X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cce4e678a3ca34f35367ad1fd85b3e3f4c9f5957;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=5f0e5d381ac962116a13004ba64ad8c1e165120b;hpb=fcb39fa3bc47777bf4e0eb209f765dd254dc3cb9;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 5f0e5d3..cce4e67 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -24,7 +24,6 @@ import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; import jalview.analysis.Dna; -import jalview.analysis.NJTree; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignExportSettingI; @@ -35,7 +34,7 @@ import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsControllerI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; -import jalview.api.analysis.DistanceModelI; +import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.commands.CommandI; @@ -54,6 +53,8 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; @@ -72,6 +73,7 @@ import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.FileParse; import jalview.io.FormatAdapter; +import jalview.io.HMMFile; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.JPredFile; @@ -85,9 +87,12 @@ 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.Comparison; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; @@ -120,7 +125,9 @@ import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; +import java.io.BufferedReader; import java.io.File; +import java.io.FileReader; import java.io.FileWriter; import java.io.PrintWriter; import java.net.URL; @@ -128,8 +135,11 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Deque; import java.util.Enumeration; +import java.util.HashMap; import java.util.Hashtable; import java.util.List; +import java.util.Map; +import java.util.Scanner; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; @@ -151,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { + Map distribution = new HashMap<>(); // temporary + public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; @@ -162,9 +174,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; + ViewportRanges vpRanges; + public AlignViewControllerI avc; - List alignPanels = new ArrayList(); + List alignPanels = new ArrayList<>(); /** * Last format used to load or save alignments in this window @@ -176,6 +190,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ String fileName = null; + /** * Creates a new AlignFrame object with specific width and height. * @@ -231,7 +246,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @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); @@ -248,7 +263,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @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); @@ -267,7 +282,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @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); @@ -286,7 +301,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - ColumnSelection hiddenColumns, int width, int height) + HiddenColumns hiddenColumns, int width, int height) { setSize(width, height); @@ -333,6 +348,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -368,7 +384,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void actionPerformed(ActionEvent e) { - new TreeChooser(AlignFrame.this); + openTreePcaDialog(); } }); buildColourMenu(); @@ -392,8 +408,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addKeyListener(); - final List selviews = new ArrayList(); - final List origview = new ArrayList(); + final List selviews = new ArrayList<>(); + final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, @@ -406,7 +422,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, origview.clear(); origview.add(alignPanel); // make an array of all alignment panels except for this one - List aps = new ArrayList( + List aps = new ArrayList<>( Arrays.asList(Desktop.getAlignmentPanels(null))); aps.remove(AlignFrame.this.alignPanel); return aps.toArray(new AlignmentPanel[aps.size()]); @@ -650,8 +666,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; - alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + .getStartRes(); + alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); break; @@ -685,23 +703,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_PAGE_UP: if (viewport.getWrapAlignment()) { - alignPanel.scrollUp(true); + vpRanges.scrollUp(true); } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); + vpRanges.pageUp(); } break; case KeyEvent.VK_PAGE_DOWN: if (viewport.getWrapAlignment()) { - alignPanel.scrollUp(false); + vpRanges.scrollUp(false); } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); + vpRanges.pageDown(); } break; } @@ -914,6 +930,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + showInformationHistogram.setSelected(av.isShowInformationHistogram()); + showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo()); + normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo()); ColourMenuHelper.setColourSelected(colourMenu, av.getGlobalColourScheme()); @@ -1187,8 +1206,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) { @@ -1266,8 +1285,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -1316,8 +1336,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignmentToExport = viewport.getAlignment(); } alignmentStartEnd = alignmentToExport - .getVisibleStartAndEndIndex(viewport.getColumnSelection() - .getHiddenColumns()); + .getVisibleStartAndEndIndex(viewport.getAlignment() + .getHiddenColumns() + .getHiddenRegions()); AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; @@ -1726,7 +1747,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, synchronized void slideSequences(boolean right, int size) { - List sg = new ArrayList(); + List