X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=6cec30a2bd7db21e3e06b4c967b466fc7b7bb43a;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=eb45fa4040094ece4fd42a66a90c9a7ba73da6bb;hpb=63a18b71aa3ed6503b6fbb8ec3543b5d66ed3f70;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index eb45fa4..6cec30a 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -1,28 +1,30 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * 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 . + * 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.viewmodel; -import jalview.analysis.AAFrequency; import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeaturesDisplayedI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; @@ -33,7 +35,6 @@ import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.Blosum62ColourScheme; -import jalview.schemes.ClustalxColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.PIDColourScheme; import jalview.schemes.ResidueProperties; @@ -212,15 +213,18 @@ public abstract class AlignmentViewport implements AlignViewportI // calculation till later or to do all calculations in thread. // via changecolour globalColourScheme = cs; - boolean recalc=false; - if (cs!=null) + boolean recalc = false; + if (cs != null) { cs.setConservationApplied(recalc = getConservationSelected()); - if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme) + if (getAbovePIDThreshold() || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) { recalc = true; cs.setThreshold(threshold, ignoreGapsInConsensusCalculation); - } else { + } + else + { cs.setThreshold(0, ignoreGapsInConsensusCalculation); } if (recalc) @@ -245,7 +249,7 @@ public abstract class AlignmentViewport implements AlignViewportI || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, getIgnoreGapsConsensus()); - recalc=true; + recalc = true; } else { @@ -255,16 +259,19 @@ public abstract class AlignmentViewport implements AlignViewportI if (getConservationSelected()) { sg.cs.setConservationApplied(true); - recalc=true; + recalc = true; } else { sg.cs.setConservation(null); // sg.cs.setThreshold(0, getIgnoreGapsConsensus()); } - if (recalc) { + if (recalc) + { sg.recalcConservation(); - } else { + } + else + { sg.cs.alignmentChanged(sg, hiddenRepSequences); } } @@ -300,13 +307,15 @@ public abstract class AlignmentViewport implements AlignViewportI * view */ protected Hashtable[] hStrucConsensus = null; - + protected Conservation hconservation = null; + @Override public void setConservation(Conservation cons) { hconservation = cons; } + /** * percentage gaps allowed in a column before all amino acid properties should * be considered unconserved @@ -437,7 +446,9 @@ public abstract class AlignmentViewport implements AlignViewportI AlignmentAnnotation alignmentAnnotation) { if (!alignmentAnnotation.autoCalculated) + { return false; + } if (calculator.workingInvolvedWith(alignmentAnnotation)) { // System.err.println("grey out ("+alignmentAnnotation.label+")"); @@ -626,10 +637,6 @@ public abstract class AlignmentViewport implements AlignViewportI public void setHiddenColumns(ColumnSelection colsel) { this.colSel = colsel; - if (colSel.getHiddenColumns() != null) - { - hasHiddenColumns = true; - } } @Override @@ -638,9 +645,14 @@ public abstract class AlignmentViewport implements AlignViewportI return colSel; } + @Override public void setColumnSelection(ColumnSelection colSel) { this.colSel = colSel; + if (colSel != null) + { + updateHiddenColumns(); + } } /** @@ -660,15 +672,22 @@ public abstract class AlignmentViewport implements AlignViewportI this.hiddenRepSequences = hiddenRepSequences; } - protected boolean hasHiddenColumns = false; + @Override + public boolean hasHiddenColumns() + { + return colSel != null && colSel.hasHiddenColumns(); + } public void updateHiddenColumns() { - hasHiddenColumns = colSel.getHiddenColumns() != null; + // this method doesn't really do anything now. But - it could, since a + // column Selection could be in the process of modification + // hasHiddenColumns = colSel.hasHiddenColumns(); } protected boolean hasHiddenRows = false; + @Override public boolean hasHiddenRows() { return hasHiddenRows; @@ -686,6 +705,7 @@ public abstract class AlignmentViewport implements AlignViewportI sequenceSetID = new String(newid); } + @Override public String getSequenceSetId() { if (sequenceSetID == null) @@ -847,7 +867,6 @@ public abstract class AlignmentViewport implements AlignViewportI colSel.hideSelectedColumns(); setSelectionGroup(null); - hasHiddenColumns = true; } public void hideColumns(int start, int end) @@ -860,23 +879,17 @@ public abstract class AlignmentViewport implements AlignViewportI { colSel.hideColumns(start, end); } - - hasHiddenColumns = true; } public void showColumn(int col) { colSel.revealHiddenColumns(col); - if (colSel.getHiddenColumns() == null) - { - hasHiddenColumns = false; - } + } public void showAllHiddenColumns() { colSel.revealAllHiddenColumns(); - hasHiddenColumns = false; } // common hide/show seq stuff @@ -889,11 +902,12 @@ public abstract class AlignmentViewport