + initAutoAnnotation(); + if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) + { + globalColourScheme = ColourSchemeProperty.getColour(alignment, + jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + + if (globalColourScheme instanceof UserColourScheme) + { + globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme) globalColourScheme).setThreshold(0, + getIgnoreGapsConsensus()); + } + + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + } + + wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); + showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", + false); + sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false); + followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", + true); + } + + /** + * set the flag + * + * @param b + * features are displayed if true + */ + public void setShowSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + + public boolean getShowSequenceFeatures() + { + return showSequenceFeatures; + } + + /** + * centre columnar annotation labels in displayed alignment annotation TODO: + * add to jalviewXML and annotation display settings + */ + boolean centreColumnLabels = false; + + private boolean showdbrefs; + + private boolean shownpfeats; + + // --------END Structure Conservation + + /** + * 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; + } + + + /** + * GUI state + * + * @return true if conservation based shading is enabled + */ + public boolean getConservationSelected() + { + return conservationColourSelected; + } + + /** + * GUI state + * + * @param b + * enable conservation based shading + */ + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } + + /** + * GUI state + * + * @return true if percent identity threshold is applied to shading + */ + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } + + /** + * GUI state + * + * + * @param b + * indicate if percent identity threshold is applied to shading + */ + public void setAbovePIDThreshold(boolean b) + { + abovePIDThreshold = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartRes() + { + return startRes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEndRes() + { + return endRes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartSeq() + { + return startSeq; + } + + /** + * DOCUMENT ME! + * + * @param res + * DOCUMENT ME! + */ + public void setStartRes(int res) + { + this.startRes = res; + } + + /** + * DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! + */ + public void setStartSeq(int seq) + { + this.startSeq = seq; + } + + /** + * DOCUMENT ME! + * + * @param res + * DOCUMENT ME! + */ + 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; + } + + /** + * DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! + */ + public void setEndSeq(int seq) + { + if (seq > alignment.getHeight()) + { + seq = alignment.getHeight(); + } + + if (seq < 0) + { + seq = 0; + } + + this.endSeq = seq; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEndSeq() + { + return endSeq; + } + + /** + * DOCUMENT ME! + * + * @param f + * DOCUMENT ME! + */ + public void setFont(Font f) + { + font = f; + + Container c = new Container(); + + java.awt.FontMetrics fm = c.getFontMetrics(font); + setCharHeight(fm.getHeight()); + setCharWidth(fm.charWidth('M')); + validCharWidth = true; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Font getFont() + { + return font; + } + + /** + * DOCUMENT ME! + * + * @param w + * DOCUMENT ME! + */ + public void setCharWidth(int w) + { + this.charWidth = w; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getCharWidth() + { + return charWidth; + } + + /** + * DOCUMENT ME! + * + * @param h + * DOCUMENT ME! + */ + public void setCharHeight(int h) + { + this.charHeight = h; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getCharHeight() + { + return charHeight; + } + + /** + * DOCUMENT ME! + * + * @param w + * DOCUMENT ME! + */ + public void setWrappedWidth(int w) + { + this.wrappedWidth = w; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedWidth() + { + return wrappedWidth; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public AlignmentI getAlignment() + { + return alignment; + } + + /** + * DOCUMENT ME! + * + * @param align + * DOCUMENT ME! + */ + public void setAlignment(AlignmentI align) + { + if (alignment != null && alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).removeMappings(alignment.getCodonFrames()); + } + this.alignment = align; + if (alignment!=null && alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); + } + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setWrapAlignment(boolean state) + { + wrapAlignment = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowText(boolean state) + { + showText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setRenderGaps(boolean state) + { + renderGaps = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourText() + { + return showColourText; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setColourText(boolean state) + { + showColourText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowBoxes(boolean state) + { + showBoxes = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getWrapAlignment() + { + return wrapAlignment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowText() + { + return showText; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowBoxes() + { + return showBoxes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char getGapCharacter() + { + return getAlignment().getGapCharacter(); + } + + /** + * DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! + */ + public void setGapCharacter(char gap) + { + if (getAlignment() != null) + { + getAlignment().setGapCharacter(gap); + } + } + + /** + * DOCUMENT ME! + * + * @param thresh + * DOCUMENT ME! + */ + public void setThreshold(int thresh) + { + threshold = thresh; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getThreshold() + { + return threshold; + } + + /** + * DOCUMENT ME! + * + * @param inc + * DOCUMENT ME! + */ + public void setIncrement(int inc) + { + increment = inc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getIncrement() + { + return increment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public ColumnSelection getColumnSelection() + { + return colSel; + } + + /** + * DOCUMENT ME! + * + * @param tree + * DOCUMENT ME! + */ + public void setCurrentTree(NJTree tree) + { + currentTree = tree; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public NJTree getCurrentTree() + { + return