From: Jim Procter Date: Tue, 27 Feb 2018 11:16:41 +0000 (+0000) Subject: Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104 X-Git-Tag: Release_2_10_4~55^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aad3640b07f836362df7ea025fa09127a0a06145;hp=-c;p=jalview.git Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104 --- aad3640b07f836362df7ea025fa09127a0a06145 diff --combined src/jalview/appletgui/AnnotationLabels.java index d8e7007,6e3257d..bbcb3b8 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@@ -23,6 -23,7 +23,7 @@@ package jalview.appletgui import jalview.analysis.AlignmentUtils; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; + import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.util.MessageManager; @@@ -31,7 -32,6 +32,7 @@@ import jalview.util.ParseHtmlBodyAndLin import java.awt.Checkbox; import java.awt.CheckboxMenuItem; import java.awt.Color; +import java.awt.Cursor; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.FontMetrics; @@@ -51,23 -51,12 +52,22 @@@ import java.awt.event.MouseListener import java.awt.event.MouseMotionListener; import java.util.Arrays; import java.util.Collections; - import java.util.Vector; public class AnnotationLabels extends Panel implements ActionListener, MouseListener, MouseMotionListener { Image image; + /** + * width in pixels within which height adjuster arrows are shown and active + */ + private static final int HEIGHT_ADJUSTER_WIDTH = 50; + + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; + boolean active = false; AlignmentPanel ap; @@@ -103,6 -92,23 +103,6 @@@ this.ap = ap; this.av = ap.av; setLayout(null); - - /** - * this retrieves the adjustable height glyph from resources. we don't use - * it at the moment. java.net.URL url = - * getClass().getResource("/images/idwidth.gif"); Image temp = null; - * - * if (url != null) { temp = - * java.awt.Toolkit.getDefaultToolkit().createImage(url); } - * - * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0); - * mt.waitForID(0); } catch (Exception ex) { } - * - * BufferedImage bi = new BufferedImage(temp.getHeight(this), - * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g = - * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90)); - * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi; - */ addMouseListener(this); addMouseMotionListener(this); } @@@ -262,10 -268,7 +262,10 @@@ @Override public void mouseMoved(MouseEvent evt) { - resizePanel = evt.getY() < 10 && evt.getX() < 14; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); int row = getSelectedRow(evt.getY() + scrollOffset); if (row > -1) @@@ -403,7 -406,6 +403,7 @@@ resizePanel = false; dragEvent = null; dragCancelled = false; + setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); repaint(); ap.annotationPanel.repaint(); } @@@ -416,8 -418,6 +416,8 @@@ resizePanel = true; repaint(); } + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); } @Override @@@ -843,8 -843,8 +843,8 @@@ + "\t" + sq.getSequenceAsString() + "\n"); if (av.hasHiddenColumns()) { - jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>( - av.getAlignment().getHiddenColumns().getHiddenColumnsCopy()); + jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } } @@@ -903,8 -903,14 +903,8 @@@ } } g.translate(0, +scrollOffset); - if (resizePanel) - { - g.setColor(Color.red); - g.setPaintMode(); - g.drawLine(2, 8, 5, 2); - g.drawLine(5, 2, 8, 8); - } - else if (!dragCancelled && dragEvent != null && aa != null) + + if (!resizePanel && !dragCancelled && dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), diff --combined src/jalview/datamodel/Alignment.java index a3b3ff6,9475f00..3ba35b6 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@@ -29,10 -29,12 +29,12 @@@ import jalview.util.MessageManager import java.util.ArrayList; import java.util.Arrays; + import java.util.BitSet; import java.util.Collections; import java.util.Enumeration; import java.util.HashSet; import java.util.Hashtable; + import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; @@@ -49,7 -51,7 +51,7 @@@ public class Alignment implements Align { private Alignment dataset; - protected List sequences; + private List sequences; protected List groups; @@@ -198,7 -200,6 +200,7 @@@ return sequences.get(i); } } + return null; } @@@ -707,7 -708,7 +709,7 @@@ public int getWidth() { int maxLength = -1; - + for (int i = 0; i < sequences.size(); i++) { if (getSequenceAt(i).getLength() > maxLength) @@@ -715,34 -716,9 +717,34 @@@ maxLength = getSequenceAt(i).getLength(); } } - + return maxLength; } + /* + @Override + public int getWidth() + { + final Wrapper temp = new Wrapper(); + + forEachSequence(new Consumer() + { + @Override + public void accept(SequenceI s) + { + if (s.getLength() > temp.inner) + { + temp.inner = s.getLength(); + } + } + }, 0, sequences.size() - 1); + + return temp.inner; + } + + public static class Wrapper + { + public int inner; + }*/ /** * DOCUMENT ME! @@@ -1629,10 -1605,7 +1631,10 @@@ AlignmentAnnotation annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH); annot.hasText = false; - annot.setCalcId(new String(calcId)); + if (calcId != null) + { + annot.setCalcId(new String(calcId)); + } annot.autoCalculated = autoCalc; if (seqRef != null) { @@@ -1924,4 -1897,117 +1926,117 @@@ { hiddenCols = cols; } + + @Override + public void setupJPredAlignment() + { + SequenceI repseq = getSequenceAt(0); + setSeqrep(repseq); + HiddenColumns cs = new HiddenColumns(); + cs.hideList(repseq.getInsertions()); + setHiddenColumns(cs); + } + + @Override + public HiddenColumns propagateInsertions(SequenceI profileseq, + AlignmentView input) + { + int profsqpos = 0; + + char gc = getGapCharacter(); + Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc); + HiddenColumns nview = (HiddenColumns) alandhidden[1]; + SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos]; + return propagateInsertions(profileseq, origseq, nview); + } + + /** + * + * @param profileseq + * sequence in al which corresponds to origseq + * @param al + * alignment which is to have gaps inserted into it + * @param origseq + * sequence corresponding to profileseq which defines gap map for + * modifying al + */ + private HiddenColumns propagateInsertions(SequenceI profileseq, + SequenceI origseq, HiddenColumns hc) + { + // take the set of hidden columns, and the set of gaps in origseq, + // and remove all the hidden gaps from hiddenColumns + + // first get the gaps as a Bitset + // then calculate hidden ^ not(gap) + BitSet gaps = origseq.gapBitset(); + hc.andNot(gaps); + + // for each sequence in the alignment, except the profile sequence, + // insert gaps corresponding to each hidden region but where each hidden + // column region is shifted backwards by the number of preceding visible + // gaps update hidden columns at the same time + HiddenColumns