X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=2f6e3e401d534283f9a6a9e0562f54945a1a9657;hb=fcb68d2ebaf7ebdde2bf6e857de856dc7f46a8da;hp=ad7e75c50b2852a8100ad6e0a81f5e81fb0b4f96;hpb=c54d46db524f1acf7cf4659a9603bbe50518440f;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index ad7e75c..2f6e3e4 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -25,7 +25,8 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; @@ -33,8 +34,10 @@ 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.ViewportRanges; import java.awt.BorderLayout; import java.awt.Color; @@ -69,6 +72,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { public AlignViewport av; + ViewportRanges vpRanges; + OverviewPanel overviewPanel; private SeqPanel seqPanel; @@ -76,6 +81,7 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; private boolean headless; + IdwidthAdjuster idwidthAdjuster; /** DOCUMENT ME!! */ @@ -90,15 +96,19 @@ public class AlignmentPanel extends GAlignmentPanel implements // this value is set false when selection area being dragged boolean fastPaint = true; - int hextent = 0; + private int hextent = 0; - int vextent = 0; + private int vextent = 0; /* * Flag set while scrolling to follow complementary cDNA/protein scroll. When * true, suppresses invoking the same method recursively. */ - private boolean followingComplementScroll; + private boolean dontScrollComplement; + + private PropertyChangeListener propertyChangeListener; + + private CalculationChooser calculationDialog; /** * Creates a new AlignmentPanel object. @@ -110,6 +120,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { alignFrame = af; this.av = av; + vpRanges = av.getRanges(); setSeqPanel(new SeqPanel(av, this)); setIdPanel(new IdPanel(av, this)); @@ -134,8 +145,9 @@ public class AlignmentPanel extends GAlignmentPanel implements vscroll.addAdjustmentListener(this); final AlignmentPanel ap = this; - av.addPropertyChangeListener(new PropertyChangeListener() + propertyChangeListener = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -144,7 +156,8 @@ public class AlignmentPanel extends GAlignmentPanel implements alignmentChanged(); } } - }); + }; + av.addPropertyChangeListener(propertyChangeListener); fontChanged(); adjustAnnotationHeight(); updateLayout(); @@ -155,10 +168,16 @@ public class AlignmentPanel extends GAlignmentPanel implements { return av; } + public void alignmentChanged() { av.alignmentChanged(this); + if (getCalculationDialog() != null) + { + getCalculationDialog().validateCalcTypes(); + } + alignFrame.updateEditMenuBar(); paintAlignment(true); @@ -177,8 +196,7 @@ public class AlignmentPanel extends GAlignmentPanel implements scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av - .getCharHeight() - + fm.getDescent())); + .getCharHeight() + fm.getDescent())); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; @@ -292,7 +310,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * Highlight the given results on the alignment. * */ - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { scrollToPosition(results); getSeqPanel().seqCanvas.highlightSearchResults(results); @@ -304,7 +322,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * * @param results */ - public boolean scrollToPosition(SearchResults results) + public boolean scrollToPosition(SearchResultsI results) { return scrollToPosition(results, 0, true, false); } @@ -317,7 +335,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param redrawOverview * @return */ - public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview) + public boolean scrollToPosition(SearchResultsI searchResults, + boolean redrawOverview) { return scrollToPosition(searchResults, 0, redrawOverview, false); } @@ -336,9 +355,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * if true, try to centre the search results horizontally in the view * @return false if results were not found */ - public boolean scrollToPosition(SearchResults results, - int verticalOffset, - boolean redrawOverview, boolean centre) + public 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 @@ -362,8 +380,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } int start = r[0]; int end = r[1]; - // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // // DEBUG + // System.err.println(this.av.viewName + " Seq : " + seqIndex + // + " Scroll to " + start + "," + end); /* * To centre results, scroll to positions half the visible width @@ -371,9 +390,9 @@ public class AlignmentPanel extends GAlignmentPanel implements */ if (centre) { - int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1; + int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1; start = Math.max(start - offset, 0); - end = Math.min(end + offset, seq.getEnd() - 1); + end = end + offset - 1; } if (start < 0) { @@ -385,11 +404,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (av.hasHiddenColumns()) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + start = hidden.findColumnPosition(start); + end = hidden.findColumnPosition(end); if (start == end) { - if (!av.getColumnSelection().isVisible(r[0])) + if (!hidden.isVisible(r[0])) { // don't scroll - position isn't visible return false; @@ -402,9 +422,12 @@ public class AlignmentPanel extends GAlignmentPanel implements */ seqIndex = Math.max(0, seqIndex - verticalOffset); + // System.out.println("start=" + start + ", end=" + end + ", startv=" + // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts=" + // + av.getStartSeq() + ", ends=" + av.getEndSeq()); if (!av.getWrapAlignment()) { - if ((startv = av.getStartRes()) >= start) + if ((startv = vpRanges.getStartRes()) >= start) { /* * Scroll left to make start of search results visible @@ -412,7 +435,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // setScrollValues(start - 1, seqIndex); // plus one residue setScrollValues(start, seqIndex); } - else if ((endv = av.getEndRes()) <= end) + else if ((endv = vpRanges.getEndRes()) <= end) { /* * Scroll right to make end of search results visible @@ -420,19 +443,20 @@ public class AlignmentPanel extends GAlignmentPanel implements // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one setScrollValues(startv + end - endv, seqIndex); } - else if ((starts = av.getStartSeq()) > seqIndex) + else if ((starts = vpRanges.getStartSeq()) > seqIndex) { /* * Scroll up to make start of search results visible */ - setScrollValues(av.getStartRes(), seqIndex); + setScrollValues(vpRanges.getStartRes(), seqIndex); } - else if ((ends = av.getEndSeq()) <= seqIndex) + else if ((ends = vpRanges.getEndSeq()) <= seqIndex) { /* * Scroll down to make end of search results visible */ - setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends + + 1); } /* * Else results are already visible - no need to scroll @@ -455,10 +479,11 @@ public class AlignmentPanel extends GAlignmentPanel implements { int cwidth = getSeqPanel().seqCanvas .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) + if (res < vpRanges.getStartRes() + || res >= (vpRanges.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); - av.startRes = vscroll.getValue() * cwidth; + vpRanges.setStartRes(vscroll.getValue() * cwidth); } } @@ -504,6 +529,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * automatically adjust annotation panel height for new annotation whilst * ensuring the alignment is still visible. */ + @Override public void adjustAnnotationHeight() { // TODO: display vertical annotation scrollbar if necessary @@ -561,6 +587,9 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationScroller.setPreferredSize(new Dimension(annotationScroller .getWidth(), annotationHeight)); + Dimension e = idPanel.getSize(); + alabels.setSize(new Dimension(e.width, annotationHeight)); + annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), annotationHeight)); annotationScroller.validate(); @@ -578,7 +607,7 @@ public class AlignmentPanel extends GAlignmentPanel implements fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - av.startSeq = 0; + vpRanges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -668,14 +697,13 @@ public class AlignmentPanel extends GAlignmentPanel implements * Adjust row/column scrollers to show a visible position in the alignment. * * @param x - * visible column to scroll to DOCUMENT ME! + * visible column to scroll to * @param y * visible row to scroll to * */ public void setScrollValues(int x, int y) { - // System.err.println("Scroll to "+x+","+y); if (av == null || av.getAlignment() == null) { return; @@ -685,12 +713,11 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { - width = av.getColumnSelection().findColumnPosition(width); + // reset the width to exclude hidden columns + width = av.getAlignment().getHiddenColumns() + .findColumnPosition(width); } - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av - .getCharWidth())) - 1); - hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); @@ -724,7 +751,18 @@ public class AlignmentPanel extends GAlignmentPanel implements x = 0; } + // update endRes after x has (possibly) been adjusted + vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); + + /* + * each scroll adjustment triggers adjustmentValueChanged, which resets the + * 'do not scroll complement' flag; ensure it is the same for both + * operations + */ + boolean flag = isDontScrollComplement(); hscroll.setValues(x, hextent, 0, width); + setDontScrollComplement(flag); vscroll.setValues(y, vextent, 0, height); } @@ -734,16 +772,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param evt * DOCUMENT ME! */ + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - int oldX = av.getStartRes(); - int oldY = av.getStartSeq(); + int oldX = vpRanges.getStartRes(); + int oldY = vpRanges.getStartSeq(); if (evt.getSource() == hscroll) { int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1); + vpRanges.setStartRes(x); + vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -756,8 +796,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { int rowSize = getSeqPanel().seqCanvas .