From: kiramt Date: Fri, 5 May 2017 09:50:22 +0000 (+0100) Subject: Merge remote-tracking branch 'origin/develop' into X-Git-Tag: Release_2_10_2~3^2~92^2~3^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3c75c089a56859ec8e7f674d7054e82af41e4b77;hp=-c;p=jalview.git Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges Conflicts: src/jalview/appletgui/TreePanel.java src/jalview/gui/AnnotationColumnChooser.java src/jalview/gui/PCAPanel.java src/jalview/gui/TreePanel.java --- 3c75c089a56859ec8e7f674d7054e82af41e4b77 diff --combined src/jalview/appletgui/AlignFrame.java index 681c777,cd1e1a9..23b8843 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@@ -22,6 -22,9 +22,9 @@@ package jalview.appletgui import jalview.analysis.AlignmentSorter; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; + import jalview.analysis.TreeBuilder; + import jalview.analysis.scoremodels.PIDModel; + import jalview.analysis.scoremodels.ScoreModels; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; @@@ -43,7 -46,6 +46,7 @@@ import jalview.datamodel.AlignmentAnnot import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; @@@ -170,14 -172,14 +173,14 @@@ public class AlignFrame extends Embmenu } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - ColumnSelection columnSelection, JalviewLite applet, + HiddenColumns hidden, JalviewLite applet, String title, boolean embedded) { - this(al, hiddenSeqs, columnSelection, applet, title, embedded, true); + this(al, hiddenSeqs, hidden, applet, title, embedded, true); } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - ColumnSelection columnSelection, JalviewLite applet, + HiddenColumns hidden, JalviewLite applet, String title, boolean embedded, boolean addToDisplay) { if (applet != null) @@@ -220,9 -222,9 +223,9 @@@ { viewport.hideSequence(hiddenSeqs); } - if (columnSelection != null) + if (hidden != null) { - viewport.setColumnSelection(columnSelection); + viewport.getAlignment().setHiddenColumns(hidden); } viewport.setScaleAboveWrapped(scaleAbove.getState()); @@@ -1925,8 -1927,7 +1928,8 @@@ { copiedHiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int[] region : viewport.getColumnSelection().getHiddenColumns()) + for (int[] region : viewport.getAlignment().getHiddenColumns() + .getListOfCols()) { copiedHiddenColumns.addElement(new int[] { region[0] - hiddenOffset, region[1] - hiddenOffset }); @@@ -2732,7 -2733,7 +2735,7 @@@ { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport - .getAlignment().getSequenceAt(0), null); + .getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); @@@ -2824,25 -2825,31 +2827,31 @@@ public void averageDistanceTreeMenuItem_actionPerformed() { - NewTreePanel("AV", "PID", "Average distance tree using PID"); + newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(), + "Average distance tree using PID"); } public void neighbourTreeMenuItem_actionPerformed() { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(), + "Neighbour joining tree using PID"); } protected void njTreeBlosumMenuItem_actionPerformed() { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance() + .getBlosum62().getName(), + "Neighbour joining tree using BLOSUM62"); } protected void avTreeBlosumMenuItem_actionPerformed() { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance() + .getBlosum62().getName(), + "Average distance tree using BLOSUM62"); } - void NewTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String pwType, String title) { // are the sequences aligned? if (!viewport.getAlignment().isAligned(false)) @@@ -4200,10 -4207,9 +4209,10 @@@ * @param csel * - columns to be selected on the alignment */ - public void select(SequenceGroup sel, ColumnSelection csel) + public void select(SequenceGroup sel, ColumnSelection csel, + HiddenColumns hidden) { - alignPanel.seqPanel.selection(sel, csel, null); + alignPanel.seqPanel.selection(sel, csel, hidden, null); } public void scrollTo(int row, int column) diff --combined src/jalview/appletgui/AlignViewport.java index 61621ae,afe57e0..c156c36 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@@ -20,14 -20,13 +20,14 @@@ */ package jalview.appletgui; - import jalview.analysis.NJTree; + import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.api.FeatureSettingsModelI; import jalview.bin.JalviewLite; import jalview.commands.CommandI; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; @@@ -53,7 -52,7 +53,7 @@@ public class AlignViewport extends Alig boolean validCharWidth = true; - NJTree currentTree = null; + TreeModel currentTree = null; public jalview.bin.JalviewLite applet; @@@ -304,12 -303,12 +304,12 @@@ ranges.setEndSeq(height / getCharHeight()); } - public void setCurrentTree(NJTree tree) + public void setCurrentTree(TreeModel tree) { currentTree = tree; } - public NJTree getCurrentTree() + public TreeModel getCurrentTree() { return currentTree; } @@@ -337,8 -336,7 +337,8 @@@ { getStructureSelectionManager().sendSelection( new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), this); } /** diff --combined src/jalview/appletgui/AnnotationColumnChooser.java index 2acb568,25ff293..cc16275 --- a/src/jalview/appletgui/AnnotationColumnChooser.java +++ b/src/jalview/appletgui/AnnotationColumnChooser.java @@@ -21,7 -21,7 +21,7 @@@ package jalview.appletgui; import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.schemes.AnnotationColourGradient; import jalview.util.MessageManager; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; @@@ -110,7 -110,7 +110,7 @@@ public class AnnotationColumnChooser ex private int actionOption = ACTION_OPTION_SELECT; - private ColumnSelection oldColumnSelection; + private HiddenColumns oldHiddenColumns; public AnnotationColumnChooser() { @@@ -140,7 -140,7 +140,7 @@@ { return; } - setOldColumnSelection(av.getColumnSelection()); + setOldHiddenColumns(av.getAlignment().getHiddenColumns()); adjusting = true; Vector list = new Vector(); int index = 1; @@@ -289,26 -289,26 +289,26 @@@ @SuppressWarnings("unchecked") public void reset() { - if (this.getOldColumnSelection() != null) + if (this.getOldHiddenColumns() != null) { av.getColumnSelection().clear(); if (av.getAnnotationColumnSelectionState() != null) { - ColumnSelection oldSelection = av + HiddenColumns oldHidden = av .getAnnotationColumnSelectionState() - .getOldColumnSelection(); - if (oldSelection != null && oldSelection.getHiddenColumns() != null - && !oldSelection.getHiddenColumns().isEmpty()) + .getOldHiddenColumns(); + if (oldHidden != null && oldHidden.getListOfCols() != null + && !oldHidden.getListOfCols().isEmpty()) { - for (Iterator itr = oldSelection.getHiddenColumns() + for (Iterator itr = oldHidden.getListOfCols() .iterator(); itr.hasNext();) { int positions[] = itr.next(); av.hideColumns(positions[0], positions[1]); } } - av.setColumnSelection(oldSelection); + av.getAlignment().setHiddenColumns(oldHidden); } ap.paintAlignment(true); } @@@ -444,7 -444,7 +444,7 @@@ // build filter params filterParams .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); - if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH) + if (getCurrentAnnotation().isQuantitative()) { filterParams .setThresholdValue(getCurrentAnnotation().threshold.value); @@@ -518,16 -518,16 +518,16 @@@ ap.paintAlignment(true); } - public ColumnSelection getOldColumnSelection() + public HiddenColumns getOldHiddenColumns() { - return oldColumnSelection; + return oldHiddenColumns; } - public void setOldColumnSelection(ColumnSelection currentColumnSelection) + public void setOldHiddenColumns(HiddenColumns currentHiddenColumns) { - if (currentColumnSelection != null) + if (currentHiddenColumns != null) { - this.oldColumnSelection = new ColumnSelection(currentColumnSelection); + this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns); } } @@@ -598,7 -598,7 +598,7 @@@ { String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW; if (av.getAlignment().getAlignmentAnnotation()[getAnnotations() - .