newhidden = new HiddenColumns(); + + int numGapsBefore = 0; + int gapPosition = 0; + Iterator it = hc.iterator(); + while (it.hasNext()) + { + int[] region = it.next(); + + // get region coordinates accounting for gaps + // we can rely on gaps not being *in* hidden regions because we already + // removed those + while (gapPosition < region[0]) + { + gapPosition++; + if (gaps.get(gapPosition)) + { + numGapsBefore++; + } + } + + int left = region[0] - numGapsBefore; + int right = region[1] - numGapsBefore; + + newhidden.hideColumns(left, right); + padGaps(left, right, profileseq); + } + return newhidden; + } + + /** + * Pad gaps in all sequences in alignment except profileseq + * + * @param left + * position of first gap to insert + * @param right + * position of last gap to insert + * @param profileseq + * sequence not to pad + */ + private void padGaps(int left, int right, SequenceI profileseq) + { + char gc = getGapCharacter(); + + // make a string with number of gaps = length of hidden region + StringBuilder sb = new StringBuilder(); + for (int g = 0; g < right - left + 1; g++) + { + sb.append(gc); + } + + // loop over the sequences and pad with gaps where required + for (int s = 0, ns = getHeight(); s < ns; s++) + { + SequenceI sqobj = getSequenceAt(s); + if ((sqobj != profileseq) && (sqobj.getLength() >= left)) + { + String sq = sqobj.getSequenceAsString(); + sqobj.setSequence( + sq.substring(0, left) + sb.toString() + sq.substring(left)); + } + } + } + } diff --combined src/jalview/gui/AlignFrame.java index e10ff4a,0c452c3..9981559 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@@ -1862,23 -1862,17 +1862,17 @@@ public class AlignFrame extends GAlignF return; } - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList<>(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); - ArrayList hiddenRegions = viewport.getAlignment() - .getHiddenColumns().getHiddenColumnsCopy(); - for (int[] region : hiddenRegions) - { - if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) - { - hiddenColumns - .add(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); - } - } + + // create new HiddenColumns object with copy of hidden regions + // between startRes and endRes, offset by startRes + hiddenColumns = new HiddenColumns( + viewport.getAlignment().getHiddenColumns(), hiddenOffset, + hiddenCutoff, hiddenOffset); } Desktop.jalviewClipboard = new Object[] { seqs, @@@ -2207,11 -2201,8 +2201,8 @@@ if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int[] region : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@@ -2266,11 -2257,8 +2257,8 @@@ if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int region[] : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is @@@ -4639,11 -4627,7 +4627,7 @@@ new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); - SequenceI repseq = viewport.getAlignment().getSequenceAt(0); - viewport.getAlignment().setSeqrep(repseq); - HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(repseq); - viewport.getAlignment().setHiddenColumns(cs); + viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) @@@ -4865,15 -4849,14 +4849,15 @@@ MessageManager.getString("option.trim_retrieved_seqs")); trimrs.setToolTipText( MessageManager.getString("label.trim_retrieved_sequences")); - trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); - Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); }; }); diff --combined src/jalview/gui/AlignmentPanel.java index 68b1998,60ca80a..f5634d2 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@@ -419,8 -419,8 +419,8 @@@ public class AlignmentPanel extends GAl if (av.hasHiddenColumns()) { HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - start = hidden.findColumnPosition(start); - end = hidden.findColumnPosition(end); + start = hidden.absoluteToVisibleColumn(start); + end = hidden.absoluteToVisibleColumn(end); if (start == end) { if (!hidden.isVisible(r[0])) @@@ -678,7 -678,7 +678,7 @@@ { // reset the width to exclude hidden columns width = av.getAlignment().getHiddenColumns() - .findColumnPosition(width); + .absoluteToVisibleColumn(width); } hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@@ -874,17 -874,15 +874,17 @@@ @Override public void paintComponent(Graphics g) { - invalidate(); + invalidate(); // needed so that the id width adjuster works correctly Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); idPanelHolder.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); - validate(); + + validate(); // needed so that the id width adjuster works correctly /* - * set scroll bar positions + * set scroll bar positions - tried to remove but necessary for split panel to resize correctly + * though I still think this call should be elsewhere. */ ViewportRanges ranges = av.getRanges(); setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); @@@ -1176,7 -1174,7 +1176,7 @@@ if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + .absoluteToVisibleColumn(maxwidth) - 1; } int resWidth = getSeqPanel().seqCanvas @@@ -1368,7 -1366,7 +1368,7 @@@ if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); + .absoluteToVisibleColumn(maxwidth); } int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) @@@ -1586,7 -1584,7 +1586,7 @@@ if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + .absoluteToVisibleColumn(maxwidth) - 1; } int height = ((maxwidth / chunkWidth) + 1) * cHeight; @@@ -1815,6 -1813,35 +1815,6 @@@ */ protected void scrollToCentre(SearchResultsI sr, int verticalOffset) { - /* - * To avoid jumpy vertical scrolling (if some sequences are gapped or not - * mapped), we can make the scroll-to location a sequence above the one - * actually mapped. - */ - SequenceI mappedTo = sr.getResults().get(0).getSequence(); - List seqs = av.getAlignment().getSequences(); - - /* - * This is like AlignmentI.findIndex(seq) but here we are matching the - * dataset sequence not the aligned sequence - */ - boolean matched = false; - for (SequenceI seq : seqs) - { - if (mappedTo == seq.getDatasetSequence()) - { - matched = true; - break; - } - } - if (!matched) - { - return; // failsafe, shouldn't happen - } - - /* - * Scroll to position but centring the target residue. - */ scrollToPosition(sr, verticalOffset, true, true); } diff --combined src/jalview/gui/AnnotationLabels.java index 15f1fe0,c883071..b58269d --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@@ -20,27 -20,26 +20,28 @@@ */ package jalview.gui; +import jalview.analysis.AlignSeq; import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; + import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.FileFormat; import jalview.io.FormatAdapter; +import jalview.util.Comparison; import jalview.util.MessageManager; +import jalview.util.Platform; import java.awt.Color; +import java.awt.Cursor; import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; -import