implements AlignViewportI selectionGroup = new SequenceGroup(); selectionGroup.setEndRes(alignment.getWidth() - 1); } - Vector tmp = alignment.getHiddenSequences().showAll( + List tmp = alignment.getHiddenSequences().showAll( hiddenRepSequences); - for (int t = 0; t < tmp.size(); t++) + for (SequenceI seq : tmp) { - selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + selectionGroup.addSequence(seq, false); + setSequenceAnnotationsVisible(seq, true); } hasHiddenRows = false; @@ -908,7 +922,8 @@ public abstract class AlignmentViewport implements AlignViewportI public void showSequence(int index) { - Vector tmp = alignment.getHiddenSequences().showSequence(index, + List tmp = alignment.getHiddenSequences().showSequence( + index, hiddenRepSequences); if (tmp.size() > 0) { @@ -918,9 +933,10 @@ public abstract class AlignmentViewport implements AlignViewportI selectionGroup.setEndRes(alignment.getWidth() - 1); } - for (int t = 0; t < tmp.size(); t++) + for (SequenceI seq : tmp) { - selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + selectionGroup.addSequence(seq, false); + setSequenceAnnotationsVisible(seq, true); } // JBPNote: refactor: only update flag if we modified visiblity (used to // do this regardless) @@ -954,12 +970,30 @@ public abstract class AlignmentViewport implements AlignViewportI for (int i = 0; i < seq.length; i++) { alignment.getHiddenSequences().hideSequence(seq[i]); + setSequenceAnnotationsVisible(seq[i], false); } hasHiddenRows = true; firePropertyChange("alignment", null, alignment.getSequences()); } } + /** + * Set visibility for any annotations for the given sequence. + * + * @param sequenceI + */ + protected void setSequenceAnnotationsVisible(SequenceI sequenceI, + boolean visible) + { + for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation()) + { + if (ann.sequenceRef == sequenceI) + { + ann.visible = visible; + } + } + } + public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) { int sSize = sg.getSize(); @@ -1008,32 +1042,24 @@ public abstract class AlignmentViewport implements AlignViewportI : hiddenRepSequences.get(seq)); } + @Override public int adjustForHiddenSeqs(int alignmentIndex) { return alignment.getHiddenSequences().adjustForHiddenSeqs( alignmentIndex); } - // Selection manipulation - /** - * broadcast selection to any interested parties - */ + @Override public abstract void sendSelection(); + @Override public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth()); } - /** - * 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 - */ + + @Override public SequenceI[] getSelectionAsNewSequence() { SequenceI[] sequences; @@ -1062,12 +1088,7 @@ public abstract class AlignmentViewport implements AlignViewportI return sequences; } - /** - * get the currently selected sequence objects or all the sequences in the - * alignment. - * - * @return array of references to sequence objects - */ + @Override public SequenceI[] getSequenceSelection() { @@ -1083,31 +1104,16 @@ public abstract class AlignmentViewport implements AlignViewportI 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[] - */ + @Override public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { - return new jalview.datamodel.CigarArray(alignment, - (hasHiddenColumns ? colSel : null), + return new jalview.datamodel.CigarArray(alignment, colSel, (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 - */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) @@ -1115,34 +1121,17 @@ public abstract class AlignmentViewport implements AlignViewportI 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 - */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly, boolean markGroups) { return new AlignmentView(alignment, colSel, selectionGroup, - hasHiddenColumns, selectedOnly, markGroups); + colSel != null && colSel.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[] - */ + @Override public String[] getViewAsString(boolean selectedRegionOnly) { @@ -1165,7 +1154,7 @@ public abstract class AlignmentViewport implements AlignViewportI } selection = new String[iSize]; - if (hasHiddenColumns) + if (colSel != null && colSel.hasHiddenColumns()) { selection = colSel.getVisibleSequenceStrings(start, end, seqs); } @@ -1180,15 +1169,8 @@ public abstract class AlignmentViewport implements AlignViewportI return selection; } - /** - * return visible region boundaries within given column range - * - * @param min - * first column (inclusive, from 0) - * @param max - * last column (exclusive) - * @return int[][] range of {start,end} visible positions - */ + + @Override public int[][] getVisibleRegionBoundaries(int min, int max) { Vector regions = new Vector(); @@ -1197,7 +1179,7 @@ public abstract class AlignmentViewport implements AlignViewportI do { - if (hasHiddenColumns) + if (colSel != null && colSel.hasHiddenColumns()) { if (start == 0) { @@ -1218,7 +1200,7 @@ public abstract class AlignmentViewport implements AlignViewportI regions.addElement(new int[] { start, end }); - if (hasHiddenColumns) + if (colSel != null && colSel.hasHiddenColumns()) { start = colSel.adjustForHiddenColumns(end); start = colSel.getHiddenBoundaryLeft(start) + 1; @@ -1233,18 +1215,37 @@ public abstract class AlignmentViewport implements AlignViewportI } - /** - * @return the padGaps - */ + @Override + public List getVisibleAlignmentAnnotation(boolean selectedOnly) + { + ArrayList ala = new ArrayList(); + AlignmentAnnotation[] aa; + if ((aa=alignment.getAlignmentAnnotation())!