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH) + .getSelectedIndex()].isQuantitative()) { currentView = AnnotationColumnChooser.GRAPH_VIEW; } diff --combined src/jalview/appletgui/PCAPanel.java index 2ef7d10,2d77c59..5dc57f9 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@@ -20,9 -20,12 +20,12 @@@ */ package jalview.appletgui; + import jalview.analysis.scoremodels.ScoreModels; + import jalview.analysis.scoremodels.SimilarityParams; + import jalview.api.analysis.ScoreModelI; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentView; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SeqCigar; import jalview.datamodel.SequenceI; import jalview.util.MessageManager; @@@ -56,7 -59,7 +59,7 @@@ public class PCAPanel extends EmbmenuFr int top = 0; - public PCAPanel(AlignViewport av) + public PCAPanel(AlignViewport viewport) { try { @@@ -73,19 -76,19 +76,19 @@@ zCombobox.addItem("dim " + i); } - this.av = av; - boolean selected = av.getSelectionGroup() != null - && av.getSelectionGroup().getSize() > 0; - AlignmentView seqstrings = av.getAlignmentView(selected); - boolean nucleotide = av.getAlignment().isNucleotide(); + this.av = viewport; + boolean selected = viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 0; + AlignmentView seqstrings = viewport.getAlignmentView(selected); + boolean nucleotide = viewport.getAlignment().isNucleotide(); SequenceI[] seqs; if (!selected) { - seqs = av.getAlignment().getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } else { - seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); + seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.getAlignment()); } SeqCigar sq[] = seqstrings.getSequences(); int length = sq[0].getWidth(); @@@ -99,9 -102,13 +102,13 @@@ return; } } - pcaModel = new PCAModel(seqstrings, seqs, nucleotide); - rc = new RotatableCanvas(av); + ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel( + !nucleotide); + pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, + SimilarityParams.SeqSpace); + + rc = new RotatableCanvas(viewport); embedMenuIfNeeded(rc); add(rc, BorderLayout.CENTER); @@@ -209,6 -216,9 +216,9 @@@ if (!pcaModel.isNucleotide()) { pcaModel.setNucleotide(true); + ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel( + false); + pcaModel.setScoreModel(scoreModel); new Thread(this).start(); } } @@@ -217,6 -227,9 +227,9 @@@ if (pcaModel.isNucleotide()) { pcaModel.setNucleotide(false); + ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel( + true); + pcaModel.setScoreModel(scoreModel); new Thread(this).start(); } } @@@ -268,7 -281,7 +281,7 @@@ } ; Object[] alAndColsel = pcaModel.getSeqtrings() - .getAlignmentAndColumnSelection(gc); + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@@ -276,8 -289,7 +289,8 @@@ AlignFrame af = new AlignFrame(al, av.applet, "Original Data for PCA", false); - af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]); + af.viewport.getAlignment().setHiddenColumns( + (HiddenColumns) alAndColsel[1]); } } diff --combined src/jalview/appletgui/SeqPanel.java index 69a0dd0,60c53dd..a40e73c --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@@ -25,7 -25,6 +25,7 @@@ import jalview.commands.EditCommand import jalview.commands.EditCommand.Action; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@@ -181,22 -180,19 +181,22 @@@ public class SeqPanel extends Panel imp seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; if (av.hasHiddenColumns() - && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + && !av.getAlignment().getHiddenColumns() + .isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) + while (!av.getAlignment().getHiddenColumns() + .isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + || !av.getAlignment().getHiddenColumns() + .isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@@ -232,7 -228,6 +232,7 @@@ else { ViewportRanges ranges = av.getRanges(); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); while (seqCanvas.cursorY < ranges.getStartSeq()) { ap.scrollUp(true); @@@ -241,8 -236,8 +241,8 @@@ { ap.scrollUp(false); } - while (seqCanvas.cursorX < av.getColumnSelection() - .adjustForHiddenColumns(ranges.getStartRes())) + while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges + .getStartRes())) { if (!ap.scrollRight(false)) @@@ -250,8 -245,8 +250,8 @@@ break; } } - while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(ranges.getEndRes())) + while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges + .getEndRes())) { if (!ap.scrollRight(true)) { @@@ -575,7 -570,7 +575,7 @@@ if (features != null && features.length > 0) { seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, features, false, ap); + new SequenceI[] { sequence }, features, false, ap, null); seqCanvas.highlightSearchResults(null); } @@@ -643,8 -638,7 +643,8 @@@ if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(res); } return res; @@@ -1137,10 -1131,8 +1137,10 @@@ if (av.hasHiddenColumns()) { fixedColumns = true; - int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); - int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + int y1 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryLeft(startres); + int y2 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryRight(startres); if ((insertGap && startres > y1 && lastres < y1) || (!insertGap && startres < y2 && lastres > y2)) @@@ -1211,8 -1203,8 +1211,8 @@@ { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av - .getColumnSelection().getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() && startres < av.getAlignment() + .getHiddenColumns().getHiddenBoundaryRight(startres))) { endEditing(); return; @@@ -1795,7 -1787,7 +1795,7 @@@ */ @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, - SelectionSource source) + HiddenColumns hidden, SelectionSource source) { // TODO: fix this hack - source of messages is align viewport, but SeqPanel // handles selection messages... @@@ -1812,7 -1804,7 +1812,7 @@@ * Check for selection in a view of which this one is a dna/protein * complement. */ - if (selectionFromTranslation(seqsel, colsel, source)) + if (selectionFromTranslation(seqsel, colsel, hidden, source)) { return; } @@@ -1878,16 -1870,15 +1878,16 @@@ } else { - av.getColumnSelection().setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel, + av.getAlignment().getHiddenColumns()); } } repaint |= av.isColSelChanged(true); } if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection() - .getHiddenColumns() == null)) + && (av.getColumnSelection() == null || av.getAlignment() + .getHiddenColumns().getListOfCols() == null)) { System.err.println("Bad things"); } @@@ -1947,8 -1938,7 +1947,8 @@@ * @param source */ protected boolean selectionFromTranslation(SequenceGroup seqsel, - ColumnSelection colsel, SelectionSource source) + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { if (!(source instanceof AlignViewportI)) { @@@ -1971,13 -1961,9 +1971,13 @@@ /* * Map column selection */ - ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, - av); + // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, + // av); + ColumnSelection cs = new ColumnSelection(); + HiddenColumns hs = new HiddenColumns(); + MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs); av.setColumnSelection(cs); + av.getAlignment().setHiddenColumns(hs); ap.scalePanelHolder.repaint(); ap.repaint(); diff --combined src/jalview/appletgui/TreePanel.java index 23b23be,8b1f79c..c7bf6aa --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@@ -20,15 -20,17 +20,17 @@@ */ package jalview.appletgui; + import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; + import jalview.analysis.TreeBuilder; + import jalview.analysis.TreeModel; + import jalview.analysis.scoremodels.ScoreModels; + import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; - import jalview.api.analysis.ViewBasedAnalysisI; import jalview.datamodel.Alignment; - import jalview.datamodel.AlignmentView; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.io.NewickFile; - import jalview.schemes.ResidueProperties; import jalview.util.MessageManager; import java.awt.BorderLayout; @@@ -58,13 -60,13 +60,13 @@@ public class TreePanel extends EmbmenuF TreeCanvas treeCanvas; - NJTree tree; + TreeModel tree; AlignmentPanel ap; AlignViewport av; - public NJTree getTree() + public TreeModel getTree() { return tree; } @@@ -79,21 -81,8 +81,8 @@@ /** * Creates a new TreePanel object. - * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! - * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - * @param s - * DOCUMENT ME! - * @param e - * DOCUMENT ME! */ - public TreePanel(AlignmentPanel ap, String type, String pwtype) + public TreePanel(AlignmentPanel alignPanel, String type, String pwtype) { try { @@@ -104,22 -93,12 +93,12 @@@ ex.printStackTrace(); } - initTreePanel(ap, type, pwtype, null); + initTreePanel(alignPanel, type, pwtype, null); } /** * Creates a new TreePanel object. * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! - * @param newtree - * DOCUMENT ME! - * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! */ public TreePanel(AlignmentPanel ap, String type, String pwtype, NewickFile newtree) @@@ -160,7 -139,7 +139,7 @@@ // yields unaligned seqs) // or create a selection box around columns in alignment view // test Alignment(SeqCigar[]) - if (tree.seqData != null) + if (tree.getOriginalData() != null) { char