X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f5bc6e4cf3014e61522070c5bffd4270d833be39;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=07a745336b2b9c14e3404e494847151655d96f2d;hpb=d69ea8f1997771890b44e4b332a7ca84fe6f0893;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java old mode 100755 new mode 100644 index 07a7453..f5bc6e4 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,6 +1,23 @@ - /* +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + */ +/* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 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 @@ -18,1396 +35,2435 @@ */ package jalview.gui; +import java.util.*; + +import java.awt.*; + import jalview.analysis.*; +import jalview.api.StructureSelectionManagerProvider; import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; - -import java.awt.*; - -import java.util.*; - +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; /** * DOCUMENT ME! - * + * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.141 $ */ -public class AlignViewport +public class AlignViewport implements SelectionSource, VamsasSource { - 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(); - } + 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; - 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))); + boolean renderGaps = true; + boolean showSequenceFeatures = false; - alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) ); + boolean showAnnotation = true; + boolean colourAppliesToAllGroups = true; - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - if(hconsensus==null && !isDataset) - { - updateConservation(); - updateConsensus(); - } + ColourSchemeI globalColourScheme = null; - if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + boolean conservationColourSelected = false; - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus()); - } + boolean abovePIDThreshold = false; - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - } - } + SequenceGroup selectionGroup; + int charHeight; + int charWidth; - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowSequenceFeatures(boolean b) + 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; + + boolean cursorMode = false; + + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ + Hashtable featuresDisplayed = null; + + /** DOCUMENT ME!! */ + public Hashtable[] hconsensus; + + public Hashtable[] hStrucConsensus; + + AlignmentAnnotation consensus; + + AlignmentAnnotation strucConsensus; + + AlignmentAnnotation conservation; + + AlignmentAnnotation quality; + + AlignmentAnnotation[] groupConsensus; + + AlignmentAnnotation[] groupConservation; + + boolean autoCalculateConsensus = true; + + boolean autoCalculateStrucConsensus = 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; + + 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) { - showSequenceFeatures = b; + Cache.log.debug("Setting viewport's view id : " + viewId); } + setAlignment(al); + init(); + } - public boolean getShowSequenceFeatures() + /** + * Create a new AlignViewport with hidden regions + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + { + setAlignment(al); + if (hiddenColumns != null) { - return showSequenceFeatures; + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } + } + init(); + } + + /** + * New viewport with hidden columns and an existing sequence set id + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid) + { + this(al, hiddenColumns, seqsetid, null); + } + + /** + * New viewport with hidden columns and an existing sequence set id and viewid + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + * @param viewid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid, String viewid) + { + sequenceSetID = seqsetid; + viewId = viewid; + // TODO remove these once 2.4.VAMSAS release finished + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + if (hiddenColumns != null) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } } + init(); + } - /** - * DOCUMENT ME! - */ - public void updateConservation() + 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")) { - if(alignment.isNucleotide()) - return; + style = 1; + } + else if (fontStyle.equals("italic")) + { + style = 2; + } - // System.out.println("UPDATING CONSERVATION"); - - try{ - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alignment.getWidth() - 1); - cons.calculate(); - cons.verdict(false, ConsPercGaps); - cons.findQuality(); - - int alWidth = alignment.getWidth(); - Annotation[] annotations = new Annotation[alWidth]; - Annotation[] qannotations = new Annotation[alWidth]; - String sequence = cons.getConsSequence().getSequence(); - float minR; - 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 - - float min = 0f; - float max = 11f; - float qmin = cons.qualityRange[0].floatValue(); - float qmax = cons.qualityRange[1].floatValue(); - - for (int i = 0; i < alWidth; i++) - { - float value = 0; + setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - try - { - value = Integer.parseInt(sequence.charAt(i) + ""); - } - catch (Exception ex) - { - if (sequence.charAt(i) == '*') - { - value = 11; - } - - if (sequence.charAt(i) == '+') - { - value = 10; - } - } + alignment + .