X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d0c5674e257ae8ff0acf41bc53e81faf0953f863;hb=caf13e6a9dc82023cd8648420201e5ad60ce0393;hp=d07b010ed81f4d75279ad3cd269f7fee8c107b77;hpb=5feda00b43b9156b7a86b232b63a5da0736113ee;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index d07b010..d0c5674 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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. * - * 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 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 @@ -49,6 +48,7 @@ import jalview.datamodel.*; import jalview.schemes.*; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; /** * DOCUMENT ME! @@ -56,7 +56,7 @@ import jalview.structure.StructureSelectionManager; * @author $author$ * @version $Revision$ */ -public class AlignViewport implements SelectionSource +public class AlignViewport implements SelectionSource, VamsasSource { private static final int RIGHT_JUSTIFY = 1; @@ -130,8 +130,10 @@ public class AlignViewport implements SelectionSource boolean cursorMode = false; - // The following vector holds the features which are - // currently visible, in the correct order or rendering + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ Hashtable featuresDisplayed = null; /** DOCUMENT ME!! */ @@ -143,6 +145,10 @@ public class AlignViewport implements SelectionSource AlignmentAnnotation quality; + AlignmentAnnotation[] groupConsensus; + + AlignmentAnnotation[] groupConservation; + boolean autoCalculateConsensus = true; /** DOCUMENT ME!! */ @@ -184,32 +190,46 @@ public class AlignViewport implements SelectionSource Hashtable hiddenRepSequences; + boolean sortByTree; + /** * Creates a new AlignViewport object. * - * @param al alignment to view + * @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) + * @param seqsetid + * (may be null - but potential for ambiguous constructor exception) */ public AlignViewport(AlignmentI al, String seqsetid) { - this(al,seqsetid,null); + 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); } + 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(); } @@ -218,9 +238,9 @@ public class AlignViewport implements SelectionSource * Create a new AlignViewport with hidden regions * * @param al - * AlignmentI + * AlignmentI * @param hiddenColumns - * ColumnSelection + * ColumnSelection */ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) { @@ -228,45 +248,71 @@ public class AlignViewport implements SelectionSource if (hiddenColumns != null) { this.colSel = hiddenColumns; - if (hiddenColumns.getHiddenColumns() != null) + 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) + * @param seqsetid + * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid) + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid) { - this(al,hiddenColumns,seqsetid,null); + 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) + * @param seqsetid + * (may be null) + * @param viewid + * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid, String viewid) + 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); } + 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) + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) { hasHiddenColumns = true; } + else + { + hasHiddenColumns = false; + } } init(); } @@ -288,9 +334,9 @@ public class AlignViewport implements SelectionSource 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); - + 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"); @@ -341,8 +387,20 @@ public class AlignViewport implements SelectionSource alignment.addAnnotation(quality); } + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + 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 + 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; @@ -373,14 +431,18 @@ public class AlignViewport implements SelectionSource } wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); - showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", 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! + * set the flag * * @param b - * DOCUMENT ME! + * features are displayed if true */ public void setShowSequenceFeatures(boolean b) { @@ -392,146 +454,6 @@ public class AlignViewport implements SelectionSource 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; - } - - float vprop = value - min; - vprop /= max; - conservation.annotations[i] = new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); - - // Quality calc - if (quality != null) - { - value = ((Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String - .valueOf(value), ' ', value, new Color(minR - + (maxR * vprop), minG + (maxG * vprop), minB - + (maxB * vprop))); - } - } - } catch (OutOfMemoryError error) - { - new OOMWarning("calculating conservation", error); - - conservation = null; - quality = null; - - } - - UPDATING_CONSERVATION = false; - updatingConservation = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - - } - } - ConservationThread conservationThread; ConsensusThread consensusThread; @@ -562,12 +484,13 @@ public class AlignViewport implements SelectionSource public void updateConservation(final AlignmentPanel ap) { // see note in mantis : issue number 8585 - if (alignment.isNucleotide() || conservation == null || !autoCalculateConsensus) + if (alignment.isNucleotide() || conservation == null + || !autoCalculateConsensus) { return; } - conservationThread = new ConservationThread(ap); + conservationThread = new ConservationThread(this, ap); conservationThread.start(); } @@ -617,12 +540,14 @@ public class AlignViewport implements