gc = '-'; try @@@ -171,9 -150,9 +150,9 @@@ } catch (Exception ex) { } - ; - Object[] alAndColsel = tree.seqData + + Object[] alAndColsel = tree.getOriginalData() - .getAlignmentAndColumnSelection(gc); + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@@ -181,8 -160,7 +160,8 @@@ AlignFrame af = new AlignFrame(al, av.applet, "Original Data for Tree", false); - af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]); + af.viewport.getAlignment().setHiddenColumns( + (HiddenColumns) alAndColsel[1]); } } else @@@ -207,58 -185,18 +186,18 @@@ { if (newtree != null) { - if (odata == null) - { - tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); - } - else - { - tree = new NJTree(av.getAlignment().getSequencesArray(), odata, - newtree); - } - + tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, + newtree); } else { - int start, end; - SequenceI[] seqs; - boolean selview = av.getSelectionGroup() != null - && av.getSelectionGroup().getSize() > 1; - AlignmentView seqStrings = av.getAlignmentView(selview); - if (!selview) - { - start = 0; - end = av.getAlignment().getWidth(); - seqs = av.getAlignment().getSequencesArray(); - } - else - { - start = av.getSelectionGroup().getStartRes(); - end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder( - av.getAlignment()); - } - ScoreModelI sm = ResidueProperties.getScoreModel(pwtype); - if (sm instanceof ViewBasedAnalysisI) - { - try - { - sm = sm.getClass().newInstance(); - ((ViewBasedAnalysisI) sm) - .configureFromAlignmentView(treeCanvas.ap); - } catch (Exception q) - { - System.err.println("Couldn't create a scoremodel instance for " - + sm.getName()); - q.printStackTrace(); - } - tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end); - } - else - { - tree = new NJTree(seqs, seqStrings, type, pwtype, null, start, - end); - } + ScoreModelI sm1 = ScoreModels.getInstance().getScoreModel(pwtype, + treeCanvas.ap); + ScoreModelI sm = sm1; + TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree( + av, sm, SimilarityParams.Jalview) + : new AverageDistanceTree(av, sm, SimilarityParams.Jalview); + tree = new TreeModel(njtree); } tree.reCount(tree.getTopNode()); diff --combined src/jalview/datamodel/AlignmentAnnotation.java index e8dbeee,543958e..1594f2b --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@@ -20,10 -20,6 +20,10 @@@ */ package jalview.datamodel; +import jalview.analysis.Rna; +import jalview.analysis.SecStrConsensus.SimpleBP; +import jalview.analysis.WUSSParseException; + import java.util.Collection; import java.util.Collections; import java.util.HashMap; @@@ -32,6 -28,10 +32,6 @@@ import java.util.List import java.util.Map; import java.util.Map.Entry; -import jalview.analysis.Rna; -import jalview.analysis.SecStrConsensus.SimpleBP; -import jalview.analysis.WUSSParseException; - /** * DOCUMENT ME! * @@@ -1150,14 -1150,14 +1150,14 @@@ public class AlignmentAnnotatio * @param colSel */ public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation, - ColumnSelection colSel) + HiddenColumns hidden) { this(alignmentAnnotation); if (annotations == null) { return; } - colSel.makeVisibleAnnotation(this); + hidden.makeVisibleAnnotation(this); } public void setPadGaps(boolean padgaps, char gapchar) @@@ -1494,4 -1494,13 +1494,13 @@@ { return counter++; } + + /** + * + * @return true for rows that have a range of values in their annotation set + */ + public boolean isQuantitative() + { + return graphMin < graphMax; + } } diff --combined src/jalview/gui/AlignFrame.java index 9cb9804,8eb09ab..ca37196 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@@ -34,7 -34,7 +34,7 @@@ import jalview.api.AlignmentViewPanel import jalview.api.FeatureSettingsControllerI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; - import jalview.api.analysis.ScoreModelI; + import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.commands.CommandI; @@@ -53,7 -53,6 +53,7 @@@ import jalview.datamodel.AlignmentI import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; @@@ -70,6 -69,7 +70,7 @@@ import jalview.io.FileFormat import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FileLoader; + import jalview.io.FileParse; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; @@@ -78,12 -78,12 +79,12 @@@ import jalview.io.JalviewFileChooser import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; + import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; import jalview.jbgui.GAlignFrame; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; - import jalview.schemes.ResidueProperties; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@@ -233,7 -233,7 +234,7 @@@ public class AlignFrame extends GAlignF * @param height * height of frame. */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height) { this(al, hiddenColumns, width, height, null); @@@ -250,7 -250,7 +251,7 @@@ * @param sequenceSetId * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height, String sequenceSetId) { this(al, hiddenColumns, width, height, sequenceSetId, null); @@@ -269,7 -269,7 +270,7 @@@ * @param viewId * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height, String sequenceSetId, String viewId) { setSize(width, height); @@@ -288,7 -288,7 +289,7 @@@ } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - ColumnSelection hiddenColumns, int width, int height) + HiddenColumns hiddenColumns, int width, int height) { setSize(width, height); @@@ -365,7 -365,15 +366,15 @@@ setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); - buildTreeMenu(); + calculateTree.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + openTreePcaDialog(); + } + }); buildColourMenu(); if (Desktop.desktop != null) @@@ -1184,8 -1192,8 +1193,8 @@@ exportData.getAlignment(), // class cast exceptions will // occur in the distant future exportData.getOmitHidden(), exportData.getStartEndPostions(), - f.getCacheSuffixDefault(format), - viewport.getColumnSelection()); + f.getCacheSuffixDefault(format), viewport.getAlignment() + .getHiddenColumns()); if (output == null) { @@@ -1263,9 -1271,8 +1272,9 @@@ cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getColumnSelection())); + exportData + .getStartEndPostions(), viewport + .getAlignment().getHiddenColumns())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); @@@ -1314,9 -1321,8 +1323,9 @@@ alignmentToExport = viewport.getAlignment(); } alignmentStartEnd = alignmentToExport - .getVisibleStartAndEndIndex(viewport.getColumnSelection() - .getHiddenColumns()); + .getVisibleStartAndEndIndex(viewport.getAlignment() + .getHiddenColumns() + .getListOfCols()); AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; @@@ -1880,8 -1886,7 +1889,8 @@@ hiddenColumns = new ArrayList(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport .getSelectionGroup().getEndRes(); - for (int[] region : viewport.getColumnSelection().getHiddenColumns()) + for (int[] region : viewport.getAlignment().getHiddenColumns() + .getListOfCols()) { if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { @@@ -3446,7 -3451,7 +3455,7 @@@ { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport - .getAlignment().getSequenceAt(0), null); + .getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true); @@@ -3540,35 -3545,6 +3549,6 @@@ } } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void PCAMenuItem_actionPerformed(ActionEvent e) - { - if (((viewport.getSelectionGroup() != null) - && (viewport.getSelectionGroup().getSize() < 4) && (viewport - .getSelectionGroup().getSize() > 0)) - || (viewport.getAlignment().getHeight() < 4)) - { - JvOptionPane - .showInternalMessageDialog( - this, - MessageManager - .