X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=dc1f95ba377622a28e0e13b82d237e4a49a7e312;hb=31b84e9690b026255a488724ef7b847da94e48af;hp=c7ef3cedf42543f8d9cbed9235a6ebd7c97b18b6;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index c7ef3ce..0ea2b8a 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,6 +20,29 @@ */ package jalview.gui; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.bin.Jalview; +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.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.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -27,8 +50,11 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; +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; @@ -41,21 +67,6 @@ 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.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; - /** * DOCUMENT ME! * @@ -63,7 +74,7 @@ import jalview.util.MessageManager; * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable, AlignmentViewPanel + AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; @@ -73,10 +84,8 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; - private boolean headless; IdwidthAdjuster idwidthAdjuster; - /** DOCUMENT ME!! */ public AlignFrame alignFrame; private ScalePanel scalePanel; @@ -85,18 +94,19 @@ public class AlignmentPanel extends GAlignmentPanel implements private AnnotationLabels alabels; - // this value is set false when selection area being dragged - boolean fastPaint = true; + private int hextent = 0; - 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 followingComplementScroll; + private boolean scrollComplementaryPanel = true; + + private PropertyChangeListener propertyChangeListener; + + private CalculationChooser calculationDialog; /** * Creates a new AlignmentPanel object. @@ -106,6 +116,7 @@ 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)); @@ -131,9 +142,39 @@ 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) { if (evt.getPropertyName().equals("alignment")) @@ -142,7 +183,10 @@ public class AlignmentPanel extends GAlignmentPanel implements alignmentChanged(); } } - }); + }; + av.addPropertyChangeListener(propertyChangeListener); + + av.getRanges().addPropertyChangeListener(this); fontChanged(); adjustAnnotationHeight(); updateLayout(); @@ -153,13 +197,20 @@ public class AlignmentPanel extends GAlignmentPanel implements { return av; } + public void alignmentChanged() { av.alignmentChanged(this); + if (getCalculationDialog() != null) + { + getCalculationDialog().validateCalcTypes(); + } + alignFrame.updateEditMenuBar(); - paintAlignment(true); + // no idea if we need to update structure + paintAlignment(true, true); } @@ -172,13 +223,13 @@ 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; + 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(); @@ -188,15 +239,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); - if (overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } - if (this.alignFrame.getSplitViewContainer() != null) - { - ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); - } - repaint(); } @@ -240,8 +282,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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; @@ -282,29 +324,21 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, - idWidth), 12); + return new Dimension( + maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** * Highlight the given results on the alignment. * */ - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { - scrollToPosition(results); - getSeqPanel().seqCanvas.highlightSearchResults(results); - } + boolean scrolled = scrollToPosition(results, 0, true, false); - /** - * Scroll the view to show the position of the highlighted region in results - * (if any) and redraw the overview - * - * @param results - */ - public boolean scrollToPosition(SearchResults results) - { - return scrollToPosition(results, true, false); + boolean fastPaint = !(scrolled && av.getWrapAlignment()); + + getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint); } /** @@ -315,138 +349,138 @@ 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, redrawOverview, false); + return scrollToPosition(searchResults, 0, redrawOverview, 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, - boolean redrawOverview, boolean centre) + protected boolean scrollToPosition(SearchResultsI results, + int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; - // TODO: properly locate search results in view when large numbers of hidden - // columns exist before highlighted region - // do we need to scroll the panel? - // TODO: tons of nullpointerexceptions raised here. - if (results != null && results.getSize() > 0 && av != null - && av.getAlignment() != null) - { - int seqIndex = av.getAlignment().findIndex(results); - if (seqIndex == -1) - { - return false; - } - SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); + ViewportRanges ranges = av.getRanges(); - int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); - if (r == null) - { - return false; - } - int start = r[0]; - int end = r[1]; - // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // - // DEBUG + 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 = Math.min(end + offset, seq.getEnd() - 1); - } - if (start < 0) + 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) { - return false; + if (!hidden.isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } } - if (end == seq.getEnd()) + } + + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + boolean scrollNeeded = true; + + if (!av.getWrapAlignment()) + { + if ((startv = ranges.getStartRes()) >= start) { - return false; + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start, seqIndex); } - if (av.hasHiddenColumns()) + else if ((endv = ranges.getEndRes()) <= end) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); - if (start == end) - { - if (!av.getColumnSelection().isVisible(r[0])) - { - // don't scroll - position isn't visible - return false; - } - } + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + end - endv, seqIndex); } - if (!av.getWrapAlignment()) + else if ((starts = ranges.getStartSeq()) > seqIndex) { - if ((startv = av.getStartRes()) >= start) - { - /* - * Scroll left to make start of search results visible - */ - setScrollValues(start - 1, seqIndex); - } - else if ((endv = av.getEndRes()) <= end) - { - /* - * Scroll right to make end of search results visible - */ - setScrollValues(startv + 1 + 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 up to make start of search results visible */ + setScrollValues(ranges.getStartRes(), seqIndex); } - else + else if ((ends = ranges.getEndSeq()) <= seqIndex) { - scrollToWrappedVisible(start); + /* + * Scroll down to make end of search results visible + */ + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + + 1); } + /* + * Else results are already visible - no need to scroll + */ + scrollNeeded = false; } - 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(redrawOverview, false); + return scrollNeeded; } /** @@ -490,6 +524,7 @@ 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 @@ -500,7 +535,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } validateAnnotationDimensions(true); addNotify(); - paintAlignment(true); + // TODO: many places call this method and also paintAlignment with various + // different settings. this means multiple redraws are triggered... + paintAlignment(true, false); } /** @@ -509,47 +546,20 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int height = getAnnotationPanel().adjustPanelHeight(); - - int theight = av.getCharHeight() - * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 - : av.getAlignment().getHiddenSequences().getSize())); - float sscaling = (float) (theight / (1.0 * theight + height)); - float ascaling = (float) (height * 1.0 / alignFrame.getHeight()); - int rheight = alignFrame.getHeight() - height - av.getCharHeight(); - if (adjustPanelHeight) - { - // NOTE: this logic is different in the applet. Need a better algorithm to - // define behaviour - // try and set height according to alignment - if (ascaling > 0 && sscaling < 0.5) - { - // if the alignment is too big then - // default is 0.5 split - height = alignFrame.getHeight() / 2; - } - else - { - // if space for more than one sequence row left when annotation is fully - // displayed then set height to annotation height - // otherwise, leave at least two lines of sequence shown. - height = (rheight > av.getCharHeight()) ? height - : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling))); - } - } - else - { - // maintain same window layout whilst updating sliders - height = annotationScroller.getSize().height; - } + int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + annotationHeight = getAnnotationPanel() + .adjustForAlignFrame(adjustPanelHeight, annotationHeight); + hscroll.addNotify(); + annotationScroller.setPreferredSize( + new Dimension(annotationScroller.getWidth(), annotationHeight)); - annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), height)); + Dimension e = idPanel.getSize(); + alabels.setSize(new Dimension(e.width, annotationHeight)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), height)); - annotationScroller.validate();// repaint(); + annotationSpaceFillerHolder.getWidth(), annotationHeight)); + annotationScroller.validate(); annotationScroller.addNotify(); } @@ -564,7 +574,8 @@ public class AlignmentPanel extends GAlignmentPanel implements fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - av.startSeq = 0; + ViewportRanges ranges = av.getRanges(); + ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -578,6 +589,27 @@ public class AlignmentPanel extends GAlignmentPanel implements { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); + validateAnnotationDimensions(false); + } + + int canvasWidth = getSeqPanel().seqCanvas.getWidth(); + if (canvasWidth > 0) + { // may not yet be laid out + if (wrap) + { + int widthInRes = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(canvasWidth); + ranges.setViewportWidth(widthInRes); + } + else + { + int widthInRes = (canvasWidth / av.getCharWidth()); + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight()); + + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); + } } idSpaceFillerPanel1.setVisible(!wrap); @@ -585,255 +617,217 @@ public class AlignmentPanel extends GAlignmentPanel implements repaint(); } - // return value is true if the scroll is valid - public boolean scrollUp(boolean up) + /** + * Adjust row/column scrollers to show a visible position in the alignment. + * + * @param x + * visible column to scroll to + * @param y + * visible row to scroll to + * + */ + public void setScrollValues(int xpos, int ypos) { - if (up) + int x = xpos; + int y = ypos; + + if (av == null || av.getAlignment() == null) { - if (vscroll.getValue() < 1) - { - return false; - } + return; + } - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); + if (av.getWrapAlignment()) + { + setScrollingForWrappedPanel(x); } else { - if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); + + if (av.hasHiddenColumns()) { - return false; + // reset the width to exclude hidden columns + width = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(width); } - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); - } + hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); + vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - fastPaint = true; + if (hextent > width) + { + hextent = width; + } - return true; - } + if (vextent > height) + { + vextent = height; + } - /** - * DOCUMENT ME! - * - * @param right - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean scrollRight(boolean right) - { - if (!right) - { - if (hscroll.getValue() < 1) + if ((hextent + x) > width) { - return false; + x = width - hextent; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); - } - else - { - if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) + if ((vextent + y) > height) { - return false; + y = height - vextent; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); - } + if (y < 0) + { + y = 0; + } - fastPaint = true; + if (x < 