SelectionSource try { - int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null - // pointer - // possibility - // here. - if (aWidth < 0) + int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null + // pointer + // possibility + // here. + if (aWidth <= 0) { + updatingConsensus = false; + UPDATING_CONSENSUS = false; return; } @@ -630,38 +555,9 @@ public class AlignViewport implements SelectionSource consensus.annotations = new Annotation[aWidth]; hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment - .getWidth(), hconsensus); - - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) - .floatValue(); - } - else - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) - .floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) - + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ((int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } + AAFrequency.calculate(alignment.getSequencesArray(), 0, + alignment.getWidth(), hconsensus, true); + updateAnnotation(true); if (globalColourScheme != null) { @@ -684,6 +580,28 @@ public class AlignViewport implements SelectionSource ap.paintAlignment(true); } } + + /** + * update the consensus annotation from the sequence profile data using + * current visualization settings. + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + protected void updateAnnotation(boolean immediate) + { + // 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 + || (!updatingConsensus && consensus != null && hconsensus != null)) + { + AAFrequency.completeConsensus(consensus, hconsensus, 0, + hconsensus.length, ignoreGapsInConsensusCalculation, + showSequenceLogo); + } + } } /** @@ -738,11 +656,11 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param sg - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSelectionGroup(SequenceGroup sg) { - selectionGroup = sg; + selectionGroup = sg; } /** @@ -759,7 +677,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setConservationSelected(boolean b) { @@ -780,7 +698,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAbovePIDThreshold(boolean b) { @@ -821,7 +739,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGlobalColourScheme(ColourSchemeI cs) { @@ -842,7 +760,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartRes(int res) { @@ -853,7 +771,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStartSeq(int seq) { @@ -864,7 +782,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param res - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndRes(int res) { @@ -887,7 +805,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEndSeq(int seq) { @@ -918,7 +836,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param f - * DOCUMENT ME! + * DOCUMENT ME! */ public void setFont(Font f) { @@ -946,7 +864,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharWidth(int w) { @@ -967,7 +885,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param h - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCharHeight(int h) { @@ -988,7 +906,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param w - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrappedWidth(int w) { @@ -1019,7 +937,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param align - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAlignment(AlignmentI align) { @@ -1040,7 +958,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean state) { @@ -1051,7 +969,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowText(boolean state) { @@ -1062,7 +980,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setRenderGaps(boolean state) { @@ -1083,7 +1001,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourText(boolean state) { @@ -1094,7 +1012,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowBoxes(boolean state) { @@ -1145,7 +1063,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param gap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setGapCharacter(char gap) { @@ -1159,7 +1077,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param thresh - * DOCUMENT ME! + * DOCUMENT ME! */ public void setThreshold(int thresh) { @@ -1180,7 +1098,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param inc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setIncrement(int inc) { @@ -1211,7 +1129,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param tree - * DOCUMENT ME! + * DOCUMENT ME! */ public void setCurrentTree(NJTree tree) { @@ -1232,7 +1150,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColourAppliesToAllGroups(boolean b) { @@ -1263,7 +1181,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowJVSuffix(boolean b) { @@ -1284,7 +1202,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowAnnotation(boolean b) { @@ -1325,7 +1243,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleAboveWrapped(boolean b) { @@ -1336,7 +1254,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleLeftWrapped(boolean b) { @@ -1347,7 +1265,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScaleRightWrapped(boolean b) { @@ -1358,7 +1276,7 @@ public class AlignViewport implements SelectionSource * Property change listener for changes in alignment * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void addPropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -1370,7 +1288,7 @@ public class AlignViewport implements SelectionSource * DOCUMENT ME! * * @param listener - * DOCUMENT ME! + * DOCUMENT ME! */ public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) @@ -1382,11 +1300,11 @@ public class AlignViewport implements SelectionSource * Property change