java.awt.Image; -import java.awt.MediaTracker; import java.awt.RenderingHints; import java.awt.Toolkit; import java.awt.datatransfer.StringSelection; @@@ -50,9 -49,10 +51,11 @@@ import java.awt.event.MouseEvent import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; + import java.awt.image.BufferedImage; +import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; + import java.util.Iterator; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@@ -63,74 -63,63 +66,74 @@@ import javax.swing.SwingUtilities import javax.swing.ToolTipManager; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * The panel that holds the labels for alignment annotations, providing + * tooltips, context menus, drag to reorder rows, and drag to adjust panel + * height */ public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { + /** + * width in pixels within which height adjuster arrows are shown and active + */ + private static final int HEIGHT_ADJUSTER_WIDTH = 50; + + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern .compile("<"); - String TOGGLE_LABELSCALE = MessageManager + private static final Font font = new Font("Arial", Font.PLAIN, 11); + + private static final String TOGGLE_LABELSCALE = MessageManager .getString("label.scale_label_to_column"); - String ADDNEW = MessageManager.getString("label.add_new_row"); + private static final String ADDNEW = MessageManager + .getString("label.add_new_row"); - String EDITNAME = MessageManager + private static final String EDITNAME = MessageManager .getString("label.edit_label_description"); - String HIDE = MessageManager.getString("label.hide_row"); + private static final String HIDE = MessageManager + .getString("label.hide_row"); - String DELETE = MessageManager.getString("label.delete_row"); + private static final String DELETE = MessageManager + .getString("label.delete_row"); - String SHOWALL = MessageManager.getString("label.show_all_hidden_rows"); + private static final String SHOWALL = MessageManager + .getString("label.show_all_hidden_rows"); - String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); + private static final String OUTPUT_TEXT = MessageManager + .getString("label.export_annotation"); - String COPYCONS_SEQ = MessageManager + private static final String COPYCONS_SEQ = MessageManager .getString("label.copy_consensus_sequence"); - boolean resizePanel = false; - - Image image; + private final boolean debugRedraw = false; - AlignmentPanel ap; + private AlignmentPanel ap; AlignViewport av; - boolean resizing = false; - - MouseEvent dragEvent; + private MouseEvent dragEvent; - int oldY; + private int oldY; - int selectedRow; + private int selectedRow; private int scrollOffset = 0; - Font font = new Font("Arial", Font.PLAIN, 11); - private boolean hasHiddenRows; + private boolean resizePanel = false; + /** - * Creates a new AnnotationLabels object. + * Creates a new AnnotationLabels object * * @param ap - * DOCUMENT ME! */ public AnnotationLabels(AlignmentPanel ap) { @@@ -138,6 -127,30 +141,6 @@@ av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); - java.net.URL url = getClass().getResource("/images/idwidth.gif"); - Image temp = null; - - if (url != null) - { - temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); - } - - try - { - MediaTracker mt = new MediaTracker(this); - mt.addImage(temp, 0); - mt.waitForID(0); - } catch (Exception ex) - { - } - - BufferedImage bi = new BufferedImage(temp.getHeight(this), - temp.getWidth(this), BufferedImage.TYPE_INT_RGB); - Graphics2D g = (Graphics2D) bi.getGraphics(); - g.rotate(Math.toRadians(90)); - g.drawImage(temp, 0, -bi.getWidth(this), this); - image = bi; - addMouseListener(this); addMouseMotionListener(this); addMouseWheelListener(ap.getAnnotationPanel()); @@@ -595,9 -608,10 +598,9 @@@ } /** - * DOCUMENT ME! + * Reorders annotation rows after a drag of a label * * @param evt - * DOCUMENT ME! */ @Override public void mouseReleased(MouseEvent evt) @@@ -612,9 -626,6 +615,9 @@@ getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; + /* + * if dragging to resize instead, start == end + */ if (start != end) { // Swap these annotations @@@ -638,13 -649,31 +641,13 @@@ } /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseEntered(MouseEvent evt) - { - if (evt.getY() < 10) - { - resizePanel = true; - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! + * Removes the height adjuster image on leaving the panel, unless currently + * dragging it */ @Override public void mouseExited(MouseEvent evt) { - if (dragEvent == null) + if (resizePanel && dragEvent == null) { resizePanel = false; repaint(); @@@ -652,11 -681,10 +655,11 @@@ } /** - * DOCUMENT ME! + * A mouse drag may be either an adjustment of the panel height (if flag + * resizePanel is set on), or a reordering of the annotation rows. The former + * is dealt with by this method, the latter in mouseReleased. * * @param evt - * DOCUMENT ME! */ @Override public void mouseDragged(MouseEvent evt) @@@ -690,14 -718,15 +693,14 @@@ } /** - * DOCUMENT ME! + * Updates the tooltip as the mouse moves over the labels * * @param evt - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) { - resizePanel = evt.getY() < 10; + showOrHideAdjuster(evt); getSelectedRow(evt.getY() - getScrollOffset()); @@@ -773,26 -802,6 +776,26 @@@ } } + /** + * Shows the height adjuster image if the mouse moves into the top left + * region, or hides it if the mouse leaves the regio + * + * @param evt + */ + protected void showOrHideAdjuster(MouseEvent evt) + { + boolean was = resizePanel; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + + if (resizePanel != was) + { + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR + : Cursor.DEFAULT_CURSOR)); + repaint(); + } + } + @Override public void mouseClicked(MouseEvent evt) { @@@ -812,9 -821,11 +815,9 @@@ // process modifiers SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null || sg == aa[selectedRow].groupRef - || !(jalview.util.Platform.isControlDown(evt) - || evt.isShiftDown())) + || !(Platform.isControlDown(evt) || evt.isShiftDown())) { - if (jalview.util.Platform.isControlDown(evt) - || evt.isShiftDown()) + if (Platform.isControlDown(evt) || evt.isShiftDown()) { // clone a new selection group from the associated group ap.av.setSelectionGroup( @@@ -873,7 -884,8 +876,7 @@@ // we make a copy rather than edit the current selection if no // modifiers pressed // see Enhancement JAL-1557 - if (!(jalview.util.Platform.isControlDown(evt) - || evt.isShiftDown())) + if (!