X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=68b1998fa92fa9f217defcac4f8ddcf5f77d0ecb;hb=8474476096a0bbce03c7748aa3c267fbf6258249;hp=b6bd4af90fa84a459997f03cbf053ac1fa10c7b5;hpb=eac3f8019fe37f2c84784adef3a7db56598c5cb8;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index b6bd4af..68b1998 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -30,10 +30,12 @@ import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.io.HTMLOutput; import jalview.jbgui.GAlignmentPanel; import jalview.math.AlignmentDimension; import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.ViewportListenerI; @@ -74,8 +76,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { public AlignViewport av; - ViewportRanges vpRanges; - OverviewPanel overviewPanel; private SeqPanel seqPanel; @@ -95,9 +95,6 @@ public class AlignmentPanel extends GAlignmentPanel implements private AnnotationLabels alabels; - // this value is set false when selection area being dragged - boolean fastPaint = true; - private int hextent = 0; private int vextent = 0; @@ -122,7 +119,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { alignFrame = af; this.av = av; - vpRanges = av.getRanges(); setSeqPanel(new SeqPanel(av, this)); setIdPanel(new IdPanel(av, this)); @@ -154,11 +150,12 @@ public class AlignmentPanel extends GAlignmentPanel implements // reset the viewport ranges when the alignment panel is resized // in particular, this initialises the end residue value when Jalview // is initialised + ViewportRanges ranges = av.getRanges(); if (av.getWrapAlignment()) { int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( getSeqPanel().seqCanvas.getWidth()); - vpRanges.setViewportWidth(widthInRes); + ranges.setViewportWidth(widthInRes); } else { @@ -167,8 +164,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int heightInSeq = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - vpRanges.setViewportWidth(widthInRes); - vpRanges.setViewportHeight(heightInSeq); + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); } } @@ -212,7 +209,8 @@ public class AlignmentPanel extends GAlignmentPanel implements alignFrame.updateEditMenuBar(); - paintAlignment(true); + // no idea if we need to update structure + paintAlignment(true, true); } @@ -229,7 +227,8 @@ public class AlignmentPanel extends GAlignmentPanel implements new Dimension(10, av.getCharHeight() + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize( new Dimension(10, av.getCharHeight() + fm.getDescent())); - + idwidthAdjuster.invalidate(); + scalePanelHolder.invalidate(); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; getAnnotationPanel().adjustPanelHeight(); @@ -240,11 +239,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); - if (this.alignFrame.getSplitViewContainer() != null) - { - ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); - } - repaint(); } @@ -340,19 +334,11 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void highlightSearchResults(SearchResultsI results) { - scrollToPosition(results); - getSeqPanel().seqCanvas.highlightSearchResults(results); - } + boolean scrolled = scrollToPosition(results, 0, true, false); - /** - * Scroll the view to show the position of the highlighted region in results - * (if any) and redraw the overview - * - * @param results - */ - public boolean scrollToPosition(SearchResultsI results) - { - return scrollToPosition(results, 0, true, false); + boolean noFastPaint = scrolled && av.getWrapAlignment(); + + getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint); } /** @@ -370,8 +356,10 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Scroll the view to show the position of the highlighted region in results - * (if any) + * Scrolls the view (if necessary) to show the position of the first + * highlighted region in results (if any). Answers true if the view was + * scrolled, or false if no matched region was found, or it is already + * visible. * * @param results * @param verticalOffset @@ -381,116 +369,118 @@ public class AlignmentPanel extends GAlignmentPanel implements * - when set, the overview will be recalculated (takes longer) * @param centre * if true, try to centre the search results horizontally in the view - * @return false if results were not found + * @return */ - public boolean scrollToPosition(SearchResultsI results, + protected boolean scrollToPosition(SearchResultsI results, int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; - // TODO: properly locate search results in view when large numbers of hidden - // columns exist before highlighted region - // do we need to scroll the panel? - // TODO: tons of nullpointerexceptions raised here. - if (results != null && results.getSize() > 0 && av != null - && av.getAlignment() != null) - { - int seqIndex = av.getAlignment().findIndex(results); - if (seqIndex == -1) - { - return false; - } - SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); + ViewportRanges ranges = av.getRanges(); - int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); - if (r == null) - { - return false; - } - int start = r[0]; - int end = r[1]; + if (results == null || results.isEmpty() || av == null + || av.getAlignment() == null) + { + return false; + } + int seqIndex = av.getAlignment().findIndex(results); + if (seqIndex == -1) + { + return false; + } + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); - /* - * To centre results, scroll to positions half the visible width - * left/right of the start/end positions - */ - if (centre) - { - int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - - 1; - start = Math.max(start - offset, 0); - end = end + offset - 1; - } - if (start < 0) - { - return false; - } - if (end == seq.getEnd()) - { - return false; - } - if (av.hasHiddenColumns()) + int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); + if (r == null) + { + return false; + } + int start = r[0]; + int end = r[1]; + + /* + * To centre results, scroll to positions half the visible width + * left/right of the start/end positions + */ + if (centre) + { + int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1; + start = Math.max(start - offset, 0); + end = end + offset - 1; + } + if (start < 0) + { + return false; + } + if (end == seq.getEnd()) + { + return false; + } + + if (av.hasHiddenColumns()) + { + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + start = hidden.findColumnPosition(start); + end = hidden.findColumnPosition(end); + if (start == end) { - HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - start = hidden.findColumnPosition(start); - end = hidden.findColumnPosition(end); - if (start == end) + if (!hidden.isVisible(r[0])) { - if (!hidden.isVisible(r[0])) - { - // don't scroll - position isn't visible - return false; - } + // don't scroll - position isn't visible + return false; } } + } - /* - * allow for offset of target sequence (actually scroll to one above it) - */ - seqIndex = Math.max(0, seqIndex - verticalOffset); + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + boolean scrollNeeded = true; - if (!av.getWrapAlignment()) + if (!av.getWrapAlignment()) + { + if ((startv = ranges.getStartRes()) >= start) { - if ((startv = vpRanges.getStartRes()) >= start) - { - /* - * Scroll left to make start of search results visible - */ - setScrollValues(start, seqIndex); - } - else if ((endv = vpRanges.getEndRes()) <= end) - { - /* - * Scroll right to make end of search results visible - */ - setScrollValues(startv + end - endv, seqIndex); - } - else if ((starts = vpRanges.getStartSeq()) > seqIndex) - { - /* - * Scroll up to make start of search results visible - */ - setScrollValues(vpRanges.getStartRes(), seqIndex); - } - else if ((ends = vpRanges.getEndSeq()) <= seqIndex) - { - /* - * Scroll down to make end of search results visible - */ - setScrollValues(vpRanges.getStartRes(), - starts + seqIndex - ends + 1); - } /* - * Else results are already visible - no need to scroll + * Scroll left to make start of search results visible */ + setScrollValues(start, seqIndex); } - else + else if ((endv = ranges.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + end - endv, seqIndex); + } + else if ((starts = ranges.getStartSeq()) > seqIndex) + { + /* + * Scroll up to make start of search results visible + */ + setScrollValues(ranges.getStartRes(), seqIndex); + } + else if ((ends = ranges.getEndSeq()) <= seqIndex) { - vpRanges.scrollToWrappedVisible(start); + /* + * Scroll down to make end of search results visible + */ + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + + 1); } + /* + * Else results are already visible - no need to scroll + */ + scrollNeeded = false; + } + else + { + scrollNeeded = ranges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); - return true; + paintAlignment(redrawOverview, false); + + return scrollNeeded; } /** @@ -545,7 +535,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } validateAnnotationDimensions(true); addNotify(); - paintAlignment(true); + // TODO: many places call this method and also paintAlignment with various + // different settings. this means multiple redraws are triggered... + paintAlignment(true, false); } /** @@ -612,7 +604,8 @@ public class AlignmentPanel extends GAlignmentPanel implements fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - vpRanges.setStartSeq(0); + ViewportRanges ranges = av.getRanges(); + ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -635,16 +628,16 @@ public class AlignmentPanel extends GAlignmentPanel implements { int widthInRes = getSeqPanel().seqCanvas .getWrappedCanvasWidth(canvasWidth); - vpRanges.setViewportWidth(widthInRes); + ranges.setViewportWidth(widthInRes); } else { - int widthInRes = (canvasWidth / av.getCharWidth()) - 1; + int widthInRes = (canvasWidth / av.getCharWidth()); int heightInSeq = (getSeqPanel().seqCanvas.getHeight() - / av.getCharHeight()) - 1; + / av.getCharHeight()); - vpRanges.setViewportWidth(widthInRes); - vpRanges.setViewportHeight(heightInSeq); + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); } } @@ -743,10 +736,12 @@ public class AlignmentPanel extends GAlignmentPanel implements return; } + ViewportRanges ranges = av.getRanges(); + if (evt.getSource() == hscroll) { - int oldX = vpRanges.getStartRes(); - int oldwidth = vpRanges.getViewportWidth(); + int oldX = ranges.getStartRes(); + int oldwidth = ranges.getViewportWidth(); int x = hscroll.getValue(); int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@ -757,12 +752,12 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - vpRanges.setViewportStartAndWidth(x, width); + ranges.setViewportStartAndWidth(x, width); } else if (evt.getSource() == vscroll) { - int oldY = vpRanges.getStartSeq(); - int oldheight = vpRanges.getViewportHeight(); + int oldY = ranges.getStartSeq(); + int oldheight = ranges.getViewportHeight(); int y = vscroll.getValue(); int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); @@ -773,12 +768,9 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - vpRanges.setViewportStartAndHeight(y, height); - } - if (!fastPaint) - { - repaint(); + ranges.setViewportStartAndHeight(y, height); } + repaint(); } /** @@ -793,6 +785,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; // no horizontal scroll when wrapped } + final ViewportRanges ranges = av.getRanges(); + if (evt.getSource() == vscroll) { int newY = vscroll.getValue(); @@ -802,8 +796,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * this prevents infinite recursion of events when the scroll/viewport * ranges values are the same */ - int oldX = vpRanges.getStartRes(); - int oldY = vpRanges.getWrappedScrollPosition(oldX); + int oldX = ranges.getStartRes(); + int oldY = ranges.getWrappedScrollPosition(oldX); if (oldY == newY) { return; @@ -813,9 +807,9 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * limit page up/down to one width's worth of positions */ - int rowSize = vpRanges.getViewportWidth(); + int rowSize = ranges.getViewportWidth(); int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; - vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize); + ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } else @@ -836,20 +830,20 @@ public class AlignmentPanel extends GAlignmentPanel implements "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel - vpRanges.setStartRes(0); - vpRanges.setStartSeq(0); + ranges.setStartRes(0); + ranges.setStartSeq(0); } }); } repaint(); } - /** - * Repaint the alignment including the annotations and overview panels (if - * shown). + /* (non-Javadoc) + * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean) */ @Override - public void paintAlignment(boolean updateOverview) + public void paintAlignment(boolean updateOverview, + boolean updateStructures) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); @@ -857,10 +851,12 @@ public class AlignmentPanel extends GAlignmentPanel implements av.getSortAnnotationsBy()); repaint(); - if (updateOverview) + if (updateStructures) { - // TODO: determine if this paintAlignment changed structure colours av.getStructureSelectionManager().sequenceColoursChanged(this); + } + if (updateOverview) + { if (overviewPanel != null) { @@ -878,17 +874,20 @@ public class AlignmentPanel extends GAlignmentPanel implements @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. */ - setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); + ViewportRanges ranges = av.getRanges(); + setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); } /** @@ -900,8 +899,9 @@ public class AlignmentPanel extends GAlignmentPanel implements */ private void setScrollingForWrappedPanel(int topLeftColumn) { - int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn); - int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn); + ViewportRanges ranges = av.getRanges(); + int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn); + int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn); /* * a scrollbar's value can be set to at most (maximum-extent) @@ -1103,8 +1103,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); - getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes, - startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, + endRes, startSeq, endSeq); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1231,7 +1231,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, totalHeight, 0); if ((pi * pheight) < totalHeight) @@ -1437,35 +1437,33 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.getAlignment().getHeight(), res, - alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize, - sy; + int