X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d07b010ed81f4d75279ad3cd269f7fee8c107b77;hb=97a31ae1fe3095b9d332f655103e334342ee9a19;hp=1f5ec798cd7277a6ecc5781eb5f92a928728472e;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index 1f5ec79..93d8c19 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,539 +1,1173 @@ -/* -* 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.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(); - - - 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() - { - showFullId = Preferences.showFullId; - showAnnotation = Preferences.showAnnotation; - showConservation = Preferences.showConservation; - showQuality = Preferences.showQuality; - showIdentity = Preferences.showIdentity; - showFullId = Preferences.showFullId; - String fontName = Preferences.fontName; - String fontStyle = Preferences.fontStyle; - String fontSize = Cache.getProperty("FONT_SIZE"); - if (fontName != null && fontStyle != null && fontSize != null) - { - int style = 0; - if(fontStyle.equals("bold")) - style = 1; - else if(fontStyle.equals("italic")) - style = 2; - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - } - else - setFont(font); - - alignment.setGapCharacter(Preferences.gapSymbol); - - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - updateConservation(); - updateConsensus(); - if(Preferences.defaultColour!=null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour); - if(globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - } - 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) + "", - "", ' ', 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("Consensus", - "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) { - // 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; - 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; - } - - - 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 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; } - // JBPNote Prolly only need this in the applet version. - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this); - public void addPropertyChangeListener(java.beans.PropertyChangeListener listener) { - changeSupport.addPropertyChangeListener(listener); - } - - public void removePropertyChangeListener(java.beans.PropertyChangeListener listener) { - changeSupport.removePropertyChangeListener(listener); - } - public void firePropertyChange(String prop, Object oldvalue, Object newvalue) { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * 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. + */ +/* + * 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 jalview.analysis.AlignmentUtils; +import jalview.analysis.AlignmentUtils.MappingResult; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.analysis.NJTree; +import jalview.api.AlignViewportI; +import jalview.api.ViewStyleI; +import jalview.bin.Cache; +import jalview.commands.CommandI; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; +import jalview.structure.CommandListener; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.params.AutoCalcSetting; + +import java.awt.Container; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.Rectangle; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.Set; +import java.util.Vector; + +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision: 1.141 $ + */ +public class AlignViewport extends AlignmentViewport implements + SelectionSource, AlignViewportI, CommandListener +{ + int startRes; + + int endRes; + + int startSeq; + + int endSeq; + + + SequenceAnnotationOrder sortAnnotationsBy = null; + + Font font; + + NJTree currentTree = null; + + boolean cursorMode = false; + + boolean antiAlias = false; + + private Rectangle explodedGeometry; + + String viewName; + + /* + * Flag set true on the view that should 'gather' multiple views of the same + * sequence set id when a project is reloaded. Set false on all views when + * they are 'exploded' into separate windows. Set true on the current view + * when 'Gather' is performed, and also on the first tab when the first new + * view is created. + */ + private boolean gatherViewsHere = false; + + private AnnotationColumnChooser annotationColumnSelectionState; + /** + * 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) + { + colSel = hiddenColumns; + } + 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) + { + colSel = hiddenColumns; + } + init(); + } + + private void applyViewProperties() + { + antiAlias = Cache.getDefault("ANTI_ALIAS", false); + + viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); + setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true)); + + setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); + setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); + autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + + setPadGaps(Cache.getDefault("PAD_GAPS", true)); + setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); + setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); + viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); + viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); + viewStyle.setShowUnconserved(Cache + .getDefault("SHOW_UNCONSERVED", false)); + sortByTree = Cache.getDefault("SORT_BY_TREE", false); + followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); + sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( + Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + showAutocalculatedAbove = Cache.getDefault( + Preferences.SHOW_AUTOCALC_ABOVE, false); + + } + + void init() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; + applyViewProperties(); + + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); + String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); + String fontSize = Cache.getDefault("FONT_SIZE", "10"); + + int style = 0; + + if (fontStyle.equals("bold")) + { + style = 1; + } + else if (fontStyle.equals("italic")) + { + style = 2; + } + + setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); + + 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); + } + initAutoAnnotation(); + String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT; + String