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), - MessageManager - .getString("label.sequence_selection_insufficient"), - JvOptionPane.WARNING_MESSAGE); - - return; - } - - new PCAPanel(alignPanel); - } - @Override public void autoCalculate_actionPerformed(ActionEvent e) { @@@ -3593,67 -3569,21 +3573,21 @@@ } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("AV", "PID", "Average distance tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - newTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! + * Constructs a tree panel and adds it to the desktop * * @param type - * DOCUMENT ME! - * @param pwType - * DOCUMENT ME! - * @param title - * DOCUMENT ME! + * tree type (NJ or AV) + * @param modelName + * name of score model used to compute the tree + * @param options + * parameters for the distance or similarity calculation */ - void newTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String modelName, SimilarityParamsI options) { + String frameTitle = ""; TreePanel tp; + boolean onSelection = false; if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 0) { @@@ -3689,45 -3619,29 +3623,29 @@@ return; } } - - title = title + " on region"; - tp = new TreePanel(alignPanel, type, pwType); + onSelection = true; } else { - // are the visible sequences aligned? - if (!viewport.getAlignment().isAligned(false)) - { - JvOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.sequences_must_be_aligned_before_creating_tree"), - MessageManager - .getString("label.sequences_not_aligned"), - JvOptionPane.WARNING_MESSAGE); - - return; - } - if (viewport.getAlignment().getHeight() < 2) { return; } - - tp = new TreePanel(alignPanel, type, pwType); } - title += " from "; + tp = new TreePanel(alignPanel, type, modelName, options); + frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : ""); + + frameTitle += " from "; if (viewport.viewName != null) { - title += viewport.viewName + " of "; + frameTitle += viewport.viewName + " of "; } - title += this.title; + frameTitle += this.title; - Desktop.addInternalFrame(tp, title, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, 600, 500); } /** @@@ -3849,48 -3763,10 +3767,10 @@@ * call. Listeners are added to remove the menu item when the treePanel is * closed, and adjust the tree leaf to sequence mapping when the alignment is * modified. - * - * @param treePanel - * Displayed tree window. - * @param title - * SortBy menu item title. */ @Override - public void buildTreeMenu() + public void buildTreeSortMenu() { - calculateTree.removeAll(); - // build the calculate menu - - for (final String type : new String[] { "NJ", "AV" }) - { - String treecalcnm = MessageManager.getString("label.tree_calc_" - + type.toLowerCase()); - for (final String pwtype : ResidueProperties.scoreMatrices.keySet()) - { - JMenuItem tm = new JMenuItem(); - ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); - if (sm.isDNA() == viewport.getAlignment().isNucleotide() - || sm.isProtein() == !viewport.getAlignment() - .isNucleotide()) - { - String smn = MessageManager.getStringOrReturn( - "label.score_model_", sm.getName()); - final String title = MessageManager.formatMessage( - "label.treecalc_title", treecalcnm, smn); - tm.setText(title);// - tm.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - newTreePanel(type, pwtype, title); - } - }); - calculateTree.add(tm); - } - - } - } sortByTreeMenu.removeAll(); List comps = PaintRefresher.components.get(viewport @@@ -4041,13 -3917,13 +3921,13 @@@ if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - jalview.io.NewickFile fin = null; + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; try { - fin = new NewickFile(choice, DataSourceType.FILE); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); + fin = new NewickFile(filePath, DataSourceType.FILE); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); } catch (Exception ex) { JvOptionPane @@@ -4069,25 -3945,19 +3949,19 @@@ } } - public TreePanel ShowNewickTree(NewickFile nf, String title) - { - return ShowNewickTree(nf, title, 600, 500, 4, 5); - } - - public TreePanel ShowNewickTree(NewickFile nf, String title, - AlignmentView input) + public TreePanel showNewickTree(NewickFile nf, String treeTitle) { - return ShowNewickTree(nf, title, input, 600, 500, 4, 5); + return showNewickTree(nf, treeTitle, 600, 500, 4, 5); } - public TreePanel ShowNewickTree(NewickFile nf, String title, int w, + public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w, int h, int x, int y) { - return ShowNewickTree(nf, title, null, w, h, x, y); + return showNewickTree(nf, treeTitle, null, w, h, x, y); } /** - * Add a treeviewer for the tree extracted from a newick file object to the + * Add a treeviewer for the tree extracted from a Newick file object to the * current alignment view * * @param nf @@@ -4106,7 -3976,7 +3980,7 @@@ * position * @return TreePanel handle */ - public TreePanel ShowNewickTree(NewickFile nf, String title, + public TreePanel showNewickTree(NewickFile nf, String treeTitle, AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; @@@ -4117,7 -3987,7 +3991,7 @@@ if (nf.getTree() != null) { - tp = new TreePanel(alignPanel, "FromFile", title, nf, input); + tp = new TreePanel(alignPanel, nf, treeTitle, input); tp.setSize(w, h); @@@ -4126,7 -3996,7 +4000,7 @@@ tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, title, w, h); + Desktop.addInternalFrame(tp, treeTitle, w, h); } } catch (Exception ex) { @@@ -4699,10 -4569,13 +4573,13 @@@ } /** - * Attempt to load a "dropped" file or URL string: First by testing whether - * it's an Annotation file, then a JNet file, and finally a features file. If - * all are false then the user may have dropped an alignment file onto this - * AlignFrame. + * Attempt to load a "dropped" file or URL string, by testing in turn for + *
    + *
  • an Annotation file
    • + *
  • a JNet file
    • + *
  • a features file
    • + *
  • else try to interpret as an alignment file
    • + *
* * @param file * either a filename or a URL string. @@@ -4776,7 -4649,18 +4653,18 @@@ { format = new IdentifyFile().identify(file, sourceType); } - if (FileFormat.Jnet.equals(format)) + if (FileFormat.ScoreMatrix == format) + { + ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file, + sourceType)); + sm.parse(); + // todo: i18n this message + statusBar + .setText(MessageManager.formatMessage( + "label.successfully_loaded_matrix", + sm.getMatrixName())); + } + else if (FileFormat.Jnet.equals(format)) { JPredFile predictions = new JPredFile(file, sourceType); new JnetAnnotationMaker(); @@@ -4784,9 -4668,9 +4672,9 @@@ viewport.getAlignment(), 0, false); SequenceI repseq = viewport.getAlignment().getSequenceAt(0); viewport.getAlignment().setSeqrep(repseq); - ColumnSelection cs = new ColumnSelection(); + HiddenColumns cs = new HiddenColumns(); cs.hideInsertionsFor(repseq); - viewport.setColumnSelection(cs); + viewport.getAlignment().setHiddenColumns(cs); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) @@@ -5711,6 -5595,18 +5599,18 @@@ ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); ColourMenuHelper.setColourSelected(colourMenu, colourScheme); } + + /** + * Open a dialog (if not already open) that allows the user to select and + * calculate PCA or Tree analysis + */ + protected void openTreePcaDialog() + { + if (alignPanel.getCalculationDialog() == null) + { + new CalculationChooser(AlignFrame.this); + } + } } class PrintThread extends Thread diff --combined src/jalview/gui/AlignViewport.java index 73f81bc,f22a911..1c53b61 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@@ -22,7 -22,7 +22,7 @@@ package jalview.gui import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; - import jalview.analysis.NJTree; + import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; @@@ -35,7 -35,6 +35,7 @@@ import jalview.datamodel.AlignedCodonFr import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@@ -77,7 -76,7 +77,7 @@@ public class AlignViewport extends Alig { Font font; - NJTree currentTree = null; + TreeModel currentTree = null; boolean cursorMode = false; @@@ -148,12 -147,12 +148,12 @@@ * @param hiddenColumns * ColumnSelection */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns) { setAlignment(al); if (hiddenColumns != null) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@@ -166,7 -165,7 +166,7 @@@ * @param seqsetid * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid) { this(al, hiddenColumns, seqsetid, null); @@@ -182,7 -181,7 +182,7 @@@ * @param viewid * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid, String viewid) { sequenceSetID = seqsetid; @@@ -200,7 -199,7 +200,7 @@@ setAlignment(al); if (hiddenColumns != null) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@@ -494,7 -493,7 +494,7 @@@ * @param tree * DOCUMENT ME! */ - public void setCurrentTree(NJTree tree) + public void setCurrentTree(TreeModel tree) { currentTree = tree; } @@@ -504,7 -503,7 +504,7 @@@ * * @return DOCUMENT ME! */ - public NJTree getCurrentTree() + public TreeModel getCurrentTree() { return currentTree; } @@@ -530,7 -529,7 +530,7 @@@ { end = alignment.getWidth(); } - viscontigs = colSel.getVisibleContigs(start, end); + viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end); return viscontigs; } @@@ -600,9 -599,7 +600,9 @@@ jalview.structure.StructureSelectionManager .getStructureSelectionManager(Desktop.instance).sendSelection( new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), + this); } /** diff --combined src/jalview/gui/AlignmentPanel.java index dc5f7cc,04de50b..885d79d --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@@ -25,7 -25,6 +25,7 @@@ import jalview.api.AlignViewportI