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - av.setStartRes(offy * rowSize); - av.setEndRes((offy + 1) * rowSize); + vpRanges.setStartRes(offy * rowSize); + vpRanges.setEndRes((offy + 1) * rowSize); } else { @@ -766,18 +806,21 @@ public class AlignmentPanel extends GAlignmentPanel implements // as preference setting SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - setScrollValues(av.getStartRes(), av.getStartSeq()); + setScrollValues(vpRanges.getStartRes(), + vpRanges.getStartSeq()); } }); } } else { - av.setStartSeq(offy); - av.setEndSeq(offy - + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())); + vpRanges.setStartSeq(offy); + vpRanges.setEndSeq(offy + + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()) + - 1); } } @@ -786,8 +829,8 @@ public class AlignmentPanel extends GAlignmentPanel implements overviewPanel.setBoxPosition(); } - int scrollX = av.startRes - oldX; - int scrollY = av.startSeq - oldY; + int scrollX = vpRanges.getStartRes() - oldX; + int scrollY = vpRanges.getStartSeq() - oldY; if (av.getWrapAlignment() || !fastPaint) { @@ -797,13 +840,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { // Make sure we're not trying to draw a panel // larger than the visible window - if (scrollX > av.endRes - av.startRes) + if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes()) { - scrollX = av.endRes - av.startRes; + scrollX = vpRanges.getEndRes() - vpRanges.getStartRes(); } - else if (scrollX < av.startRes - av.endRes) + else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes()) { - scrollX = av.startRes - av.endRes; + scrollX = vpRanges.getStartRes() - vpRanges.getEndRes(); } if (scrollX != 0 || scrollY != 0) @@ -822,9 +865,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * If there is one, scroll the (Protein/cDNA) complementary alignment to * match, unless we are ourselves doing that. */ - if (isFollowingComplementScroll()) + if (isDontScrollComplement()) { - setFollowingComplementScroll(false); + setDontScrollComplement(false); } else { @@ -836,17 +879,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * Repaint the alignment including the annotations and overview panels (if * shown). */ + @Override public void paintAlignment(boolean updateOverview) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); - sorter.sort(getAlignment() - .getAlignmentAnnotation(), + sorter.sort(getAlignment().getAlignmentAnnotation(), av.getSortAnnotationsBy()); repaint(); if (updateOverview) { + // TODO: determine if this paintAlignment changed structure colours av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) @@ -862,6 +906,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { invalidate(); @@ -871,13 +916,20 @@ public class AlignmentPanel extends GAlignmentPanel implements hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); validate(); + /* + * set scroll bar positions; first suppress this being 'followed' in any + * complementary split pane + */ + setDontScrollComplement(true); + if (av.getWrapAlignment()) { int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int canvasWidth = getSeqPanel().seqCanvas @@ -895,7 +947,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - setScrollValues(av.getStartRes(), av.getStartSeq()); + setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); } } @@ -914,6 +966,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -924,11 +977,11 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.getWrapAlignment()) { - return printWrappedAlignment(pg, pwidth, pheight, pi); + return printWrappedAlignment(pwidth, pheight, pi, pg); } else { - return printUnwrapped(pg, pwidth, pheight, pi); + return printUnwrapped(pwidth, pheight, pi, pg, pg); } } @@ -949,84 +1002,103 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) + /** + * Draws the alignment image, including sequence ids, sequences, and + * annotation labels and annotations if shown, on either one or two Graphics + * context. + * + * @param pageWidth + * @param pageHeight + * @param pi + * @param idGraphics + * the graphics context for sequence ids and annotation labels + * @param alignmentGraphics + * the graphics context for sequences and annotations (may or may not + * be the same context as idGraphics) + * @return + * @throws PrinterException + */ + public int printUnwrapped(int pageWidth, int pageHeight, int pi, + Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { - int idWidth = getVisibleIdWidth(false); - FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.getCharHeight() + fm.getDescent(); + final int idWidth = getVisibleIdWidth(false); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); - - // ////////////////////////////////// - // / How many sequences and residues can we fit on a printable page? - int totalRes = (pwidth - idWidth) / av.getCharWidth(); + /* + * Get the horizontal offset to where we draw the sequences. + * This is idWidth if using a single Graphics context, else