X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=dee56b0c91953e3e39cbb81ca86190845ba3b614;hb=3f53fef393541cb63beb8766a4f3922b8c420579;hp=199c4e599a9ff1e5cc0cf83a272f668e993b91b1;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 199c4e5..dee56b0 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -23,12 +23,15 @@ package jalview.gui; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.renderer.AnnotationRenderer; import jalview.renderer.AwtRenderPanelI; import jalview.schemes.ResidueProperties; import jalview.util.Comparison; import jalview.util.MessageManager; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; import java.awt.AlphaComposite; import java.awt.Color; @@ -49,13 +52,13 @@ import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.awt.image.BufferedImage; +import java.beans.PropertyChangeEvent; import java.util.ArrayList; import java.util.Collections; import java.util.List; import javax.swing.JColorChooser; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.Scrollable; @@ -70,7 +73,7 @@ import javax.swing.ToolTipManager; */ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, MouseListener, MouseWheelListener, MouseMotionListener, - ActionListener, AdjustmentListener, Scrollable + ActionListener, AdjustmentListener, Scrollable, ViewportListenerI { String HELIX = MessageManager.getString("label.helix"); @@ -156,6 +159,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // and then set our own listener to consume all mousewheel events ap.annotationScroller.addMouseWheelListener(this); renderer = new AnnotationRenderer(); + + av.getRanges().addPropertyChangeListener(this); } public AnnotationPanel(AlignViewport av) @@ -170,13 +175,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (e.isShiftDown()) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { - ap.scrollRight(true); + av.getRanges().scrollRight(true); } - else + else if (wheelRotation < 0) { - ap.scrollRight(false); + av.getRanges().scrollRight(false); } } else @@ -280,7 +286,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (anot.length < av.getColumnSelection().getMax()) { - Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2]; + Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + + 2]; System.arraycopy(anot, 0, temp, 0, anot.length); anot = temp; aa[activeRow].annotations = anot; @@ -291,7 +298,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { for (int index : av.getColumnSelection().getSelected()) { - if (av.getColumnSelection().isVisible(index)) + if (av.getAlignment().getHiddenColumns().isVisible(index)) { anot[index] = null; } @@ -300,7 +307,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, else if (action.equals(LABEL)) { String exMesg = collectAnnotVals(anot, LABEL); - String label = JOptionPane.showInputDialog(this, + String label = JvOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"), exMesg); if (label == null) @@ -315,7 +322,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, for (int index : av.getColumnSelection().getSelected()) { - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) { continue; } @@ -338,7 +345,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, for (int index : av.getColumnSelection().getSelected()) { - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) { continue; } @@ -380,7 +387,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].hasIcons = true; } - String label = JOptionPane.showInputDialog(MessageManager + String label = JvOptionPane.showInputDialog(MessageManager .getString("label.enter_label_for_the_structure"), symbol); if (label == null) @@ -398,7 +405,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } for (int index : av.getColumnSelection().getSelected()) { - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) { continue; } @@ -408,8 +415,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, anot[index] = new Annotation(label, "", type, 0); } - anot[index].secondaryStructure = type != 'S' ? type : label - .length() == 0 ? ' ' : label.charAt(0); + anot[index].secondaryStructure = type != 'S' ? type + : label.length() == 0 ? ' ' : label.charAt(0); anot[index].displayCharacter = label; } @@ -441,17 +448,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, StringBuilder collatedInput = new StringBuilder(64); String last = ""; ColumnSelection viscols = av.getColumnSelection(); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); /* * the selection list (read-only view) is in selection order, not * column order; make a copy so we can sort it */ - List selected = new ArrayList(viscols.getSelected()); + List selected = new ArrayList<>(viscols.getSelected()); Collections.sort(selected); for (int index : selected) { // always check for current display state - just in case - if (!viscols.isVisible(index)) + if (!hidden.isVisible(index)) { continue; } @@ -652,15 +660,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { if (graphStretch > -1) { - av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - - evt.getY(); - if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0) + av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY + - evt.getY(); + if (av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graphHeight < 0) { - av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0; + av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graphHeight = 0; } graphStretchY = evt.getY(); adjustPanelHeight(); - ap.paintAlignment(true); + ap.paintAlignment(false, false); } else { @@ -708,11 +719,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - int column = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + int column = (evt.getX() / av.getCharWidth()) + + av.getRanges().getStartRes(); if (av.hasHiddenColumns()) { - column = av.getColumnSelection().adjustForHiddenColumns(column); + column = av.getAlignment().getHiddenColumns() + .visibleToAbsoluteColumn(column); } AlignmentAnnotation ann = aa[row]; @@ -770,6 +783,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { this.setToolTipText(JvSwingUtils.wrapTooltip(true, description)); } + else + { + this.setToolTipText(null); // no tooltip if null or empty description + } } else { @@ -812,8 +829,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int seqIndex = av.getAlignment().findIndex(seqref); if (seqIndex != -1) { - text.append(", ") - .append(MessageManager.getString("label.sequence")) + text.append(", ").append(MessageManager.getString("label.sequence")) .append(" ").append(seqIndex + 1); char residue = seqref.getCharAt(column); if (!Comparison.isGap(residue)) @@ -822,16 +838,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, String name; if (av.getAlignment().isNucleotide()) { - name = ResidueProperties.nucleotideName.get(String - .valueOf(residue)); - text.append(" Nucleotide: ").append( - name != null ? name : residue); + name = ResidueProperties.nucleotideName + .get(String.valueOf(residue)); + text.append(" Nucleotide: ") + .append(name != null ? name : residue); } else { - name = 'X' == residue ? "X" : ('*' == residue ? "STOP" - : ResidueProperties.aa2Triplet.get(String - .valueOf(residue))); + name = 'X' == residue ? "X" + : ('*' == residue ? "STOP" + : ResidueProperties.aa2Triplet + .get(String.valueOf(residue))); text.append(" Residue: ").append(name != null ? name : residue); } int residuePos = seqref.findPosition(column); @@ -892,6 +909,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void paintComponent(Graphics g) { + super.paintComponent(g); + g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); @@ -905,7 +924,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } } - imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth(); + imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + + 1) * av.getCharWidth(); if (imgWidth < 1) { return; @@ -915,8 +935,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { try { - image = new BufferedImage(imgWidth, ap.getAnnotationPanel() - .getHeight(), BufferedImage.TYPE_INT_RGB); + image = new BufferedImage(imgWidth, + ap.getAnnotationPanel().getHeight(), + BufferedImage.TYPE_INT_RGB); } catch (OutOfMemoryError oom) { try @@ -945,8 +966,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.fillRect(0, 0, imgWidth, image.getHeight()); imageFresh = true; } - - drawComponent(gg, av.startRes, av.endRes + 1); + + drawComponent(gg, av.getRanges().getStartRes(), + av.getRanges().getEndRes() + 1); imageFresh = false; g.drawImage(image, 0, 0, this); } @@ -972,13 +994,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, repaint(); return; } - long stime = System.currentTimeMillis(); + + int sr = av.getRanges().getStartRes(); + int er = av.getRanges().getEndRes() + 1; + int transX = 0; + gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.getCharWidth(), 0); - long mtime = System.currentTimeMillis(); - int sr = av.startRes; - int er = av.endRes + 1; - int transX = 0; if (horizontal > 0) // scrollbar pulled right, image to the left { @@ -995,17 +1017,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, drawComponent(gg, sr, er); gg.translate(-transX, 0); - long dtime = System.currentTimeMillis(); + fastPaint = true; - repaint(); - long rtime = System.currentTimeMillis(); - if (debugRedraw) - { - System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t" - + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime) - + "\tRepaint call:\t" + (rtime - dtime)); - } + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the overview + // window and others may be adversely affected. + av.getAlignPanel().repaint(); } private volatile boolean lastImageGood = false; @@ -1034,8 +1052,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // and draw a faded image until the calculation // has completed if (lastImageGood - && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage - .getHeight() != image.getHeight())) + && (fadedImage == null || fadedImage.getWidth() != imgWidth + || fadedImage.getHeight() != image.getHeight())) { // System.err.println("redraw faded image ("+(fadedImage==null ? // "null image" : "") + " lastGood="+lastImageGood+")"); @@ -1047,8 +1065,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, fadedG.setColor(Color.white); fadedG.fillRect(0, 0, imgWidth, image.getHeight()); - fadedG.setComposite(AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, .3f)); + fadedG.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f)); fadedG.drawImage(image, 0, 0, this); } @@ -1089,8 +1107,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - lastImageGood = renderer.drawComponent(this, av, g, activeRow, - startRes, endRes); + lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes, + endRes); if (!lastImageGood && fadedImage == null) { fadedImage = oldFaded; @@ -1154,4 +1172,28 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, renderer.dispose(); } } + + @Override + public void propertyChange(PropertyChangeEvent evt) + { + // Respond to viewport range changes (e.g. alignment panel was scrolled) + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (evt.getPropertyName().equals(ViewportRanges.STARTRES)) + { + fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)) + { + fastPaint(((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]); + } + else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) + { + repaint(); + } + } }