import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@@ -107,6 -106,8 +107,8 @@@ public class AlignmentPanel extends GAl private PropertyChangeListener propertyChangeListener; + private CalculationChooser calculationDialog; + /** * Creates a new AlignmentPanel object. * @@@ -170,6 -171,11 +172,11 @@@ { av.alignmentChanged(this); + if (getCalculationDialog() != null) + { + getCalculationDialog().validateCalcTypes(); + } + alignFrame.updateEditMenuBar(); paintAlignment(true); @@@ -396,12 -402,11 +403,12 @@@ } if (av.hasHiddenColumns()) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + start = hidden.findColumnPosition(start); + end = hidden.findColumnPosition(end); if (start == end) { - if (!av.getColumnSelection().isVisible(r[0])) + if (!hidden.isVisible(r[0])) { // don't scroll - position isn't visible return false; @@@ -706,8 -711,7 +713,8 @@@ if (av.hasHiddenColumns()) { // reset the width to exclude hidden columns - width = av.getColumnSelection().findColumnPosition(width); + width = av.getAlignment().getHiddenColumns() + .findColumnPosition(width); } hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@@ -920,8 -924,7 +927,8 @@@ if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int canvasWidth = getSeqPanel().seqCanvas @@@ -1209,8 -1212,7 +1216,8 @@@ int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth @@@ -1404,8 -1406,7 +1411,8 @@@ int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); } int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) @@@ -1635,8 -1636,7 +1642,8 @@@ int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int height = ((maxwidth / chunkWidth) + 1) * cHeight; @@@ -1654,6 -1654,8 +1661,8 @@@ PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); + closeChildFrames(); + /* * try to ensure references are nulled */ @@@ -1685,6 -1687,17 +1694,17 @@@ } /** + * Close any open dialogs that would be orphaned when this one is closed + */ + protected void closeChildFrames() + { + if (calculationDialog != null) + { + calculationDialog.closeFrame(); + } + } + + /** * hides or shows dynamic annotation rows based on groups and av state flags */ public void updateAnnotation() @@@ -1913,4 -1926,24 +1933,24 @@@ repaint(); } } + + /** + * Set the reference to the PCA/Tree chooser dialog for this panel. This + * reference should be nulled when the dialog is closed. + * + * @param calculationChooser + */ + public void setCalculationDialog(CalculationChooser calculationChooser) + { + calculationDialog = calculationChooser; + } + + /** + * Returns the reference to the PCA/Tree chooser dialog for this panel (null + * if none is open) + */ + public CalculationChooser getCalculationDialog() + { + return calculationDialog; + } } diff --combined src/jalview/gui/AnnotationColumnChooser.java index 0fe6462,999d217..dedb8b8 --- a/src/jalview/gui/AnnotationColumnChooser.java +++ b/src/jalview/gui/AnnotationColumnChooser.java @@@ -21,8 -21,7 +21,7 @@@ package jalview.gui; - import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.schemes.AnnotationColourGradient; import jalview.util.MessageManager; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; @@@ -30,6 -29,7 +29,7 @@@ import java.awt.BorderLayout; import java.awt.CardLayout; import java.awt.Color; + import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; @@@ -86,8 -86,12 +86,12 @@@ public class AnnotationColumnChooser ex private int actionOption = ACTION_OPTION_SELECT; - private ColumnSelection oldColumnSelection; + private HiddenColumns oldHiddenColumns; + protected int MIN_WIDTH = 420; + + protected int MIN_HEIGHT = 430; + public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap) { super(av, ap); @@@ -97,6 -101,7 +101,7 @@@ Desktop.addInternalFrame(frame, MessageManager.getString("label.select_by_annotation"), 520, 215); + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); addSliderChangeListener(); addSliderMouseListeners(); @@@ -105,7 -110,7 +110,7 @@@ { return; } - setOldColumnSelection(av.getColumnSelection()); + setOldHiddenColumns(av.getAlignment().getHiddenColumns()); adjusting = true; setAnnotations(new JComboBox(getAnnotationItems(false))); @@@ -231,26 -236,26 +236,26 @@@ @Override protected void reset() { - if (this.getOldColumnSelection() != null) + if (this.getOldHiddenColumns() != null) { av.getColumnSelection().clear(); if (av.getAnnotationColumnSelectionState() != null) { - ColumnSelection oldSelection = av + HiddenColumns oldHidden = av .getAnnotationColumnSelectionState() - .getOldColumnSelection(); - if (oldSelection != null && oldSelection.getHiddenColumns() != null - && !oldSelection.getHiddenColumns().isEmpty()) + .getOldHiddenColumns(); + if (oldHidden != null && oldHidden.getListOfCols() != null + && !oldHidden.getListOfCols().isEmpty()) { - for (Iterator itr = oldSelection.getHiddenColumns() + for (Iterator itr = oldHidden.getListOfCols() .iterator(); itr.hasNext();) { int positions[] = itr.next(); av.hideColumns(positions[0], positions[1]); } } - av.setColumnSelection(oldSelection); + av.getAlignment().setHiddenColumns(oldHidden); } ap.paintAlignment(true); } @@@ -328,7 -333,7 +333,7 @@@ // build filter params filterParams .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); - if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH) + if (getCurrentAnnotation().isQuantitative()) { filterParams .setThresholdValue(getCurrentAnnotation().threshold.value); @@@ -403,16 -408,17 +408,16 @@@ ap.paintAlignment(true); } - - public ColumnSelection getOldColumnSelection() + public HiddenColumns getOldHiddenColumns() { - return oldColumnSelection; + return oldHiddenColumns; } - public void setOldColumnSelection(ColumnSelection currentColumnSelection) + public void setOldHiddenColumns(HiddenColumns currentHiddenColumns) { - if (currentColumnSelection != null) + if (currentHiddenColumns != null) { - this.oldColumnSelection = new ColumnSelection(currentColumnSelection); + this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns); } } @@@ -488,8 -494,9 +493,9 @@@ public void selectedAnnotationChanged() { String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW; - if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations() - .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH) + if (av.getAlignment() + .getAlignmentAnnotation()[annmap[getAnnotations() + .getSelectedIndex()]].isQuantitative()) { currentView = AnnotationColumnChooser.GRAPH_VIEW; } diff --combined src/jalview/gui/Jalview2XML.java index 962dc0d,02136f9..5f1fe73 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@@ -1107,7 -1107,7 +1107,7 @@@ public class Jalview2XM Tree tree = new Tree(); tree.setTitle(tp.getTitle()); tree.setCurrentTree((av.currentTree == tp.getTree())); - tree.setNewick(tp.getTree().toString()); + tree.setNewick(tp.getTree().print()); tree.setThreshold(tp.treeCanvas.threshold); tree.setFitToWindow(tp.fitToWindow.getState()); @@@ -1413,18 -1413,17 +1413,18 @@@ if (av.hasHiddenColumns()) { - if (av.getColumnSelection() == null - || av.getColumnSelection().getHiddenColumns() == null) + jalview.datamodel.HiddenColumns hidden = av.getAlignment() + .getHiddenColumns(); + if (hidden == null || hidden.getListOfCols() == null) { warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); } else { - for (int c = 0; c < av.getColumnSelection().getHiddenColumns() + for (int c = 0; c < hidden.getListOfCols() .size(); c++) { - int[] region = av.getColumnSelection().getHiddenColumns() + int[] region = hidden.getListOfCols() .get(c); HiddenColumns hc = new HiddenColumns(); hc.setStart(region[0]); @@@ -3681,7 -3680,7 +3681,7 @@@ TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); if (tp == null) { - tp = af.ShowNewickTree( + tp = af.showNewickTree( new jalview.io.NewickFile(tree.getNewick()), tree.getTitle(), tree.getWidth(), tree.getHeight(), tree.getXpos(), tree.getYpos()); diff --combined src/jalview/gui/PCAPanel.java index 1f68124,e9ba1e7..d8e6b06 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@@ -20,20 -20,23 +20,23 @@@ */ package jalview.gui; + import jalview.analysis.scoremodels.ScoreModels; + import jalview.analysis.scoremodels.SimilarityParams; + import jalview.api.analysis.ScoreModelI; + import jalview.api.analysis.SimilarityParamsI; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; - import jalview.datamodel.SeqCigar; import jalview.datamodel.SequenceI; import jalview.jbgui.GPCAPanel; - import jalview.schemes.ResidueProperties; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; import java.awt.BorderLayout; import java.awt.Color; + import java.awt.Dimension; import java.awt.Graphics; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@@ -70,29 -73,54 +73,54 @@@ public class PCAPanel extends GPCAPane PCAModel pcaModel; + private static final int MIN_WIDTH = 470; + + private static final int MIN_HEIGHT = 250; + int top = 0; /** - * Creates a new PCAPanel object. + * Creates a new PCAPanel object using default score model and parameters * - * @param av - * DOCUMENT ME! - * @param s - * DOCUMENT ME! + * @param alignPanel */ - public PCAPanel(AlignmentPanel ap) + public PCAPanel(AlignmentPanel alignPanel) + { + this(alignPanel, ScoreModels.getInstance() + .