listener for changes in alignment * * @param prop - * DOCUMENT ME! + * DOCUMENT ME! * @param oldvalue - * DOCUMENT ME! + * DOCUMENT ME! * @param newvalue - * DOCUMENT ME! + * DOCUMENT ME! */ public void firePropertyChange(String prop, Object oldvalue, Object newvalue) @@ -1604,9 +1522,9 @@ public class AlignViewport implements SelectionSource for (int i = 0; i < sequences.length; i++) { sequences[i] = new Sequence(sequences[i], annots); // construct new - // sequence with - // subset of visible - // annotation + // sequence with + // subset of visible + // annotation } } else @@ -1625,14 +1543,14 @@ public class AlignViewport implements SelectionSource */ public SequenceI[] getSequenceSelection() { - SequenceI[] sequences; - if (selectionGroup == null) + SequenceI[] sequences = null; + if (selectionGroup != null) { - sequences = alignment.getSequencesArray(); + sequences = selectionGroup.getSequencesInOrder(alignment); } - else + if (sequences == null) { - sequences = selectionGroup.getSequencesInOrder(alignment); + sequences = alignment.getSequencesArray(); } return sequences; } @@ -1648,90 +1566,7 @@ public class AlignViewport implements SelectionSource 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 new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null)); } /** @@ -1739,24 +1574,27 @@ public class AlignViewport implements SelectionSource * to an analysis function * * @param selectedOnly - * boolean true to just return the selected view + * boolean true to just return the selected view * @return AlignmentView */ - jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + public 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; + 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); } /** @@ -1866,22 +1704,22 @@ public class AlignViewport implements SelectionSource return sequenceSetID; } + /** - * unique viewId for synchronizing state with stored Jalview Project + * unique viewId for synchronizing state with stored Jalview Project * */ - private String viewId=null; + private String viewId = null; - public String getViewId() { - if (viewId==null) + if (viewId == null) { - viewId = this.getSequenceSetId()+"."+this.hashCode()+""; + viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; } return viewId; } - + public void alignmentChanged(AlignmentPanel ap) { if (padGaps) @@ -1938,8 +1776,8 @@ public class AlignViewport implements SelectionSource { Alignment al = (Alignment) alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, al - .getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); c.calculate(); c.verdict(false, ConsPercGaps); @@ -1953,8 +1791,8 @@ public class AlignViewport implements SelectionSource SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme) sg.cs).resetClustalX(sg - .getSequences(hiddenRepSequences), sg.getWidth()); + ((ClustalxColourScheme) sg.cs).resetClustalX( + sg.getSequences(hiddenRepSequences), sg.getWidth()); } sg.recalcConservation(); } @@ -1993,8 +1831,8 @@ public class AlignViewport implements SelectionSource * returns the visible column regions of the alignment * * @param selectedRegionOnly - * true to just return the contigs intersecting with the - * selected area + * true to just return the contigs intersecting with the selected + * area * @return */ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) @@ -2033,7 +1871,7 @@ public class AlignViewport implements SelectionSource * the undo and redo list. * * @param undoredo - * the stored set of hashcodes as returned by getUndoRedoHash + * 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 */ @@ -2091,11 +1929,12 @@ public class AlignViewport implements SelectionSource } /** - * enable or disable the display of Database Cross References in the sequence ID tooltip - */ + * enable or disable the display of Database Cross References in the sequence + * ID tooltip + */ public void setShowDbRefs(boolean show) { - showdbrefs=show; + showdbrefs = show; } /** @@ -2115,14 +1954,18 @@ public class AlignViewport implements SelectionSource { return shownpfeats; } + /** - * enable or disable the display of Non-Positional sequence features in the sequence ID tooltip - * @param show + * enable or disable the display of Non-Positional sequence features in the + * sequence ID tooltip + * + * @param show */ public void setShowNpFeats(boolean show) { - shownpfeats=show; + shownpfeats = show; } + /** * * @return true if view has hidden rows @@ -2131,6 +1974,7 @@ public class AlignViewport implements SelectionSource { return hasHiddenRows; } + /** * * @return true if view has hidden columns @@ -2139,72 +1983,264 @@ public class AlignViewport implements SelectionSource { return hasHiddenColumns; } + /** * when set, view will scroll to show the highlighted position */ - public boolean followHighlight=true; + public boolean followHighlight = true; + /** - * @return true if view should scroll to show the highlighted region of a sequence + * @return true if view should scroll to show the highlighted region of a + * sequence * @return */ - public boolean getFollowHighlight() { + public boolean getFollowHighlight() + { return followHighlight; } - public boolean followSelection=true; + + public boolean followSelection = true; + /** - * @return true if view selection should always follow the selections broadcast by other selection sources + * @return true if view selection should always follow the selections + * broadcast by other selection sources */ - public boolean getFollowSelection() { + public boolean getFollowSelection() + { return followSelection; } - private long sgrouphash=-1,colselhash=-1; + + private long sgrouphash = -1, colselhash = -1; boolean showSeqFeaturesHeight; + /** - * checks current SelectionGroup against record of last hash value, and updates record. + * checks current SelectionGroup against record of last hash value, and + * updates record. + * * @return true if SelectionGroup changed since last call */ - boolean isSelectionGroupChanged() { - int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode(); - if (hc!