X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=6d6531f27ff92c21518cf5a28249446080c0ef99;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=fb3d4df9946ff566d17bb2794b486b322c16dc39;hpb=cc02d3050be98385d6558af2b2513bacce82417d;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index fb3d4df..6d6531f --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,26 @@ - /* +/* + * 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -18,1485 +38,1230 @@ */ package jalview.gui; -import jalview.analysis.*; - -import jalview.bin.*; - -import jalview.datamodel.*; - -import jalview.schemes.*; - -import java.awt.*; - -import java.util.*; - +import jalview.analysis.NJTree; +import jalview.api.AlignViewportI; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +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.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.params.AutoCalcSetting; + +import java.awt.Color; +import java.awt.Container; +import java.awt.Font; +import java.awt.Rectangle; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.Stack; +import java.util.Vector; /** * DOCUMENT ME! - * + * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport +public class AlignViewport extends AlignmentViewport implements + SelectionSource, VamsasSource, AlignViewportI { - 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 showIdentity = true; - boolean colourAppliesToAllGroups = true; - ColourSchemeI globalColourScheme = null; - boolean conservationColourSelected = false; - boolean abovePIDThreshold = false; - SequenceGroup selectionGroup; - int charHeight; - int charWidth; - boolean validCharWidth; - int wrappedWidth; - Font font; - AlignmentI alignment; - ColumnSelection colSel = new ColumnSelection(); - int threshold; - int increment; - NJTree currentTree = null; - boolean scaleAboveWrapped = false; - boolean scaleLeftWrapped = true; - boolean scaleRightWrapped = true; - boolean hasHiddenColumns = false; - boolean hasHiddenRows = false; - boolean showHiddenMarkers = true; - - boolean cursorMode = false; - - // The following vector holds the features which are - // currently visible, in the correct order or rendering - Hashtable featuresDisplayed = null; - - - /** DOCUMENT ME!! */ - public Hashtable [] hconsensus; - AlignmentAnnotation consensus; - AlignmentAnnotation conservation; - AlignmentAnnotation quality; - boolean autoCalculateConsensus = true; - - /** DOCUMENT ME!! */ - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - - // JBPNote Prolly only need this in the applet version. - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this); - - boolean ignoreGapsInConsensusCalculation = false; - - boolean isDataset = false; - - boolean antiAlias = false; - - boolean padGaps = false; - - Rectangle explodedPosition; - - String viewName; - - String sequenceSetID; - - boolean gatherViewsHere = false; - - - public AlignViewport(AlignmentI al, boolean dataset) - { - isDataset = dataset; - setAlignment(al); - init(); - } - /** - * Creates a new AlignViewport object. - * - * @param al DOCUMENT ME! - */ - public AlignViewport(AlignmentI al) - { - 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) - hasHiddenColumns = true; - } - init(); - } - - void init() - { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 1; + int startRes; - antiAlias = Cache.getDefault("ANTI_ALIAS", false); + int endRes; - showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); - showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); - showConservation = Cache.getDefault("SHOW_CONSERVATION", true); + int startSeq; - showQuality = Cache.getDefault("SHOW_QUALITY", true); - showIdentity = Cache.getDefault("SHOW_IDENTITY", true); + int endSeq; - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + boolean showJVSuffix = true; - padGaps = Cache.getDefault("PAD_GAPS", false); + boolean showText = true; - String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); - String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ; - String fontSize = Cache.getDefault("FONT_SIZE", "10"); + boolean showColourText = false; - int style = 0; + boolean showBoxes = true; - if (fontStyle.equals("bold")) - { - style = 1; - } - else if (fontStyle.equals("italic")) - { - style = 2; - } + boolean wrapAlignment = false; - 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()) - { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", - new Annotation[1], 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); - conservation.hasText = true; - - if (showConservation) - { - alignment.addAnnotation(conservation); - } - - if (showQuality) - { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], - 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - - alignment.addAnnotation(quality); - } - } + boolean renderGaps = true; - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; + boolean showSequenceFeatures = false; - if (showIdentity) - { - alignment.addAnnotation(consensus); - } + boolean showAnnotation = true; - } + int charHeight; - if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + int charWidth; - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus()); - } + boolean validCharWidth; - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - } - } + int wrappedWidth; + Font font; + boolean seqNameItalics; - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } + NJTree currentTree = null; - public boolean getShowSequenceFeatures() - { - return showSequenceFeatures; - } + boolean scaleAboveWrapped = false; + boolean scaleLeftWrapped = true; + boolean scaleRightWrapped = true; - class ConservationThread extends Thread - { - AlignmentPanel ap; - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } + boolean showHiddenMarkers = true; - public void run() - { - try - { - int alWidth = alignment.getWidth(); + boolean cursorMode = false; - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alWidth -1); + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ + Hashtable featuresDisplayed = null; - cons.calculate(); - cons.verdict(false, ConsPercGaps); + boolean antiAlias = false; - if (quality!