X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=19ec9e0065a1b3524eca4889afa9b3602beff12b;hb=075b2506c45bf8ae70e7a3ce3bb29029a21824b1;hp=5edb65b1bc4d74b94751d7476f87c8f0460d3c56;hpb=d545553b53ac1bd1e29eb72250cdb29745f7292f;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 5edb65b..19ec9e0 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,24 @@ - /* +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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 + */ +/* * 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 @@ -18,6 +36,10 @@ */ package jalview.gui; +import java.util.*; + +import java.awt.*; + import jalview.analysis.*; import jalview.bin.*; @@ -25,221 +47,405 @@ import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; - -import java.awt.*; - -import java.util.*; - +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class AlignViewport +public class AlignViewport implements SelectionSource { - 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 Vector vconsensus; - 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; - - - 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(); - } + private static final int RIGHT_JUSTIFY = 1; - void init() - { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 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; + + ColourSchemeI globalColourScheme = null; + + boolean conservationColourSelected = false; + + boolean abovePIDThreshold = false; + + SequenceGroup selectionGroup; + + int charHeight; + + int charWidth; + + boolean validCharWidth; + + int wrappedWidth; + + Font font; + + boolean seqNameItalics; + + 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; - antiAlias = Cache.getDefault("ANTI_ALIAS", false); + boolean cursorMode = false; - showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); - showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); - showConservation = Cache.getDefault("SHOW_CONSERVATION", true); + // The following vector holds the features which are + // currently visible, in the correct order or rendering + Hashtable featuresDisplayed = null; - showQuality = Cache.getDefault("SHOW_QUALITY", true); - showIdentity = Cache.getDefault("SHOW_IDENTITY", true); + /** DOCUMENT ME!! */ + public Hashtable[] hconsensus; - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + AlignmentAnnotation consensus; - padGaps = Cache.getDefault("PAD_GAPS", false); + AlignmentAnnotation conservation; - String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); - String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ; - String fontSize = Cache.getDefault("FONT_SIZE", "10"); + AlignmentAnnotation quality; - int style = 0; + boolean autoCalculateConsensus = true; - if (fontStyle.equals("bold")) - { - style = 1; - } - else if (fontStyle.equals("italic")) - { - style = 2; - } + /** DOCUMENT ME!! */ + public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + // JBPNote Prolly only need this in the applet version. + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); + boolean ignoreGapsInConsensusCalculation = false; - alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) ); + boolean isDataset = false; + boolean antiAlias = false; - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - if(vconsensus==null && !isDataset) + boolean padGaps = false; + + Rectangle explodedPosition; + + String viewName; + + String sequenceSetID; + + 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; + + Hashtable hiddenRepSequences; + + boolean sortByTree; + + /** + * 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) + { + hasHiddenColumns = true; + } + } + 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) + { + hasHiddenColumns = true; + } + } + 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); + + padGaps = 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()) + { + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + ConsPercGaps + + "% gaps", new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + conservation.autoCalculated = true; + + if (Cache.getDefault("SHOW_CONSERVATION", true)) { - updateConservation(); - updateConsensus(); + alignment.addAnnotation(conservation); } - if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) + if (Cache.getDefault("SHOW_QUALITY", true)) { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); - - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus()); - } + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(vconsensus); - } + alignment.addAnnotation(quality); } + } + // TODO: add menu option action that nulls or creates consensus object depending on if the user wants to see the annotation or not in a specific alignment + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + + if (Cache.getDefault("SHOW_IDENTITY", true)) + { + alignment.addAnnotation(consensus); + } } + 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()); + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowSequenceFeatures(boolean b) - { - showSequenceFeatures = b; + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } } - public boolean getShowSequenceFeatures() + 