sSize = av.getAlignment().getHeight(); + int alwidth = av.getAlignment().getWidth(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); - out.println(jalview.io.HTMLOutput.getImageMapHTML()); + out.println(HTMLOutput.getImageMapHTML()); out.println("" + ""); - for (s = 0; s < sSize; s++) + for (int s = 0; s < sSize; s++) { - sy = s * av.getCharHeight() + scaleHeight; + int sy = s * av.getCharHeight() + scaleHeight; SequenceI seq = av.getAlignment().getSequenceAt(s); - SequenceFeature[] features = seq.getSequenceFeatures(); SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); - for (res = 0; res < alwidth; res++) + for (int column = 0; column < alwidth; column++) { - StringBuilder text = new StringBuilder(); + StringBuilder text = new StringBuilder(512); String triplet = null; if (av.getAlignment().isNucleotide()) { - triplet = ResidueProperties.nucleotideName - .get(seq.getCharAt(res) + ""); + triplet = ResidueProperties.nucleotideName.get(seq + .getCharAt(column) + ""); } else { - triplet = ResidueProperties.aa2Triplet - .get(seq.getCharAt(res) + ""); + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) + + ""); } if (triplet == null) @@ -1473,84 +1471,73 @@ public class AlignmentPanel extends GAlignmentPanel implements continue; } - int alIndex = seq.findPosition(res); - gSize = groups.length; - for (g = 0; g < gSize; g++) + int seqPos = seq.findPosition(column); + int gSize = groups.length; + for (int g = 0; g < gSize; g++) { if (text.length() < 1) { text.append(" res) + if (groups[g].getStartRes() < column + && groups[g].getEndRes() > column) { text.append("
").append(groups[g].getName()) .append(""); } } - if (features != null) + if (text.length() < 1) { - if (text.length() < 1) - { - text.append(" features = seq.findFeatures(column, column); + for (SequenceFeature sf : features) { - - if ((features[f].getBegin() <= seq.findPosition(res)) - && (features[f].getEnd() >= seq.findPosition(res))) + if (sf.isContactFeature()) { - if (features[f].isContactFeature()) - { - if (features[f].getBegin() == seq.findPosition(res) - || features[f].getEnd() == seq - .findPosition(res)) - { - text.append("
").append(features[f].getType()) - .append(" ").append(features[f].getBegin()) - .append(":").append(features[f].getEnd()); - } - } - else + text.append("
").append(sf.getType()).append(" ") + .append(sf.getBegin()).append(":") + .append(sf.getEnd()); + } + else + { + text.append("
"); + text.append(sf.getType()); + String description = sf.getDescription(); + if (description != null + && !sf.getType().equals(description)) { - text.append("
"); - text.append(features[f].getType()); - if (features[f].getDescription() != null && !features[f] - .getType().equals(features[f].getDescription())) - { - text.append(" ").append(features[f].getDescription()); - } - - if (features[f].getValue("status") != null) - { - text.append(" (") - .append(features[f].getValue("status")) - .append(")"); - } + description = description.replace("\"", """); + text.append(" ").append(description); } } - + String status = sf.getStatus(); + if (status != null && !"".equals(status)) + { + text.append(" (").append(status).append(")"); + } + } + if (text.length() > 1) + { + text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); + out.println(text.toString()); } - } - if (text.length() > 1) - { - text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); - out.println(text.toString()); } } } @@ -1631,8 +1618,8 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av != null) { av.removePropertyChangeListener(propertyChangeListener); - jalview.structure.StructureSelectionManager ssm = av - .getStructureSelectionManager(); + propertyChangeListener = null; + StructureSelectionManager ssm = av.getStructureSelectionManager(); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); ssm.removeCommandListener(av); @@ -1826,37 +1813,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param verticalOffset * the number of visible sequences to show above the mapped region */ - public void scrollToCentre(SearchResultsI sr, int verticalOffset) + 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); } @@ -1893,7 +1851,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (adjustHeight) { // sort, repaint, update overview - paintAlignment(true); + paintAlignment(true, false); } else { @@ -1910,8 +1868,9 @@ public class AlignmentPanel extends GAlignmentPanel implements public void propertyChange(PropertyChangeEvent evt) { // update this panel's scroll values based on the new viewport ranges values - int x = vpRanges.getStartRes(); - int y = vpRanges.getStartSeq(); + ViewportRanges ranges = av.getRanges(); + int x = ranges.getStartRes(); + int y = ranges.getStartSeq(); setScrollValues(x, y); // now update any complementary alignment (its viewport ranges object