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide()) + .getName(), SimilarityParams.SeqSpace); + } + + /** + * Constructor given sequence data, a similarity (or distance) score model + * name, and score calculation parameters + * + * @param alignPanel + * @param modelName + * @param params + */ + public PCAPanel(AlignmentPanel alignPanel, String modelName, + SimilarityParamsI params) { super(); - this.av = ap.av; - this.ap = ap; + this.av = alignPanel.av; + this.ap = alignPanel; + boolean nucleotide = av.getAlignment().isNucleotide(); progressBar = new ProgressBar(statusPanel, statusBar); - boolean sameLength = true; + addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent e) + { + close_actionPerformed(); + } + }); + boolean selected = av.getSelectionGroup() != null && av.getSelectionGroup().getSize() > 0; AlignmentView seqstrings = av.getAlignmentView(selected); - boolean nucleotide = av.getAlignment().isNucleotide(); SequenceI[] seqs; if (!selected) { @@@ -102,41 -130,14 +130,14 @@@ { seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } - SeqCigar sq[] = seqstrings.getSequences(); - int length = sq[0].getWidth(); - - for (int i = 0; i < seqs.length; i++) - { - if (sq[i].getWidth() != length) - { - sameLength = false; - break; - } - } - - if (!sameLength) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.getString("label.pca_sequences_not_aligned"), - MessageManager.getString("label.sequences_not_aligned"), - JvOptionPane.WARNING_MESSAGE); - return; - } - - addInternalFrameListener(new InternalFrameAdapter() - { - @Override - public void internalFrameClosed(InternalFrameEvent e) - { - close_actionPerformed(); - } - }); - - pcaModel = new PCAModel(seqstrings, seqs, nucleotide); + ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel( + modelName, ap); + pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, + params); PaintRefresher.Register(this, av.getSequenceSetId()); - rc = new RotatableCanvas(ap); + rc = new RotatableCanvas(alignPanel); this.getContentPane().add(rc, BorderLayout.CENTER); Thread worker = new Thread(this); worker.start(); @@@ -151,40 -152,52 +152,52 @@@ pcaModel = null; } + /** + * Repopulate the options and actions under the score model menu when it is + * selected. Options will depend on whether 'nucleotide' or 'peptide' + * modelling is selected (and also possibly on whether any additional score + * models have been added). + */ @Override - protected void scoreMatrix_menuSelected() + protected void scoreModel_menuSelected() { - scoreMatrixMenu.removeAll(); - for (final String sm : ResidueProperties.scoreMatrices.keySet()) + scoreModelMenu.removeAll(); + for (final ScoreModelI sm : ScoreModels.getInstance().getModels()) { - if (ResidueProperties.getScoreMatrix(sm) != null) + final String name = sm.getName(); + JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name); + + /* + * if the score model doesn't provide a description, try to look one + * up in the text bundle, falling back on its name + */ + String tooltip = sm.getDescription(); + if (tooltip == null) + { + tooltip = MessageManager.getStringOrReturn("label.score_model_", + name); + } + jm.setToolTipText(tooltip); + jm.setSelected(pcaModel.getScoreModelName().equals(name)); + if ((pcaModel.isNucleotide() && sm.isDNA()) + || (!pcaModel.isNucleotide() && sm.isProtein())) { - // create an entry for this score matrix for use in PCA - JCheckBoxMenuItem jm = new JCheckBoxMenuItem(); - jm.setText(MessageManager.getStringOrReturn("label.score_model_", - sm)); - jm.setSelected(pcaModel.getScore_matrix().equals(sm)); - if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices - .get(sm).isProtein()) - || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices - .get(sm).isDNA()) + jm.addActionListener(new ActionListener() { - final PCAPanel us = this; - jm.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent e) { - @Override - public void actionPerformed(ActionEvent e) + if (!pcaModel.getScoreModelName().equals(name)) { - if (!pcaModel.getScore_matrix().equals(sm)) - { - pcaModel.setScore_matrix(sm); - Thread worker = new Thread(us); - worker.start(); - } + ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel( + name, ap); + pcaModel.setScoreModel(sm2); + Thread worker = new Thread(PCAPanel.this); + worker.start(); } - }); - scoreMatrixMenu.add(jm); - } + } + }); + scoreModelMenu.add(jm); } } } @@@ -231,7 -244,6 +244,6 @@@ // rc.invalidate(); nuclSetting.setSelected(pcaModel.isNucleotide()); protSetting.setSelected(!pcaModel.isNucleotide()); - jvVersionSetting.setSelected(pcaModel.isJvCalcMode()); top = pcaModel.getTop(); } catch (OutOfMemoryError er) @@@ -249,6 -261,7 +261,7 @@@ addKeyListener(rc); Desktop.addInternalFrame(this, MessageManager .getString("label.principal_component_analysis"), 475, 450); + this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } } @@@ -258,7 -271,8 +271,8 @@@ if (!pcaModel.isNucleotide()) { pcaModel.setNucleotide(true); - pcaModel.setScore_matrix("DNA"); + pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel( + false)); Thread worker = new Thread(this); worker.start(); } @@@ -272,20 -286,13 +286,13 @@@ if (pcaModel.isNucleotide()) { pcaModel.setNucleotide(false); - pcaModel.setScore_matrix("BLOSUM62"); + pcaModel.setScoreModel(ScoreModels.getInstance() + .getDefaultModel(true)); Thread worker = new Thread(this); worker.start(); } } - @Override - protected void jvVersionSetting_actionPerfomed(ActionEvent arg0) - { - pcaModel.setJvCalcMode(jvVersionSetting.isSelected()); - Thread worker = new Thread(this); - worker.start(); - } - /** * DOCUMENT ME! */ @@@ -399,7 -406,7 +406,7 @@@ } ; Object[] alAndColsel = pcaModel.getSeqtrings() - .getAlignmentAndColumnSelection(gc); + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@@ -416,8 -423,8 +423,8 @@@ if (true) { // make a new frame! - AlignFrame af = new AlignFrame(al, - (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH, + AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // >>>This is a fix for the moment, until a better solution is diff --combined src/jalview/gui/PopupMenu.java index 38f409f,1685721..09e3263 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@@ -31,8 -31,8 +31,8 @@@ import jalview.commands.EditCommand.Act import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; -import jalview.datamodel.ColumnSelection; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; @@@ -55,6 -55,7 +55,7 @@@ import jalview.util.UrlLink import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; + import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Collections; @@@ -1445,21 -1446,13 +1446,21 @@@ public class PopupMenu extends JPopupMe { if (sequence != null) { - ColumnSelection cs = ap.av.getColumnSelection(); - if (cs == null) - { - cs = new ColumnSelection(); + /* ColumnSelection cs = ap.av.getColumnSelection(); + if (cs == null) + { + cs = new ColumnSelection(); + } + cs.hideInsertionsFor(sequence); + ap.av.setColumnSelection(cs);*/ + + HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); + if (hidden == null) + { + hidden = new HiddenColumns(); } - cs.hideInsertionsFor(sequence); - ap.av.setColumnSelection(cs); + hidden.hideInsertionsFor(sequence); + ap.av.getAlignment().setHiddenColumns(hidden); } refresh(); } @@@ -1888,30 -1881,28 +1889,28 @@@ return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + List seqs = new ArrayList(); + List features = new ArrayList(); + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + int gSize = sg.getSize(); for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i).getDatasetSequence()); + features.add(new SequenceFeature(null, null, null, start, end, + "Jalview")); } } - rseqs = new SequenceI[rsize]; - tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs, 0, rseqs, 0, rsize); - System.arraycopy(features, 0, tfeatures, 0, rsize); - features = tfeatures; - seqs = rseqs; + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + features, true, ap, null)) { ap.alignFrame.setShowSeqFeatures(true); ap.highlightSearchResults(null); diff --combined src/jalview/gui/SeqPanel.java index 31fe2b6,1432fcb..749b390 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@@ -27,7 -27,6 +27,7 @@@ import jalview.commands.EditCommand.Act import jalview.commands.EditCommand.Edit; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@@ -60,6 -59,7 +60,7 @@@ import java.awt.event.MouseMotionListen import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.util.ArrayList; + import java.util.Collections; import java.util.List; import javax.swing.JPanel; @@@ -233,8 -233,7 +234,8 @@@ public class SeqPanel extends JPanel im if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(res); } return res; @@@ -340,23 -339,20 +341,23 @@@ { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; + + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + if (av.hasHiddenColumns() - && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + && !hidden.