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); - 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))); - - // 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))); + // 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)) + { + alignment.addAnnotation(conservation); } - if (conservation == null) + if (Cache.getDefault("SHOW_QUALITY", true)) { - 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); + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; - if (showQuality) - { - alignment.addAnnotation(quality); - } + alignment.addAnnotation(quality); } - else + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); + { - conservation.annotations = annotations; - quality.annotations = qannotations; - quality.graphMax = cons.qualityRange[1].floatValue(); + } } - catch (OutOfMemoryError error) + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); + showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); + // 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 (alignment.isNucleotide() && alignment.hasRNAStructure()) + { + strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + strucConsensus.hasText = true; + strucConsensus.autoCalculated = true; + } + + if (Cache.getDefault("SHOW_IDENTITY", true)) { - javax.swing.SwingUtilities.invokeLater(new Runnable() + alignment.addAnnotation(consensus); + // TODO: Make own if for structure + if (alignment.isNucleotide() && alignment.hasRNAStructure()) { - 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); - } - }); + alignment.addAnnotation(strucConsensus); + } + } - System.out.println("Conservation calculation: " + error); - System.gc(); + } + + if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) + { + globalColourScheme = ColourSchemeProperty.getColour(alignment, + jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + if (globalColourScheme instanceof UserColourScheme) + { + globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme) globalColourScheme).setThreshold(0, + getIgnoreGapsConsensus()); + } + + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); } } + wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); + showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", + false); + sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false); + followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", + true); + } - /** - * DOCUMENT ME! - */ - public void updateConsensus() - { - try{ - int aWidth = alignment.getWidth(); + /** + * set the flag + * + * @param b + * features are displayed if true + */ + public void setShowSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } - Annotation[] annotations = new Annotation[aWidth]; + public boolean getShowSequenceFeatures() + { + return showSequenceFeatures; + } - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); + ConservationThread conservationThread; - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - value = ( (Float) hconsensus[i].get("pid_nogaps")).floatValue(); - else - value = ( (Float) hconsensus[i].get("pid_gaps")).floatValue(); + ConsensusThread consensusThread; - String maxRes = hconsensus[i].get("maxResidue").toString(); - String mouseOver = hconsensus[i].get("maxResidue") + " "; + StrucConsensusThread strucConsensusThread; - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } + boolean consUpdateNeeded = false; - mouseOver += ( (int) value + "%"); - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - } + static boolean UPDATING_CONSENSUS = false; - if (consensus == null) - { - consensus = new AlignmentAnnotation("Consensus", "PID", - annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH); + static boolean UPDATING_STRUC_CONSENSUS = false; - if (showIdentity) - { - alignment.addAnnotation(consensus); - } - } - else - { - consensus.annotations = annotations; - } + static boolean UPDATING_CONSERVATION = false; - if (globalColourScheme != null) - globalColourScheme.setConsensus(hconsensus); + boolean updatingConsensus = false; - }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); - } - }); + boolean updatingStrucConsensus = false; + boolean updatingConservation = false; - System.out.println("Consensus calculation: " + error); - System.gc(); - } + /** + * centre columnar annotation labels in displayed alignment annotation TODO: + * add to jalviewXML and annotation display settings + */ + boolean centreColumnLabels = 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(); - if (consensus==null) - return null; - StringBuffer seqs=new StringBuffer(); - for (int i=0; i (alignment.getWidth() - 1)) + updatingStrucConsensus = true; + while (UPDATING_STRUC_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } + + Thread.sleep(200); + } catch (Exception ex) { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; + ex.printStackTrace(); } + } - if (res < 0) + UPDATING_STRUC_CONSENSUS = true; + + try + { + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) { - res = 0; + updatingStrucConsensus = false; + UPDATING_STRUC_CONSENSUS = false; + return; } - this.endRes = res; - } + strucConsensus.annotations = null; + strucConsensus.annotations = new Annotation[aWidth]; - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setEndSeq(int seq) - { - if (seq > alignment.getHeight()) + hStrucConsensus = new Hashtable[aWidth]; + + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation rnaStruc = null; + for (int i = 0; i < aa.length; i++) { - seq = alignment.getHeight(); + if (aa[i].getRNAStruc() != null) + { + rnaStruc = aa[i]; + break; + } } - if (seq < 0) + AlignmentAnnotation rna = ap.av.getAlignment() + .getAlignmentAnnotation()[0]; + StructureFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hStrucConsensus, true, rnaStruc); + // TODO AlignmentAnnotation rnaStruc!!! + updateAnnotation(true); + if (globalColourScheme != null) { - seq = 0; + globalColourScheme.setConsensus(hStrucConsensus); } - this.endSeq = seq; + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(strucConsensus); + + strucConsensus = null; + hStrucConsensus = null; + new OOMWarning("calculating structure consensus", error); + } + UPDATING_STRUC_CONSENSUS = false; + updatingStrucConsensus = false; + + if (ap != null) + { + ap.paintAlignment(true); + } } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * update the consensus annotation from the sequence profile data using + * current visualization settings. */ - public int getEndSeq() + public void updateAnnotation() { - return endSeq; + updateAnnotation(false); } - /** - * DOCUMENT ME! - * - * @param f DOCUMENT ME! - */ - public void setFont(Font f) + protected void updateAnnotation(boolean immediate) { - font = f; - - Container c = new Container(); - - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; + // TODO: make calls thread-safe, so if another thread calls this method, + // it will either return or wait until one calculation is finished. + if (immediate + || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null)) + { + StructureFrequency.completeConsensus(strucConsensus, + hStrucConsensus, 0, hStrucConsensus.length, false, + showSequenceLogo); + } } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() - { - return font; - } + // --------END Structure Conservation - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setCharWidth(int w) + /** + * 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) { - this.charWidth = w; + updateConsensus(null); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() + if (consensus == null) { - return charWidth; + return null; } - - /** - * DOCUMENT ME! - * - * @param h DOCUMENT ME! - */ - public void setCharHeight(int h) + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) { - this.charHeight = h; + 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! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() + SequenceI sq = new Sequence("Consensus", seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); + return sq; + } + + /** + * + * + * @return null or the currently selected sequence region + */ + public SequenceGroup getSelectionGroup() + { + return selectionGroup; + } + + /** + * Set the selection group for this window. + * + * @param sg + * - group holding references to sequences in this alignment view + * + */ + public void setSelectionGroup(SequenceGroup sg) + { + selectionGroup = sg; + } + + /** + * GUI state + * + * @return true if conservation based shading is enabled + */ + public boolean getConservationSelected() + { + return conservationColourSelected; + } + + /** + * GUI state + * + * @param b + * enable conservation based shading + */ + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } + + /** + * GUI state + * + * @return true if percent identity threshold is applied to shading + */ + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } + + /** + * GUI state + * + * + * @param b + * indicate if percent identity threshold is applied to shading + */ + public void setAbovePIDThreshold(boolean b) + { + abovePIDThreshold = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartRes() + { + return startRes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEndRes() + { + return endRes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartSeq() + { + return startSeq; + } + + /** + * DOCUMENT ME! + * + * @param 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( + Desktop.instance).removeMappings(alignment.getCodonFrames()); + } + this.alignment = align; + if (alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).addMappings(alignment.getCodonFrames()); + } + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setWrapAlignment(boolean state) + { + wrapAlignment = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowText(boolean state) + { + showText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setRenderGaps(boolean state) + { + renderGaps = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourText() + { + return showColourText; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setColourText(boolean state) + { + showColourText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowBoxes(boolean state) + { + showBoxes = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getWrapAlignment() + { + return wrapAlignment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowText() + { + return showText; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowBoxes() + { + return showBoxes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char getGapCharacter() + { + return getAlignment().getGapCharacter(); + } + + /** + * DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! + */ + public void setGapCharacter(char gap) + { + if (getAlignment() != null) + { + getAlignment().setGapCharacter(gap); + } + } + + /** + * DOCUMENT ME! + * + * @param thresh + * DOCUMENT ME! + */ + public void setThreshold(int thresh) + { + threshold = thresh; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getThreshold() + { + return threshold; + } + + /** + * DOCUMENT ME! + * + * @param inc + * DOCUMENT ME! + */ + public void setIncrement(int inc) + { + increment = inc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getIncrement() + { + return increment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public ColumnSelection getColumnSelection() + { + return colSel; + } + + /** + * DOCUMENT ME! + * + * @param tree + * DOCUMENT ME! + */ + public void setCurrentTree(NJTree tree) + { + currentTree = tree; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public NJTree getCurrentTree() + { + return currentTree; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setColourAppliesToAllGroups(boolean