zero. + */ + final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth; - int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1; + FontMetrics fm = getFontMetrics(av.getFont()); + int charHeight = av.getCharHeight(); + int scaleHeight = charHeight + fm.getDescent(); - int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; + idGraphics.setColor(Color.white); + idGraphics.fillRect(0, 0, pageWidth, pageHeight); + idGraphics.setFont(av.getFont()); - // /////////////////////////// - // / Only print these sequences and residues on this page - int startRes; + /* + * How many sequences and residues can we fit on a printable page? + */ + int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - // /////////////////////////// - // / Only print these sequences and residues on this page - int endRes; + int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - // /////////////////////////// - // / Only print these sequences and residues on this page - int startSeq; + int alignmentWidth = av.getAlignment().getWidth(); + int pagesWide = (alignmentWidth / totalRes) + 1; - // /////////////////////////// - // / Only print these sequences and residues on this page - int endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = (startRes + totalRes) - 1; + final int startRes = (pi % pagesWide) * totalRes; + int endRes = (startRes + totalRes) - 1; - if (endRes > (av.getAlignment().getWidth() - 1)) + if (endRes > (alignmentWidth - 1)) { - endRes = av.getAlignment().getWidth() - 1; + endRes = alignmentWidth - 1; } - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; + final int startSeq = (pi / pagesWide) * totalSeq; + int endSeq = startSeq + totalSeq; - if (endSeq > av.getAlignment().getHeight()) + int alignmentHeight = av.getAlignment().getHeight(); + if (endSeq > alignmentHeight) { - endSeq = av.getAlignment().getHeight(); + endSeq = alignmentHeight; } - int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) - * pheight; + int pagesHigh = ((alignmentHeight / totalSeq) + 1) + * pageHeight; if (av.isShowAnnotation()) { pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; } - pagesHigh /= pheight; + pagesHigh /= pageHeight; if (pi >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } + final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + + 3; - // draw Scale - pg.translate(idWidth, 0); - getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth, - scaleHeight); - pg.translate(-idWidth, scaleHeight); + /* + * draw the Scale at horizontal offset, then reset to top left (0, 0) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, 0); + getScalePanel().drawScale(alignmentGraphics, startRes, endRes, + pageWidth - idWidth, scaleHeight); + alignmentGraphics.translate(-alignmentGraphicsOffset, 0); - // ////////////// - // Draw the ids + /* + * Draw the sequence ids, offset for scale height, + * then reset to top left (0, 0) + */ + idGraphics.translate(0, scaleHeight); + idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont()); Color currentColor = null; Color currentTextColor = null; - pg.setFont(getIdPanel().getIdCanvas().getIdfont()); - SequenceI seq; for (int i = startSeq; i < endSeq; i++) { @@ -1034,6 +1106,9 @@ public class AlignmentPanel extends GAlignmentPanel implements if ((av.getSelectionGroup() != null) && av.getSelectionGroup().getSequences(null).contains(seq)) { + /* + * gray out ids of sequences in selection group (if any) + */ currentColor = Color.gray; currentTextColor = Color.black; } @@ -1043,46 +1118,58 @@ public class AlignmentPanel extends GAlignmentPanel implements currentTextColor = Color.black; } - pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, - av.getCharHeight()); + idGraphics.setColor(currentColor); + idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth, + charHeight); - pg.setColor(currentTextColor); + idGraphics.setColor(currentTextColor); int xPos = 0; + String displayId = seq.getDisplayId(av.getShowJVSuffix()); if (av.isRightAlignIds()) { - fm = pg.getFontMetrics(); + fm = idGraphics.getFontMetrics(); xPos = idWidth - - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) + - fm.stringWidth(displayId) - 4; } - pg.drawString( - seq.getDisplayId(av.getShowJVSuffix()), - xPos, - (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); + idGraphics.drawString(displayId, xPos, + (((i - startSeq) * charHeight) + charHeight) + - (charHeight / 5)); } + idGraphics.setFont(av.getFont()); + idGraphics.translate(0, -scaleHeight); - pg.setFont(av.getFont()); - - // draw main sequence panel - pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); + /* + * draw the sequences, offset for scale height, and id width (if using a + * single graphics context), then reset to (0, scale height) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); + getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes, + startSeq, endSeq, 0); + alignmentGraphics.translate(-alignmentGraphicsOffset, 0); - if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) + if (av.isShowAnnotation() && (endSeq == alignmentHeight)) { - // draw annotation - need to offset for current scroll position - int offset = -getAlabels().getScrollOffset(); - pg.translate(0, offset); - pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight() - + 3); - getAlabels().drawComponent(pg, idWidth); - pg.translate(idWidth + 3, 0); + /* + * draw annotation labels; drawComponent() translates by + * getScrollOffset(), so compensate for that first; + * then reset to (0, scale height) + */ + int offset = getAlabels().getScrollOffset(); + idGraphics.translate(0, -offset); + idGraphics.translate(0, alignmentDrawnHeight); + getAlabels().drawComponent(idGraphics, idWidth); + idGraphics.translate(0, -alignmentDrawnHeight); + + /* + * draw the annotations starting at + * (idOffset, alignmentHeight) from (0, scaleHeight) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, - pg, -1, startRes, endRes + 1); - pg.translate(0, -offset); + alignmentGraphics, -1, startRes, endRes + 1); } return Printable.PAGE_EXISTS; @@ -1105,8 +1192,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ - public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, - int pi) throws PrinterException + public int printWrappedAlignment(int pwidth, int pheight, int pi, + Graphics pg) throws PrinterException { int annotationHeight = 0; AnnotationLabels labels = null; @@ -1130,7 +1217,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth @@ -1171,12 +1259,14 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (labels != null) { - pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.getCharHeight())); + pg.translate(-3, + ypos + (av.getAlignment().getHeight() * av.getCharHeight())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos + pg.translate( + +3, + -ypos - (av.getAlignment().getHeight() * av .getCharHeight())); } @@ -1186,8 +1276,8 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, - 0); + getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + totalHeight, 0); if ((pi * pheight) < totalHeight) { @@ -1231,22 +1321,26 @@ public class AlignmentPanel extends GAlignmentPanel implements if (onscreen || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { - return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth() - : calculateIdWidth().width + 4); + int w = getIdPanel().getWidth(); + return (w > 0 ? w : calculateIdWidth().width + 4); } return idwidth.intValue() + 4; } void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) { - long progress = System.currentTimeMillis(); + int boarderBottomOffset = 5; + long pSessionId = System.currentTimeMillis(); headless = (System.getProperty("java.awt.headless") != null && System .getProperty("java.awt.headless").equals("true")); if (alignFrame != null && !headless) { - alignFrame.setProgressBar(MessageManager.formatMessage( - "status.saving_file", new Object[] - { type.getLabel() }), progress); + if (file != null) + { + alignFrame.setProgressBar(MessageManager.formatMessage( + "status.saving_file", new Object[] { type.getLabel() }), + pSessionId); + } } try { @@ -1272,26 +1366,30 @@ public class AlignmentPanel extends GAlignmentPanel implements } im = new jalview.util.ImageMaker(this, type, imageAction, - aDimension.getWidth(), aDimension.getHeight(), file, - imageTitle); + aDimension.getWidth(), aDimension.getHeight() + + boarderBottomOffset, file, imageTitle, + alignFrame, pSessionId, headless); + Graphics graphics = im.getGraphics(); if (av.getWrapAlignment()) { - if (im.getGraphics() != null) + if (graphics != null) { - printWrappedAlignment(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight(), 0); + printWrappedAlignment(aDimension.getWidth(), + aDimension.getHeight() + boarderBottomOffset, 0, + graphics); im.writeImage(); } } else { - if (im.getGraphics() != null) + if (graphics != null) { - printUnwrapped(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight(), 0); + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), + 0, graphics, graphics); im.writeImage(); } } + } catch (OutOfMemoryError err) { // Be noisy here. @@ -1305,10 +1403,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } finally { - if (alignFrame != null && !headless) - { - alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); - } + } } @@ -1317,7 +1412,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); } int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) @@ -1372,9 +1468,10 @@ public class AlignmentPanel extends GAlignmentPanel implements { makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); } + public void makePNGImageMap(File imgMapFile, String imageName) { - // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS + // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); @@ -1388,7 +1485,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { int s, sSize = av.getAlignment().getHeight(), res, alwidth = av .getAlignment().getWidth(), g, gSize, f, fSize, sy; - StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(jalview.io.HTMLOutput.getImageMapHTML()); out.println(" res) { - text.append("