sg = new ArrayList<>(); if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( @@ -1745,7 +1766,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - List invertGroup = new ArrayList(); + List invertGroup = new ArrayList<>(); for (SequenceI seq : viewport.getAlignment().getSequences()) { @@ -1878,10 +1899,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ArrayList hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList(); + hiddenColumns = new ArrayList<>(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport .getSelectionGroup().getEndRes(); - for (int[] region : viewport.getColumnSelection().getHiddenColumns()) + for (int[] region : viewport.getAlignment().getHiddenColumns() + .getHiddenRegions()) { if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { @@ -1987,7 +2009,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } int alwidth = 0; - ArrayList newGraphGroups = new ArrayList(); + ArrayList newGraphGroups = new ArrayList<>(); int fgroup = -1; if (newAlignment) @@ -2151,7 +2173,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.setEndSeq(alignment.getHeight()); + vpRanges.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2555,7 +2577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - viewport.setStartRes(0); + vpRanges.setStartRes(0); } else { @@ -2622,13 +2644,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2661,12 +2683,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2754,6 +2776,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ newap.av.replaceMappings(viewport.getAlignment()); + /* + * start up cDNA consensus (if applicable) now mappings are in place + */ + if (newap.av.initComplementConsensus()) + { + newap.refresh(true); // adjust layout of annotations + } + newap.av.viewName = getNewViewName(viewTitle); addAlignmentPanel(newap, true); @@ -2811,7 +2841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ protected List getExistingViewNames(List comps) { - List existingNames = new ArrayList(); + List existingNames = new ArrayList<>(); for (Component comp : comps) { if (comp instanceof AlignmentPanel) @@ -3263,7 +3293,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frame.setContentPane(overview); Desktop.addInternalFrame(frame, MessageManager.formatMessage( "label.overview_params", new Object[] { this.getTitle() }), - frame.getWidth(), frame.getHeight()); + true, frame.getWidth(), frame.getHeight(), true, true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() @@ -3331,7 +3361,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ if (ResidueColourScheme.USER_DEFINED.equals(name)) { - new UserDefinedColours(alignPanel, null); + new UserDefinedColours(alignPanel); return; } @@ -3352,10 +3382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void changeColour(ColourSchemeI cs) { // TODO: pull up to controller method - if (cs != null) - { - ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName()); - } + ColourMenuHelper.setColourSelected(colourMenu, cs); viewport.setGlobalColourScheme(cs); @@ -3441,7 +3468,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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); @@ -3535,35 +3562,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - /** - * 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) { @@ -3588,35 +3586,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * 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) { - if (viewport.getSelectionGroup().getSize() < 3) - { - JvOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.you_need_more_two_sequences_selected_build_tree"), - MessageManager - .getString("label.not_enough_sequences"), - JvOptionPane.WARNING_MESSAGE); - return; - } - SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ @@ -3636,45 +3623,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } /** @@ -3804,7 +3775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - List treePanels = new ArrayList(); + List treePanels = new ArrayList<>(); for (Component comp : comps) { if (comp instanceof TreePanel) @@ -3950,13 +3921,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 @@ -3978,25 +3949,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - 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 @@ -4015,7 +3980,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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; @@ -4026,7 +3991,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (nf.getTree() != null) { - tp = new TreePanel(alignPanel, NJTree.FROM_FILE, title, nf, input); + tp = new TreePanel(alignPanel, nf, treeTitle, input); tp.setSize(w, h); @@ -4035,7 +4000,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, title, w, h); + Desktop.addInternalFrame(tp, treeTitle, w, h); } } catch (Exception ex) { @@ -4070,7 +4035,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - final List legacyItems = new ArrayList(); + final List legacyItems = new ArrayList<>(); try { // System.err.println("Building ws menu again " @@ -4085,7 +4050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // TODO: group services by location as well as function and/or // introduce // object broker mechanism. - final Vector wsmenu = new Vector(); + final Vector wsmenu = new Vector<>(); final IProgressIndicator af = me; /* @@ -4453,8 +4418,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - List files = new ArrayList(); - List protocols = new ArrayList(); + List files = new ArrayList<>(); + List protocols = new ArrayList<>(); try { @@ -4474,8 +4439,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Object[] { String,SequenceI} */ - ArrayList filesmatched = new ArrayList(); - ArrayList