X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=c43e0b6bd6f72dc49e74cbc00c5fac7bbfa16277;hb=801c367379086cc38bf4d3059a8e30ca9f4e78c0;hp=0040dd7e0bf71343fe16e6d9dc0f1ea460e82639;hpb=2ea1fb1e8751ac7272c421820000449525664f02;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 0040dd7..c43e0b6 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -23,6 +23,7 @@ package jalview.gui; import jalview.analysis.AnnotationSorter; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.SequenceRenderer; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; @@ -55,6 +56,7 @@ import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; +import java.awt.image.BufferedImage; import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; @@ -65,10 +67,15 @@ import java.io.FileWriter; import java.io.PrintWriter; import java.util.List; -import javax.swing.SwingUtilities; - /** - * DOCUMENT ME! + * The main panel of an AlignFrame, containing holders for the IdPanel, + * SeqPanel, AnnotationLabels (a JPanel), and AnnotationPanel. + * + * Additional holders contain an IdPanelWidthAdjuster space above the idPanel, + * AnnotationScroller (JScrollPane for AnnotationPanel), and vertical and + * horizontal scrollbars. + * + * * * @author $author$ * @version $Revision: 1.161 $ @@ -117,7 +124,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { -// setBackground(Color.white); // BH 2019 + setBackground(Color.white); // BH 2019 + setOpaque(true); alignFrame = af; this.av = av; setSeqPanel(new SeqPanel(av, this)); @@ -134,7 +142,11 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationScroller.setViewportView(getAnnotationPanel()); annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); - + if (!av.isShowAnnotation()) + { + annotationScroller.setVisible(false); + annotationSpaceFillerHolder.setVisible(false); + } scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER); seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER); @@ -167,6 +179,9 @@ public class AlignmentPanel extends GAlignmentPanel implements ranges.setViewportWidth(widthInRes); ranges.setViewportHeight(heightInSeq); + ViewportRanges.sTest += "AP.resize chht=" + av.getCharHeight() + + "canvHt=" + getSeqPanel().seqCanvas.getHeight() + " " + + heightInSeq + "\n"; } } @@ -578,7 +593,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void updateLayout() { - fontChanged(); + fontChanged(); // fires repaint setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); ViewportRanges ranges = av.getRanges(); @@ -732,6 +747,7 @@ public class AlignmentPanel extends GAlignmentPanel implements 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 @@ -739,6 +755,11 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } + + ViewportRanges.sTest += "AP.valChanged chht=" + av.getCharHeight() + + "canvHt=" + getSeqPanel().seqCanvas.getHeight() + " " + + height + "\n"; + ranges.setViewportStartAndHeight(y, height); } repaint(); @@ -788,7 +809,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -828,7 +849,6 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (updateOverview) { - if (overviewPanel != null) { overviewPanel.updateOverviewImage(); @@ -845,6 +865,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void paintComponent(Graphics g) { + invalidate(); // needed so that the id width adjuster works correctly Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); @@ -1065,6 +1086,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, Graphics g) throws PrinterException { + int annotationHeight = 0; if (av.isShowAnnotation()) { @@ -1089,6 +1111,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int totalHeight = cHeight * (maxwidth / resWidth + 1); + g = g.create(); + g.setColor(Color.white); g.fillRect(0, 0, pageWidth, pageHeight); g.setFont(av.getFont()); @@ -1102,7 +1126,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ g.translate(0, -pageNumber * pageHeight); - g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight); + // BH 2020.03.19 avoiding g.setClip + g.clipRect(0, pageNumber * pageHeight, pageWidth, pageHeight); /* * draw sequence ids and annotation labels (if shown) @@ -1115,6 +1140,7 @@ public class AlignmentPanel extends GAlignmentPanel implements getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, totalHeight, 0); + g.dispose(); if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; @@ -1722,4 +1748,154 @@ public class AlignmentPanel extends GAlignmentPanel implements return calculationDialog; } + @Override + public SequenceRenderer getSequenceRenderer() + { + return seqPanel.seqCanvas.getSequenceRenderer(); + } + + public boolean scrollTo(int ostart, int end, int seqIndex, + boolean scrollToNearest, boolean redrawOverview) + { + int startv, endv, starts, ends;// , width; + + int start = -1; + if (av.hasHiddenColumns()) + { + AlignmentI al = av.getAlignment(); + start = al.getHiddenColumns().absoluteToVisibleColumn(ostart); + end = al.getHiddenColumns().absoluteToVisibleColumn(end); + if (start == end) + { + if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart)) + { + // don't scroll - position isn't visible + return false; + } + } + } + else + { + start = ostart; + } + + ViewportRanges ranges = av.getRanges(); + if (!av.getWrapAlignment()) + { + /* + * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv = + * av.getStartRes()) >= start) { spos=start-1; // seqIn // + * setScrollValues(start - 1, seqIndex); } else if ((endv = + * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end - + * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts = + * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), + * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) { + * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } + */ + + // below is scrolling logic up to Jalview 2.8.2 + // if ((av.getStartRes() > end) + // || (av.getEndRes() < start) + // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + // { + // if (start > av.getAlignment().getWidth() - hextent) + // { + // start = av.getAlignment().getWidth() - hextent; + // if (start < 0) + // { + // start = 0; + // } + // + // } + // if (seqIndex > av.getAlignment().getHeight() - vextent) + // { + // seqIndex = av.getAlignment().getHeight() - vextent; + // if (seqIndex < 0) + // { + // seqIndex = 0; + // } + // } + // setScrollValues(start, seqIndex); + // } + // logic copied from jalview.gui.AlignmentPanel: + if ((startv = ranges.getStartRes()) >= start) + { + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start - 1, seqIndex); + } + else if ((endv = ranges.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + 1 + 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 + */ + } + else + { + ranges.scrollToWrappedVisible(start); + } + + paintAlignment(redrawOverview, false); + return true; + } + + @Override + public void overviewDone(BufferedImage miniMe) + { + overviewPanel.canvas.finalizeDraw(miniMe); + } + + + private boolean holdRepaint = false; + + public boolean getHoldRepaint() + { + return holdRepaint; + } + + public void setHoldRepaint(boolean b) + { + if (holdRepaint == b) + { + return; + } + holdRepaint = b; + if (!b) + { + repaint(); + } + } + + @Override + public void repaint() + { + if (holdRepaint) + { + // System.out.println("AP repaint holding"); + // Platform.stackTrace(); + return; + } + super.repaint(); + } + }