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) + while (!hidden.isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + || !hidden.isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@@ -402,17 -398,16 +403,17 @@@ } if (!av.getWrapAlignment()) { - while (seqCanvas.cursorX < av.getColumnSelection() - .adjustForHiddenColumns(av.getRanges().getStartRes())) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av + .getRanges().getStartRes())) { if (!ap.scrollRight(false)) { break; } } - while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(av.getRanges().getEndRes())) + while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av + .getRanges().getEndRes())) { if (!ap.scrollRight(true)) { @@@ -1149,10 -1144,8 +1150,10 @@@ if (av.hasHiddenColumns()) { fixedColumns = true; - int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); - int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + int y1 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryLeft(startres); + int y2 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryRight(startres); if ((insertGap && startres > y1 && lastres < y1) || (!insertGap && startres < y2 && lastres > y2)) @@@ -1227,8 -1220,8 +1228,8 @@@ { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av - .getColumnSelection().getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() && startres < av.getAlignment() + .getHiddenColumns().getHiddenBoundaryRight(startres))) { endEditing(); return; @@@ -1492,6 -1485,11 +1493,11 @@@ } } + /** + * Handler for double-click on a position with one or more sequence features. + * Opens the Amend Features dialog to allow feature details to be amended, or + * the feature deleted. + */ @Override public void mouseClicked(MouseEvent evt) { @@@ -1510,20 -1508,23 +1516,23 @@@ .findFeaturesAtRes(sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); - if (features != null && features.size() > 0) + if (!features.isEmpty()) { + /* + * highlight the first feature at the position on the alignment + */ SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); - } - if (features != null && features.size() > 0) - { - seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, - features.toArray(new SequenceFeature[features.size()]), - false, ap); + /* + * open the Amend Features dialog; clear highlighting afterwards, + * whether changes were made or not + */ + List seqs = Collections.singletonList(sequence); + seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, + ap, null); seqCanvas.highlightSearchResults(null); } } @@@ -1678,7 -1679,7 +1687,7 @@@ * * @param evt * @param res - * @param sequence + * @param sequences */ void showPopupMenu(MouseEvent evt) { @@@ -1956,7 -1957,7 +1965,7 @@@ */ @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, - SelectionSource source) + HiddenColumns hidden, SelectionSource source) { // TODO: fix this hack - source of messages is align viewport, but SeqPanel // handles selection messages... @@@ -1964,9 -1965,20 +1973,20 @@@ // shared between viewports. boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))); - if (iSentTheSelection || !av.followSelection) + + if (iSentTheSelection) { - return; + // respond to our own event by updating dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + + // process further ? + if (!av.followSelection) + { + return; + } } /* @@@ -1981,7 -1993,7 +2001,7 @@@ * Check for selection in a view of which this one is a dna/protein * complement. */ - if (selectionFromTranslation(seqsel, colsel, source)) + if (selectionFromTranslation(seqsel, colsel, hidden, source)) { return; } @@@ -2044,8 -2056,7 +2064,8 @@@ } else { - av.getColumnSelection().setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel, + av.getAlignment().getHiddenColumns()); } } av.isColSelChanged(true); @@@ -2054,8 -2065,8 +2074,8 @@@ if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection() - .getHiddenColumns() == null)) + && (av.getAlignment().getHiddenColumns() == null || av + .getAlignment().getHiddenColumns().getListOfCols() == null)) { System.err.println("Bad things"); } @@@ -2065,6 -2076,13 +2085,13 @@@ PaintRefresher.Refresh(this, av.getSequenceSetId()); // ap.paintAlignment(false); } + + // lastly, update dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + } /** @@@ -2077,8 -2095,7 +2104,8 @@@ * @param source */ protected boolean selectionFromTranslation(SequenceGroup seqsel, - ColumnSelection colsel, SelectionSource source) + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { if (!(source instanceof AlignViewportI)) { @@@ -2101,14 -2118,16 +2128,20 @@@ /* * Map column selection */ - ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, - av); + // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, + // av); + ColumnSelection cs = new ColumnSelection(); + HiddenColumns hs = new HiddenColumns(); + MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs); av.setColumnSelection(cs); + av.getAlignment().setHiddenColumns(hs); + // lastly, update any dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + PaintRefresher.Refresh(this, av.getSequenceSetId()); return true; diff --combined src/jalview/gui/TreePanel.java index 96d0746,9dd805e..35998eb --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@@ -21,9 -21,13 +21,13 @@@ package jalview.gui; import jalview.analysis.AlignmentSorter; + import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; + import jalview.analysis.TreeBuilder; + import jalview.analysis.TreeModel; + import jalview.analysis.scoremodels.ScoreModels; import jalview.api.analysis.ScoreModelI; - import jalview.api.analysis.ViewBasedAnalysisI; + import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.OrderCommand; @@@ -31,8 -35,8 +35,8 @@@ import jalview.datamodel.Alignment import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.BinaryNode; -import jalview.datamodel.ColumnSelection; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.NodeTransformI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@@ -41,7 -45,6 +45,6 @@@ import jalview.io.JalviewFileChooser import jalview.io.JalviewFileView; import jalview.io.NewickFile; import jalview.jbgui.GTreePanel; - import jalview.schemes.ResidueProperties; import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@@ -71,68 -74,46 +74,46 @@@ import org.jibble.epsgraphics.EpsGraphi */ public class TreePanel extends GTreePanel { - String type; + String treeType; - String pwtype; + String scoreModelName; // if tree computed + + String treeTitle; // if tree loaded + + SimilarityParamsI similarityParams; TreeCanvas treeCanvas; - NJTree tree; + TreeModel tree; AlignViewport av; /** * Creates a new TreePanel object. * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! + * @param ap * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - * @param s - * DOCUMENT ME! - * @param e - * DOCUMENT ME! + * @param modelName + * @param options */ - public TreePanel(AlignmentPanel ap, String type, String pwtype) + public TreePanel(AlignmentPanel ap, String type, String modelName, + SimilarityParamsI options) { super(); - initTreePanel(ap, type, pwtype, null, null); + this.similarityParams = options; + initTreePanel(ap, type, modelName, null, null); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default // showDistances(true); } - /** - * Creates a new TreePanel object. - * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! - * @param newtree - * DOCUMENT ME! - * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - */ - public TreePanel(AlignmentPanel ap, String type, String pwtype, - NewickFile newtree) - { - super(); - initTreePanel(ap, type, pwtype, newtree, null); - } - - public TreePanel(AlignmentPanel av, String type, String pwtype, - NewickFile newtree, AlignmentView inputData) + public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, + String theTitle, AlignmentView