0) + { + x = 0; + } - return true; + // update the scroll values + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); + } } /** - * Adjust row/column scrollers to show a visible position in the alignment. - * - * @param x - * visible column to scroll to DOCUMENT ME! - * @param y - * visible row to scroll to + * Respond to adjustment event when horizontal or vertical scrollbar is + * changed * + * @param evt + * adjustment event encoding whether hscroll or vscroll changed */ - public void setScrollValues(int x, int y) + @Override + public void adjustmentValueChanged(AdjustmentEvent evt) { - // System.err.println("Scroll to "+x+","+y); - if (av == null || av.getAlignment() == null) + if (av.getWrapAlignment()) { + adjustScrollingWrapped(evt); return; } - int width = av.getAlignment().getWidth(); - int height = av.getAlignment().getHeight(); - - if (av.hasHiddenColumns()) - { - width = av.getColumnSelection().findColumnPosition(width); - } - - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av - .getCharWidth())) - 1); - - hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); - vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - - if (hextent > width) - { - hextent = width; - } - if (vextent > height) - { - vextent = height; - } + ViewportRanges ranges = av.getRanges(); - if ((hextent + x) > width) + if (evt.getSource() == hscroll) { - x = width - hextent; - } + int oldX = ranges.getStartRes(); + int oldwidth = ranges.getViewportWidth(); + int x = hscroll.getValue(); + int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); - if ((vextent + y) > height) - { - y = height - vextent; + // 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)) + { + return; + } + ranges.setViewportStartAndWidth(x, width); } - - if (y < 0) + else if (evt.getSource() == vscroll) { - y = 0; - } + int oldY = ranges.getStartSeq(); + int oldheight = ranges.getViewportHeight(); + int y = vscroll.getValue(); + int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - if (x < 0) - { - x = 0; + // 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)) + { + return; + } + ranges.setViewportStartAndHeight(y, height); } - - hscroll.setValues(x, hextent, 0, width); - vscroll.setValues(y, vextent, 0, height); + repaint(); } /** - * DOCUMENT ME! + * Responds to a scroll change by setting the start position of the viewport. + * Does * * @param evt - * DOCUMENT ME! */ - public void adjustmentValueChanged(AdjustmentEvent evt) + protected void adjustScrollingWrapped(AdjustmentEvent evt) { - int oldX = av.getStartRes(); - int oldY = av.getStartSeq(); - if (evt.getSource() == hscroll) { - int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1); + return; // no horizontal scroll when wrapped } + final ViewportRanges ranges = av.getRanges(); if (evt.getSource() == vscroll) { - int offy = vscroll.getValue(); + int newY = vscroll.getValue(); - 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 + */ + int oldX = ranges.getStartRes(); + int oldY = ranges.getWrappedScrollPosition(oldX); + if (oldY == newY) { - 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() - { - public void run() - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } - }); - } + return; } - else + if (newY > -1) { - av.setStartSeq(offy); - av.setEndSeq(offy - + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())); + /* + * 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 (overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } - - int scrollX = av.startRes - oldX; - int scrollY = av.startSeq - oldY; - - if (av.getWrapAlignment() || !fastPaint) - { - repaint(); - } else { - // Make sure we're not trying to draw a panel - // larger than the visible window - if (scrollX > av.endRes - av.startRes) + // 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() { - scrollX = av.endRes - av.startRes; - } - else if (scrollX < av.startRes - av.endRes) - { - scrollX = av.startRes - av.endRes; - } - - if (scrollX != 0 || scrollY != 0) - { - getIdPanel().getIdCanvas().fastPaint(scrollY); - getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY); - getScalePanel().repaint(); - - if (av.isShowAnnotation() && scrollX != 0) + @Override + public void run() { - getAnnotationPanel().fastPaint(scrollX); + // 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 + Cache.log.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); } - } - } - /* - * If there is one, scroll the (Protein/cDNA) complementary alignment to - * match, unless we are ourselves doing that. - */ - if (isFollowingComplementScroll()) - { - setFollowingComplementScroll(false); - } - else - { - av.scrollComplementaryAlignment(); + }); } + repaint(); } - /** - * Repaint the alignment including the annotations and overview panels (if - * shown). + /* (non-Javadoc) + * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean) */ - public void paintAlignment(boolean updateOverview) + @Override + public void paintAlignment(boolean updateOverview, + boolean updateStructures) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); - sorter.sort(getAlignment() - .getAlignmentAnnotation(), + sorter.sort(getAlignment().getAlignmentAnnotation(), av.getSortAnnotationsBy()); repaint(); - if (updateOverview) + if (updateStructures) { av.getStructureSelectionManager().sequenceColoursChanged(this); + } + if (updateOverview) + { if (overviewPanel != null) { @@ -848,41 +842,45 @@ public class AlignmentPanel extends GAlignmentPanel implements * @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(); - if (av.getWrapAlignment()) - { - int maxwidth = av.getAlignment().getWidth(); + validate(); // needed so that the id width adjuster works correctly - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } + /* + * 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); + } - 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()); - } + /** + * 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); + + /* + * 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); } /** @@ -900,6 +898,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -910,196 +909,166 @@ 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()); + final int idWidth = getVisibleIdWidth(false); - // ////////////////////////////////// - // / 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; + /* + * 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().getWidth(); + final 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); - - 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); - 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().