X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=ccc086ccc5d589670203d7d571d35ef14e63f84c;hb=0d326d33340305d0eaa539cbf903f778001ebeb7;hp=bf8c70945d9d4d5297dc13cc6cb83d04bf4c5b6c;hpb=dcda5b75e1bbbce40799573d39d6e7298a17b361;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index bf8c709..ccc086c 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -20,19 +20,6 @@ */ 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; import java.awt.Dimension; @@ -57,14 +44,32 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import javax.swing.JColorChooser; -import javax.swing.JDialog; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.Scrollable; import javax.swing.ToolTipManager; +import jalview.api.AlignViewportI; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactRange; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SequenceI; +import jalview.gui.JalviewColourChooser.ColourChooserListener; +import jalview.renderer.AnnotationRenderer; +import jalview.renderer.AwtRenderPanelI; +import jalview.renderer.ContactGeometry; +import jalview.schemes.ResidueProperties; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + /** * AnnotationPanel displays visible portion of annotation rows below unwrapped * alignment @@ -76,6 +81,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, MouseListener, MouseWheelListener, MouseMotionListener, ActionListener, AdjustmentListener, Scrollable, ViewportListenerI { + enum DragMode + { + Select, Resize, Undefined, MatrixSelect + }; + String HELIX = MessageManager.getString("label.helix"); String SHEET = MessageManager.getString("label.sheet"); @@ -108,7 +118,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public volatile BufferedImage fadedImage; - Graphics2D gg; + // private Graphics2D gg; public FontMetrics fm; @@ -119,11 +129,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // Used For mouse Dragging and resizing graphs int graphStretch = -1; - int graphStretchY = -1; + int mouseDragLastX = -1; - int min; // used by mouseDragged to see if user + int mouseDragLastY = -1; - int max; // used by mouseDragged to see if user + int firstDragX = -1; + + int firstDragY = -1; + + DragMode dragMode = DragMode.Undefined; boolean mouseDragging = false; @@ -207,7 +221,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public Dimension getPreferredScrollableViewportSize() { - return getPreferredSize(); + Dimension ps = getPreferredSize(); + return new Dimension(ps.width, adjustForAlignFrame(false, ps.height)); } @Override @@ -308,7 +323,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, else if (action.equals(LABEL)) { String exMesg = collectAnnotVals(anot, LABEL); - String label = JvOptionPane.showInputDialog(this, + String label = JvOptionPane.showInputDialog( MessageManager.getString("label.enter_label"), exMesg); if (label == null) @@ -341,14 +356,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, else if (action.equals(COLOUR)) { final Annotation[] fAnot = anot; - JColorChooser colorChooser = new JColorChooser(); - colorChooser.setColor(Color.black); - String title = MessageManager.getString("label.select_foreground_colour"); - ActionListener listener = new ActionListener() { + String title = MessageManager + .getString("label.select_foreground_colour"); + ColourChooserListener listener = new ColourChooserListener() + { @Override - public void actionPerformed(ActionEvent e) + public void colourSelected(Color c) { - HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); + HiddenColumns hiddenColumns = av.getAlignment() + .getHiddenColumns(); for (int index : av.getColumnSelection().getSelected()) { if (hiddenColumns.isVisible(index)) @@ -357,12 +373,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { fAnot[index] = new Annotation("", "", ' ', 0); } - fAnot[index].colour = colorChooser.getColor(); + fAnot[index].colour = c; } - }}; + } + }; }; - JDialog dialog = JColorChooser.createDialog(this, title, true, colorChooser, listener, null); - dialog.setVisible(true); + JalviewColourChooser.showColourChooser(this, title, Color.black, + listener); } else // HELIX, SHEET or STEM @@ -503,10 +520,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * DOCUMENT ME! + * Action on right mouse pressed on Mac is to show a pop-up menu for the + * annotation. Action on left mouse pressed is to find which annotation is + * pressed and mark the start of a column selection or graph resize operation. * * @param evt - * DOCUMENT ME! */ @Override public void mousePressed(MouseEvent evt) @@ -517,11 +535,19 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { return; } + mouseDragLastX = evt.getX(); + mouseDragLastY = evt.getY(); + /* + * add visible annotation heights until we reach the y + * position, to find which annotation it is in + */ int height = 0; activeRow = -1; - + int yOffset = 0; + // todo could reuse getRowIndexAndOffset ? final int y = evt.getY(); + for (int i = 0; i < aa.length; i++) { if (aa[i].visible) @@ -535,13 +561,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { activeRow = i; } - else if (aa[i].graph > 0) + else if (aa[i].graph != 0) { - // Stretch Graph + /* + * we have clicked on a resizable graph annotation + */ graphStretch = i; - graphStretchY = y; + yOffset = height - y; } - break; } } @@ -556,7 +583,44 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - ap.getScalePanel().mousePressed(evt); + if (graphStretch != -1) + { + + if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER) + { + if (evt.isAltDown() || evt.isAltGraphDown()) + { + dragMode = DragMode.MatrixSelect; + firstDragX = mouseDragLastX; + firstDragY = mouseDragLastY; + } + else + { + int currentX = getColumnForXPos(evt.getX()); + ContactListI forCurrentX = av.getContactList(aa[graphStretch], + currentX); + if (forCurrentX != null) + { + ContactGeometry cXcgeom = new ContactGeometry(forCurrentX, + aa[graphStretch].graphHeight); + ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset, + yOffset); + int fr, to; + fr = Math.min(cXci.cStart, cXci.cEnd); + to = Math.max(cXci.cStart, cXci.cEnd); + for (int c = fr; c <= to; c++) + { + av.getColumnSelection().addElement(c); + } + av.getColumnSelection().addElement(currentX); + } + } + } + } + else + { + ap.getScalePanel().mousePressed(evt); + } } /** @@ -607,17 +671,30 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * DOCUMENT ME! + * Action on mouse up is to clear mouse drag data and call mouseReleased on + * ScalePanel, to deal with defining the selection group (if any) defined by + * the mouse drag * * @param evt - * DOCUMENT ME! */ @Override public void mouseReleased(MouseEvent evt) { + if (dragMode == DragMode.MatrixSelect) + { + matrixSelectRange(evt); + } graphStretch = -1; - graphStretchY = -1; + mouseDragLastX = -1; + mouseDragLastY = -1; + firstDragX = -1; + firstDragY = -1; mouseDragging = false; + if (dragMode == DragMode.Resize) + { + ap.adjustAnnotationHeight(); + } + dragMode = DragMode.Undefined; ap.getScalePanel().mouseReleased(evt); /* @@ -640,14 +717,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseEntered(MouseEvent evt) { + this.mouseDragging = false; ap.getScalePanel().mouseEntered(evt); } /** - * DOCUMENT ME! + * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling + * with column selection on a mouse drag * * @param evt - * DOCUMENT ME! */ @Override public void mouseExited(MouseEvent evt) @@ -656,33 +734,191 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * DOCUMENT ME! + * Action on starting or continuing a mouse drag. There are two possible + * actions: + * + * A drag on a graph annotation is treated as column selection if it starts + * with more horizontal than vertical movement, and as resize if it starts + * with more vertical than horizontal movement. Once started, the drag does + * not change mode. * * @param evt - * DOCUMENT ME! */ @Override public void mouseDragged(MouseEvent evt) { - if (graphStretch > -1) + /* + * if dragMode is Undefined: + * - set to Select if dx > dy + * - set to Resize if dy > dx + * - do nothing if dx == dy + */ + final int x = evt.getX(); + final int y = evt.getY(); + if (dragMode == DragMode.Undefined) { - av.getAlignment() - .