inputData) { super(); - initTreePanel(av, type, pwtype, newtree, inputData); + this.treeTitle = theTitle; + initTreePanel(alignPanel, null, null, newtree, inputData); } public AlignmentI getAlignment() @@@ -145,13 -126,13 +126,13 @@@ return treeCanvas.av; } - void initTreePanel(AlignmentPanel ap, String type, String pwtype, + void initTreePanel(AlignmentPanel ap, String type, String modelName, NewickFile newTree, AlignmentView inputData) { av = ap.av; - this.type = type; - this.pwtype = pwtype; + this.treeType = type; + this.scoreModelName = modelName; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@@ -181,7 -162,7 +162,7 @@@ .println("new alignment sequences vector value is null"); } - tree.UpdatePlaceHolders((List) evt.getNewValue()); + tree.updatePlaceHolders((List) evt.getNewValue()); treeCanvas.nameHash.clear(); // reset the mapping between canvas // rectangles and leafnodes repaint(); @@@ -189,11 -170,7 +170,7 @@@ } }); - TreeLoader tl = new TreeLoader(newTree); - if (inputData != null) - { - tl.odata = inputData; - } + TreeLoader tl = new TreeLoader(newTree, inputData); tl.start(); } @@@ -265,19 -242,21 +242,21 @@@ class TreeLoader extends Thread { - NewickFile newtree; + private NewickFile newtree; - jalview.datamodel.AlignmentView odata = null; + private AlignmentView odata = null; - public TreeLoader(NewickFile newtree) + public TreeLoader(NewickFile newickFile, AlignmentView inputData) { - this.newtree = newtree; - if (newtree != null) + this.newtree = newickFile; + this.odata = inputData; + + if (newickFile != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - showBootstrap(newtree.HasBootstrap()); - showDistances(newtree.HasDistances()); + showBootstrap(newickFile.HasBootstrap()); + showDistances(newickFile.HasDistances()); } } @@@ -287,60 -266,21 +266,21 @@@ if (newtree != null) { - if (odata == null) - { - tree = new NJTree(av.getAlignment().getSequencesArray(), newtree); - } - else + tree = new TreeModel(av.getAlignment().getSequencesArray(), odata, + newtree); + if (tree.getOriginalData() == null) { - tree = new NJTree(av.getAlignment().getSequencesArray(), odata, - newtree); - } - if (!tree.hasOriginalSequenceData()) - { - allowOriginalSeqData(false); + originalSeqData.setVisible(false); } } else { - int start, end; - SequenceI[] seqs; - boolean selview = av.getSelectionGroup() != null - && av.getSelectionGroup().getSize() > 1; - AlignmentView seqStrings = av.getAlignmentView(selview); - if (!selview) - { - start = 0; - end = av.getAlignment().getWidth(); - seqs = av.getAlignment().getSequencesArray(); - } - else - { - start = av.getSelectionGroup().getStartRes(); - end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder( - av.getAlignment()); - } - ScoreModelI sm = ResidueProperties.getScoreModel(pwtype); - if (sm instanceof ViewBasedAnalysisI) - { - try - { - sm = sm.getClass().newInstance(); - ((ViewBasedAnalysisI) sm) - .configureFromAlignmentView(treeCanvas.ap); - } catch (Exception q) - { - Cache.log.error("Couldn't create a scoremodel instance for " - + sm.getName()); - } - tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end); - } - else - { - tree = new NJTree(seqs, seqStrings, type, pwtype, null, start, - end); - } + ScoreModelI sm = ScoreModels.getInstance().getScoreModel( + scoreModelName, treeCanvas.ap); + TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree( + av, sm, similarityParams) : new AverageDistanceTree(av, sm, + similarityParams); + tree = new TreeModel(njtree); showDistances(true); } @@@ -374,17 -314,12 +314,12 @@@ treeCanvas.setMarkPlaceholders(b); } - private void allowOriginalSeqData(boolean b) - { - originalSeqData.setVisible(b); - } - /** * DOCUMENT ME! * * @return DOCUMENT ME! */ - public NJTree getTree() + public TreeModel getTree() { return tree; } @@@ -400,33 -335,14 +335,14 @@@ { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - StringBuffer buffer = new StringBuffer(); + String newTitle = getPanelTitle(); - if (type.equals("AV")) - { - buffer.append("Average distance tree using "); - } - else - { - buffer.append("Neighbour joining tree using "); - } - - if (pwtype.equals("BL")) - { - buffer.append("BLOSUM62"); - } - else - { - buffer.append("PID"); - } - - jalview.io.NewickFile fout = new jalview.io.NewickFile( - tree.getTopNode()); + NewickFile fout = new NewickFile(tree.getTopNode()); try { - cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), - tree.isHasRootDistance())); - Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); + cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(), + tree.hasRootDistance())); + Desktop.addInternalFrame(cap, newTitle, 500, 100); } catch (OutOfMemoryError oom) { new OOMWarning("generating newick tree file", oom); @@@ -463,8 -379,8 +379,8 @@@ { jalview.io.NewickFile fout = new jalview.io.NewickFile( tree.getTopNode()); - String output = fout.print(tree.isHasBootstrap(), - tree.isHasDistances(), tree.isHasRootDistance()); + String output = fout.print(tree.hasBootstrap(), + tree.hasDistances(), tree.hasRootDistance()); java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(choice)); out.println(output); @@@ -492,7 -408,8 +408,8 @@@ @Override public void originalSeqData_actionPerformed(ActionEvent e) { - if (!tree.hasOriginalSequenceData()) + AlignmentView originalData = tree.getOriginalData(); + if (originalData == null) { jalview.bin.Cache.log .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); @@@ -514,8 -431,9 +431,8 @@@ } catch (Exception ex) { } - ; - Object[] alAndColsel = tree.seqData.getAlignmentAndHiddenColumns(gc); + - Object[] alAndColsel = originalData - .getAlignmentAndColumnSelection(gc); ++ Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@@ -532,8 -450,8 +449,8 @@@ if (true) { // make a new frame! - AlignFrame af = new AlignFrame(al, - (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH, + AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // >>>This is a fix for the moment, until a better solution is @@@ -632,11 -550,11 +549,11 @@@ public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignmentViewport av = ap.av; - SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(av.getAlignment(), tree); + AlignmentViewport viewport = ap.av; + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(viewport.getAlignment(), tree); CommandI undo; - undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment()); + undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment()); ap.paintAlignment(true); return undo; @@@ -664,11 -582,11 +581,11 @@@ return treeCanvas.font; } - public void setTreeFont(Font font) + public void setTreeFont(Font f) { if (treeCanvas != null) { - treeCanvas.setFont(font); + treeCanvas.setFont(f); } } @@@ -891,12 -809,46 +808,46 @@@ } if (newname != null) { - String oldname = ((SequenceNode) node).getName(); - // TODO : save in the undo object for this modification. + // String oldname = ((SequenceNode) node).getName(); + // TODO : save oldname in the undo object for this modification. ((SequenceNode) node).setName(newname); } } } }); } + + /** + * Formats a localised title for the tree panel, like + *

+ * Neighbour Joining Using BLOSUM62 + *

+ * For a tree loaded from file, just uses the file name + * @return + */ + public String getPanelTitle() + { + if (treeTitle != null) + { + return treeTitle; + } + + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager.getString("label.tree_calc_" + + treeType.toLowerCase()); + + /* + * short score model name (long description can be too long) + */ + String smn = scoreModelName; + + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.treecalc_title", + treecalcnm, smn); + return ttl; + } } diff --combined src/jalview/structure/StructureSelectionManager.java index 0acb786,0990b56..72da7ae --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@@ -29,7 -29,6 +29,7 @@@ import jalview.datamodel.AlignedCodonFr import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@@ -455,7 -454,7 +455,7 @@@ public class StructureSelectionManage * Attempt pairwise alignment of the sequence with each chain in the PDB, * and remember the highest scoring chain */ - int max = -10; + float max = -10; AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; @@@ -1202,14 -1201,13 +1202,14 @@@ public synchronized void sendSelection( jalview.datamodel.SequenceGroup selection, - jalview.datamodel.ColumnSelection colsel, SelectionSource source) + jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { for (SelectionListener slis : sel_listeners) { if (slis != source) { - slis.selection(selection, colsel, source); + slis.selection(selection, colsel, hidden, source); } } }