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); + } + + /** + * set the flag + * + * @param b + * features are displayed if true + */ + public void setShowSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + + public boolean getShowSequenceFeatures() + { + return showSequenceFeatures; + } + + class ConservationThread extends Thread + { + AlignmentPanel ap; + + public ConservationThread(AlignmentPanel ap) { - return showSequenceFeatures; + this.ap = ap; } - /** - * DOCUMENT ME! - */ - public void updateConservation() + public void run() { - if(alignment.isNucleotide()) + try + { + updatingConservation = true; + + while (UPDATING_CONSERVATION) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } + Thread.sleep(200); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_CONSERVATION = true; + + int alWidth = alignment.getWidth(); + if (alWidth < 0) + { return; + } - try{ Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alignment.getWidth() - 1); + jalview.schemes.ResidueProperties.propHash, 3, alignment + .getSequences(), 0, alWidth - 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(); + if (quality != null) + { + cons.findQuality(); + } + + char[] sequence = cons.getConsSequence().getSequence(); float minR; float minG; float minB; @@ -251,1161 +457,1783 @@ public class AlignViewport minB = 0f; maxR = 1.0f - minR; maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and Quality + 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(); + float qmin = 0f; + float qmax = 0f; + + char c; + + conservation.annotations = new Annotation[alWidth]; + + if (quality != null) + { + quality.graphMax = cons.qualityRange[1].floatValue(); + quality.annotations = new Annotation[alWidth]; + qmin = cons.qualityRange[0].floatValue(); + qmax = cons.qualityRange[1].floatValue(); + } for (int i = 0; i < alWidth; i++) { float value = 0; - try + c = sequence[i]; + + if (Character.isDigit(c)) { - value = Integer.parseInt(sequence.charAt(i) + ""); + value = (int) (c - '0'); } - catch (Exception ex) + else if (c == '*') { - if (sequence.charAt(i) == '*') - { - value = 11; - } - - if (sequence.charAt(i) == '+') - { - value = 10; - } + value = 11; + } + else if (c == '+') + { + value = 10; } float vprop = value - min; vprop /= max; - annotations[i] = new Annotation(sequence.charAt(i) + "", - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); + 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 - 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() - AlignmentAnnotation.BAR_GRAPH); - - if (showConservation) - { - alignment.addAnnotation(conservation); - } - - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), - AlignmentAnnotation.BAR_GRAPH); - - if (showQuality) + if (quality != null) { - alignment.addAnnotation(quality); + 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))); } } - else - { - conservation.annotations = annotations; - quality.annotations = qannotations; - quality.graphMax = cons.qualityRange[1].floatValue(); - } - } - catch (OutOfMemoryError error) + } catch (OutOfMemoryError error) { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - 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); - } - }); + new OOMWarning("calculating conservation", error); - System.out.println("Conservation calculation: " + error); - System.gc(); + conservation = null; + quality = null; } - } - - /** - * DOCUMENT ME! - */ - public void updateConsensus() - { - try{ - 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(); + UPDATING_CONSERVATION = false; + updatingConservation = false; - Enumeration e = temp.elements(); + if (ap != null) + { + ap.paintAlignment(true); + } - while (e.hasMoreElements()) - { - vconsensus.add(e.nextElement()); - } - } + } + } - Hashtable hash = null; + ConservationThread conservationThread; - for (int i = 0; i < alignment.getWidth(); i++) - { - hash = (Hashtable) vconsensus.elementAt(i); + ConsensusThread consensusThread; - float value = 0; - if (ignoreGapsInConsensusCalculation) - value = ( (Float) hash.get("pid_nogaps")).floatValue(); - else - value = ( (Float) hash.get("pid_gaps")).floatValue(); + boolean consUpdateNeeded = false; - String maxRes = hash.get("maxResidue").toString(); - String mouseOver = hash.get("maxResidue") + " "; + static boolean UPDATING_CONSENSUS = false; - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } + static boolean UPDATING_CONSERVATION = false; - mouseOver += ( (int) value + "%"); - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - } + boolean updatingConsensus = false; - if (consensus == null) - { - consensus = new AlignmentAnnotation("Consensus", "PID", - annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH); + boolean updatingConservation = false; - if (showIdentity) - { - alignment.addAnnotation(consensus); - } - } - else - { - consensus.annotations = annotations; - } + /** + * centre columnar annotation labels in displayed alignment annotation TODO: + * add to jalviewXML and annotation display settings + */ + boolean centreColumnLabels = false; - if (globalColourScheme != null) - globalColourScheme.setConsensus(vconsensus); + private boolean showdbrefs; - }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(); - } - - } - /** - * 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(); - if (consensus==null) - return null; - StringBuffer seqs=new StringBuffer(); - for (int i=0; i (alignment.getWidth() - 1)) + for (int i = 0; i < aWidth; i++) { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; - } + float value = 0; + if (ignoreGapsInConsensusCalculation) + { + value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) + .floatValue(); + } + else + { + value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) + .floatValue(); + } - if (res < 0) - { - res = 0; - } + String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) + .toString(); + String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + + " "; - this.endRes = res; - } + if (maxRes.length() > 1) + { + mouseOver = "[" + maxRes + "] "; + maxRes = "+"; + } - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setEndSeq(int seq) - { - if (seq > alignment.getHeight()) - { - seq = alignment.getHeight(); + mouseOver += ((int) value + "%"); + consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', + value); } - if (seq < 0) + if (globalColourScheme != null) { - seq = 0; + globalColourScheme.setConsensus(hconsensus); } - 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; + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(consensus); - Container c = new Container(); + consensus = null; + hconsensus = null; + new OOMWarning("calculating consensus", error); + } + UPDATING_CONSENSUS = false; + updatingConsensus = false; - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; + if (ap != null) + { + ap.paintAlignment(true); + } } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() + /** + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * + * @return consensus sequence as a new sequence object + */ + public SequenceI getConsensusSeq() + { + if (consensus == null) { - return font; + updateConsensus(null); } - - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setCharWidth(int w) + if (consensus == null) { - this.charWidth = w; + return null; } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) { - return charWidth; + 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); + } + } } - /** - * DOCUMENT ME! - * - * @param h DOCUMENT ME! - */ - public void setCharHeight(int h) + SequenceI sq = new Sequence("Consensus", seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); + return sq; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceGroup getSelectionGroup() + { + return selectionGroup; + } + + /** + * DOCUMENT ME! + * + * @param sg + * DOCUMENT ME! + */ + public void setSelectionGroup(SequenceGroup sg) + { + selectionGroup = sg; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getConservationSelected() + { + return conservationColourSelected; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + 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 cs + * DOCUMENT ME! + */ + public void setGlobalColourScheme(ColourSchemeI cs) + { + globalColourScheme = cs; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public ColourSchemeI getGlobalColourScheme() + { + return globalColourScheme; + } + + /** + * 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() + .removeMappings(alignment.getCodonFrames()); + } + this.alignment = align; + if (alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager().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; + } + + /** + * 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) + { + globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + ignoreGapsInConsensusCalculation); + } + } + + 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 hideRepSequences(SequenceI repSequence, SequenceGroup sg) + { + int sSize = sg.getSize(); + if (sSize < 2) { - this.charHeight = h; + return; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() + if (hiddenRepSequences == null) { - return charHeight; + hiddenRepSequences = new Hashtable(); } - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setWrappedWidth(int w) - { - this.wrappedWidth = w; - } + hiddenRepSequences.put(repSequence, sg); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() + // Hide all sequences except the repSequence + SequenceI[] seqs = new SequenceI[sSize - 1]; + int index = 0; + for (int i = 0; i < sSize; i++) { - return wrappedWidth; + if (sg.getSequenceAt(i) != repSequence) + { + if (index == sSize - 1) + { + return; + } + + seqs[index++] = sg.getSequenceAt(i); + } } + sg.setSeqrep(repSequence); + sg.setHidereps(true); + hideSequence(seqs); + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public AlignmentI getAlignment() + public void hideAllSelectedSeqs() + { + if (selectionGroup == null || selectionGroup.getSize() < 1) { - return alignment; + return; } - /** - * DOCUMENT ME! - * - * @param align DOCUMENT ME! - */ - public void setAlignment(AlignmentI align) - { - this.alignment = align; - } + SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setWrapAlignment(boolean