X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fe216c07622fca5b240d593b6e094aba605ac236;hb=1140532d01b32b648e7e5b17ea717ae790625f8f;hp=b16e2436bc6938bd5abab4d6773f1e9a11ee5838;hpb=b07c7cb77f73eecaea77b66b9b5f7f9071e0e1e0;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index b16e243..fe6477e 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,22 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.jbgui.GAlignmentPanel; -import jalview.math.AlignmentDimension; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; -import jalview.util.Platform; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -43,9 +27,11 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; -import java.awt.Insets; +import java.awt.Graphics2D; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; @@ -58,15 +44,48 @@ import java.util.List; import javax.swing.SwingUtilities; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.bin.Jalview; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.io.HTMLOutput; +import jalview.io.exceptions.ImageOutputException; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.imagemaker.BitmapImageSizing; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + /** * DOCUMENT ME! * * @author $author$ * @version $Revision: 1.161 $ */ +@SuppressWarnings("serial") public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable, AlignmentViewPanel + AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { + /* + * spare space in pixels between sequence id and alignment panel + */ + private static final int ID_WIDTH_PADDING = 4; + public AlignViewport av; OverviewPanel overviewPanel; @@ -75,11 +94,8 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; - private boolean headless; - IdwidthAdjuster idwidthAdjuster; - /** DOCUMENT ME!! */ public AlignFrame alignFrame; private ScalePanel scalePanel; @@ -88,18 +104,19 @@ public class AlignmentPanel extends GAlignmentPanel implements private AnnotationLabels alabels; - // 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. + * false, suppresses invoking the same method recursively. */ - private boolean dontScrollComplement; + private boolean scrollComplementaryPanel = true; + + private PropertyChangeListener propertyChangeListener; + + private CalculationChooser calculationDialog; /** * Creates a new AlignmentPanel object. @@ -109,6 +126,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { + // setBackground(Color.white); // BH 2019 alignFrame = af; this.av = av; setSeqPanel(new SeqPanel(av, this)); @@ -134,8 +152,37 @@ public class AlignmentPanel extends GAlignmentPanel implements hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); + addComponentListener(new ComponentAdapter() + { + @Override + public void componentResized(ComponentEvent evt) + { + // 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()); + ranges.setViewportWidth(widthInRes); + } + else + { + int widthInRes = getSeqPanel().seqCanvas.getWidth() + / av.getCharWidth(); + int heightInSeq = getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight(); + + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); + } + } + + }); + final AlignmentPanel ap = this; - av.addPropertyChangeListener(new PropertyChangeListener() + propertyChangeListener = new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) @@ -146,7 +193,10 @@ public class AlignmentPanel extends GAlignmentPanel implements alignmentChanged(); } } - }); + }; + av.addPropertyChangeListener(propertyChangeListener); + + av.getRanges().addPropertyChangeListener(this); fontChanged(); adjustAnnotationHeight(); updateLayout(); @@ -162,9 +212,15 @@ public class AlignmentPanel extends GAlignmentPanel implements { av.alignmentChanged(this); + if (getCalculationDialog() != null) + { + getCalculationDialog().validateCalcTypes(); + } + alignFrame.updateEditMenuBar(); - paintAlignment(true); + // no idea if we need to update structure + paintAlignment(true, true); } @@ -177,49 +233,46 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() - + fm.getDescent())); - idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av - .getCharHeight() + fm.getDescent())); - - getIdPanel().getIdCanvas().gg = null; + // update the flag controlling whether the grid is too small to render the + // font + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); + + scalePanelHolder.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idwidthAdjuster.invalidate(); + scalePanelHolder.invalidate(); + // BH 2018 getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; getAnnotationPanel().adjustPanelHeight(); Dimension d = calculateIdWidth(); - - d.setSize(d.width + 4, d.height); getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); - if (overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } - if (this.alignFrame.getSplitViewContainer() != null) - { - ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); - } - repaint(); } /** - * Calculate the width of the alignment labels based on the displayed names + * Calculates the width of the alignment labels based on the displayed names * and any bounds on label width set in preferences. * + * The calculated width is set as a property of the viewport and the layout is + * updated. + * * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ public Dimension calculateIdWidth() { + int oldWidth = av.getIdWidth(); + // calculate sensible default width when no preference is available Dimension r = null; if (av.getIdWidth() < 0) { - int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3)); - r = calculateIdWidth(maxwidth); + r = calculateDefaultAlignmentIdWidth(); av.setIdWidth(r.width); } else @@ -228,87 +281,144 @@ public class AlignmentPanel extends GAlignmentPanel implements r.width = av.getIdWidth(); r.height = 0; } + + /* + * fudge: if desired width has changed, update layout + * (see also paintComponent - updates layout on a repaint) + */ + if (r.width != oldWidth) + { + idPanelHolder.setPreferredSize(r); + validate(); + } return r; } + public Dimension calculateDefaultAlignmentIdWidth() + { + return calculateIdWidth(-1, false, false); + } + /** + * pre 2.11.3 Id width