X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=92b9a5065cd1b64168b5eb2ffa4a4b0a40023d33;hb=1b0014839c94c711c09a94641ecb5036072bb5b3;hp=1ac553668f2a9230ae5af6b1c3cb40fd6835755d;hpb=b2829c5d7e7815e5e261d39964ade91ed5225510;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 1ac5536..92b9a50 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -37,7 +37,6 @@ import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; -import jalview.util.Platform; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; @@ -329,12 +328,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Highlight the given results on the alignment. + * Highlight the given results on the alignment * */ public void highlightSearchResults(SearchResultsI results) { - boolean scrolled = scrollToPosition(results, 0, true, false); + boolean scrolled = scrollToPosition(results, 0, false); boolean noFastPaint = scrolled && av.getWrapAlignment(); @@ -346,13 +345,11 @@ public class AlignmentPanel extends GAlignmentPanel implements * (if any) * * @param searchResults - * @param redrawOverview * @return */ - public boolean scrollToPosition(SearchResultsI searchResults, - boolean redrawOverview) + public boolean scrollToPosition(SearchResultsI searchResults) { - return scrollToPosition(searchResults, 0, redrawOverview, false); + return scrollToPosition(searchResults, 0, false); } /** @@ -365,14 +362,12 @@ public class AlignmentPanel extends GAlignmentPanel implements * @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 */ protected boolean scrollToPosition(SearchResultsI results, - int verticalOffset, boolean redrawOverview, boolean centre) + int verticalOffset, boolean centre) { int startv, endv, starts, ends; ViewportRanges ranges = av.getRanges(); @@ -478,7 +473,7 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollNeeded = ranges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview, false); + paintAlignment(false, false); return scrollNeeded; } @@ -537,7 +532,7 @@ public class AlignmentPanel extends GAlignmentPanel implements addNotify(); // TODO: many places call this method and also paintAlignment with various // different settings. this means multiple redraws are triggered... - paintAlignment(true, false); + paintAlignment(true, av.needToUpdateStructureViews()); } /** @@ -547,37 +542,10 @@ public class AlignmentPanel extends GAlignmentPanel implements protected void validateAnnotationDimensions(boolean adjustPanelHeight) { int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + annotationHeight = getAnnotationPanel() + .adjustForAlignFrame(adjustPanelHeight, annotationHeight); - if (adjustPanelHeight) - { - int rowHeight = av.getCharHeight(); - int alignmentHeight = rowHeight * av.getAlignment().getHeight(); - - /* - * Estimate available height in the AlignFrame for alignment + - * annotations. Deduct an estimate for title bar, menu bar, scale panel, - * hscroll, status bar, insets. - */ - int stuff = Platform.isAMac() ? 120 : 140; - int availableHeight = alignFrame.getHeight() - stuff; - - /* - * 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)); @@ -616,6 +584,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); + validateAnnotationDimensions(false); } int canvasWidth = getSeqPanel().seqCanvas.getWidth(); @@ -668,16 +637,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - int width = av.getAlignment().getWidth(); + int width = av.getAlignment().getVisibleWidth(); int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns()) - { - // reset the width to exclude hidden columns - width = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(width); - } - hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); @@ -989,8 +951,8 @@ public class AlignmentPanel extends GAlignmentPanel implements final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - final int alignmentWidth = av.getAlignment().getWidth(); - final int pagesWide = (alignmentWidth / totalRes) + 1; + final int alignmentWidth = av.getAlignment().getVisibleWidth(); + int pagesWide = (alignmentWidth / totalRes) + 1; final int startRes = (pageIndex % pagesWide) * totalRes; final int endRes = Math.min(startRes + totalRes - 1, @@ -1073,31 +1035,27 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * 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(int pwidth, int pheight, int pi, - Graphics pg) 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(); @@ -1111,72 +1069,42 @@ public class AlignmentPanel extends GAlignmentPanel implements int idWidth = getVisibleIdWidth(false); - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(maxwidth) - 1; - } + int maxwidth = av.getAlignment().getVisibleWidth(); int resWidth = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(pwidth - idWidth); + .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); + 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; - - 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())); + /* + * 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); - 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.drawWrappedPanelForPrinting(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, totalHeight, 0); - if ((pi * pheight) < totalHeight) + if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; - } else { @@ -1303,12 +1231,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public AlignmentDimension getAlignmentDimension() { - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getAlignment().getHiddenColumns() - .absoluteToVisibleColumn(maxwidth); - } + int maxwidth = av.getAlignment().getVisibleWidth(); int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + getScalePanel().getHeight(); @@ -1623,7 +1546,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public String getViewName() { - return av.viewName; + return av.getViewName(); } /** @@ -1754,7 +1677,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void scrollToCentre(SearchResultsI sr, int verticalOffset) { - scrollToPosition(sr, verticalOffset, true, true); + scrollToPosition(sr, verticalOffset, true); } /**