state) - { - wrapAlignment = state; - } + hideSequence(seqs); - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setShowText(boolean state) - { - showText = state; - } + setSelectionGroup(null); + } - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setRenderGaps(boolean state) + public void hideSequence(SequenceI[] seq) + { + if (seq != null) { - renderGaps = state; + for (int i = 0; i < seq.length; i++) + { + alignment.getHiddenSequences().hideSequence(seq[i]); + } + hasHiddenRows = true; + firePropertyChange("alignment", null, alignment.getSequences()); } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourText() + public void showSequence(int index) + { + Vector tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); + if (tmp.size() > 0) { - return showColourText; - } + if (selectionGroup == null) + { + selectionGroup = new SequenceGroup(); + selectionGroup.setEndRes(alignment.getWidth() - 1); + } - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setColourText(boolean state) - { - showColourText = state; + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + } + firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); } - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setShowBoxes(boolean state) + if (alignment.getHiddenSequences().getSize() < 1) { - showBoxes = state; + hasHiddenRows = false; } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getWrapAlignment() + public void showColumn(int col) + { + colSel.revealHiddenColumns(col); + if (colSel.getHiddenColumns() == null) { - return wrapAlignment; + hasHiddenColumns = false; } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowText() - { - return showText; - } + public void showAllHiddenColumns() + { + colSel.revealAllHiddenColumns(); + hasHiddenColumns = false; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowBoxes() + public void showAllHiddenSeqs() + { + if (alignment.getHiddenSequences().getSize() > 0) { - return showBoxes; + if (selectionGroup == null) + { + selectionGroup = new SequenceGroup(); + selectionGroup.setEndRes(alignment.getWidth() - 1); + } + Vector tmp = alignment.getHiddenSequences().showAll( + hiddenRepSequences); + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + } + firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); + hasHiddenRows = false; + hiddenRepSequences = null; + } + } + + public void invertColumnSelection() + { + colSel.invertColumnSelection(0, alignment.getWidth()); + } + + public int adjustForHiddenSeqs(int alignmentIndex) + { + return alignment.getHiddenSequences().adjustForHiddenSeqs( + alignmentIndex); + } + + /** + * This method returns an array of new SequenceI objects derived from the + * whole alignment or just the current selection with start and end points + * adjusted + * + * @note if you need references to the actual SequenceI objects in the + * alignment or currently selected then use getSequenceSelection() + * @return selection as new sequenceI objects + */ + public SequenceI[] getSelectionAsNewSequence() + { + SequenceI[] sequences; + + if (selectionGroup == null) + { + sequences = alignment.getSequencesArray(); + AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); + for (int i = 0; i < sequences.length; i++) + { + sequences[i] = new Sequence(sequences[i], annots); // construct new + // sequence with + // subset of visible + // annotation + } } + else + { + sequences = selectionGroup.getSelectionAsNewSequences(alignment); + } + + return sequences; + } + + /** + * get the currently selected sequence objects or all the sequences in the + * alignment. + * + * @return array of references to sequence objects + */ + public SequenceI[] getSequenceSelection() + { + SequenceI[] sequences=null; + if (selectionGroup!=null) + { + sequences = selectionGroup.getSequencesInOrder(alignment); + } + if (sequences == null) + { + sequences = alignment.getSequencesArray(); + } + return sequences; + } + + /** + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * + * @return String[] + */ + public jalview.datamodel.CigarArray getViewAsCigars( + boolean selectedRegionOnly) + { + CigarArray selection = null; + SequenceI[] seqs = null; + int i, iSize; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + iSize = selectionGroup.getSize(); + seqs = selectionGroup.getSequencesInOrder(alignment); + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes(); // inclusive for start and end in + // SeqCigar constructor + } + else + { + iSize = alignment.getHeight(); + seqs = alignment.getSequencesArray(); + end = alignment.getWidth() - 1; + } + SeqCigar[] selseqs = new SeqCigar[iSize]; + for (i = 0; i < iSize; i++) + { + selseqs[i] = new SeqCigar(seqs[i], start, end); + } + selection = new CigarArray(selseqs); + // now construct the CigarArray operations + if (hasHiddenColumns) + { + Vector regions = colSel.getHiddenColumns(); + int[] region; + int hideStart, hideEnd; + int last = start; + for (int j = 0; last < end & j < regions.size(); j++) + { + region = (int[]) regions.elementAt(j); + hideStart = region[0]; + hideEnd = region[1]; + // edit hidden regions to selection range + if (hideStart < last) + { + if (hideEnd > last) + { + hideStart = last; + } + else + { + continue; + } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getGapCharacter() - { - return getAlignment().getGapCharacter(); - } + if (hideStart > end) + { + break; + } - /** - * DOCUMENT ME! - * - * @param gap DOCUMENT ME! - */ - public void setGapCharacter(char gap) - { - if (getAlignment() != null) + if (hideEnd > end) { - getAlignment().setGapCharacter(gap); + hideEnd = end; } - } - /** - * DOCUMENT ME! - * - * @param thresh DOCUMENT ME! - */ - public void setThreshold(int thresh) - { - threshold = thresh; + if (hideStart > hideEnd) + { + break; + } + /** + * form operations... + */ + if (last < hideStart) + { + selection.addOperation(CigarArray.M, hideStart - last); + } + selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart); + last = hideEnd + 1; + } + // Final match if necessary. + if (last < end) + { + selection.addOperation(CigarArray.M, end - last + 1); + } } + else + { + selection.addOperation(CigarArray.M, end - start + 1); + } + return selection; + } + + /** + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view + * @return AlignmentView + */ + jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + { + // JBPNote: + // this is here because the AlignmentView constructor modifies the + // CigarArray + // object. Refactoring of Cigar and alignment view representation should + // be done to remove redundancy. + CigarArray aligview = getViewAsCigars(selectedOnly); + if (aligview != null) + { + return new AlignmentView(aligview, + (selectedOnly && selectionGroup != null) ? selectionGroup + .getStartRes() : 0); + } + return null; + } + + /** + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * + * @return String[] + */ + public String[] getViewAsString(boolean selectedRegionOnly) + { + String[] selection = null; + SequenceI[] seqs = null; + int i, iSize; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + iSize = selectionGroup.getSize(); + seqs = selectionGroup.getSequencesInOrder(alignment); + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + iSize = alignment.getHeight(); + seqs = alignment.getSequencesArray(); + end = alignment.getWidth(); + } + + selection = new String[iSize]; + if (hasHiddenColumns) + { + selection = colSel.getVisibleSequenceStrings(start, end, seqs); + } + else + { + for (i = 0; i < iSize; i++) + { + selection[i] = seqs[i].getSequenceAsString(start, end); + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getThreshold() - { - return threshold; } + return selection; + } - /** - * DOCUMENT ME! - * - * @param inc DOCUMENT ME! - */ - public void setIncrement(int inc) - { - increment = inc; - } + public int[][] getVisibleRegionBoundaries(int min, int max) + { + Vector regions = new Vector(); + int start = min; + int end = max; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIncrement() + do { - return increment; - } + if (hasHiddenColumns) + { + if (start == 0) + { + start = colSel.adjustForHiddenColumns(start); + } + end = colSel.getHiddenBoundaryRight(start); + if (start == end) + { + end = max; + } + if (end > max) + { + end = max; + } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColumnSelection getColumnSelection() - { - return colSel; - } + regions.addElement(new int[] + { start, end }); + if (hasHiddenColumns) + { + start = colSel.adjustForHiddenColumns(end); + start = colSel.getHiddenBoundaryLeft(start) + 1; + } + } while (end < max); - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - public void setCurrentTree(NJTree tree) - { - currentTree = tree; - } + int[][] startEnd = new int[regions.size()][2]; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getCurrentTree() - { - return currentTree; - } + regions.copyInto(startEnd); - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } + return startEnd; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowJVSuffix() - { - return showJVSuffix; - } + public boolean getShowHiddenMarkers() + { + return showHiddenMarkers; + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowJVSuffix(boolean b) - { - showJVSuffix = b; - } + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; + } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowAnnotation() + public String getSequenceSetId() + { + if (sequenceSetID == null) { - return showAnnotation; + sequenceSetID = alignment.hashCode() + ""; } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowAnnotation(boolean b) - { - showAnnotation = b; - } + return sequenceSetID; + } + /** + * unique viewId for synchronizing state with stored Jalview Project + * + */ + private String viewId=null; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() + + public String getViewId() + { + if (viewId==null) { - return scaleAboveWrapped; + viewId = this.getSequenceSetId()+"."