calculation - used when importing old projects only + * @return + */ + public int getLegacyIdWidth() + { + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3); + int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth); + Dimension w = calculateIdWidthOrLegacy(true, maxwidth, false, false); + return w.width; + } + + /** + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. Also includes annotations + * not actually visible. + * + * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation + * label decorators and only called during tests + * + * @param maxwidth + * -1 or maximum width allowed for IdWidth + * @return Dimension giving the maximum width of the alignment label panel + * that should be used. + */ + protected Dimension calculateIdWidth(int maxwidth) + { + return calculateIdWidth(maxwidth, true, false); + } /** * Calculate the width of the alignment labels based on the displayed names * and any bounds on label width set in preferences. * * @param maxwidth * -1 or maximum width allowed for IdWidth + * @param includeAnnotations - when true includes width of any additional marks in annotation id panel + * @param visibleOnly - when true, ignore label widths for hidden annotation rows * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ - public Dimension calculateIdWidth(int maxwidth) + public Dimension calculateIdWidth(int maxwidth, + boolean includeAnnotations, boolean visibleOnly) + { + return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations, visibleOnly); + } + + /** + * legacy mode or post 2.11.3 ID width calculation + * @param legacy - uses annotation labels, not rendered label width (excludes additional decorators) + * @param maxwidth + * @param includeAnnotations + * @param visibleOnly + * @return + */ + private Dimension calculateIdWidthOrLegacy(boolean legacy, int maxwidth, + boolean includeAnnotations, boolean visibleOnly) { Container c = new Container(); - FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), - Font.ITALIC, av.font.getSize())); + FontMetrics fm = c.getFontMetrics( + new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); int i = 0; int idWidth = 0; - String id; while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) { SequenceI s = al.getSequenceAt(i); - - id = s.getDisplayId(av.getShowJVSuffix()); - - if (fm.stringWidth(id) > idWidth) - { - idWidth = fm.stringWidth(id); - } - + String id = s.getDisplayId(av.getShowJVSuffix()); + int stringWidth = fm.stringWidth(id); + idWidth = Math.max(idWidth, stringWidth); i++; } // Also check annotation label widths - i = 0; - - if (al.getAlignmentAnnotation() != null) + if (includeAnnotations && al.getAlignmentAnnotation() != null) { fm = c.getFontMetrics(getAlabels().getFont()); - while (i < al.getAlignmentAnnotation().length) + if (!legacy || Jalview.isHeadlessMode()) { - String label = al.getAlignmentAnnotation()[i].label; - - if (fm.stringWidth(label) > idWidth) + AnnotationLabels aal = getAlabels(); + int stringWidth = aal.drawLabels(null, false, idWidth, false, false, + fm, !visibleOnly); + idWidth = Math.max(idWidth, stringWidth); + } + else + { + for (i = 0; i < al.getAlignmentAnnotation().length; i++) { - idWidth = fm.stringWidth(label); + AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; + if (visibleOnly && !aa.visible) + { + continue; + } + String label = aa.label; + int stringWidth = fm.stringWidth(label); + idWidth = Math.max(idWidth, stringWidth); } - - i++; } } - return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, - idWidth), 12); - } + int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth); + w += ID_WIDTH_PADDING; - /** - * Highlight the given results on the alignment. - * - */ - public void highlightSearchResults(SearchResults results) - { - scrollToPosition(results); - getSeqPanel().seqCanvas.highlightSearchResults(results); + return new Dimension(w, 12); } /** - * Scroll the view to show the position of the highlighted region in results - * (if any) and redraw the overview + * Highlight the given results on the alignment * - * @param results */ - public boolean scrollToPosition(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { - return scrollToPosition(results, 0, true, false); + boolean scrolled = scrollToPosition(results, 0, false); + + boolean fastPaint = !(scrolled && av.getWrapAlignment()); + + getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint); } /** @@ -316,157 +426,136 @@ public class AlignmentPanel extends GAlignmentPanel implements * (if any) * * @param searchResults - * @param redrawOverview * @return */ - public boolean scrollToPosition(SearchResults searchResults, - boolean redrawOverview) + public boolean scrollToPosition(SearchResultsI searchResults) { - return scrollToPosition(searchResults, 0, redrawOverview, false); + return scrollToPosition(searchResults, 0, false); } /** - * 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 * if greater than zero, allows scrolling to a position below the * first displayed sequence - * @param redrawOverview - * - 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(SearchResults results, - int verticalOffset, boolean redrawOverview, boolean centre) + protected boolean scrollToPosition(SearchResultsI results, + int verticalOffset, 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]; - // DEBUG - // System.err.println(this.av.viewName + " Seq : " + seqIndex - // + " Scroll to " + start + "," + end); + 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 = (av.getEndRes() - av.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.absoluteToVisibleColumn(start); + end = hidden.absoluteToVisibleColumn(end); + if (start == end) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); - if (start == end) + if (!hidden.isVisible(r[0])) { - if (!av.getColumnSelection().