(Platform.isControlDown(evt) || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@@ -881,7 -893,7 +884,7 @@@ } else { - if (jalview.util.Platform.isControlDown(evt)) + if (Platform.isControlDown(evt)) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); } @@@ -926,16 -938,17 +929,17 @@@ if (dseqs[0] == null) { dseqs[0] = new Sequence(sq); - dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, sq.getSequenceAsString())); + dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, + sq.getSequenceAsString())); sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getAlignment().getHiddenColumns() - .getVisibleSequenceStrings(0, sq.getLength(), seqs); + Iterator it = av.getAlignment().getHiddenColumns() + .getVisContigsIterator(0, sq.getLength(), false); + omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; } int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; @@@ -951,12 -964,12 +955,12 @@@ Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (av.hasHiddenColumns()) { - hiddenColumns = av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy(); + hiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset @@@ -1009,6 -1022,8 +1013,6 @@@ drawComponent(g, false, width); } - private final boolean debugRedraw = false; - /** * Draw the full set of annotation Labels for the alignment at the given * cursor @@@ -1191,7 -1206,11 +1195,7 @@@ } } - if (resizePanel) - { - g.drawImage(image, 2, 0 - getScrollOffset(), this); - } - else if (dragEvent != null && aa != null) + if (!resizePanel && dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), @@@ -1210,9 -1229,4 +1214,9 @@@ { return scrollOffset; } + + @Override + public void mouseEntered(MouseEvent e) + { + } } diff --combined src/jalview/gui/AnnotationPanel.java index c39a87d,f8e8a78..71cdc9c --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@@ -724,7 -724,7 +724,7 @@@ public class AnnotationPanel extends JP if (av.hasHiddenColumns()) { column = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(column); + .visibleToAbsoluteColumn(column); } AlignmentAnnotation ann = aa[row]; @@@ -904,8 -904,6 +904,8 @@@ @Override public void paintComponent(Graphics g) { + super.paintComponent(g); + g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); @@@ -961,7 -959,7 +961,7 @@@ gg.fillRect(0, 0, imgWidth, image.getHeight()); imageFresh = true; } - + drawComponent(gg, av.getRanges().getStartRes(), av.getRanges().getEndRes() + 1); imageFresh = false; @@@ -994,8 -992,10 +994,8 @@@ int er = av.getRanges().getEndRes() + 1; int transX = 0; - long stime = System.currentTimeMillis(); gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.getCharWidth(), 0); - long mtime = System.currentTimeMillis(); if (horizontal > 0) // scrollbar pulled right, image to the left { @@@ -1012,13 -1012,17 +1012,13 @@@ drawComponent(gg, sr, er); gg.translate(-transX, 0); - long dtime = System.currentTimeMillis(); + fastPaint = true; - repaint(); - long rtime = System.currentTimeMillis(); - if (debugRedraw) - { - System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t" - + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime) - + "\tRepaint call:\t" + (rtime - dtime)); - } + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the overview + // window and others may be adversely affected. + av.getAlignPanel().repaint(); } private volatile boolean lastImageGood = false; diff --combined src/jalview/gui/IdCanvas.java index 8f13eca,ab96d80..cd7b0b7 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@@ -83,7 -83,7 +83,7 @@@ public class IdCanvas extends JPanel im this.av = av; PaintRefresher.Register(this, av.getSequenceSetId()); av.getRanges().addPropertyChangeListener(this); - } + } /** * DOCUMENT ME! @@@ -204,11 -204,7 +204,11 @@@ gg.translate(0, -transY); fastPaint = true; - repaint(); + + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the overview + // window and others may be adversely affected. + av.getAlignPanel().repaint(); } /** @@@ -220,43 -216,41 +220,43 @@@ @Override public void paintComponent(Graphics g) { + super.paintComponent(g); + g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - + if (fastPaint) { fastPaint = false; g.drawImage(image, 0, 0, this); - + return; } - + int oldHeight = imgHeight; - + imgHeight = getHeight(); imgHeight -= (imgHeight % av.getCharHeight()); - + if (imgHeight < 1) { return; } - + if (oldHeight != imgHeight || image.getWidth(this) != getWidth()) { - image = new BufferedImage(getWidth(), imgHeight, - BufferedImage.TYPE_INT_RGB); + image = new BufferedImage(getWidth(), imgHeight, + BufferedImage.TYPE_INT_RGB); } - + gg = (Graphics2D) image.getGraphics(); - + // Fill in the background gg.setColor(Color.white); gg.fillRect(0, 0, getWidth(), imgHeight); - + drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq()); - + g.drawImage(image, 0, 0, this); } @@@ -380,7 -374,7 +380,7 @@@ if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth) - 1; + .absoluteToVisibleColumn(maxwidth) - 1; } int annotationHeight = 0; diff --combined src/jalview/gui/ScalePanel.java index cb7f0da,f772a1f..e6bba02 --- a/src/jalview/gui/ScalePanel.java +++ b/src/jalview/gui/ScalePanel.java @@@ -42,6 -42,7 +42,7 @@@ import java.awt.event.MouseEvent import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.beans.PropertyChangeEvent; + import java.util.Iterator; import java.util.List; import javax.swing.JMenuItem; @@@ -112,7 -113,7 +113,7 @@@ public class ScalePanel extends JPane if (av.hasHiddenColumns()) { - x = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x); + x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x); } if (x >= av.getAlignment().getWidth()) @@@ -174,7 -175,7 +175,7 @@@ }); pop.add(item); - if (av.getAlignment().getHiddenColumns().hasHiddenColumns()) + if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions()) { item = new JMenuItem(MessageManager.getString("action.reveal_all")); item.addActionListener(new ActionListener() @@@ -281,7 -282,7 +282,7 @@@ if (av.hasHiddenColumns()) { res = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(res); + .visibleToAbsoluteColumn(res); } if (res >= av.getAlignment().getWidth()) @@@ -336,7 -337,7 +337,7 @@@ int res = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes(); res = Math.max(0, res); - res = hidden.adjustForHiddenColumns(res); + res = hidden.visibleToAbsoluteColumn(res); res = Math.min(res, av.getAlignment().getWidth() - 1); min = Math.min(res, min); max = Math.max(res, max); @@@ -392,7 -393,7 +393,7 @@@ reveal = av.getAlignment().getHiddenColumns() .getRegionWithEdgeAtRes(res); - res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res); ToolTipManager.sharedInstance().registerComponent(this); this.setToolTipText( @@@ -409,8 -410,6 +410,8 @@@ @Override public void paintComponent(Graphics g) { + super.paintComponent(g); + /* * shouldn't get called in wrapped mode as the scale above is * drawn instead by SeqCanvas.drawNorthScale @@@ -459,7 -458,7 +460,7 @@@ { if (hidden.isVisible(sel)) { - sel = hidden.findColumnPosition(sel); + sel = hidden.absoluteToVisibleColumn(sel); } else { @@@ -489,23 -488,18 +490,18 @@@ if (av.getShowHiddenMarkers()) { - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) + Iterator it = hidden.getStartRegionIterator(startx, + startx + widthx + 1); + while (it.hasNext()) { - res = pos - startx; - - if (res < 0 || res > widthx) - { - continue; - } + res = it.next() - startx; gg.fillPolygon( new int[] - { -1 + res * avCharWidth - avCharHeight / 4, - -1 + res * avCharWidth + avCharHeight / 4, - -1 + res * avCharWidth }, - new int[] - { y, y, y + 2 * yOf }, 3); + { -1 + res * avCharWidth - avCharHeight / 4, + -1 + res * avCharWidth + avCharHeight / 4, + -1 + res * avCharWidth }, new int[] + { y, y, y + 2 * yOf }, 3); } } } @@@ -556,11 -550,7 +552,11 @@@ || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) { // scroll event, repaint panel - repaint(); + + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the overview + // window and others may be adversely affected. + av.getAlignPanel().repaint(); } } diff --combined src/jalview/gui/SeqCanvas.java index 7d182b2,fb81f4d..2d8eb7d --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@@ -25,6 -25,7 +25,7 @@@ import jalview.datamodel.HiddenColumns import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; + import jalview.datamodel.VisibleContigsIterator; import jalview.renderer.ScaleRenderer; import jalview.renderer.ScaleRenderer.ScaleMark; import jalview.util.Comparison; @@@ -42,6 -43,7 +43,7 @@@ import java.awt.RenderingHints import java.awt.Shape; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; + import java.util.Iterator; import java.util.List; import javax.swing.JComponent; @@@ -198,8 -200,8 +200,8 @@@ public class SeqCanvas extends JCompone if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); - startX = hiddenColumns.adjustForHiddenColumns(startx); - endX = hiddenColumns.adjustForHiddenColumns(endx); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(endx); } FontMetrics fm = getFontMetrics(av.getFont()); @@@ -295,7 -297,7 +297,7 @@@ int endSeq = ranges.getEndSeq(); int transX = 0; int transY = 0; - + gg.copyArea(horizontal * charWidth, vertical * charHeight, img.getWidth(), img.getHeight(), -horizontal * charWidth, -vertical * charHeight); @@@ -337,10 -339,7 +339,10 @@@ drawPanel(gg, startRes, endRes, startSeq, endSeq, 0); gg.translate(-transX, -transY); - repaint(); + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the + // overview window and others may be adversely affected. + av.getAlignPanel().repaint(); } finally { fastpainting = false; @@@ -354,20 -353,20 +356,20 @@@ int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); - + ViewportRanges ranges = av.getRanges(); - + int width = getWidth(); int height = getHeight(); - + width -= (width % charWidth); height -= (height % charHeight); - + // selectImage is the selection group outline image BufferedImage selectImage = drawSelectionGroup( ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq()); - + if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g.getClipBounds().height))) @@@ -391,16 -390,16 +393,16 @@@ gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); } - + if (av.antiAlias) { gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } - + gg.setColor(Color.white); gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - + if (av.getWrapAlignment()) { drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); @@@ -410,7 -409,7 +412,7 @@@ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq(), 0); } - + // lcimg is a local *copy* of img which we'll draw selectImage on top of BufferedImage lcimg = buildLocalImage(selectImage); g.drawImage(lcimg, 0, 0, this); @@@ -507,11 -506,8 +509,11 @@@ private BufferedImage buildLocalImage(BufferedImage selectImage) { // clone the cached image - BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), - img.getType()); + BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + img.getType()); + + // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + // img.getType()); Graphics2D g2d = lcimg.createGraphics(); g2d.drawImage(img, 0, 0, null); @@@ -551,8 -547,8 +553,8 @@@ try { - lcimg = new BufferedImage(width, height, - BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + lcimg = new BufferedImage(width, height, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works } catch (OutOfMemoryError er) { System.gc(); @@@ -896,11 -892,14 +898,14 @@@ int charWidth = av.getCharWidth(); g.setColor(Color.blue); + int res; HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - List positions = hidden.findHiddenRegionPositions(); - for (int pos : positions) + + Iterator it = hidden.getStartRegionIterator(startColumn, + endColumn); + while (it.hasNext()) { - int res = pos - startColumn; + res = it.next() - startColumn; if (res < 0 || res > endColumn - startColumn + 1) { @@@ -949,7 -948,7 +954,7 @@@ if (av.hasHiddenColumns()) { maxwidth = av.getAlignment().getHiddenColumns() - .findColumnPosition(maxwidth); + .absoluteToVisibleColumn(maxwidth); } // chop the wrapped alignment extent up into panel-sized blocks and treat @@@ -1027,29 -1026,23 +1032,23 @@@ else { int screenY = 0; - final int screenYMax = endRes - startRes; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) - { - int hideStart = region[0]; - int hideEnd = region[1]; + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } + while (regions.hasNext()) + { + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; /* * draw up to just before the next hidden region, or the end of * the visible region, whichever comes first */ - blockEnd = Math.min(hideStart - 1, blockStart + screenYMax - - screenY); - g1.translate(screenY * charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); @@@ -1058,7 -1051,8 +1057,8 @@@ * draw the downline of the hidden column marker (ScalePanel draws the * triangle on top) if we reached it */ - if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1) + if (av.getShowHiddenMarkers() + && (regions.hasNext() || regions.endsAtHidden())) { g1.setColor(Color.blue); @@@ -1069,23 -1063,6 +1069,6 @@@ g1.