+this.hashCode()+""; } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() + return viewId; + } + + public void alignmentChanged(AlignmentPanel ap) + { + if (padGaps) { - return scaleLeftWrapped; + alignment.padGaps(); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() + if (hconsensus != null && autoCalculateConsensus) { - return scaleRightWrapped; + updateConservation(ap); } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleAboveWrapped(boolean b) + if (autoCalculateConsensus) { - scaleAboveWrapped = b; + updateConsensus(ap); } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) + // Reset endRes of groups if beyond alignment width + int alWidth = alignment.getWidth(); + Vector groups = alignment.getGroups(); + if (groups != null) { - scaleLeftWrapped = b; + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if (sg.getEndRes() > alWidth) + { + sg.setEndRes(alWidth - 1); + } + } } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) + if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) { - scaleRightWrapped = b; + selectionGroup.setEndRes(alWidth - 1); } - /** - * Property change listener for changes in alignment - * - * @param listener DOCUMENT ME! - */ - public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(listener); - } + resetAllColourSchemes(); - /** - * DOCUMENT ME! - * - * @param listener DOCUMENT ME! - */ - public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) - { - changeSupport.removePropertyChangeListener(listener); - } + // alignment.adjustSequenceAnnotations(); + } - /** - * 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) + void resetAllColourSchemes() + { + ColourSchemeI cs = globalColourScheme; + if (cs != null) { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); - } + if (cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), + alignment.getWidth()); + } - public void setIgnoreGapsConsensus(boolean b) - { - ignoreGapsInConsensusCalculation = b; - updateConsensus(); - if(globalColourScheme!=null) + cs.setConsensus(hconsensus); + if (cs.conservationApplied()) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation); + Alignment al = (Alignment) alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, al.getSequences(), 0, al + .getWidth() - 1); + c.calculate(); + c.verdict(false, ConsPercGaps); + + cs.setConservation(c); } } - public boolean getIgnoreGapsConsensus() + int s, sSize = alignment.getGroups().size(); + for (s = 0; s < sSize; s++) { - return ignoreGapsInConsensusCalculation; + SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); + if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme) sg.cs).resetClustalX(sg + .getSequences(hiddenRepSequences), sg.getWidth()); + } + sg.recalcConservation(); } + } - public void setDataset(boolean b) + public Color getSequenceColour(SequenceI seq) + { + if (sequenceColours == null || !sequenceColours.containsKey(seq)) { - isDataset = b; + return Color.white; } - - public boolean isDataset() + else { - return isDataset; + return (Color) sequenceColours.get(seq); } + } - - public void hideSelectedColumns() + public void setSequenceColour(SequenceI seq, Color col) + { + if (sequenceColours == null) { - if (colSel.size() < 1) - return; - - colSel.hideSelectedColumns(); - setSelectionGroup(null); - - hasHiddenColumns = true; + sequenceColours = new Hashtable(); } - - public void hideColumns(int start, int end) + if (col == null) { - if(start==end) - colSel.hideColumns(start); - else - colSel.hideColumns(start, end); - - hasHiddenColumns = true; + sequenceColours.remove(seq); } - - public void hideAllSelectedSeqs() + else { - if (selectionGroup == null) - return; - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - for (int i = 0; i < seqs.length; i++) - { - alignment.getHiddenSequences().hideSequence(seqs[i]); - } - firePropertyChange("alignment", null, alignment.getSequences()); - hasHiddenRows = true; - setSelectionGroup(null); + sequenceColours.put(seq, col); } + } - public void hideSequence(SequenceI seq) + /** + * 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) { - if(seq!=null) - { - alignment.getHiddenSequences().hideSequence(seq); - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); - } + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; } - - public void showSequence(int index) + else { - Vector tmp = alignment.getHiddenSequences().showSequence(index); - if(tmp.size()>0) - { - 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()); - } - - if(alignment.getHiddenSequences().getSize()<1) - hasHiddenRows = false; + end = alignment.getWidth(); } + viscontigs = colSel.getVisibleContigs(start, end); + return viscontigs; + } - public void showColumn(int col) + /** + * 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) { - colSel.revealHiddenColumns(col); - if(colSel.getHiddenColumns()==null) - hasHiddenColumns = false; + return true; } - - public void showAllHiddenColumns() + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) { - colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; + return true; } - public void showAllHiddenSeqs() + for (int i = 0; i < cstate.length; i++) { - if(alignment.getHiddenSequences().getSize()>0) + if (cstate[i] != undoredo[i]) { - if(selectionGroup==null) - { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); - } - Vector tmp = alignment.getHiddenSequences().showAll(); - for(int t=0; t