b) + { + colourAppliesToAllGroups = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourAppliesToAllGroups() + { + return colourAppliesToAllGroups; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowJVSuffix() + { + return showJVSuffix; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowJVSuffix(boolean b) + { + showJVSuffix = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowAnnotation() + { + return showAnnotation; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowAnnotation(boolean b) + { + showAnnotation = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleAboveWrapped() + { + return scaleAboveWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleLeftWrapped() + { + return scaleLeftWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleRightWrapped() + { + return scaleRightWrapped; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleAboveWrapped(boolean b) + { + scaleAboveWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleLeftWrapped(boolean b) + { + scaleLeftWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleRightWrapped(boolean b) + { + scaleRightWrapped = b; + } + + /** + * 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) { - return charHeight; + return; } - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setWrappedWidth(int w) + if (hiddenRepSequences == null) { - this.wrappedWidth = w; + hiddenRepSequences = new Hashtable(); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() + hiddenRepSequences.put(repSequence, sg); + + // 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) + { + return new jalview.datamodel.CigarArray(alignment, + (hasHiddenColumns ? colSel : null), + (selectedRegionOnly ? selectionGroup : null)); + } + + /** + * 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 + */ + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly) + { + return getAlignmentView(selectedOnly, false); + } + + /** + * 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 + * @param markGroups + * boolean true to annotate the alignment view with groups on the + * alignment (and intersecting with selected region if selectedOnly + * is true) + * @return AlignmentView + */ + public jalview.datamodel.AlignmentView getAlignmentView( + boolean selectedOnly, boolean markGroups) + { + return new AlignmentView(alignment, colSel, selectionGroup, + hasHiddenColumns, selectedOnly, markGroups); + } + + /** + * 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 char getGapCharacter() - { - return getAlignment().getGapCharacter(); } + return selection; + } - /** - * DOCUMENT ME! - * - * @param gap DOCUMENT ME! - */ - public void setGapCharacter(char gap) + public int[][] getVisibleRegionBoundaries(int min, int max) + { + Vector regions = new Vector(); + int start = min; + int end = max; + + do { - if (getAlignment() != null) + if (hasHiddenColumns) + { + if (start == 0) { - getAlignment().setGapCharacter(gap); + start = colSel.adjustForHiddenColumns(start); } - } - /** - * DOCUMENT ME! - * - * @param thresh DOCUMENT ME! - */ - public void setThreshold(int thresh) - { - threshold = thresh; - } + end = colSel.getHiddenBoundaryRight(start); + if (start == end) + { + end = max; + } + if (end > max) + { + end = max; + } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getThreshold() - { - return threshold; - } + regions.addElement(new int[] + { start, end }); - /** - * DOCUMENT ME! - * - * @param inc DOCUMENT ME! - */ - public void setIncrement(int inc) - { - increment = inc; - } + if (hasHiddenColumns) + { + start = colSel.adjustForHiddenColumns(end); + start = colSel.getHiddenBoundaryLeft(start) + 1; + } + } while (end < max); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIncrement() - { - return increment; - } + int[][] startEnd = new int[regions.size()][2]; + regions.copyInto(startEnd); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColumnSelection getColumnSelection() - { - return colSel; - } + return startEnd; + } - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - public void setCurrentTree(NJTree tree) - { - currentTree = tree; - } + public boolean getShowHiddenMarkers() + { + return showHiddenMarkers; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getCurrentTree() - { - return currentTree; - } + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; + } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setColourAppliesToAllGroups(boolean b) + public String getSequenceSetId() + { + if (sequenceSetID == null) { - colourAppliesToAllGroups = b; + sequenceSetID = alignment.hashCode() + ""; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } + return sequenceSetID; + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowJVSuffix() - { - return showJVSuffix; - } + /** + * unique viewId for synchronizing state with stored Jalview Project + * + */ + private String viewId = null; - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowJVSuffix(boolean b) + public String getViewId() + { + if (viewId == null) { - showJVSuffix = b; + viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; } + return viewId; + } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowAnnotation() + public void alignmentChanged(AlignmentPanel ap) + { + if (padGaps) { - return showAnnotation; + alignment.padGaps(); } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowAnnotation(boolean b) + if (hconsensus != null && autoCalculateConsensus) { - showAnnotation = b; + updateConservation(ap); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() + if (autoCalculateConsensus) { - return