X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=10f4c6e02e89be2c515153d2e0a3a62fdf492c80;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=1b3af30457edc9f103bd93f1815d8c9c4d3e2089;hpb=14ff1fd59357c8967a6f6d673e48ff0516bce5d6;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java old mode 100755 new mode 100644 index 1b3af30..10f4c6e --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,20 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; @@ -23,11 +23,16 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; +import jalview.api.AlignViewportI; import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.VamsasSource; +import jalview.viewmodel.AlignmentViewport; -public class AlignViewport +public class AlignViewport extends AlignmentViewport implements + AlignViewportI, SelectionSource, VamsasSource { int startRes; @@ -55,24 +60,8 @@ public class AlignViewport boolean showAnnotation = true; - boolean showConservation = true; - - boolean showQuality = true; - - boolean showConsensus = true; - boolean upperCasebold = false; - boolean colourAppliesToAllGroups = true; - - ColourSchemeI globalColourScheme = null; - - boolean conservationColourSelected = false; - - boolean abovePIDThreshold = false; - - SequenceGroup selectionGroup; - int charHeight; int charWidth; @@ -83,10 +72,6 @@ public class AlignViewport boolean validCharWidth = true; - AlignmentI alignment; - - ColumnSelection colSel = new ColumnSelection(); - int threshold; int increment; @@ -103,32 +88,9 @@ public class AlignViewport // currently visible, in the correct order or rendering public Hashtable featuresDisplayed; - boolean hasHiddenColumns = false; - - boolean hasHiddenRows = false; - boolean showHiddenMarkers = true; - public Hashtable[] hconsensus; - - AlignmentAnnotation consensus; - - AlignmentAnnotation conservation; - - AlignmentAnnotation quality; - AlignmentAnnotation[] groupConsensus; - AlignmentAnnotation[] groupConservation; - - boolean autocalculateConsensus = true; - - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( - this); - - boolean ignoreGapsInConsensusCalculation = false; - - jalview.bin.JalviewLite applet; + public jalview.bin.JalviewLite applet; Hashtable sequenceColours; @@ -138,55 +100,72 @@ public class AlignViewport Stack redoList = new Stack(); - String sequenceSetID; - - Hashtable hiddenRepSequences; + public void finalize() + { + applet = null; + quality = null; + alignment = null; + colSel = null; + } public AlignViewport(AlignmentI al, JalviewLite applet) { + calculator = new jalview.workers.AlignCalcManager(); this.applet = applet; setAlignment(al); + // we always pad gaps + this.setPadGaps(true); this.startRes = 0; this.endRes = al.getWidth() - 1; this.startSeq = 0; this.endSeq = al.getHeight() - 1; - if (applet!=null) + if (applet != null) { // get the width and height scaling factors if they were specified String param = applet.getParameter("widthScale"); - if (param!=null) + if (param != null) { - try { + try + { widthScale = new Float(param).floatValue(); } catch (Exception e) { } - if (widthScale<=1.0) + if (widthScale <= 1.0) { - System.err.println("Invalid alignment character width scaling factor ("+widthScale+"). Ignoring."); + System.err + .println("Invalid alignment character width scaling factor (" + + widthScale + "). Ignoring."); widthScale = 1; } if (applet.debug) { - System.err.println("Alignment character width scaling factor is now "+widthScale); + System.err + .println("Alignment character width scaling factor is now " + + widthScale); } } param = applet.getParameter("heightScale"); - if (param!=null) + if (param != null) { - try { + try + { heightScale = new Float(param).floatValue(); } catch (Exception e) { } - if (heightScale<=1.0) + if (heightScale <= 1.0) { - System.err.println("Invalid alignment character height scaling factor ("+heightScale+"). Ignoring."); + System.err + .println("Invalid alignment character height scaling factor (" + + heightScale + "). Ignoring."); heightScale = 1; } if (applet.debug) { - System.err.println("Alignment character height scaling factor is now "+heightScale); + System.err + .println("Alignment character height scaling factor is now " + + heightScale); } } } @@ -196,43 +175,23 @@ public class AlignViewport if (applet != null) { - String param = applet.getParameter("showFullId"); - if (param != null) - { - showJVSuffix = Boolean.valueOf(param).booleanValue(); - } + showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix); - param = applet.getParameter("showAnnotation"); - if (param != null) - { - showAnnotation = Boolean.valueOf(param).booleanValue(); - } + showAnnotation = applet.getDefaultParameter("showAnnotation", + showAnnotation); - param = applet.getParameter("showConservation"); - if (param != null) - { - showConservation = Boolean.valueOf(param).booleanValue(); - } + showConservation = applet.getDefaultParameter("showConservation", + showConservation); - param = applet.getParameter("showQuality"); - if (param != null) - { - showQuality = Boolean.valueOf(param).booleanValue(); - } + showQuality = applet.getDefaultParameter("showQuality", showQuality); - param = applet.getParameter("showConsensus"); - if (param != null) - { - showConsensus = Boolean.valueOf(param).booleanValue(); - } + showConsensus = applet.getDefaultParameter("showConsensus", + showConsensus); - param = applet.getParameter("showUnconserved"); - if (param != null) - { - this.showUnconserved = Boolean.valueOf(param).booleanValue(); - } + showUnconserved = applet.getDefaultParameter("showUnconserved", + showUnconserved); - param = applet.getParameter("upperCase"); + String param = applet.getParameter("upperCase"); if (param != null) { if (param.equalsIgnoreCase("bold")) @@ -240,11 +199,27 @@ public class AlignViewport upperCasebold = true; } } - param = applet.getParameter("sortByTree"); - if (param != null) - { - sortByTree=Boolean.valueOf(param).booleanValue(); - } + sortByTree = applet.getDefaultParameter("sortByTree", sortByTree); + + followHighlight = applet.getDefaultParameter("automaticScrolling", + followHighlight); + followSelection = followHighlight; + + showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", + showSequenceLogo); + + normaliseSequenceLogo = applet.getDefaultParameter( + "normaliseSequenceLogo", applet.getDefaultParameter( + "normaliseLogo", normaliseSequenceLogo)); + + showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", + showGroupConsensus); + + showGroupConservation = applet.getDefaultParameter( + "showGroupConservation", showGroupConservation); + + showConsensusHistogram = applet.getDefaultParameter( + "showConsensusHistogram", showConsensusHistogram); } @@ -277,44 +252,7 @@ public class AlignViewport .getParameter("userDefinedColour")); } } - if (hconsensus == null) - { - 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 (showConservation) - { - alignment.addAnnotation(conservation); - } - - if (showQuality) - { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - quality.autoCalculated = true; - - alignment.addAnnotation(quality); - } - } - - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; - - if (showConsensus) - { - alignment.addAnnotation(consensus); - } - } + initAutoAnnotation(); } @@ -328,252 +266,6 @@ public class AlignViewport return showSequenceFeatures; } - class ConservationThread extends Thread - { - AlignmentPanel ap; - - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - 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; - } - - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, alignment - .getSequences(), 0, alWidth - 1); - - cons.calculate(); - cons.verdict(false, ConsPercGaps); - - if (quality != null) - { - cons.findQuality(); - } - - char[] 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 = 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; - - c = sequence[i]; - - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') - { - value = 11; - } - else if (c == '+') - { - value = 10; - } - // TODO - refactor to use a graduatedColorScheme to calculate the histogram colors. - float vprop = value - min; - vprop /= max; - conservation.annotations[i] = new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); - - // Quality calc - if (quality != null) - { - value = ((Double) cons.quality.elementAt(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String - .valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); - } - } - } catch (OutOfMemoryError error) - { - System.out.println("Out of memory calculating conservation!!"); - conservation = null; - quality = null; - System.gc(); - } - - UPDATING_CONSERVATION = false; - updatingConservation = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - - } - } - - ConservationThread