=null) + { + for (AlignmentAnnotation annot:aa) + { + AlignmentAnnotation clone = new AlignmentAnnotation(annot); + if (selectedOnly && selectionGroup!=null) + { + colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone); + } else { + colSel.makeVisibleAnnotation(clone); + } + ala.add(clone); + } + } + return ala; + } + + + @Override public boolean isPadGaps() { return padGaps; } - /** - * @param padGaps - * the padGaps to set - */ + + @Override public void setPadGaps(boolean padGaps) { this.padGaps = padGaps; @@ -1256,6 +1257,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @param ap */ + @Override public void alignmentChanged(AlignmentViewPanel ap) { if (isPadGaps()) @@ -1371,15 +1373,15 @@ public abstract class AlignmentViewport implements AlignViewportI { conservation = new AlignmentAnnotation("Conservation", "Conservation of total alignment less than " - + getConsPercGaps() + "% gaps", - new Annotation[1], 0f, 11f, - AlignmentAnnotation.BAR_GRAPH); + + getConsPercGaps() + "% gaps", new Annotation[1], + 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; alignment.addAnnotation(conservation); } } } + private void initQuality() { if (showQuality) @@ -1388,21 +1390,20 @@ public abstract class AlignmentViewport implements AlignViewportI { quality = new AlignmentAnnotation("Quality", "Alignment Quality based on Blosum62 scores", - new Annotation[1], 0f, 11f, - AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); quality.hasText = true; quality.autoCalculated = true; alignment.addAnnotation(quality); } } } + private void initRNAStructure() { - if (alignment.hasRNAStructure() && strucConsensus==null) + if (alignment.hasRNAStructure() && strucConsensus == null) { strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); strucConsensus.hasText = true; strucConsensus.autoCalculated = true; @@ -1412,11 +1413,13 @@ public abstract class AlignmentViewport implements AlignViewportI } } } + /* * (non-Javadoc) * * @see jalview.api.AlignViewportI#calcPanelHeight() */ + @Override public int calcPanelHeight() { // setHeight of panels @@ -1512,7 +1515,7 @@ public abstract class AlignmentViewport implements AlignViewportI if (aan[an].autoCalculated && aan[an].groupRef != null) { oldrfs.add(aan[an].groupRef); - alignment.deleteAnnotation(aan[an],false); + alignment.deleteAnnotation(aan[an], false); } } } @@ -1557,11 +1560,13 @@ public abstract class AlignmentViewport implements AlignViewportI */ private boolean colourByReferenceSeq=false; + @Override public boolean isDisplayReferenceSeq() { return alignment.hasSeqrep() && displayReferenceSeq; } + @Override public void setDisplayReferenceSeq(boolean displayReferenceSeq) { this.displayReferenceSeq = displayReferenceSeq; @@ -1580,11 +1585,12 @@ public abstract class AlignmentViewport implements AlignViewportI @Override public Color getSequenceColour(SequenceI seq) { - Color sqc=Color.white; + Color sqc = Color.white; if (sequenceColours != null) { sqc = (Color) sequenceColours.get(seq); - if (sqc == null) { + if (sqc == null) + { sqc = Color.white; } } @@ -1633,4 +1639,90 @@ public abstract class AlignmentViewport implements AlignViewportI { sequenceColours = null; }; + + FeaturesDisplayedI featuresDisplayed = null; + + @Override + public FeaturesDisplayedI getFeaturesDisplayed() + { + return featuresDisplayed; + } + + @Override + public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) + { + featuresDisplayed = featuresDisplayedI; + } + + @Override + public boolean areFeaturesDisplayed() + { + return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0; + } + + /** + * display setting for showing/hiding sequence features on alignment view + */ + boolean showSequenceFeatures = false; + + /** + * set the flag + * + * @param b + * features are displayed if true + */ + @Override + public void setShowSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + @Override + public boolean isShowSequenceFeatures() + { + return showSequenceFeatures; + } + + boolean showSeqFeaturesHeight; + + @Override + public void setShowSequenceFeaturesHeight(boolean selected) + { + showSeqFeaturesHeight = selected; + } + + @Override + public boolean isShowSequenceFeaturesHeight() + { + return showSeqFeaturesHeight; + } + + private boolean showAnnotation = true; + + private boolean rightAlignIds = false; + + + @Override + public void setShowAnnotation(boolean b) + { + showAnnotation = b; + } + + @Override + public boolean isShowAnnotation() + { + return showAnnotation; + } + + @Override + public boolean isRightAlignIds() + { + return rightAlignIds; + } + + @Override + public void setRightAlignIds(boolean rightAlignIds) + { + this.rightAlignIds = rightAlignIds; + } + }