" + groups[g].getName() + ""); + text.append("
").append(groups[g].getName()) + .append(""); } } - if (features != null) + if (text.length() < 1) { - if (text.length() < 1) - { - text.append(" features = seq.getFeatures() + .findFeatures(seqPos, seqPos); + for (SequenceFeature sf : features) { - - if ((features[f].getBegin() <= seq.findPosition(res)) - && (features[f].getEnd() >= seq.findPosition(res))) + if (sf.isContactFeature()) { - if (features[f].getType().equals("disulfide bond")) - { - if (features[f].getBegin() == seq.findPosition(res) - || features[f].getEnd() == seq - .findPosition(res)) - { - text.append("
disulfide bond " - + features[f].getBegin() + ":" - + 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(" " + features[f].getDescription()); - } - - if (features[f].getValue("status") != null) - { - text.append(" (" + features[f].getValue("status") - + ")"); - } + 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()); } } } @@ -1547,7 +1632,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int height = ((maxwidth / chunkWidth) + 1) * cHeight; @@ -1564,8 +1650,20 @@ public class AlignmentPanel extends GAlignmentPanel implements PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas); PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); + + closeChildFrames(); + + /* + * try to ensure references are nulled + */ + if (annotationPanel != null) + { + annotationPanel.dispose(); + } + if (av != null) { + av.removePropertyChangeListener(propertyChangeListener); jalview.structure.StructureSelectionManager ssm = av .getStructureSelectionManager(); ssm.removeStructureViewerListener(getSeqPanel(), null); @@ -1573,7 +1671,7 @@ public class AlignmentPanel extends GAlignmentPanel implements ssm.removeCommandListener(av); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); - av.setAlignment(null); + av.dispose(); av = null; } else @@ -1586,6 +1684,17 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** + * Close any open dialogs that would be orphaned when this one is closed + */ + protected void closeChildFrames() + { + if (calculationDialog != null) + { + calculationDialog.closeFrame(); + } + } + + /** * hides or shows dynamic annotation rows based on groups and av state flags */ public void updateAnnotation() @@ -1609,10 +1718,9 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public AlignmentI getAlignment() { - return av.getAlignment(); + return av == null ? null : av.getAlignment(); } - @Override public String getViewName() { @@ -1664,12 +1772,15 @@ public class AlignmentPanel extends GAlignmentPanel implements return new FeatureRenderer(this); } - @Override + + @Override public jalview.api.FeatureRenderer getFeatureRenderer() { return seqPanel.seqCanvas.getFeatureRenderer(); } - public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr) + + public void updateFeatureRenderer( + jalview.renderer.seqfeatures.FeatureRenderer fr) { fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer()); } @@ -1742,14 +1853,14 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param verticalOffset * the number of visible sequences to show above the mapped region */ - public void scrollToCentre(SearchResults sr, int verticalOffset) + public 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.getResultSequence(0); + SequenceI mappedTo = sr.getResults().get(0).getSequence(); List seqs = av.getAlignment().getSequences(); /* @@ -1777,17 +1888,59 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Set a flag to say we are scrolling to follow a (cDNA/protein) complement. + * Set a flag to say do not scroll any (cDNA/protein) complement. * * @param b */ - protected void setFollowingComplementScroll(boolean b) + protected void setDontScrollComplement(boolean b) + { + this.dontScrollComplement = b; + } + + protected boolean isDontScrollComplement() + { + return this.dontScrollComplement; + } + + /** + * Redraw sensibly. + * + * @adjustHeight if true, try to recalculate panel height for visible + * annotations + */ + protected void refresh(boolean adjustHeight) + { + validateAnnotationDimensions(adjustHeight); + addNotify(); + if (adjustHeight) + { + // sort, repaint, update overview + paintAlignment(true); + } + else + { + // lightweight repaint + repaint(); + } + } + + /** + * Set the reference to the PCA/Tree chooser dialog for this panel. This + * reference should be nulled when the dialog is closed. + * + * @param calculationChooser + */ + public void setCalculationDialog(CalculationChooser calculationChooser) { - this.followingComplementScroll = b; + calculationDialog = calculationChooser; } - protected boolean isFollowingComplementScroll() + /** + * Returns the reference to the PCA/Tree chooser dialog for this panel (null + * if none is open) + */ + public CalculationChooser getCalculationDialog() { - return this.followingComplementScroll; + return calculationDialog; } }