conservationThread; - - ConsensusThread consensusThread; - - boolean consUpdateNeeded = false; - - static boolean UPDATING_CONSENSUS = false; - - static boolean UPDATING_CONSERVATION = false; - - boolean updatingConsensus = false; - - boolean updatingConservation = false; - - /** - * DOCUMENT ME! - */ - public void updateConservation(final AlignmentPanel ap) - { - if (alignment.isNucleotide() || conservation == null) - { - return; - } - - conservationThread = new ConservationThread(ap); - conservationThread.start(); - } - - /** - * DOCUMENT ME! - */ - public void updateConsensus(final AlignmentPanel ap) - { - consensusThread = new ConsensusThread(ap); - consensusThread.start(); - } - - class ConsensusThread extends Thread - { - AlignmentPanel ap; - - public ConsensusThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - updatingConsensus = true; - while (UPDATING_CONSENSUS) - { - try - { - if (ap != null) - { - ap.paintAlignment(false); - } - - Thread.sleep(200); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSENSUS = true; - - try - { - int aWidth = alignment.getWidth(); - if (aWidth < 0) - { - return; - } - - consensus.annotations = null; - consensus.annotations = new Annotation[aWidth]; - - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus, includeAllConsensusSymbols); - AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols); - - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } - - } catch (OutOfMemoryError error) - { - alignment.deleteAnnotation(consensus); - - consensus = null; - hconsensus = null; - System.out.println("Out of memory calculating consensus!!"); - System.gc(); - } - UPDATING_CONSENSUS = false; - updatingConsensus = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - } - } - /** * get the consensus sequence as displayed under the PID consensus annotation * row. @@ -584,6 +276,10 @@ public class AlignViewport { if (consensus == null) { + updateConsensus(null); + } + if (consensus == null) + { return null; } StringBuffer seqs = new StringBuffer(); @@ -607,36 +303,6 @@ public class AlignViewport return sq; } - public SequenceGroup getSelectionGroup() - { - return selectionGroup; - } - - public void setSelectionGroup(SequenceGroup sg) - { - selectionGroup = sg; - } - - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - public int getStartRes() { return startRes; @@ -652,16 +318,6 @@ public class AlignViewport return startSeq; } - public void setGlobalColourScheme(ColourSchemeI cs) - { - globalColourScheme = cs; - } - - public ColourSchemeI getGlobalColourScheme() - { - return globalColourScheme; - } - public void setStartRes(int res) { this.startRes = res; @@ -709,7 +365,7 @@ public class AlignViewport protected FeatureSettings featureSettings = null; - private float heightScale=1,widthScale=1; + private float heightScale = 1, widthScale = 1; public void setFont(Font f) { @@ -721,14 +377,14 @@ public class AlignViewport } java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font); - setCharHeight((int)(heightScale*fm.getHeight())); - charWidth = (int)(widthScale*fm.charWidth('M')); + setCharHeight((int) (heightScale * fm.getHeight())); + charWidth = (int) (widthScale * fm.charWidth('M')); if (upperCasebold) { Font f2 = new Font(f.getName(), Font.BOLD, f.getSize()); fm = nullFrame.getGraphics().getFontMetrics(f2); - charWidth = (int)(widthScale*(fm.stringWidth("MMMMMMMMMMM") / 10)); + charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)); } } @@ -850,20 +506,6 @@ public class AlignViewport return increment; } - public void setHiddenColumns(ColumnSelection colsel) - { - this.colSel = colsel; - if (colSel.getHiddenColumns() != null) - { - hasHiddenColumns = true; - } - } - - public ColumnSelection getColumnSelection() - { - return colSel; - } - public void resetSeqLimits(int height) { setEndSeq(height / getCharHeight()); @@ -879,16 +521,6 @@ public class AlignViewport return currentTree; } - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } - - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } - public boolean getShowJVSuffix() { return showJVSuffix; @@ -951,445 +583,6 @@ public class AlignViewport } } - /** - * 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 boolean getIgnoreGapsConsensus() - { - return ignoreGapsInConsensusCalculation; - } - - public void hideSelectedColumns() - { - if (colSel.size() < 