=null) - { - cons.findQuality(); - } + Rectangle explodedPosition; + String viewName; - String sequence = cons.getConsSequence().getSequence(); - float minR; - float minG; - float minB; - float maxR; - float maxG; - float maxB; - minR = 0.3f; - minG = 0.0f; - minB = 0f; - maxR = 1.0f - minR; - maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and Quality + boolean gatherViewsHere = false; - float min = 0f; - float max = 11f; - float qmin = 0f; - float qmax = 0f; + Stack historyList = new Stack(); - char c; + Stack redoList = new Stack(); - conservation.annotations = new Annotation[alWidth]; + int thresholdTextColour = 0; - if (quality!=null) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - quality.annotations = new Annotation[alWidth]; - qmin = cons.qualityRange[0].floatValue(); - qmax = cons.qualityRange[1].floatValue(); - } + Color textColour = Color.black; - for (int i = 0; i < alWidth; i++) - { - float value = 0; - - c = sequence.charAt(i); - - if (Character.isDigit(c)) - value = (int) (c - '0'); - else if (c == '*') - value = 11; - else if (c == '+') - value = 10; - - float vprop = value - min; - vprop /= max; - conservation.annotations[i] = - new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - - // Quality calc - if (quality!=null) - { - value = ( (Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ', - value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - } - } - } - catch (OutOfMemoryError error) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { + Color textColour2 = Color.white; + boolean rightAlignIds = false; - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating conservation!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); + /** + * Creates a new AlignViewport object. + * + * @param al + * alignment to view + */ + public AlignViewport(AlignmentI al) + { + setAlignment(al); + init(); + } - conservation = null; - quality = null; + /** + * 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); + } - System.out.println("Conservation calculation: " + error); - System.gc(); - - } - - if(ap!=null) - { - ap.repaint(); - } - updatingConservation = false; - } + 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); } - - - ConservationThread conservationThread; - - ConsensusThread consensusThread; - - boolean consUpdateNeeded = false; - - boolean updatingConsensus = false; - - boolean updatingConservation = false; - - /** - * DOCUMENT ME! - */ - public void updateConservation(AlignmentPanel ap) + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) { - if (alignment.isNucleotide()) - return; - - updatingConservation = true; - - if (conservationThread == null || !conservationThread.isAlive()) - { - conservationThread = new ConservationThread(ap); - conservationThread.start(); - } - else - { - consUpdateNeeded = true; - System.out.println("come back later"); - } + Cache.log.debug("Setting viewport's view id : " + viewId); } + setAlignment(al); + init(); + } - /** - * DOCUMENT ME! - */ - public void updateConsensus(AlignmentPanel ap) + /** + * Create a new AlignViewport with hidden regions + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + { + setAlignment(al); + if (hiddenColumns != null) { - updatingConsensus = true; - - if (consensusThread == null || !consensusThread.isAlive()) + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { - consensusThread = new ConsensusThread(ap); - consensusThread.start(); + hasHiddenColumns = true; } else { - consUpdateNeeded = true; - System.out.println("come back later"); + hasHiddenColumns = false; } } - - - class ConsensusThread extends Thread - { - AlignmentPanel ap; - public ConsensusThread(AlignmentPanel ap) + 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) { - this.ap = ap; + hasHiddenColumns = true; } - public void run() + else { - try - { - int aWidth = alignment.getWidth(); - - consensus.annotations = null; - consensus.annotations = new Annotation[aWidth]; - - - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)). - floatValue(); - else - value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)). - floatValue(); - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ( (int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - } - - - if (globalColourScheme != null) - globalColourScheme.setConsensus(hconsensus); - - } - catch (OutOfMemoryError error) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating consensus!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - - System.out.println("Consensus calculation: " + error); - System.gc(); - } - - if (ap != null) - { - ap.repaint(); - } - - - updatingConsensus = false; - } - } - /** - * 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 (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; } + init(); + } - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setEndSeq(int seq) - { - if (seq > alignment.getHeight()) - { - seq = alignment.getHeight(); - } - - if (seq < 0) - { - seq = 0; - } + void init() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; - this.endSeq = seq; - } + antiAlias = Cache.getDefault("ANTI_ALIAS", false); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndSeq() - { - return endSeq; - } + showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); + showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); - /** - * DOCUMENT ME! - * - * @param f DOCUMENT ME! - */ - public void setFont(Font f) - { - font = f; + rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); + centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); + autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); - Container c = new Container(); + setPadGaps(Cache.getDefault("PAD_GAPS", true)); + shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); + showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; - } + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); + String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); + String fontSize = Cache.getDefault("FONT_SIZE", "10"); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() - { - return font; - } + seqNameItalics = Cache.getDefault("ID_ITALICS", true); - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setCharWidth(int w) - { - this.charWidth = w; - } + int style = 0; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() + if (fontStyle.equals("bold")) { - return charWidth; + style = 1; } - - /** - * DOCUMENT ME! - * - * @param h DOCUMENT ME! - */ - public void setCharHeight(int h) + else if (fontStyle.equals("italic")) { - this.charHeight = h; + style = 2; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() - { - return charHeight; - } + setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setWrappedWidth(int w) - { - this.wrappedWidth = w; - } + alignment + .