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; - // System.out.println("start=" + start + ", end=" + end + ", startv=" - // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts=" - // + av.getStartSeq() + ", ends=" + av.getEndSeq()); - if (!av.getWrapAlignment()) + if (!av.getWrapAlignment()) + { + if ((startv = ranges.getStartRes()) >= start) { - if ((startv = av.getStartRes()) >= start) - { - /* - * Scroll left to make start of search results visible - */ - // setScrollValues(start - 1, seqIndex); // plus one residue - setScrollValues(start, seqIndex); - } - else if ((endv = av.getEndRes()) <= end) - { - /* - * Scroll right to make end of search results visible - */ - // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one - setScrollValues(startv + end - endv, seqIndex); - } - else if ((starts = av.getStartSeq()) > seqIndex) - { - /* - * Scroll up to make start of search results visible - */ - setScrollValues(av.getStartRes(), seqIndex); - } - else if ((ends = av.getEndSeq()) <= seqIndex) - { - /* - * Scroll down to make end of search results visible - */ - setScrollValues(av.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) { - scrollToWrappedVisible(start); + /* + * 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) + { + /* + * 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; } - if (redrawOverview && overviewPanel != null) + else { - overviewPanel.setBoxPosition(); + scrollNeeded = ranges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); - return true; - } - void scrollToWrappedVisible(int res) - { - int cwidth = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) - { - vscroll.setValue((res / cwidth)); - av.startRes = vscroll.getValue() * cwidth; - } + paintAlignment(false, false); + return scrollNeeded; } /** @@ -517,11 +606,13 @@ public class AlignmentPanel extends GAlignmentPanel implements // this is called after loading new annotation onto alignment if (alignFrame.getHeight() == 0) { - System.out.println("NEEDS FIXING"); + jalview.bin.Console.error("adjustAnnotationHeight called with zero height alignment window"); } 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, av.needToUpdateStructureViews()); } /** @@ -530,51 +621,38 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int annotationHeight = getAnnotationPanel().adjustPanelHeight(); - - if (adjustPanelHeight) - { - int rowHeight = av.getCharHeight(); - int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + // BH 2018.04.18 comment: addNotify() is not appropriate here. We + // are not changing ancestors, and keyboard action listeners do + // not need to be reset. addNotify() is a very expensive operation, + // requiring a full re-layout of all parents and children. + // Note in JComponent: + // This method is called by the toolkit internally and should + // not be called directly by programs. + // I note that addNotify() is called in several areas of Jalview. + + AnnotationPanel ap = getAnnotationPanel(); + int annotationHeight = ap.adjustPanelHeight(); + annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight, + annotationHeight); - /* - * Estimate available height in the AlignFrame for alignment + - * annotations. Deduct an estimate for title bar, menu bar, scale panel, - * hscroll, status bar (as these are not laid out we can't inspect their - * actual heights). Insets gives frame borders. - */ - int stuff = Platform.isAMac() ? 80 : 100; - Insets insets = alignFrame.getInsets(); - int availableHeight = alignFrame.getHeight() - stuff - insets.top - - insets.bottom; - - /* - * If not enough vertical space, maximize annotation height while keeping - * at least two rows of alignment visible - */ - if (annotationHeight + alignmentHeight > availableHeight) - { - annotationHeight = Math.min(annotationHeight, availableHeight - 2 - * rowHeight); - } - } - else - { - // maintain same window layout whilst updating sliders - annotationHeight = annotationScroller.getSize().height; - } hscroll.addNotify(); - - annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), annotationHeight)); - Dimension e = idPanel.getSize(); - alabels.setSize(new Dimension(e.width, annotationHeight)); + int idWidth = e.width; + boolean manuallyAdjusted = this.getIdPanel().getIdCanvas() + .isManuallyAdjusted(); + annotationScroller.setPreferredSize(new Dimension( + manuallyAdjusted ? idWidth : annotationScroller.getWidth(), + annotationHeight)); + + alabels.setPreferredSize(new Dimension(idWidth, annotationHeight)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), annotationHeight)); + manuallyAdjusted ? idWidth + : annotationSpaceFillerHolder.getWidth(), + annotationHeight)); annotationScroller.validate(); annotationScroller.addNotify(); + ap.validate(); } /** @@ -588,10 +666,12 @@ public class AlignmentPanel extends GAlignmentPanel implements fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - av.startSeq = 0; - scalePanelHolder.setVisible(!wrap); + ViewportRanges ranges = av.getRanges(); + ranges.setStartSeq(0); + // scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); - idwidthAdjuster.setVisible(!wrap); + // Allow idPanel width adjustment in wrap mode + idwidthAdjuster.setVisible(true); if (wrap) { @@ -602,76 +682,32 @@ public class AlignmentPanel extends GAlignmentPanel implements { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); + validateAnnotationDimensions(false); } - idSpaceFillerPanel1.setVisible(!wrap); - - repaint(); - } - - // return value is true if the scroll is valid - public boolean scrollUp(boolean up) - { - if (up) - { - if (vscroll.getValue() < 1) - { - return false; - } - - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); - } - else - { - if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) + int canvasWidth = getSeqPanel().seqCanvas.getWidth(); + if (canvasWidth > 0) + { // may not yet be laid out + if (wrap) { - return false; + int widthInRes = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(canvasWidth); + ranges.setViewportWidth(widthInRes); } - - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); - } - - fastPaint = true; - - return true; - } - - /** - * DOCUMENT ME! - * - * @param right - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean scrollRight(boolean right) - { - if (!right) - { - if (hscroll.getValue() < 1) + else { - return false; - } + int widthInRes = (canvasWidth / av.getCharWidth()); + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight()); - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); - } - else - { - if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) - { - return false; + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); } - - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); } - fastPaint = true; + // idSpaceFillerPanel1.setVisible(!wrap); - return true; + repaint(); } /** @@ -683,181 +719,188 @@ public class AlignmentPanel extends GAlignmentPanel implements * visible row to scroll to * */ - public void setScrollValues(int x, int y) + public void setScrollValues(int xpos, int ypos) { - // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y); + int x = xpos; + int y = ypos; + if (av == null || av.getAlignment() == null) { return; } - int width = av.getAlignment().getWidth(); - int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns()) + if (av.getWrapAlignment()) { - width = av.getColumnSelection().findColumnPosition(width); + setScrollingForWrappedPanel(x); } + else + { + int width = av.getAlignment().getVisibleWidth(); + int height = av.getAlignment().getHeight(); - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av - .getCharWidth())) - 1); + hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); + vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); - vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); + if (hextent > width) + { + hextent = width; + } - if (hextent > width) - { - hextent = width; - } + if (vextent > height) + { + vextent = height; + } - if (vextent > height) - { - vextent = height; - } + if ((hextent + x) > width) + { + x = width - hextent; + } - if ((hextent + x) > width) - { - x = width - hextent; - } + if ((vextent + y) > height) + { + y = height - vextent; + } - if ((vextent + y) > height) - { - y = height - vextent; - } + if (y < 0) + { + y = 0; + } - if (y < 0) - { - y = 0; - } + if (x < 0) + { + x = 0; + } - if (x < 0) - { - x = 0; + // update the scroll values + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); } - - /* - * 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); } /** - * DOCUMENT ME! + * Respond to adjustment event when horizontal or vertical scrollbar is + * changed * * @param evt - * DOCUMENT ME! + * adjustment event encoding whether hscroll or vscroll changed */ @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - int oldX = av.getStartRes(); - int oldY = av.getStartSeq(); - - if (evt.getSource() == hscroll) + if (av.getWrapAlignment()) { - int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av - .getCharWidth())) - 1); + adjustScrollingWrapped(evt); + return; } - if (evt.getSource() == vscroll) + ViewportRanges ranges = av.getRanges(); + + if (evt.getSource() == hscroll) { - int offy = vscroll.getValue(); + int oldX = ranges.getStartRes(); + int oldwidth = ranges.getViewportWidth(); + int x = hscroll.getValue(); + int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); - if (av.getWrapAlignment()) + // if we're scrolling to the position we're already at, stop + // this prevents infinite recursion of events when the scroll/viewport + // ranges values are the same + if ((x == oldX) && (width == oldwidth)) { - if (offy > -1) - { - int rowSize = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - av.setStartRes(offy * rowSize); - av.setEndRes((offy + 1) * rowSize); - } - else - { - // This is only called if file loaded is a jar file that - // was wrapped when saved and user has wrap alignment true - // as preference setting - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } - }); - } + return; } - else + ranges.setViewportStartAndWidth(x, width); + } + else if (evt.getSource() == vscroll) + { + int oldY = ranges.getStartSeq(); + int oldheight = ranges.getViewportHeight(); + int y = vscroll.getValue(); + int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); + + // if we're scrolling to the position we're already at, stop + // this prevents infinite recursion of events when the scroll/viewport + // ranges values are the same + if ((y == oldY) && (height == oldheight)) { - av.setStartSeq(offy); - av.setEndSeq(offy - + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())); + return; } + ranges.setViewportStartAndHeight(y, height); } + repaint(); + } - if (overviewPanel != null) + /** + * Responds to a scroll change by setting the start position of the viewport. + * Does + * + * @param evt + */ + protected void adjustScrollingWrapped(AdjustmentEvent evt) + { + if (evt.getSource() == hscroll) { - overviewPanel.setBoxPosition(); + return; // no horizontal scroll when wrapped } + final ViewportRanges ranges = av.getRanges(); - int scrollX = av.startRes - oldX; - int scrollY = av.startSeq - oldY; - - if (av.getWrapAlignment() || !fastPaint) - { - repaint(); - } - else + if (evt.getSource() == vscroll) { - // Make sure we're not trying to draw a panel - // larger than the visible window - if (scrollX > av.endRes - av.startRes) - { - scrollX = av.endRes - av.startRes; - } - else if (scrollX < av.startRes - av.endRes) + int newY = vscroll.getValue(); + + /* + * if we're scrolling to the position we're already at, stop + * this prevents infinite recursion of events when the scroll/viewport + * ranges values are the same + */ + int oldX = ranges.getStartRes(); + int oldY = ranges.getWrappedScrollPosition(oldX); + if (oldY == newY) { - scrollX = av.startRes - av.endRes; + return; } - - if (scrollX != 0 || scrollY != 0) + if (newY > -1) { - getIdPanel().getIdCanvas().fastPaint(scrollY); - getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY); - getScalePanel().repaint(); - - if (av.isShowAnnotation() && scrollX != 0) - { - getAnnotationPanel().fastPaint(scrollX); - } + /* + * limit page up/down to one width's worth of positions + */ + int rowSize = ranges.getViewportWidth(); + int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; + ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } - /* - * If there is one, scroll the (Protein/cDNA) complementary alignment to - * match, unless we are ourselves doing that. - */ - if (isDontScrollComplement()) - { - setDontScrollComplement(false); - } else { - av.scrollComplementaryAlignment(); + // This is only called if file loaded is a jar file that + // was wrapped when saved and user has wrap alignment true + // as preference setting + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + // When updating scrolling to use ViewportChange events, this code + // could not be validated and it is not clear if it is now being + // called. Log warning here in case it is called and unforeseen + // problems occur + Console.warn( + "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); + + // scroll to start of panel + 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()); @@ -865,10 +908,12 @@ 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) { @@ -877,54 +922,62 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - */ @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(); - - /* - * set scroll bar positions; first suppress this being 'followed' in any - * complementary split pane - */ - setDontScrollComplement(true); + int idWidth = d.width; + // check wrapped alignment as at least 1 residue width if (av.getWrapAlignment()) { - int maxwidth = av.getAlignment().getWidth(); - - if (av.hasHiddenColumns()) + SeqCanvas sc = this.getSeqPanel().seqCanvas; + if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + // need to make some adjustments + idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth()); + av.setIdWidth(idWidth); + av.getAlignPanel().getIdPanel().getIdCanvas() + .setManuallyAdjusted(true); + + validateAnnotationDimensions(false); } + } + + idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height)); + hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12)); + + validate(); // needed so that the id width adjuster works correctly + + /* + * 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()); + super.paintComponent(g); + } + + /** + * Set vertical scroll bar position, and number of increments, for wrapped + * panel + * + * @param topLeftColumn + * the column position at top left (0..) + */ + private void setScrollingForWrappedPanel(int topLeftColumn) + { + ViewportRanges ranges = av.getRanges(); + int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn); + int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn); - int canvasWidth = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - if (canvasWidth > 0) - { - int max = maxwidth - / getSeqPanel().seqCanvas - .getWrappedCanvasWidth(getSeqPanel().seqCanvas - .getWidth()) + 1; - vscroll.setMaximum(max); - vscroll.setUnitIncrement(1); - vscroll.setVisibleAmount(1); - } - } - else - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } + /* + * a scrollbar's value can be set to at most (maximum-extent) + * so we add extent (1) to the maxScroll value + */ + vscroll.setUnitIncrement(1); + vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1); } /** @@ -953,195 +1006,181 @@ 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); } } /** - * DOCUMENT ME! - * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Draws the alignment image, including sequence ids, sequences, and + * annotation labels and annotations if shown, on either one or two Graphics + * contexts. * + * @param pageWidth + * in pixels + * @param pageHeight + * in pixels + * @param pageIndex + * (0, 1, ...) + * @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 - * DOCUMENT ME! */ - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) + public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex, + Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { - int idWidth = getVisibleIdWidth(false); - FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.getCharHeight() + fm.getDescent(); - - 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(); - - int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1; - - int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; + final int idWidth, idWidthForGui; + // otherwise calculate it + idWidth = getVisibleIdWidth(false); +// if (getIdPanel()!=null && getIdPanel().getWidth()>0) +// { +// // use the current IdPanel's width, if its set and non-zero +// idWidthForGui = getIdPanel().getWidth(); +// } else { +// idWidthForGui=0; +// } + /* + * 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; - // /////////////////////////// - // / Only print these sequences and residues on this page - int startRes; + FontMetrics fm = getFontMetrics(av.getFont()); + final int charHeight = av.getCharHeight(); + final int scaleHeight = charHeight + fm.getDescent(); - // /////////////////////////// - // / Only print these sequences and residues on this page - int endRes; + idGraphics.setColor(Color.white); + idGraphics.fillRect(0, 0, pageWidth, pageHeight); + idGraphics.setFont(av.getFont()); - // /////////////////////////// - // / Only print these sequences and residues on this page - int startSeq; + /* + * How many sequences and residues can we fit on a printable page? + */ + final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - // /////////////////////////// - // / Only print these sequences and residues on this page - int endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = (startRes + totalRes) - 1; + final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - if (endRes > (av.getAlignment().getWidth() - 1)) - { - endRes = av.getAlignment().getWidth() - 1; - } + final int alignmentWidth = av.getAlignment().getVisibleWidth(); + int pagesWide = (alignmentWidth / totalRes) + 1; - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; + final int startRes = (pageIndex % pagesWide) * totalRes; + final int endRes = Math.min(startRes + totalRes - 1, + alignmentWidth - 1); - if (endSeq > av.getAlignment().getHeight()) - { - endSeq = av.getAlignment().getHeight(); - } + final int startSeq = (pageIndex / pagesWide) * totalSeq; + final int alignmentHeight = av.getAlignment().getHeight(); + final int endSeq = Math.min(startSeq + totalSeq, 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)) + if (pageIndex >= (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 ids - Color currentColor = null; - Color currentTextColor = null; - - pg.setFont(getIdPanel().getIdCanvas().getIdfont()); - - SequenceI seq; - for (int i = startSeq; i < endSeq; i++) - { - seq = av.getAlignment().getSequenceAt(i); - if ((av.getSelectionGroup() != null) - && av.getSelectionGroup().getSequences(null).contains(seq)) - { - currentColor = Color.gray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(seq); - currentTextColor = Color.black; - } - - pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, - av.getCharHeight()); - - pg.setColor(currentTextColor); + alignmentGraphics.setColor(Color.white); + alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight+scaleHeight); - int xPos = 0; - if (av.isRightAlignIds()) - { - fm = pg.getFontMetrics(); - xPos = idWidth - - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) - - 4; - } + /* + * 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); - pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, - (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); - } + /* + * Draw the sequence ids, offset for scale height, + * then reset to top left (0, 0) + */ + idGraphics.translate(0, scaleHeight); + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + List selection = av.getSelectionGroup() == null ? null + : av.getSelectionGroup().getSequences(null); + + idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, + selection, false,idWidth); - pg.setFont(av.getFont()); + idGraphics.setFont(av.getFont()); + idGraphics.translate(0, -scaleHeight); - // 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.drawPanelForPrinting(alignmentGraphics, + startRes, endRes, startSeq, endSeq - 1); + 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().drawComponentNotGUI(idGraphics, idWidth); + idGraphics.translate(0, -alignmentDrawnHeight); + + /* + * draw the annotations starting at + * (idOffset, alignmentHeight) from (0, scaleHeight) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, + alignmentDrawnHeight); + updateLayout(); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, - pg, -1, startRes, endRes + 1); - pg.translate(0, -offset); + alignmentGraphics, -1, startRes, endRes + 1); } return Printable.PAGE_EXISTS; } /** - * DOCUMENT ME! + * Prints one page of an alignment in wrapped mode. Returns + * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if + * no page could be drawn (page number out of range). * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! + * @param pageWidth + * @param pageHeight + * @param pageNumber + * (0, 1, ...) + * @param g * - * @return DOCUMENT ME! + * @return * * @throws PrinterException - * DOCUMENT ME! */ - public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, - int pi) throws PrinterException + public int printWrappedAlignment(int pageWidth, int pageHeight, + int pageNumber, Graphics g) throws PrinterException { + getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(), + getHeight()); int annotationHeight = 0; - AnnotationLabels labels = null; if (av.isShowAnnotation()) { annotationHeight = getAnnotationPanel().adjustPanelHeight(); - labels = new AnnotationLabels(av); } int hgap = av.getCharHeight(); @@ -1155,74 +1194,43 @@ public class AlignmentPanel extends GAlignmentPanel implements int idWidth = getVisibleIdWidth(false); - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } + int maxwidth = av.getAlignment().getVisibleWidth(); - int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); + int resWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(pageWidth - idWidth); + av.getRanges().setViewportStartAndWidth(0, resWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); - - // ////////////// - // Draw the ids - pg.setColor(Color.black); + g.setColor(Color.white); + g.fillRect(0, 0, pageWidth, pageHeight); + g.setFont(av.getFont()); + g.setColor(Color.black); - pg.translate(0, -pi * pheight); - - pg.setClip(0, pi * pheight, pwidth, pheight); - - int ypos = hgap; + /* + * method: print the whole wrapped alignment, but with a clip region that + * is restricted to the requested page; this supports selective print of + * single pages or ranges, (at the cost of repeated processing in the + * 'normal' case, when all pages are printed) + */ + g.translate(0, -pageNumber * pageHeight); - do - { - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - pg.setFont(getIdPanel().getIdCanvas().getIdfont()); - SequenceI s = av.getAlignment().getSequenceAt(i); - String string = s.getDisplayId(av.getShowJVSuffix()); - int xPos = 0; - if (av.isRightAlignIds()) - { - FontMetrics fm = pg.getFontMetrics(); - xPos = idWidth - fm.stringWidth(string) - 4; - } - pg.drawString(string, xPos, - ((i * av.getCharHeight()) + ypos + av.getCharHeight()) - - (av.getCharHeight() / 5)); - } - if (labels != null) - { - pg.translate(-3, - ypos + (av.getAlignment().getHeight() * av.getCharHeight())); - - pg.setFont(av.getFont()); - labels.drawComponent(pg, idWidth); - pg.translate( - +3, - -ypos - - (av.getAlignment().getHeight() * av - .getCharHeight())); - } + g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); - ypos += cHeight; - } while (ypos < totalHeight); + /* + * draw sequence ids and annotation labels (if shown) + */ + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight); - pg.translate(idWidth, 0); + g.