1) - { - return; - } - - colSel.hideSelectedColumns(); - setSelectionGroup(null); - - hasHiddenColumns = true; - } - - public void invertColumnSelection() - { - for (int i = 0; i < alignment.getWidth(); i++) - { - if (colSel.contains(i)) - { - colSel.removeElement(i); - } - else - { - if (!hasHiddenColumns || colSel.isVisible(i)) - { - colSel.addElement(i); - } - } - } - } - - 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; - } - - if (hiddenRepSequences == null) - { - hiddenRepSequences = new Hashtable(); - } - - 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++) - { - if (sg.getSequenceAt(i) != repSequence) - { - if (index == sSize - 1) - { - return; - } - - seqs[index++] = sg.getSequenceAt(i); - } - } - - hideSequence(seqs); - - } - - public void hideAllSelectedSeqs() - { - if (selectionGroup == null || selectionGroup.getSize() < 1) - { - return; - } - - SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment); - - hideSequence(seqs); - - setSelectionGroup(null); - } - - public void hideSequence(SequenceI[] seq) - { - if (seq != null) - { - for (int i = 0; i < seq.length; i++) - { - alignment.getHiddenSequences().hideSequence(seq[i]); - } - - hasHiddenRows = true; - firePropertyChange("alignment", null, alignment.getSequences()); - } - } - - public void showColumn(int col) - { - colSel.revealHiddenColumns(col); - if (colSel.getHiddenColumns() == null) - { - hasHiddenColumns = false; - } - } - - public void showAllHiddenColumns() - { - colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; - } - - public void showAllHiddenSeqs() - { - if (alignment.getHiddenSequences().getSize() > 0) - { - 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()); - hasHiddenRows = false; - hiddenRepSequences = null; - } - } - - public int adjustForHiddenSeqs(int alignmentIndex) - { - return alignment.getHiddenSequences().adjustForHiddenSeqs( - alignmentIndex); - } - - /** - * This method returns the a new SequenceI [] with the selection sequence and - * start and end points adjusted - * - * @return String[] - */ - public SequenceI[] getSelectionAsNewSequence() - { - SequenceI[] sequences; - - if (selectionGroup == null) - { - sequences = alignment.getSequencesArray(); - } - else - { - sequences = selectionGroup.getSelectionAsNewSequences(alignment); - } - - return sequences; - } - /** - * 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; - } - } - - if (hideStart > end) - { - break; - } - - if (hideEnd > end) - { - hideEnd = end; - } - - 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]; - - for (i = 0; i < iSize; i++) - { - if (hasHiddenColumns) - { - StringBuffer visibleSeq = new StringBuffer(); - Vector regions = colSel.getHiddenColumns(); - - int blockStart = start, blockEnd = end; - int[] region; - int hideStart, hideEnd; - - for (int j = 0; j < regions.size(); j++) - { - region = (int[]) regions.elementAt(j); - hideStart = region[0]; - hideEnd = region[1]; - - if (hideStart < start) - { - continue; - } - - blockStart = Math.min(blockStart, hideEnd + 1); - blockEnd = Math.min(blockEnd, hideStart); - - if (blockStart > blockEnd) - { - break; - } - - visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd)); - - blockStart = hideEnd + 1; - blockEnd = end; - } - - if (end > blockStart) - { - visibleSeq.append(seqs[i].getSequence(blockStart, end)); - } - - selection[i] = visibleSeq.toString(); - } - else - { - selection[i] = seqs[i].getSequenceAsString(start, end); - } - } - - return selection; - } - public boolean getShowHiddenMarkers() { return showHiddenMarkers; @@ -1429,92 +622,8 @@ public class AlignViewport } } - public String getSequenceSetId() - { - if (sequenceSetID == null) - { - sequenceSetID = alignment.hashCode() + ""; - } - - return sequenceSetID; - } - - public void alignmentChanged(AlignmentPanel ap) - { - alignment.padGaps(); - - if (hconsensus != null && autocalculateConsensus) - { - updateConsensus(ap); - updateConservation(ap); - } - - // Reset endRes of groups if beyond alignment width - int alWidth = alignment.getWidth(); - Vector groups = alignment.getGroups(); - if (groups != null) - { - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (sg.getEndRes() > alWidth) - { - sg.setEndRes(alWidth - 1); - } - } - } - - if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) - { - selectionGroup.setEndRes(alWidth - 1); - } - - resetAllColourSchemes(); - - // AW alignment.adjustSequenceAnnotations(); - } - - void