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; } /** - * 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 { int annotationHeight = 0; - AnnotationLabels labels = null; if (av.isShowAnnotation()) { annotationHeight = getAnnotationPanel().adjustPanelHeight(); - labels = new AnnotationLabels(av); } int hgap = av.getCharHeight(); @@ -1116,69 +1085,44 @@ 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 resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); + int resWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(pageWidth - idWidth); 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); - - pg.translate(0, -pi * pheight); - - pg.setClip(0, pi * pheight, pwidth, pheight); + g.setColor(Color.white); + g.fillRect(0, 0, pageWidth, pageHeight); + g.setFont(av.getFont()); + g.setColor(Color.black); - 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 some 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.drawIdsWrapped((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 { @@ -1214,96 +1158,68 @@ public class AlignmentPanel extends GAlignmentPanel implements return calculateIdWidth(-1).width + 4; } Integer idwidth = null; - if (onscreen - || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + 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) + /** + * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and + * writes it to the specified file + * + * @param type + * @param file + */ + void makeAlignmentImage(ImageMaker.TYPE type, File file) { - long progress = 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); - } - try + 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(), file, - imageTitle); if (av.getWrapAlignment()) { - if (im.getGraphics() != null) - { - printWrappedAlignment(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight(), 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 - { - if (alignFrame != null && !headless) - { - alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); - } - } + }; + + 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); } + /** + * 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); + maxwidth = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(maxwidth); } int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) @@ -1313,16 +1229,15 @@ 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 { @@ -1338,29 +1253,9 @@ 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) { - // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS + // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); @@ -1372,35 +1267,32 @@ 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) - + ""); + .getCharAt(column) + ""); } else { - triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) + ""); } @@ -1409,83 +1301,73 @@ public class AlignmentPanel extends GAlignmentPanel implements continue; } - int alIndex = seq.findPosition(res); - gSize = groups.length; - for (g = 0; g < gSize; g++) + int seqPos = seq.findPosition(column); + int gSize = groups.length; + for (int g = 0; g < gSize; g++) { if (text.length() < 1) { - text.append(" res) + if (groups[g].getStartRes() < column + && groups[g].getEndRes() > column) { - text.append("
" + 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()); } } } @@ -1533,7 +1415,8 @@ 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; @@ -1550,16 +1433,29 @@ 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 @@ -1572,6 +1468,23 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** + * 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() @@ -1595,14 +1508,13 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public AlignmentI getAlignment() { - return av.getAlignment(); + return av == null ? null : av.getAlignment(); } - @Override public String getViewName() { - return av.viewName; + return av.getViewName(); } /** @@ -1614,11 +1526,17 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { + if (alignFrame.getSplitViewContainer() != null) + { + /* + * bring enclosing SplitFrame to front first if there is one + */ + ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b); + } alignFrame.setSelected(b); } catch (Exception ex) { } - ; if (b) { @@ -1644,12 +1562,15 @@ 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()); } @@ -1719,60 +1640,96 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param sr * holds mapped region(s) of this alignment that we are scrolling * 'to'; may be modified for sequence offset by this method - * @param seqOffset + * @param verticalOffset * the number of visible sequences to show above the mapped region */ - public void scrollToCentre(SearchResults sr, int seqOffset) + 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, true); + } - /* - * This is like AlignmentI.findIndex(seq) but here we are matching the - * dataset sequence not the aligned sequence - */ - int sequenceIndex = 0; - 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; - } - sequenceIndex++; + // sort, repaint, update overview + paintAlignment(true, false); } - if (!matched) + else { - return; // failsafe, shouldn't happen + // lightweight repaint + repaint(); } - sequenceIndex = Math.max(0, sequenceIndex - seqOffset); - sr.getResults().get(0) - .setSequence(av.getAlignment().getSequenceAt(sequenceIndex)); + } - /* - * Scroll to position but centring the target residue. - */ - scrollToPosition(sr, 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 we are scrolling to follow a (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 */ - protected void setFollowingComplementScroll(boolean b) + 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; } }