currentTree; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setColourAppliesToAllGroups(boolean b) + { + colourAppliesToAllGroups = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourAppliesToAllGroups() + { + return colourAppliesToAllGroups; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowJVSuffix() + { + return showJVSuffix; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowJVSuffix(boolean b) + { + showJVSuffix = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowAnnotation() + { + return showAnnotation; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowAnnotation(boolean b) + { + showAnnotation = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleAboveWrapped() + { + return scaleAboveWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleLeftWrapped() + { + return scaleLeftWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleRightWrapped() + { + return scaleRightWrapped; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleAboveWrapped(boolean b) + { + scaleAboveWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleLeftWrapped(boolean b) + { + scaleLeftWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleRightWrapped(boolean b) + { + scaleRightWrapped = b; + } + + + public void setDataset(boolean b) + { + isDataset = b; + } + + public boolean isDataset() + { + return isDataset; + } + + + + 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); + } + } + + /** + * returns the visible column regions of the alignment + * + * @param selectedRegionOnly + * true to just return the contigs intersecting with the selected + * area + * @return + */ + public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) + { + int[] viscontigs = null; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + end = alignment.getWidth(); + } + viscontigs = colSel.getVisibleContigs(start, end); + return viscontigs; + } + + /** + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; + */ + public long[] getUndoRedoHash() + { + if (historyList == null || redoList == null) + return new long[] + { -1, -1 }; + return new long[] + { historyList.hashCode(), this.redoList.hashCode() }; + } + + /** + * test if a particular set of hashcodes are different to the hashcodes for + * the undo and redo list. + * + * @param undoredo + * the stored set of hashcodes as returned by getUndoRedoHash + * @return true if the hashcodes differ (ie the alignment has been edited) or + * the stored hashcode array differs in size + */ + public boolean isUndoRedoHashModified(long[] undoredo) + { + if (undoredo == null) + { + return true; + } + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) + { + return true; + } + + for (int i = 0; i < cstate.length; i++) + { + if (cstate[i] != undoredo[i]) + { + return true; + } + } + return false; + } + + public boolean getCentreColumnLabels() + { + return centreColumnLabels; + } + + public void setCentreColumnLabels(boolean centrecolumnlabels) + { + centreColumnLabels = centrecolumnlabels; + } + + public void updateSequenceIdColours() + { + Vector groups = alignment.getGroups(); + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + for (int ig = 0, igSize = groups.size(); ig < igSize; ig++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); + if (sg.idColour != null) + { + Vector sqs = sg.getSequences(getHiddenRepSequences()); + for (int s = 0, sSize = sqs.size(); s < sSize; s++) + { + sequenceColours.put(sqs.elementAt(s), sg.idColour); + } + } + } + } + + /** + * enable or disable the display of Database Cross References in the sequence + * ID tooltip + */ + public void setShowDbRefs(boolean show) + { + showdbrefs = show; + } + + /** + * + * @return true if Database References are to be displayed on tooltips. + */ + public boolean isShowDbRefs() + { + return showdbrefs; + } + + /** + * + * @return true if Non-positional features are to be displayed on tooltips. + */ + public boolean isShowNpFeats() + { + return shownpfeats; + } + + /** + * enable or disable the display of Non-Positional sequence features in the + * sequence ID tooltip + * + * @param show + */ + public void setShowNpFeats(boolean show) + { + shownpfeats = show; + } + + /** + * + * @return true if view has hidden rows + */ + public boolean hasHiddenRows() + { + return hasHiddenRows; + } + + /** + * + * @return true if view has hidden columns + */ + public boolean hasHiddenColumns() + { + return hasHiddenColumns; + } + + /** + * when set, view will scroll to show the highlighted position + */ + public boolean followHighlight = true; + + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ + 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; + } + + boolean showSeqFeaturesHeight; + + public void sendSelection() + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + public void setShowSequenceFeaturesHeight(boolean selected) + { + showSeqFeaturesHeight = selected; + } + + public boolean getShowSequenceFeaturesHeight() + { + return showSeqFeaturesHeight; + } + + /** + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. + * + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference + */ + public AlignmentPanel getAlignPanel() + { + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this + .getSequenceSetId()); + AlignmentPanel ap = null; + for (int p = 0; aps != null && p < aps.length; p++) + { + if (aps[p].av == this) + { + return aps[p]; + } + } + return null; + } + + public boolean getSortByTree() + { + return sortByTree; + } + + public void setSortByTree(boolean sort) + { + sortByTree = sort; + } + + /** + * 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); + } + } + } + + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + } + + /** + * + * @param pdbEntries + * @return a series of SequenceI arrays, one for each PDBEntry, listing which + * sequence in the alignment holds a reference to it + */ + public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) + { + ArrayList seqvectors = new ArrayList(); + for (PDBEntry pdb : pdbEntries) + { + ArrayList seqs = new ArrayList(); + for (int i = 0; i < alignment.getHeight(); i++) + { + Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() + .getPDBId(); + if (pdbs == null) + continue; + SequenceI sq; + for (int p = 0; p < pdbs.size(); p++) + { + PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq = alignment.getSequenceAt(i))) + seqs.add(sq); + + continue; + } + } + } + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + } + return seqvectors.toArray(new SequenceI[seqvectors.size()][]); + } + + + 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; + } +}