filesnotmatched = new ArrayList(); + ArrayList filesmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); for (int i = 0; i < files.size(); i++) { String file = files.get(i).toString(); @@ -4699,6 +4664,160 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "label.successfully_loaded_matrix", sm.getMatrixName())); } + else if (FileFormat.HMMER3.equals(format)) + { + HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO + // need + // to + // follow + // standard + // pipeline + hmmFile.parse(); + HiddenMarkovModel hmm = hmmFile.getHMM(); + AlignmentAnnotation annotation = hmm.createAnnotation( + getViewport().getAlignment().getWidth()); + getViewport().getAlignment().addAnnotation(annotation); + annotation.setHMM(hmm); + isAnnotation = true; + + BufferedReader input = new BufferedReader(new FileReader( + "H:/Desktop/Distributions/BadAlignment-8.csv")); + String line = input.readLine(); + + while (!("".equals(line)) && line != null) + { + Scanner scanner = new Scanner(line); + if (scanner.hasNext()) + { + scanner.useDelimiter(","); + String value = scanner.next(); + + distribution.put(value, scanner.nextFloat()); + line = input.readLine(); + } + } + + + AlignmentI alignment = getViewport().getAlignment(); + Integer alpha = 0; + final int AMINO = 0; + final int DNA = 1; + if ("amino".equals(hmm.getAlphabetType())) + { + alpha = AMINO; + } + else if ("DNA".equals(hmm.getAlphabetType())) + { + alpha = DNA; + } + + + int size = 0; + + for (int l = 1; l < hmm.getLength() + 1; l++) + { + for (int n = 0; n < alignment.getHeight(); n++) + { + + char character = alignment.getSequenceAt(n) + .getCharAt(hmm.getNodeAlignmentColumn(l)); + character = Character.toUpperCase(character); + + boolean containedN; + boolean containedA; + + containedN = ResidueProperties.nucleotideBackgroundFrequencies + .containsKey(character); + containedA = ResidueProperties.aminoBackgroundFrequencies + .containsKey(character); + + if (!Comparison.isGap(character) + && ((alpha == DNA && containedN) + || (alpha == AMINO && containedA))) + { + size++; + } + + } + } + + for (int l = 1; l < hmm.getLength() + 1; l++) + { + for (int n = 0; n < alignment.getHeight(); n++) + { + Double prob; + char character; + character = alignment.getSequenceAt(n) + .getCharAt(hmm.getNodeAlignmentColumn(l)); + character = Character.toUpperCase(character); + boolean containedN; + boolean containedA; + + containedN = ResidueProperties.nucleotideBackgroundFrequencies + .containsKey(character); + containedA = ResidueProperties.aminoBackgroundFrequencies + .containsKey(character); + + if (!Comparison.isGap(character) + && ((alpha == DNA && containedN) + || (alpha == AMINO && containedA))) + { + prob = hmm.getMatchEmissionProbability( + hmm.getNodeAlignmentColumn(l), character); + if (prob == 0d) + { + System.out.println("?"); + } + + double freq = 0; + if (alpha == AMINO) + { + freq = ResidueProperties.aminoBackgroundFrequencies + .get(character); + } + if (alpha == DNA) + { + freq = ResidueProperties.nucleotideBackgroundFrequencies + .get(character); + } + Double doubleValue = Math.log(prob / freq); + + String value = String.format("%.1f", doubleValue); + if ("-0.0".equals(value)) + { + value = "0.0"; + } + if (distribution.containsKey(value)) + { + float prev = distribution.get(value); + prev = prev + (10000f / size); + distribution.put(value, prev); + } + else + { + distribution.put(value, 10000f / size); + } + + + } + + } + } + + PrintWriter writer = new PrintWriter( + new File( + "H:/Desktop/Distributions/BadAlignment-8.csv")); + for (Map.Entry entry : distribution + .entrySet()) + { + writer.println(entry.getKey() + "," + entry.getValue()); + + } + + writer.close(); + + + } else if (FileFormat.Jnet.equals(format)) { JPredFile predictions = new JPredFile(file, sourceType); @@ -4707,9 +4826,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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)) @@ -5317,6 +5436,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + protected void showInformationHistogram_actionPerformed(ActionEvent e) + { + viewport.setShowInformationHistogram( + showInformationHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void showHMMSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override + protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e) + { + showHMMSequenceLogo.setState(true); + viewport.setShowHMMSequenceLogo(true); + viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + @Override protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); @@ -5466,7 +5609,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return; } - List cdnaSeqs = new ArrayList(); + List cdnaSeqs = new ArrayList<>(); for (SequenceI aaSeq : alignment.getSequences()) { for (AlignedCodonFrame acf : mappings) @@ -5632,17 +5775,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(annotationColour); ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); - String schemeName = colourScheme == null ? null : colourScheme - .getSchemeName(); - - ColourMenuHelper.setColourSelected(colourMenu, schemeName); + ColourMenuHelper.setColourSelected(colourMenu, colourScheme); } - public void newTreePanel(String treeType, DistanceModelI sm) + /** + * Open a dialog (if not already open) that allows the user to select and + * calculate PCA or Tree analysis + */ + protected void openTreePcaDialog() { - String scoreModelName = sm.getName(); - final String ttl = TreePanel.getPanelTitle(treeType, scoreModelName); - newTreePanel(treeType, scoreModelName, ttl); + if (alignPanel.getCalculationDialog() == null) + { + new CalculationChooser(AlignFrame.this); + } } }