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, - totalHeight, 0); + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, + pageWidth - idWidth, totalHeight, 0); - if ((pi * pheight) < totalHeight) + if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; - } else { @@ -1250,108 +1258,86 @@ public class AlignmentPanel extends GAlignmentPanel implements * be returned * @return */ - public int getVisibleIdWidth(boolean onscreen) + protected int getVisibleIdWidth(boolean onscreen) { // see if rendering offscreen - check preferences and calc width accordingly if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) { - return calculateIdWidth(-1).width + 4; + return calculateIdWidth(-1,true,true).width; } - Integer idwidth = null; - if (onscreen - || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + Integer idwidth = onscreen ? null + : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); + if (idwidth != null) { - return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth() - : calculateIdWidth().width + 4); + return idwidth.intValue() + ID_WIDTH_PADDING; } - return idwidth.intValue() + 4; + + int w = getIdPanel().getWidth(); + w = calculateIdWidth(-1, true, true).width; + return (w > 0 ? w : calculateIdWidth().width); } - void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) + throws ImageOutputException { - int boarderBottomOffset = 0; - long pSessionId = System.currentTimeMillis(); - headless = (System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true")); - if (alignFrame != null && !headless) - { - if (file != null) - { - alignFrame.setProgressBar(MessageManager.formatMessage( - "status.saving_file", new Object[] { type.getLabel() }), - pSessionId); - } - } - try + makeAlignmentImage(type, file, renderer, + BitmapImageSizing.defaultBitmapImageSizing()); + } + + /** + * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and + * writes it to the specified file + * + * @param type + * @param file + * @param textrenderer + * @param bitmapscale + */ + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer, + BitmapImageSizing userBis) throws ImageOutputException + { + final int borderBottomOffset = 5; + + AlignmentDimension aDimension = getAlignmentDimension(); + + // todo use a lambda function in place of callback here? + ImageWriterI writer = new ImageWriterI() { - AlignmentDimension aDimension = getAlignmentDimension(); - try + @Override + public void exportImage(Graphics graphics) throws Exception { - jalview.util.ImageMaker im; - final String imageAction, imageTitle; - if (type == jalview.util.ImageMaker.TYPE.PNG) - { - imageAction = "Create PNG image from alignment"; - imageTitle = null; - } - else if (type == jalview.util.ImageMaker.TYPE.EPS) - { - imageAction = "Create EPS file from alignment"; - imageTitle = alignFrame.getTitle(); - } - else - { - imageAction = "Create SVG file from alignment"; - imageTitle = alignFrame.getTitle(); - } - - im = new jalview.util.ImageMaker(this, type, imageAction, - aDimension.getWidth(), aDimension.getHeight() - + boarderBottomOffset, file, - imageTitle, alignFrame, pSessionId, headless); if (av.getWrapAlignment()) { - if (im.getGraphics() != null) - { - printWrappedAlignment(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight() + boarderBottomOffset, 0); - im.writeImage(); - } + printWrappedAlignment(aDimension.getWidth(), + aDimension.getHeight() + borderBottomOffset, 0, graphics); } else { - if (im.getGraphics() != null) - { - printUnwrapped(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight(), 0); - im.writeImage(); - } + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, + graphics, graphics); } - - } catch (OutOfMemoryError err) - { - // Be noisy here. - System.out.println("########################\n" + "OUT OF MEMORY " - + file + "\n" + "########################"); - new OOMWarning("Creating Image for " + file, err); - // System.out.println("Create IMAGE: " + err); - } catch (Exception ex) - { - ex.printStackTrace(); } - } finally - { - - } + }; + + String fileTitle = alignFrame.getTitle(); + ImageExporter exporter = new ImageExporter(writer, alignFrame, type, + fileTitle); + int imageWidth = aDimension.getWidth(); + int imageHeight = aDimension.getHeight() + borderBottomOffset; + String of = MessageManager.getString("label.alignment"); + exporter.doExport(file, this, imageWidth, imageHeight, of, renderer, + userBis); } + /** + * Calculates and returns a suitable width and height (in pixels) for an + * exported image + * + * @return + */ public AlignmentDimension getAlignmentDimension() { - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); - } + int maxwidth = av.getAlignment().getVisibleWidth(); int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + getScalePanel().getHeight(); @@ -1360,16 +1346,15 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.getWrapAlignment()) { height = getWrappedHeight(); - if (headless) + if (Jalview.isHeadlessMode()) { // need to obtain default alignment width and then add in any // additional allowance for id margin // this duplicates the calculation in getWrappedHeight but adjusts for // offscreen idWith width = alignFrame.getWidth() - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right - getVisibleIdWidth() - + getVisibleIdWidth(false); + - alignFrame.getInsets().left - alignFrame.getInsets().right + - getVisibleIdWidth() + getVisibleIdWidth(false); } else { @@ -1385,30 +1370,10 @@ public class AlignmentPanel extends GAlignmentPanel implements } - /** - * DOCUMENT ME! - */ - public void makeEPS(File epsFile) - { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); - } - - /** - * DOCUMENT ME! - */ - public void makePNG(File pngFile) - { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile); - } - - public void makeSVG(File svgFile) - { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); - } - public void makePNGImageMap(File imgMapFile, String imageName) + throws ImageOutputException { - // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS + // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); @@ -1420,35 +1385,33 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.getAlignment().getHeight(), res, alwidth = av - .getAlignment().getWidth(), g, gSize, f, fSize, sy; - StringBuffer text = new StringBuffer(); + 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++) { - text = new StringBuffer(); + 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) @@ -1456,81 +1419,75 @@ 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("