resetAllColourSchemes() - { - ColourSchemeI cs = globalColourScheme; - if (cs != null) - { - 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); - } - } - - int s, sSize = alignment.getGroups().size(); - for (s = 0; s < sSize; s++) - { - 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(); - } - } - boolean centreColumnLabels; - public boolean getCentreColumnLabels() { return centreColumnLabels; @@ -1522,110 +631,101 @@ public class AlignViewport public void updateSequenceIdColours() { - Vector groups = alignment.getGroups(); - for (int ig = 0, igSize = groups.size(); ig < igSize; ig++) + + for (SequenceGroup sg : alignment.getGroups()) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); if (sg.idColour != null) { - Vector sqs = sg.getSequences(hiddenRepSequences); - for (int s = 0, sSize = sqs.size(); s < sSize; s++) + for (SequenceI s : sg.getSequences(getHiddenRepSequences())) { - this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour); + this.setSequenceColour(s, sg.idColour); } } } } - public boolean followHighlight=false; - public boolean getFollowHighlight() { + + public boolean followHighlight = true; + + public boolean getFollowHighlight() + { return followHighlight; } - /** - * show non-conserved residues only - */ - public boolean showUnconserved=false; - /** - * when set, alignment should be reordered according to a newly opened tree - */ - public boolean sortByTree=false; + public boolean followSelection = true; /** - * @return the showUnconserved + * @return true if view selection should always follow the selections + * broadcast by other selection sources */ - public boolean getShowunconserved() + public boolean getFollowSelection() { - return showUnconserved; + return followSelection; } - /** - * @param showUnconserved the showUnconserved to set - */ - public void setShowunconserved(boolean displayNonconserved) + public void sendSelection() { - this.showUnconserved = displayNonconserved; + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(applet).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); } /** - * consensus annotation includes all percentage for all symbols in column - * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible) - */ - private boolean includeAllConsensusSymbols=false; - - /** - * should conservation rows be shown for groups - * DISABLED FOR 2.5 RELEASE (bug 62446) - */ - boolean showGroupConservation = false; - /** - * should consensus rows be shown for groups - * DISABLED FOR 2.5 RELEASE (bug 62446) - */ - boolean showGroupConsensus = false; - /** - * should consensus profile be rendered by default - * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible) - */ - public boolean showSequenceLogo = false; - /** - * should consensus histograms be rendered by default - */ - public boolean showConsensusHistogram = true; - /** - * @return the showConsensusProfile + * synthesize a column selection if none exists so it covers the given + * selection group. if wholewidth is false, no column selection is made if the + * selection group covers the whole alignment width. + * + * @param sg + * @param wholewidth */ - public boolean isShowSequenceLogo() + public void expandColSelection(SequenceGroup sg, boolean wholewidth) { - return showSequenceLogo; + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } } - /** - * @param showSequenceLogo the new value - public void setShowSequenceLogo(boolean showSequenceLogo) + + @Override + public boolean hasHiddenColumns() { - this.showSequenceLogo = showSequenceLogo; + return hasHiddenColumns; } - */ - /** - * @param showGroupConsensus the showGroupConsensus to set - */ - public void setShowGroupConsensus(boolean showGroupConsensus) + + public boolean isNormaliseSequenceLogo() { - this.showGroupConsensus = showGroupConsensus; + return normaliseSequenceLogo; } - /** - * @return the includeAllConsensusSymbols - */ - public boolean isIncludeAllConsensusSymbols() + + public void setNormaliseSequenceLogo(boolean state) { - return false; + normaliseSequenceLogo = state; } - + /** * - * @return flag to indicate if the consensus histogram should be rendered by default + * @return true if alignment characters should be displayed */ - public boolean isShowConsensusHistogram() + public boolean isValidCharWidth() { - return this.showConsensusHistogram; + return validCharWidth; } + }