scaleAboveWrapped; + updateConsensus(ap); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() + if (autoCalculateStrucConsensus) { - return scaleLeftWrapped; + updateStrucConsensus(ap); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() + // Reset endRes of groups if beyond alignment width + int alWidth = alignment.getWidth(); + Vector groups = alignment.getGroups(); + if (groups != null) { - return scaleRightWrapped; + 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 setScaleAboveWrapped(boolean b) + if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) { - scaleAboveWrapped = b; + selectionGroup.setEndRes(alWidth - 1); } - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } + resetAllColourSchemes(); - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) + // alignment.adjustSequenceAnnotations(); + } + + void resetAllColourSchemes() + { + ColourSchemeI cs = globalColourScheme; + if (cs != null) { - scaleRightWrapped = b; + if (cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), + alignment.getWidth()); + } + + cs.setConsensus(hconsensus); + if (cs.conservationApplied()) + { + 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); + } } - /** - * Property change listener for changes in alignment - * - * @param listener DOCUMENT ME! - */ - public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) + int s, sSize = alignment.getGroups().size(); + for (s = 0; s < sSize; s++) { - changeSupport.addPropertyChangeListener(listener); + 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(); } + } - /** - * DOCUMENT ME! - * - * @param listener DOCUMENT ME! - */ - public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) + public Color getSequenceColour(SequenceI seq) + { + if (sequenceColours == null || !sequenceColours.containsKey(seq)) { - changeSupport.removePropertyChangeListener(listener); + return Color.white; } - - /** - * 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) + else { - changeSupport.firePropertyChange(prop, oldvalue, newvalue); + return (Color) sequenceColours.get(seq); } + } - public void setIgnoreGapsConsensus(boolean b) + public void setSequenceColour(SequenceI seq, Color col) + { + if (sequenceColours == null) { - ignoreGapsInConsensusCalculation = b; - updateConsensus(); - if(globalColourScheme!=null) - { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation); - } + sequenceColours = new Hashtable(); } - public boolean getIgnoreGapsConsensus() + if (col == null) { - return ignoreGapsInConsensusCalculation; + sequenceColours.remove(seq); } - - public void setDataset(boolean b) + else { - isDataset = b; + sequenceColours.put(seq, col); } + } - public boolean isDataset() + /** + * 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) { - return isDataset; + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; } - - - public void hideSelectedColumns() + else { - if (colSel.size() < 1) - return; - - colSel.hideSelectedColumns(); - setSelectionGroup(null); - - hasHiddenColumns = true; + end = alignment.getWidth(); } + viscontigs = colSel.getVisibleContigs(start, end); + return viscontigs; + } + /** + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; + */ + public long[] getUndoRedoHash() + { + if (historyList == null || redoList == null) + return new long[] + { -1, -1 }; + return new long[] + { historyList.hashCode(), this.redoList.hashCode() }; + } - public void hideColumns(int start, int end) + /** + * 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) { - if(start==end) - colSel.hideColumns(start); - else - colSel.hideColumns(start, end); - - hasHiddenColumns = true; + return true; } - - public void hideAllSelectedSeqs() + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) { - if (selectionGroup == null) - return; - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - hideSequence(seqs); - - setSelectionGroup(null); + return true; } - public void hideSequence(SequenceI [] seq) + for (int i = 0; i < cstate.length; i++) { - if(seq!=null) + if (cstate[i] != undoredo[i]) { - for (int i = 0; i < seq.length; i++) - alignment.getHiddenSequences().hideSequence(seq[i]); - - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); + return true; } } + return false; + } - public void showSequence(int index) - { - 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()); - } + public boolean getCentreColumnLabels() + { + return centreColumnLabels; + } - if(alignment.getHiddenSequences().getSize()<1) - hasHiddenRows = false; - } + public void setCentreColumnLabels(boolean centrecolumnlabels) + { + centreColumnLabels = centrecolumnlabels; + } - public void showColumn(int col) + public void updateSequenceIdColours() + { + Vector groups = alignment.getGroups(); + if (sequenceColours == null) { - colSel.revealHiddenColumns(col); - if(colSel.getHiddenColumns()==null) - hasHiddenColumns = false; + sequenceColours = new Hashtable(); } - - public void showAllHiddenColumns() + for (int ig = 0, igSize = groups.size(); ig < igSize; ig++) { - colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; - } - - public void showAllHiddenSeqs() - { - if(alignment.getHiddenSequences().getSize()>0) + SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); + if (sg.idColour != null) { - if(selectionGroup==null) + Vector sqs = sg.getSequences(hiddenRepSequences); + for (int s = 0, sSize = sqs.size(); s < sSize; s++) { - selectionGroup = new SequenceGroup(); - selectionGroup.setEndRes(alignment.getWidth()-1); + sequenceColours.put(sqs.elementAt(s), sg.idColour); } - Vector tmp = alignment.getHiddenSequences().showAll(); - for(int t=0; t