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() + // We must set conservation and consensus before setting colour, + // as Blosum and Clustal require this to be done + if (hconsensus == null && !isDataset) { - return wrappedWidth; - } - - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public AlignmentI getAlignment() - { - return alignment; - } - - /** - * DOCUMENT ME! - * - * @param align DOCUMENT ME! - */ - public void setAlignment(AlignmentI align) - { - this.alignment = align; - } - - /** - * 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; - } - - /** - * 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 void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap) - { - ignoreGapsInConsensusCalculation = b; - updateConsensus(ap); - if(globalColourScheme!=null) + if (!alignment.isNucleotide()) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation); + showConservation = Cache.getDefault("SHOW_CONSERVATION", true); + showQuality = Cache.getDefault("SHOW_QUALITY", true); + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); } - } - - public boolean getIgnoreGapsConsensus() - { - return ignoreGapsInConsensusCalculation; - } - - public void setDataset(boolean b) - { - isDataset = b; - } - - public boolean isDataset() - { - return isDataset; - } - - - public void hideSelectedColumns() - { - if (colSel.size() < 1) - return; - - colSel.hideSelectedColumns(); - setSelectionGroup(null); - - hasHiddenColumns = true; - } - - - public void hideColumns(int start, int end) - { - if(start==end) - colSel.hideColumns(start); - else - colSel.hideColumns(start, end); - - hasHiddenColumns = true; - } - - public void hideAllSelectedSeqs() - { - if (selectionGroup == null) - return; - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - hideSequence(seqs); - - setSelectionGroup(null); - } + 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")); - public void hideSequence(SequenceI [] seq) - { - if(seq!=null) + if (globalColourScheme instanceof UserColourScheme) { - for (int i = 0; i < seq.length; i++) - alignment.getHiddenSequences().hideSequence(seq[i]); - - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); + globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme) globalColourScheme).setThreshold(0, + getIgnoreGapsConsensus()); } - } - public void showSequence(int index) - { - Vector tmp = alignment.getHiddenSequences().showSequence(index); - if(tmp.size()>0) + if (globalColourScheme != null) { - if(selectionGroup==null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); - } - - for (int t = 0; t < tmp.size(); t++) - { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); - } - firePropertyChange("alignment", null, alignment.getSequences()); + globalColourScheme.setConsensus(hconsensus); } - - if(alignment.getHiddenSequences().getSize()<1) - hasHiddenRows = false; - } - - public void showColumn(int col) - { - colSel.revealHiddenColumns(col); - if(colSel.getHiddenColumns()==null) - hasHiddenColumns = false; } - public void showAllHiddenColumns() + 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) { - colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; + return null; } - - public void showAllHiddenSeqs() + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) { - if(alignment.getHiddenSequences().getSize()>0) + if (consensus.annotations[i] != null) { - if(selectionGroup==null) + if (consensus.annotations[i].description.charAt(0) == '[') { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); + seqs.append(consensus.annotations[i].description.charAt(1)); } - Vector tmp = alignment.getHiddenSequences().showAll(); - for(int t=0; t (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! + * + * @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! + * + * @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; + } + + /** + * 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]) { - column = i; - - if(colSel.contains(column)) - colSel.removeElement(column); - else - colSel.addElement(column); - + return true; } - - } - - public int adjustForHiddenSeqs(int alignmentIndex) - { - return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex); - } - - /** - * This method returns the a new SequenceI [] with - * the selection sequence and start and end points adjusted - * @return String[] - */ - public SequenceI[] getSelectionAsNewSequence() - { - SequenceI[] sequences; - - if (selectionGroup == null) - sequences = alignment.getSequencesArray(); - else - sequences = selectionGroup.getSelectionAsNewSequences(alignment); - - return sequences; } - - /** - * This method returns the visible alignment as text, as - * seen on the GUI, ie if columns are hidden they will not - * be returned in the result. - * Use this for calculating trees, PCA, redundancy etc on views - * which contain hidden columns. - * @return String[] - */ - public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly) - { - CigarArray selection=null; - SequenceI [] seqs= null; - int i, iSize; - int start = 0, end = 0; - if(selectedRegionOnly && selectionGroup!=null) + return false; + } + + public boolean getCentreColumnLabels() + { + return centreColumnLabels; + } + + public void setCentreColumnLabels(boolean centrecolumnlabels) + { + centreColumnLabels = centrecolumnlabels; + } + + /** + * 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) { - iSize = selectionGroup.getSize(false); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor + return aps[p]; } - else + } + 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)) { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth()-1; + // do nothing + return; } - SeqCigar[] selseqs = new SeqCigar[iSize]; - for(i=0; i