=sgrouphash) + boolean isSelectionGroupChanged() + { + int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); + if (hc != sgrouphash) { sgrouphash = hc; return true; } return false; } + /** - * checks current colsel against record of last hash value, and updates record. + * checks current colsel against record of last hash value, and updates + * record. + * * @return true if colsel changed since last call */ - boolean isColSelChanged() { - int hc=(colSel==null) ? -1 : colSel.hashCode(); - if (hc!=colselhash) + boolean isColSelChanged() + { + int hc = (colSel == null) ? -1 : colSel.hashCode(); + if (hc != colselhash) { colselhash = hc; return true; } return false; } + public void sendSelection() { - jalview.structure.StructureSelectionManager.getStructureSelectionManager().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this); + jalview.structure.StructureSelectionManager + .getStructureSelectionManager().sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); } + public void setShowSequenceFeaturesHeight(boolean selected) { - showSeqFeaturesHeight = selected; + showSeqFeaturesHeight = selected; } + public boolean getShowSequenceFeaturesHeight() { - return showSeqFeaturesHeight; + return showSeqFeaturesHeight; } - boolean showUnconserved=false; + + boolean showUnconserved = false; + public boolean getShowUnconserved() { return showUnconserved; } + public void setShowUnconserved(boolean showunconserved) { - showUnconserved=showunconserved; + showUnconserved = showunconserved; + } + + /** + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. + * + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference + */ + public AlignmentPanel getAlignPanel() + { + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this + .getSequenceSetId()); + AlignmentPanel ap = null; + for (int p = 0; aps != null && p < aps.length; p++) + { + if (aps[p].av == this) + { + return aps[p]; + } + } + return null; + } + + public boolean getSortByTree() + { + return sortByTree; + } + + public void setSortByTree(boolean sort) + { + sortByTree = sort; + } + + /** + * should conservation rows be shown for groups + */ + boolean showGroupConservation = false; + + /** + * should consensus rows be shown for groups + */ + boolean showGroupConsensus = false; + + /** + * should consensus profile be rendered by default + */ + public boolean showSequenceLogo = false; + + /** + * should consensus histograms be rendered by default + */ + public boolean showConsensusHistogram = true; + + /** + * @return the showConsensusProfile + */ + public boolean isShowSequenceLogo() + { + return showSequenceLogo; + } + + /** + * @param showSequenceLogo + * the new value + */ + public void setShowSequenceLogo(boolean showSequenceLogo) + { + if (showSequenceLogo != this.showSequenceLogo) + { + // TODO: decouple settings setting from calculation when refactoring + // annotation update method from alignframe to viewport + this.showSequenceLogo = showSequenceLogo; + if (consensusThread != null) + { + consensusThread.updateAnnotation(); + } + } + this.showSequenceLogo = showSequenceLogo; + } + + /** + * @param showConsensusHistogram + * the showConsensusHistogram to set + */ + public void setShowConsensusHistogram(boolean showConsensusHistogram) + { + this.showConsensusHistogram = showConsensusHistogram; + } + + /** + * @return the showGroupConservation + */ + public boolean isShowGroupConservation() + { + return showGroupConservation; + } + + /** + * @param showGroupConservation + * the showGroupConservation to set + */ + public void setShowGroupConservation(boolean showGroupConservation) + { + this.showGroupConservation = showGroupConservation; + } + + /** + * @return the showGroupConsensus + */ + public boolean isShowGroupConsensus() + { + return showGroupConsensus; + } + + /** + * @param showGroupConsensus + * the showGroupConsensus to set + */ + public void setShowGroupConsensus(boolean showGroupConsensus) + { + this.showGroupConsensus = showGroupConsensus; + } + + /** + * + * @return flag to indicate if the consensus histogram should be rendered by + * default + */ + public boolean isShowConsensusHistogram() + { + return this.showConsensusHistogram; + } + + /** + * synthesize a column selection if none exists so it covers the given + * selection group. if wholewidth is false, no column selection is made if the + * selection group covers the whole alignment width. + * + * @param sg + * @param wholewidth + */ + public void expandColSelection(SequenceGroup sg, boolean wholewidth) + { + int sgs, sge; + if (sg != null + && (sgs = sg.getStartRes()) >= 0 + && sg.getStartRes() <= (sge = sg.getEndRes()) + && (colSel == null || colSel.getSelected() == null || colSel + .getSelected().size() == 0)) + { + if (!wholewidth && alignment.getWidth() == (1 + sge - sgs)) + { + // do nothing + return; + } + if (colSel == null) + { + colSel = new ColumnSelection(); + } + for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++) + { + colSel.addElement(cspos); + } + } } }