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - - evt.getY(); - if (av.getAlignment() - .getAlignmentAnnotation()[graphStretch].graphHeight < 0) + int dx = Math.abs(x - mouseDragLastX); + int dy = Math.abs(y - mouseDragLastY); + if (graphStretch == -1 || dx > dy) { - av.getAlignment() - .getAlignmentAnnotation()[graphStretch].graphHeight = 0; + /* + * mostly horizontal drag, or not a graph annotation + */ + dragMode = DragMode.Select; + } + else if (dy > dx) + { + /* + * mostly vertical drag + */ + dragMode = DragMode.Resize; + + /* + * but could also be a matrix drag + */ + if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)) + { + /* + * dragging in a matrix + */ + dragMode = DragMode.MatrixSelect; + firstDragX = mouseDragLastX; + firstDragY = mouseDragLastY; + } } - graphStretchY = evt.getY(); - adjustPanelHeight(); - ap.paintAlignment(false, false); } - else + + if (dragMode == DragMode.Undefined) + { - ap.getScalePanel().mouseDragged(evt); + /* + * drag is diagonal - defer deciding whether to + * treat as up/down or left/right + */ + return; + } + + try + { + if (dragMode == DragMode.Resize) + { + /* + * resize graph annotation if mouse was dragged up or down + */ + int deltaY = mouseDragLastY - evt.getY(); + if (deltaY != 0) + { + AlignmentAnnotation graphAnnotation = av.getAlignment() + .getAlignmentAnnotation()[graphStretch]; + int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY); + graphAnnotation.graphHeight = newHeight; + adjustPanelHeight(); + ap.paintAlignment(false, false); + } + } + else if (dragMode == DragMode.MatrixSelect) + { + /* + * TODO draw a rubber band for range + */ + mouseDragLastX = x; + mouseDragLastY = y; + ap.paintAlignment(false, false); + } + else + { + /* + * for mouse drag left or right, delegate to + * ScalePanel to adjust the column selection + */ + ap.getScalePanel().mouseDragged(evt); + } + } finally + { + mouseDragLastX = x; + mouseDragLastY = y; + } + } + + public void matrixSelectRange(MouseEvent evt) + { + /* + * get geometry of drag + */ + int fromY = Math.min(firstDragY, evt.getY()); + int toY = Math.max(firstDragY, evt.getY()); + int deltaY = toY - fromY; + + int[] rowIndex = getRowIndexAndOffset(fromY, + av.getAlignment().getAlignmentAnnotation()); + int[] toRowIndex = getRowIndexAndOffset(toY, + av.getAlignment().getAlignmentAnnotation()); + + if (rowIndex == null || toRowIndex == null) + { + System.out.println("Drag out of range. needs to be clipped"); + + } + if (rowIndex[0] != toRowIndex[0]) + { + System.out.println("Drag went to another row. needs to be clipped"); + } + + // rectangular selection on matrix style annotation + AlignmentAnnotation cma = av.getAlignment() + .getAlignmentAnnotation()[rowIndex[0]]; + + int fromXp = Math.min(firstDragX, evt.getX()); + int toXp = Math.max(firstDragX, evt.getX()); + int lastX = getColumnForXPos(fromXp); + int currentX = getColumnForXPos(toXp); + ContactListI forLastX = av.getContactList(cma, lastX); + ContactListI forCurrentX = av.getContactList(cma, currentX); + if (forLastX != null && forCurrentX != null) + { + ContactGeometry lastXcgeom = new ContactGeometry(forLastX, + cma.graphHeight); + ContactGeometry.contactInterval lastXci = lastXcgeom.mapFor( + rowIndex[1], + rowIndex[1] + ((fromY == firstDragY) ? -deltaY : deltaY)); + ContactGeometry cXcgeom = new ContactGeometry(forCurrentX, + cma.graphHeight); + ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1], + rowIndex[1] + deltaY); + // mark rectangular region formed by drag + System.err.println("Matrix Selection from last(" + lastXci.cStart + + "," + lastXci.cEnd + ") to cur(" + cXci.cStart + "," + + cXci.cEnd + ")"); + int fr, to; + fr = Math.min(lastXci.cStart, lastXci.cEnd); + to = Math.max(lastXci.cStart, lastXci.cEnd); + System.err.println("Marking " + fr + " to " + to); + for (int c = fr; c <= to; c++) + { + av.getColumnSelection().addElement(c); + } + fr = Math.min(cXci.cStart, cXci.cEnd); + to = Math.max(cXci.cStart, cXci.cEnd); + System.err.println("Marking " + fr + " to " + to); + for (int c = fr; c <= to; c++) + { + av.getColumnSelection().addElement(c); + } + fr = Math.min(lastX, currentX); + to = Math.max(lastX, currentX); + + System.err.println("Marking " + fr + " to " + to); + for (int c = fr; c <= to; c++) + { + av.getColumnSelection().addElement(c); + } } + } /** @@ -694,120 +930,173 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseMoved(MouseEvent evt) { + int yPos = evt.getY(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); + int rowAndOffset[] = getRowIndexAndOffset(yPos, aa); + int row = rowAndOffset[0]; - if (aa == null) + if (row == -1) { this.setToolTipText(null); return; } - int row = -1; - int height = 0; + int column = getColumnForXPos(evt.getX()); - for (int i = 0; i < aa.length; i++) + AlignmentAnnotation ann = aa[row]; + if (row > -1 && ann.annotations != null + && column < ann.annotations.length) { - if (aa[i].visible) - { - height += aa[i].height; - } - - if (evt.getY() < height) - { - row = i; - break; - } + String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av, + ap); + setToolTipText(toolTip == null ? null + : JvSwingUtils.wrapTooltip(true, toolTip)); + String msg = getStatusMessage(av.getAlignment(), column, ann, + rowAndOffset[1], av); + ap.alignFrame.setStatus(msg); } - - if (row == -1) + else { this.setToolTipText(null); - return; + ap.alignFrame.setStatus(" "); } + } - int column = (evt.getX() / av.getCharWidth()) - + av.getRanges().getStartRes(); + private int getColumnForXPos(int x) + { + int column = (x / av.getCharWidth()) + av.getRanges().getStartRes(); + column = Math.min(column, av.getRanges().getEndRes()); if (av.hasHiddenColumns()) { column = av.getAlignment().getHiddenColumns() .visibleToAbsoluteColumn(column); } + return column; + } - AlignmentAnnotation ann = aa[row]; - if (row > -1 && ann.annotations != null - && column < ann.annotations.length) + /** + * Answers the index in the annotations array of the visible annotation at the + * given y position. This is done by adding the heights of visible annotations + * until the y position has been exceeded. Answers -1 if no annotations are + * visible, or the y position is below all annotations. + * + * @param yPos + * @param aa + * @return + */ + static int getRowIndex(int yPos, AlignmentAnnotation[] aa) + { + if (aa == null) { - buildToolTip(ann, column, aa); - setStatusMessage(column, ann); + return -1; } - else + return getRowIndexAndOffset(yPos, aa)[0]; + } + + static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa) + { + int[] res = new int[2]; + if (aa == null) { - this.setToolTipText(null); - ap.alignFrame.statusBar.setText(" "); + res[0] = -1; + res[1] = 0; + return res; + } + int row = -1; + int height = 0, lheight = 0; + + for (int i = 0; i < aa.length; i++) + { + if (aa[i].visible) + { + lheight = height; + height += aa[i].height; + } + + if (height > yPos) + { + row = i; + res[0] = row; + res[1] = height - yPos; + break; + } } + return res; } /** - * Builds a tooltip for the annotation at the current mouse position. + * Answers a tooltip for the annotation at the current mouse position, not + * wrapped in <html> tags (apply if wanted). Answers null if there is no + * tooltip to show. * * @param ann * @param column * @param anns + * @param rowAndOffset */ - void buildToolTip(AlignmentAnnotation ann, int column, - AlignmentAnnotation[] anns) + static String buildToolTip(AlignmentAnnotation ann, int column, + AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av, + AlignmentPanel ap) { + String tooltip = null; if (ann.graphGroup > -1) { StringBuilder tip = new StringBuilder(32); - tip.append(""); + boolean first = true; for (int i = 0; i < anns.length; i++) { if (anns[i].graphGroup == ann.graphGroup && anns[i].annotations[column] != null) { + if (!first) + { + tip.append("