propertyValue = Cache.getProperty(colourProperty); + if (propertyValue == null) + { + // fall back on this property for backwards compatibility + propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR); + } + if (propertyValue != null) + { + globalColourScheme = ColourSchemeProperty.getColour(alignment, + propertyValue); + + if (globalColourScheme instanceof UserColourScheme) + { + globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme) globalColourScheme).setThreshold(0, + isIgnoreGapsConsensus()); + } + + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + } + } + + /** + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * + * @return consensus sequence as a new sequence object + */ + 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; + } + + /** + * 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; + } + + boolean validCharWidth; + + /** + * update view settings with the given font. You may need to call + * alignPanel.fontChanged to update the layout geometry + * + * @param setGrid + * when true, charWidth/height is set according to font mentrics + */ + public void setFont(Font f, boolean setGrid) + { + font = f; + + Container c = new Container(); + + java.awt.FontMetrics fm = c.getFontMetrics(font); + int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle + .getCharHeight(); + if (setGrid) + { + setCharHeight(fm.getHeight()); + setCharWidth(ww); + } + viewStyle.setFontName(font.getName()); + viewStyle.setFontStyle(font.getStyle()); + viewStyle.setFontSize(font.getSize()); + + validCharWidth = true; + } + + @Override + public void setViewStyle(ViewStyleI settingsForView) + { + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); + + } + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Font getFont() + { + return font; + } + + /** + * 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! + * + * @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! + * + * @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; + } + + /** + * 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() + { + // TODO: JAL-1126 + 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; + } + + /** + * 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; + } + + /** + * Send the current selection to be broadcast to any selection listeners. + */ + public void sendSelection() + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(Desktop.instance).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + /** + * 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()); + 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); + } + } + } + + /** + * Returns the (Desktop) instance of the StructureSelectionManager + */ + @Override + 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; + } + + private Hashtable calcIdParams = new Hashtable(); + + private boolean showAutocalculatedAbove; + + public AutoCalcSetting getCalcIdSettingsFor(String calcId) + { + return calcIdParams.get(calcId); + } + + public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, + boolean needsUpdate) + { + calcIdParams.put(calcId, settings); + // TODO: create a restart list to trigger any calculations that need to be + // restarted after load + // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) + if (needsUpdate) + { + Cache.log.debug("trigger update for " + calcId); + } + } + + protected SequenceAnnotationOrder getSortAnnotationsBy() + { + return sortAnnotationsBy; + } + + protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) + { + this.sortAnnotationsBy = sortAnnotationsBy; + } + + protected boolean isShowAutocalculatedAbove() + { + return showAutocalculatedAbove; + } + + protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove) + { + this.showAutocalculatedAbove = showAutocalculatedAbove; + } + + /** + * Method called when another alignment's edit (or possibly other) command is + * broadcast to here. + * + * To allow for sequence mappings (e.g. protein to cDNA), we have to first + * 'unwind' the command on the source sequences (in simulation, not in fact), + * and then for each edit in turn: + *
    + *
  • compute the equivalent edit on the mapped sequences
    • + *
  • apply the mapped edit
    • + *
  • 'apply' the source edit to the working copy of the source sequences
    • + *
+ * + * @param command + * @param undo + * @param ssm + */ + @Override + public void mirrorCommand(CommandI command, boolean undo, + StructureSelectionManager ssm, VamsasSource source) + { + /* + * Do nothing unless we are a 'complement' of the source. May replace this + * with direct calls not via SSM. + */ + if (source instanceof AlignViewportI + && ((AlignViewportI) source).getCodingComplement() == this) + { + // ok to continue; + } + else + { + return; + } + + CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), + getGapCharacter()); + if (mappedCommand != null) + { + AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); + mappedCommand.doCommand(views); + getAlignPanel().alignmentChanged(); + } + } + + /** + * Add the sequences from the given alignment to this viewport. Optionally, + * may give the user the option to open a new frame, or split panel, with cDNA + * and protein linked. + * + * @param al + * @param title + */ + public void addAlignment(AlignmentI al, String title) + { + // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different + + // JBPComment: title is a largely redundant parameter at the moment + // JBPComment: this really should be an 'insert/pre/append' controller + // JBPComment: but the DNA/Protein check makes it a bit more complex + + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with + // this comment: + // TODO: create undo object for this JAL-1101 + + /* + * If one alignment is protein and one nucleotide, with at least one + * sequence name in common, offer to open a linked alignment. + */ + if (getAlignment().isNucleotide() != al.isNucleotide()) + { + // TODO: JAL-845 try a bit harder to link up imported sequences + final Set sequenceNames = getAlignment().getSequenceNames(); + sequenceNames.retainAll(al.getSequenceNames()); + if (!sequenceNames.isEmpty()) // at least one sequence name in both + { + if (openLinkedAlignment(al, title)) + { + return; + } + } + } + // TODO: JAL-407 regardless of above - identical sequences (based on ID and + // provenance) should share the same dataset sequence + + for (int i = 0; i < al.getHeight(); i++) + { + getAlignment().addSequence(al.getSequenceAt(i)); + } + // TODO this call was done by SequenceFetcher but not FileLoader or + // CutAndPasteTransfer. Is it needed? + // JBPComment: this repositions the view to show the new sequences + // JBPComment: so it is needed for UX + setEndSeq(getAlignment().getHeight()); + firePropertyChange("alignment", null, getAlignment().getSequences()); + } + + /** + * Show a dialog with the option to open and link (cDNA <-> protein) as a new + * alignment. Returns true if the new alignment was opened, false if not, + * because the user declined the offer. + * + * @param title + */ + protected boolean openLinkedAlignment(AlignmentI al, String title) + { + String[] options = new String[] + { MessageManager.getString("action.no"), + MessageManager.getString("label.split_window"), + MessageManager.getString("label.new_window"), }; + final String question = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.open_split_window?")); + int response = JOptionPane.showOptionDialog(Desktop.desktop, question, + MessageManager.getString("label.open_split_window"), + JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + + if (response != 1 && response != 2) + { + return false; + } + final boolean openSplitPane = (response == 1); + final boolean openInNewWindow = (response == 2); + + /* + * Create the AlignFrame first (which creates the new alignment's datasets), + * before attempting sequence mapping. + */ + AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + newAlignFrame.setTitle(title); + + /* + * Identify protein and dna alignments. Make a copy of this one if opening + * in a new split pane. + */ + AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment()) + : getAlignment(); + AlignmentI protein = al.isNucleotide() ? thisAlignment : al; + final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; + + newAlignFrame.statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_file", new Object[] + { title })); + + // TODO if we want this (e.g. to enable reload of the alignment from file), + // we will need to add parameters to the stack. + // if (!protocol.equals(AppletFormatAdapter.PASTE)) + // { + // alignFrame.setFileName(file, format); + // } + + if (openInNewWindow) + { + Desktop.addInternalFrame(newAlignFrame, title, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + + /* + * Try to find mappings for at least one sequence. Any mappings made will be + * added to the protein alignment. + */ + MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna); + if (mapped != MappingResult.Mapped) + { + /* + * No mapping possible - warn the user, but leave window open. + */ + final String msg = JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.mapping_failed")); + JOptionPane.showInternalMessageDialog(Desktop.desktop, msg, + MessageManager.getString("label.no_mappings"), + JOptionPane.WARNING_MESSAGE); + } + + try + { + newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( + "SHOW_FULLSCREEN", + false)); + } catch (java.beans.PropertyVetoException ex) + { + } + + if (openSplitPane) + { + protein = openSplitFrame(newAlignFrame, + thisAlignment.getSequencesArray(), protein.getCodonFrames()); + } + + /* + * Register the mappings (held on the protein alignment) with the + * StructureSelectionManager (for mouseover linking). + */ + final StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.addMappings(protein.getCodonFrames()); + + return true; + } + + /** + * Helper method to open a new SplitFrame holding linked dna and protein + * alignments. + * + * @param newAlignFrame + * containing a new alignment to be shown + * @param seqs + * 'complementary' sequences to show in the other split half + * @param mappings + * @return the protein alignment in the split frame + */ + protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, + SequenceI[] seqs, Set mappings) + { + AlignmentI complementAlignment = new Alignment(seqs); + // TODO: move this to a factory/controller method ? + /* + * Open in split pane. DNA sequence above, protein below. + */ + AlignFrame copyMe = new AlignFrame(complementAlignment, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); + + AlignmentI al = newAlignFrame.viewport.getAlignment(); + final AlignFrame proteinFrame = al.isNucleotide() ? copyMe + : newAlignFrame; + final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame + : copyMe; + AlignmentI protein = proteinFrame.viewport.getAlignment(); + protein.setCodonFrames(mappings); + + cdnaFrame.setVisible(true); + proteinFrame.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); + JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); + Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1); + + return protein; + } + + public AnnotationColumnChooser getAnnotationColumnSelectionState() + { + return annotationColumnSelectionState; + } + + public void setAnnotationColumnSelectionState( + AnnotationColumnChooser currentAnnotationColumnSelectionState) + { + this.annotationColumnSelectionState = currentAnnotationColumnSelectionState; + } + + @Override + public void setIdWidth(int i) + { + super.setIdWidth(i); + AlignmentPanel ap = getAlignPanel(); + if (ap != null) + { + // modify GUI elements to reflect geometry change + Dimension idw = getAlignPanel().getIdPanel().getIdCanvas() + .getPreferredSize(); + idw.width = i; + getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw); + } + } + + public Rectangle getExplodedGeometry() + { + return explodedGeometry; + } + + public void setExplodedGeometry(Rectangle explodedPosition) + { + this.explodedGeometry = explodedPosition; + } + + public boolean isGatherViewsHere() + { + return gatherViewsHere; + } + + public void setGatherViewsHere(boolean gatherViewsHere) + { + this.gatherViewsHere = gatherViewsHere; + } +}