" + 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.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].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()); } } } @@ -1539,18 +1496,24 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { - ex.printStackTrace(); + throw new ImageOutputException( + "couldn't write ImageMap due to unexpected error", ex); } } // /////////END OF IMAGE MAP } + /** + * Answers the height of the entire alignment in pixels, assuming it is in + * wrapped mode + * + * @return + */ int getWrappedHeight() { int seqPanelWidth = getSeqPanel().seqCanvas.getWidth(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + if (Jalview.isHeadlessMode()) { seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth() - vscroll.getPreferredSize().width @@ -1569,6 +1532,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int annotationHeight = 0; if (av.isShowAnnotation()) { + hgap += SeqCanvas.SEQS_ANNOTATION_GAP; annotationHeight = getAnnotationPanel().adjustPanelHeight(); } @@ -1578,7 +1542,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(maxwidth) - 1; } int height = ((maxwidth / chunkWidth) + 1) * cHeight; @@ -1595,28 +1560,58 @@ 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(); + annotationPanel = null; + } + if (av != null) { - jalview.structure.StructureSelectionManager ssm = av - .getStructureSelectionManager(); + av.removePropertyChangeListener(propertyChangeListener); + propertyChangeListener = null; + StructureSelectionManager ssm = av.getStructureSelectionManager(); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); ssm.removeCommandListener(av); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); - av.setAlignment(null); + av.dispose(); av = null; } else { - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.warn("Closing alignment panel which is already closed."); + Console.warn("Closing alignment panel which is already closed."); } } } /** + * Close any open dialogs that would be orphaned when this one is closed + */ + protected void closeChildFrames() + { + if (overviewPanel != null) + { + overviewPanel.dispose(); + overviewPanel = null; + } + if (calculationDialog != null) + { + calculationDialog.closeFrame(); + calculationDialog = null; + } + } + + /** * hides or shows dynamic annotation rows based on groups and av state flags */ public void updateAnnotation() @@ -1646,7 +1641,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public String getViewName() { - return av.viewName; + return av.getViewName(); } /** @@ -1669,13 +1664,17 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { } - if (b) { - alignFrame.setDisplayedView(this); + setAlignFrameView(); } } + public void setAlignFrameView() + { + alignFrame.setDisplayedView(this); + } + @Override public StructureSelectionManager getStructureSelectionManager() { @@ -1775,52 +1774,131 @@ 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) + 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.getResultSequence(0); - List seqs = av.getAlignment().getSequences(); + scrollToPosition(sr, verticalOffset, true); + } - /* - * 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) + /** + * Set a flag to say do not scroll any (cDNA/protein) complement. + * + * @param b + */ + protected void setToScrollComplementPanel(boolean b) + { + this.scrollComplementaryPanel = b; + } + + /** + * Get whether to scroll complement panel + * + * @return true if cDNA/protein complement panels should be scrolled + */ + protected boolean isSetToScrollComplementPanel() + { + return this.scrollComplementaryPanel; + } + + /** + * Redraw sensibly. + * + * @adjustHeight if true, try to recalculate panel height for visible + * annotations + */ + protected void refresh(boolean adjustHeight) + { + validateAnnotationDimensions(adjustHeight); + addNotify(); + if (adjustHeight) { - if (mappedTo == seq.getDatasetSequence()) - { - matched = true; - break; - } + // sort, repaint, update overview + paintAlignment(true, false); } - if (!matched) + else { - return; // failsafe, shouldn't happen + // lightweight repaint + repaint(); } + } - /* - * Scroll to position but centring the target residue. - */ - scrollToPosition(sr, verticalOffset, true, true); + @Override + /** + * Property change event fired when a change is made to the viewport ranges + * object associated with this alignment panel's viewport + */ + public void propertyChange(PropertyChangeEvent evt) + { + // update this panel's scroll values based on the new viewport ranges values + ViewportRanges ranges = av.getRanges(); + int x = ranges.getStartRes(); + int y = ranges.getStartSeq(); + setScrollValues(x, y); + + // now update any complementary alignment (its viewport ranges object + // is different so does not get automatically updated) + if (isSetToScrollComplementPanel()) + { + setToScrollComplementPanel(false); + av.scrollComplementaryAlignment(); + setToScrollComplementPanel(true); + } } /** - * Set a flag to say do not scroll any (cDNA/protein) complement. + * Set the reference to the PCA/Tree chooser dialog for this panel. This + * reference should be nulled when the dialog is closed. * - * @param b + * @param calculationChooser + */ + public void setCalculationDialog(CalculationChooser calculationChooser) + { + calculationDialog = calculationChooser; + } + + /** + * Returns the reference to the PCA/Tree chooser dialog for this panel (null + * if none is open) */ - protected void setDontScrollComplement(boolean b) + public CalculationChooser getCalculationDialog() { - this.dontScrollComplement = b; + return calculationDialog; } - protected boolean isDontScrollComplement() + /** + * Constructs and sets the title for the Overview window (if there is one), + * including the align frame's title, and view name (if applicable). Returns + * the title, or null if this panel has no Overview window open. + * + * @param alignFrame + * @return + */ + public String setOverviewTitle(AlignFrame alignFrame) + { + if (this.overviewPanel == null) + { + return null; + } + String overviewTitle = MessageManager + .formatMessage("label.overview_params", new Object[] + { alignFrame.getTitle() }); + String viewName = getViewName(); + if (viewName != null) + { + overviewTitle += (" " + viewName); + } + overviewPanel.setTitle(overviewTitle); + return overviewTitle; + } + + /** + * If this alignment panel has an Overview panel open, closes it + */ + public void closeOverviewPanel() { - return this.dontScrollComplement; + if (overviewPanel != null) + { + overviewPanel.close(); + overviewPanel = null; + } } }