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > screenYMax) - { - // already rendered last block - return; - } - } - - if (screenY <= screenYMax) - { - // remaining visible region to render - blockEnd = blockStart + screenYMax - screenY; - g1.translate(screenY * charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset); - - g1.translate(-screenY * charWidth, 0); } } @@@ -1143,16 -1120,16 +1126,16 @@@ if (av.hasSearchResults()) { SearchResultsI searchResults = av.getSearchResults(); - int[] visibleResults = searchResults.getResults(nextSeq, - startRes, endRes); + int[] visibleResults = searchResults.getResults(nextSeq, startRes, + endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) { seqRdr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], (visibleResults[r] - startRes) - * charWidth, offset - + ((i - startSeq) * charHeight)); + visibleResults[r + 1], + (visibleResults[r] - startRes) * charWidth, + offset + ((i - startSeq) * charHeight)); } } } @@@ -1284,7 -1261,7 +1267,7 @@@ // convert the cursorX into a position on the visible alignment int cursor_xpos = av.getAlignment().getHiddenColumns() - .findColumnPosition(cursorX); + .absoluteToVisibleColumn(cursorX); if (av.getAlignment().getHiddenColumns().isVisible(cursorX)) { @@@ -1383,22 -1360,17 +1366,17 @@@ { // package into blocks of visible columns int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; + int blockStart; + int blockEnd; - for (int[] region : av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + VisibleContigsIterator regions = hidden + .getVisContigsIterator(startRes, endRes + 1, true); + while (regions.hasNext()) { - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; + int[] region = regions.next(); + blockEnd = region[1]; + blockStart = region[0]; g.translate(screenY * charWidth, 0); drawPartialGroupOutline(g, group, @@@ -1406,24 -1378,6 +1384,6 @@@ g.translate(-screenY * charWidth, 0); screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - - if (screenY > (endRes - startRes)) - { - // already rendered last block - break; - } - } - - if (screenY <= (endRes - startRes)) - { - // remaining visible region to render - blockEnd = blockStart + (endRes - startRes) - screenY; - g.translate(screenY * charWidth, 0); - drawPartialGroupOutline(g, group, - blockStart, blockEnd, startSeq, endSeq, offset); - - g.translate(-screenY * charWidth, 0); } } } @@@ -1687,9 -1641,9 +1647,9 @@@ if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } for (int seqNo = ranges.getStartSeq(); seqNo <= ranges @@@ -1732,8 -1686,8 +1692,8 @@@ if (av.hasHiddenColumns()) { firstCol = alignment.getHiddenColumns() - .findColumnPosition(firstCol); - lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol); + .absoluteToVisibleColumn(firstCol); + lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol); } int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth(); int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight(); @@@ -1790,14 -1744,30 +1750,30 @@@ scrollX = -range; } } - // Both scrolling and resizing change viewport ranges: scrolling changes - // both start and end points, but resize only changes end values. - // Here we only want to fastpaint on a scroll, with resize using a normal - // paint, so scroll events are identified as changes to the horizontal or - // vertical start value. - if (eventName.equals(ViewportRanges.STARTRES)) - { - if (av.getWrapAlignment()) + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (eventName.equals(ViewportRanges.STARTRES)) + { + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); + } + else + { + fastPaint(scrollX, 0); + } + } + else if (eventName.equals(ViewportRanges.STARTSEQ)) + { + // scroll + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + if (av.getWrapAlignment()) { fastPaintWrapped(scrollX); } @@@ -1817,14 -1787,6 +1793,6 @@@ { fastPaintWrapped(scrollX); } - else - { - fastPaint(scrollX, 0); - } - // bizarrely, we only need to scroll on the x value here as fastpaint - // copies the full height of the image anyway. Passing in the y value - // causes nasty repaint artefacts, which only disappear on a full - // repaint. } } @@@ -1841,7 -1803,9 +1809,7 @@@ { ViewportRanges ranges = av.getRanges(); - // if (Math.abs(scrollX) > ranges.getViewportWidth()) - // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3 - if (true) + if (Math.abs(scrollX) > ranges.getViewportWidth()) { /* * shift of more than one view width is @@@ -2119,9 -2083,9 +2087,9 @@@ if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); @@@ -2160,7 -2124,7 +2128,7 @@@ if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /* diff --combined src/jalview/viewmodel/AlignmentViewport.java index bca3c85,01ec8b1..1366ada --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@@ -67,6 -67,7 +67,7 @@@ import java.util.BitSet import java.util.Deque; import java.util.HashMap; import java.util.Hashtable; + import java.util.Iterator; import java.util.List; import java.util.Map; @@@ -1740,8 -1741,12 +1741,12 @@@ public abstract class AlignmentViewpor if (alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns()) { - selection = alignment.getHiddenColumns() - .getVisibleSequenceStrings(start, end, seqs); + for (i = 0; i < iSize; i++) + { + Iterator blocks = alignment.getHiddenColumns() + .getVisContigsIterator(start, end + 1, false); + selection[i] = seqs[i].getSequenceStringFromIterator(blocks); + } } else { @@@ -1768,10 -1773,10 +1773,10 @@@ { if (start == 0) { - start = hidden.adjustForHiddenColumns(start); + start = hidden.visibleToAbsoluteColumn(start); } - end = hidden.getHiddenBoundaryRight(start); + end = hidden.getNextHiddenBoundary(false, start); if (start == end) { end = max; @@@ -1786,8 -1791,8 +1791,8 @@@ if (hidden != null && hidden.hasHiddenColumns()) { - start = hidden.adjustForHiddenColumns(end); - start = hidden.getHiddenBoundaryLeft(start) + 1; + start = hidden.visibleToAbsoluteColumn(end); + start = hidden.getNextHiddenBoundary(true, start) + 1; } } while (end < max); @@@ -1809,13 -1814,13 +1814,13 @@@ AlignmentAnnotation clone = new AlignmentAnnotation(annot); if (selectedOnly && selectionGroup != null) { - alignment.getHiddenColumns().makeVisibleAnnotation( + clone.makeVisibleAnnotation( selectionGroup.getStartRes(), selectionGroup.getEndRes(), - clone); + alignment.getHiddenColumns()); } else { - alignment.getHiddenColumns().makeVisibleAnnotation(clone); + clone.makeVisibleAnnotation(alignment.getHiddenColumns()); } ala.add(clone); } @@@ -2781,7 -2786,7 +2786,7 @@@ int lastSeq = alignment.getHeight() - 1; List seqMappings = null; for (int seqNo = ranges - .