X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=dfe0ffaeaba2721aa0d7399a30cd452ecd00218d;hb=aeb6256bd008584086db3c7be28bee2d42580e61;hp=c03b56dacd0fa6d9d5933940d001f577775255a1;hpb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index c03b56d..dfe0ffa 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -73,6 +73,11 @@ import javax.swing.SwingUtilities; public class AlignmentPanel extends GAlignmentPanel implements 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; @@ -233,8 +238,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getAnnotationPanel().adjustPanelHeight(); Dimension d = calculateIdWidth(); - - d.setSize(d.width + 4, d.height); getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); @@ -242,20 +245,24 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * Calculate the width of the alignment labels based on the displayed names - * and any bounds on label width set in preferences. + * 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 + * also set as a property of the viewport. * * @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)); + int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3); + int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth); r = calculateIdWidth(maxwidth); av.setIdWidth(r.width); } @@ -265,6 +272,16 @@ 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; } @@ -277,7 +294,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ - public Dimension calculateIdWidth(int maxwidth) + protected Dimension calculateIdWidth(int maxwidth) { Container c = new Container(); @@ -287,19 +304,13 @@ public class AlignmentPanel extends GAlignmentPanel implements 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++; } @@ -313,27 +324,25 @@ public class AlignmentPanel extends GAlignmentPanel implements while (i < al.getAlignmentAnnotation().length) { String label = al.getAlignmentAnnotation()[i].label; - - if (fm.stringWidth(label) > idWidth) - { - idWidth = fm.stringWidth(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; + + return new Dimension(w, 12); } /** - * 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(); @@ -345,13 +354,11 @@ 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); } /** @@ -364,14 +371,12 @@ 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(); @@ -477,7 +482,7 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollNeeded = ranges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview, false); + paintAlignment(false, false); return scrollNeeded; } @@ -536,7 +541,7 @@ 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()); } /** @@ -641,16 +646,9 @@ 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(); @@ -835,12 +833,6 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - */ @Override public void paintComponent(Graphics g) { @@ -962,8 +954,8 @@ 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, @@ -1063,6 +1055,8 @@ public class AlignmentPanel extends GAlignmentPanel implements public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, Graphics g) throws PrinterException { + getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(), + getHeight()); int annotationHeight = 0; if (av.isShowAnnotation()) { @@ -1080,15 +1074,11 @@ 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(pageWidth - idWidth); + av.getRanges().setViewportStartAndWidth(0, resWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -1100,8 +1090,8 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * 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) + * single pages or ranges, (at the cost of repeated processing in the + * 'normal' case, when all pages are printed) */ g.translate(0, -pageNumber * pageHeight); @@ -1148,21 +1138,22 @@ 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).width; } - Integer idwidth = null; - if (onscreen || (idwidth = Cache - .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + Integer idwidth = onscreen ? null + : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); + if (idwidth != null) { - int w = getIdPanel().getWidth(); - return (w > 0 ? w : calculateIdWidth().width + 4); + return idwidth.intValue() + ID_WIDTH_PADDING; } - return idwidth.intValue() + 4; + + int w = getIdPanel().getWidth(); + return (w > 0 ? w : calculateIdWidth().width); } void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) @@ -1247,12 +1238,7 @@ 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(); @@ -1435,6 +1421,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } + /** + * Answers the height of the entire alignment in pixels, assuming it is in + * wrapped mode + * + * @return + */ int getWrappedHeight() { int seqPanelWidth = getSeqPanel().seqCanvas.getWidth(); @@ -1459,6 +1451,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int annotationHeight = 0; if (av.isShowAnnotation()) { + hgap += SeqCanvas.SEQS_ANNOTATION_GAP; annotationHeight = getAnnotationPanel().adjustPanelHeight(); } @@ -1698,7 +1691,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void scrollToCentre(SearchResultsI sr, int verticalOffset) { - scrollToPosition(sr, verticalOffset, true, true); + scrollToPosition(sr, verticalOffset, true); } /**