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) diff --combined src/jalview/viewmodel/OverviewDimensionsHideHidden.java index f58e711,0ca1cc3..de90a21 --- a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java +++ b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java @@@ -50,8 -50,6 +50,8 @@@ public class OverviewDimensionsHideHidd public void updateViewportFromMouse(int mousex, int mousey, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { + resetAlignmentDims(); + int xAsRes = getLeftXFromCentreX(mousex, hiddenCols); int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs); @@@ -63,29 -61,24 +63,29 @@@ public void adjustViewportFromMouse(int mousex, int mousey, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { + resetAlignmentDims(); + // calculate translation in pixel terms: // get mouse location in viewport coords, add translation in viewport // coords, and update viewport as usual - int vpx = Math.round((float) mousex * alwidth / width); - int vpy = Math.round((float) mousey * alheight / sequencesHeight); + int vpx = Math.round(mousex * widthRatio); + int vpy = Math.round(mousey * heightRatio); updateViewportFromTopLeft(vpx + xdiff, vpy + ydiff, hiddenSeqs, hiddenCols); } + /** + * {@inheritDoc} Callers should have already called resetAlignmentDims to + * refresh alwidth, alheight and width/height ratios + */ @Override protected void updateViewportFromTopLeft(int leftx, int topy, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { int xAsRes = leftx; int yAsSeq = topy; - resetAlignmentDims(); if (xAsRes < 0) { @@@ -154,7 -147,7 +154,7 @@@ public AlignmentColsCollectionI getColumns(AlignmentI al) { return new VisibleColsCollection(0, - ranges.getAbsoluteAlignmentWidth() - 1, al); + ranges.getAbsoluteAlignmentWidth() - 1, al.getHiddenColumns()); } @Override @@@ -169,30 -162,19 +169,30 @@@ { alwidth = ranges.getVisibleAlignmentWidth(); alheight = ranges.getVisibleAlignmentHeight(); + + widthRatio = (float) alwidth / width; + heightRatio = (float) alheight / sequencesHeight; } + /** + * {@inheritDoc} Callers should have already called resetAlignmentDims to + * refresh widthRatio + */ @Override protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden) { - int vpx = Math.round((float) mousex * alwidth / width); + int vpx = Math.round(mousex * widthRatio); return vpx - ranges.getViewportWidth() / 2; } + /** + * {@inheritDoc} Callers should have already called resetAlignmentDims to + * refresh heightRatio + */ @Override protected int getTopYFromCentreY(int mousey, HiddenSequences hidden) { - int vpy = Math.round((float) mousey * alheight / sequencesHeight); + int vpy = Math.round(mousey * heightRatio); return vpy - ranges.getViewportHeight() / 2; } @@@ -200,12 -182,10 +200,12 @@@ public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { + resetAlignmentDims(); + // get alignment position of x and box (can get directly from vpranges) and // calculate difference between the positions - int vpx = Math.round((float) x * alwidth / width); - int vpy = Math.round((float) y * alheight / sequencesHeight); + int vpx = Math.round(x * widthRatio); + int vpy = Math.round(y * heightRatio); xdiff = ranges.getStartRes() - vpx; ydiff = ranges.getStartSeq() - vpy; diff --combined src/jalview/viewmodel/OverviewDimensionsShowHidden.java index eaa3413,79e1c47..3aa6e1b --- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java +++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java @@@ -72,15 -72,13 +72,15 @@@ public class OverviewDimensionsShowHidd public void updateViewportFromMouse(int mousex, int mousey, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { + resetAlignmentDims(); + // convert mousex and mousey to alignment units as well as // translating to top left corner of viewport - this is an absolute position int xAsRes = getLeftXFromCentreX(mousex, hiddenCols); int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs); // convert to visible positions - int visXAsRes = hiddenCols.findColumnPosition(xAsRes); + int visXAsRes = hiddenCols.absoluteToVisibleColumn(xAsRes); yAsSeq = hiddenSeqs.adjustForHiddenSeqs( hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq)); yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence @@@ -95,32 -93,27 +95,32 @@@ public void adjustViewportFromMouse(int mousex, int mousey, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { + resetAlignmentDims(); + // calculate translation in pixel terms: // get mouse location in viewport coords, add translation in viewport // coords, // convert back to pixel coords - int vpx = Math.round(mousex * widthRatio); - int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff; + int vpx = Math.round((float) mousex * alwidth / width); + int visXAsRes = hiddenCols.absoluteToVisibleColumn(vpx) + xdiff; - int vpy = Math.round((float) mousey * alheight / sequencesHeight); + int vpy = Math.round(mousey * heightRatio); int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff; // update viewport accordingly updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols); } + /** + * {@inheritDoc} Callers should have already called resetAlignmentDims to + * refresh alwidth, alheight and width/height ratios + */ @Override protected void updateViewportFromTopLeft(int leftx, int topy, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { int visXAsRes = leftx; int visYAsSeq = topy; - resetAlignmentDims(); if (visXAsRes < 0) { @@@ -143,7 -136,7 +143,7 @@@ int vpwidth = ranges.getViewportWidth(); // check in case we went off the edge of the alignment - int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1); + int visAlignWidth = hiddenCols.absoluteToVisibleColumn(alwidth - 1); if (visXAsRes + vpwidth - 1 > visAlignWidth) { // went past the end of the alignment, adjust backwards @@@ -151,8 -144,8 +151,8 @@@ // if last position was before the end of the alignment, need to update if (ranges.getEndRes() < visAlignWidth) { - visXAsRes = hiddenCols.findColumnPosition(hiddenCols - .subtractVisibleColumns(vpwidth - 1, alwidth - 1)); + visXAsRes = hiddenCols.absoluteToVisibleColumn(hiddenCols + .offsetByVisibleColumns(-(vpwidth - 1), alwidth - 1)); } else { @@@ -202,8 -195,8 +202,8 @@@ HiddenColumns hiddenCols) { // work with absolute values of startRes and endRes - int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes()); - int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes()); + int startRes = hiddenCols.visibleToAbsoluteColumn(ranges.getStartRes()); + int endRes = hiddenCols.visibleToAbsoluteColumn(ranges.getEndRes()); // work with absolute values of startSeq and endSeq int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq()); @@@ -232,32 -225,20 +232,32 @@@ { alwidth = ranges.getAbsoluteAlignmentWidth(); alheight = ranges.getAbsoluteAlignmentHeight(); + + widthRatio = (float) alwidth / width; + heightRatio = (float) alheight / sequencesHeight; } + + /** + * {@inheritDoc} Callers should have already called resetAlignmentDims to + * refresh widthRatio + */ @Override protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden) { - int vpx = Math.round(mousex * widthRatio); - return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2, + int vpx = Math.round((float) mousex * alwidth / width); + return hidden.offsetByVisibleColumns(-ranges.getViewportWidth() / 2, vpx); } + /** + * {@inheritDoc} Callers should have already called resetAlignmentDims to + * refresh heightRatio + */ @Override protected int getTopYFromCentreY(int mousey, HiddenSequences hidden) { - int vpy = Math.round((float) mousey * alheight / sequencesHeight); + int vpy = Math.round(mousey * heightRatio); return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy); } @@@ -265,14 -246,12 +265,14 @@@ public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { + resetAlignmentDims(); + // get alignment position of x and box (can get directly from vpranges) and // calculate difference between the positions - int vpx = Math.round((float) x * alwidth / width); - int vpy = Math.round((float) y * alheight / sequencesHeight); + int vpx = Math.round(x * widthRatio); + int vpy = Math.round(y * heightRatio); - xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx); + xdiff = ranges.getStartRes() - hiddenCols.absoluteToVisibleColumn(vpx); ydiff = ranges.getStartSeq() - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy); } diff --combined test/jalview/datamodel/AlignmentTest.java index 74ac146,ddba949..266b90a --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@@ -34,6 -34,7 +34,7 @@@ import jalview.io.DataSourceType import jalview.io.FileFormat; import jalview.io.FileFormatI; import jalview.io.FormatAdapter; + import jalview.util.Comparison; import jalview.util.MapList; import java.io.IOException; @@@ -668,17 -669,6 +669,17 @@@ public class AlignmentTes // third found.. so assertFalse(iter.hasNext()); + // search for annotation on one sequence with a particular label - expect + // one + SequenceI sqfound; + anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null, + "Secondary Structure"); + iter = anns.iterator(); + assertTrue(iter.hasNext()); + // expect reference to sequence 1 in the alignment + assertTrue(sqfound == iter.next().sequenceRef); + assertFalse(iter.hasNext()); + // null on all parameters == find all annotations anns = al.findAnnotations(null, null, null); iter = anns.iterator(); @@@ -1333,21 -1323,134 +1334,152 @@@ // hidden sequences, properties } + /** + * test that calcId == null on findOrCreate doesn't raise an NPE, and yields + * an annotation with a null calcId + * + */ + @Test(groups = "Functional") + public void testFindOrCreateForNullCalcId() + { + SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-"); + AlignmentI alignment = new Alignment(new SequenceI[] { seq }); + + AlignmentAnnotation ala = alignment.findOrCreateAnnotation( + "Temperature Factor", null, false, seq, null); + assertNotNull(ala); + assertEquals(seq, ala.sequenceRef); + assertEquals("", ala.calcId); + } ++ + @Test(groups = "Functional") + public void testPropagateInsertions() + { + // create an alignment with no gaps - this will be the profile seq and other + // JPRED seqs + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI al = gen.generate(25, 10, 1234, 0, 0); + + // get the profileseq + SequenceI profileseq = al.getSequenceAt(0); + SequenceI gappedseq = new Sequence(profileseq); + gappedseq.insertCharAt(5, al.getGapCharacter()); + gappedseq.insertCharAt(6, al.getGapCharacter()); + gappedseq.insertCharAt(7, al.getGapCharacter()); + gappedseq.insertCharAt(8, al.getGapCharacter()); + + // force different kinds of padding + al.getSequenceAt(3).deleteChars(2, 23); + al.getSequenceAt(4).deleteChars(2, 27); + al.getSequenceAt(5).deleteChars(10, 27); + + // create an alignment view with the gapped sequence + SequenceI[] seqs = new SequenceI[1]; + seqs[0] = gappedseq; + AlignmentI newal = new Alignment(seqs); + HiddenColumns hidden = new HiddenColumns(); + hidden.hideColumns(15, 17); + + AlignmentView view = new AlignmentView(newal, hidden, null, true, false, + false); + + // confirm that original contigs are as expected + Iterator visible = hidden.getVisContigsIterator(0, 25, false); + int[] region = visible.next(); + assertEquals("[0, 14]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[18, 24]", Arrays.toString(region)); + + // propagate insertions + HiddenColumns result = al.propagateInsertions(profileseq, view); + + // confirm that the contigs have changed to account for the gaps + visible = result.getVisContigsIterator(0, 25, false); + region = visible.next(); + assertEquals("[0, 10]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[14, 24]", Arrays.toString(region)); + + // confirm the alignment has been changed so that the other sequences have + // gaps inserted where the columns are hidden + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13])); + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14])); + + } + + @Test(groups = "Functional") + public void testPropagateInsertionsOverlap() + { + // test propagateInsertions where gaps and hiddenColumns overlap + + // create an alignment with no gaps - this will be the profile seq and other + // JPRED seqs + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI al = gen.generate(20, 10, 1234, 0, 0); + + // get the profileseq + SequenceI profileseq = al.getSequenceAt(0); + SequenceI gappedseq = new Sequence(profileseq); + gappedseq.insertCharAt(5, al.getGapCharacter()); + gappedseq.insertCharAt(6, al.getGapCharacter()); + gappedseq.insertCharAt(7, al.getGapCharacter()); + gappedseq.insertCharAt(8, al.getGapCharacter()); + + // create an alignment view with the gapped sequence + SequenceI[] seqs = new SequenceI[1]; + seqs[0] = gappedseq; + AlignmentI newal = new Alignment(seqs); + + // hide columns so that some overlap with the gaps + HiddenColumns hidden = new HiddenColumns(); + hidden.hideColumns(7, 10); + + AlignmentView view = new AlignmentView(newal, hidden, null, true, false, + false); + + // confirm that original contigs are as expected + Iterator visible = hidden.getVisContigsIterator(0, 20, false); + int[] region = visible.next(); + assertEquals("[0, 6]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[11, 19]", Arrays.toString(region)); + assertFalse(visible.hasNext()); + + // propagate insertions + HiddenColumns result = al.propagateInsertions(profileseq, view); + + // confirm that the contigs have changed to account for the gaps + visible = result.getVisContigsIterator(0, 20, false); + region = visible.next(); + assertEquals("[0, 4]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[7, 19]", Arrays.toString(region)); + assertFalse(visible.hasNext()); + + // confirm the alignment has been changed so that the other sequences have + // gaps inserted where the columns are hidden + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6])); + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7])); + } + + @Test(groups = { "Functional" }) + public void testPadGaps() + { + SequenceI seq1 = new Sequence("seq1", "ABCDEF--"); + SequenceI seq2 = new Sequence("seq2", "-JKLMNO--"); + SequenceI seq3 = new Sequence("seq2", "-PQR"); + AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); + a.setGapCharacter('.'); // this replaces existing gaps + assertEquals("ABCDEF..", seq1.getSequenceAsString()); + a.padGaps(); + // trailing gaps are pruned, short sequences padded with gap character + assertEquals("ABCDEF.", seq1.getSequenceAsString()); + assertEquals(".JKLMNO", seq2.getSequenceAsString()); + assertEquals(".PQR...", seq3.getSequenceAsString()); + } }