"); + } + first = false; tip.append(anns[i].label); String description = anns[i].annotations[column].description; if (description != null && description.length() > 0) { tip.append(" ").append(description); } - tip.append("
"); } } - if (tip.length() != 6) - { - tip.setLength(tip.length() - 4); - this.setToolTipText(tip.toString() + ""); - } + tooltip = first ? null : tip.toString(); } - else if (ann.annotations[column] != null) + else if (column < ann.annotations.length + && ann.annotations[column] != null) { - String description = ann.annotations[column].description; - if (description != null && description.length() > 0) - { - this.setToolTipText(JvSwingUtils.wrapTooltip(true, description)); - } - else - { - this.setToolTipText(null); // no tooltip if null or empty description - } + tooltip = ann.annotations[column].description; } - else + // TODO abstract tooltip generator so different implementations can be built + if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER) { - // clear the tooltip. - this.setToolTipText(null); + ContactListI clist = av.getContactList(ann, column); + if (clist != null) + { + ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight); + ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset, + rowAndOffset); + tooltip += "Contact from " + ci.cStart + " to " + ci.cEnd; + + // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef, + // new int[] {column, ci.cStart,ci.cEnd}, -1, null) + } } + return tooltip; } /** - * Constructs and displays the status bar message + * Constructs and returns the status bar message * + * @param al * @param column * @param ann + * @param rowAndOffset */ - void setStatusMessage(int column, AlignmentAnnotation ann) + static String getStatusMessage(AlignmentI al, int column, + AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av) { /* * show alignment column and annotation description if any @@ -816,7 +1105,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, text.append(MessageManager.getString("label.column")).append(" ") .append(column + 1); - if (ann.annotations[column] != null) + if (column < ann.annotations.length && ann.annotations[column] != null) { String description = ann.annotations[column].description; if (description != null && description.trim().length() > 0) @@ -832,7 +1121,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, SequenceI seqref = ann.sequenceRef; if (seqref != null) { - int seqIndex = av.getAlignment().findIndex(seqref); + int seqIndex = al.findIndex(seqref); if (seqIndex != -1) { text.append(", ").append(MessageManager.getString("label.sequence")) @@ -842,7 +1131,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { text.append(" "); String name; - if (av.getAlignment().isNucleotide()) + if (al.isNucleotide()) { name = ResidueProperties.nucleotideName .get(String.valueOf(residue)); @@ -863,7 +1152,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } - ap.alignFrame.statusBar.setText(text.toString()); + return text.toString(); } /** @@ -906,6 +1195,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, private volatile boolean imageFresh = false; + private Rectangle visibleRect = new Rectangle(), + clipBounds = new Rectangle(); + /** * DOCUMENT ME! * @@ -915,16 +1207,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void paintComponent(Graphics g) { - super.paintComponent(g); + + // BH: note that this method is generally recommended to + // call super.paintComponent(g). Otherwise, the children of this + // component will not be rendered. That is not needed here + // because AnnotationPanel does not have any children. It is + // just a JPanel contained in a JViewPort. + + computeVisibleRect(visibleRect); g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); + g.fillRect(0, 0, visibleRect.width, visibleRect.height); if (image != null) { - if (fastPaint || (getVisibleRect().width != g.getClipBounds().width) - || (getVisibleRect().height != g.getClipBounds().height)) + // BH 2018 optimizing generation of new Rectangle(). + if (fastPaint + || (visibleRect.width != (clipBounds = g + .getClipBounds(clipBounds)).width) + || (visibleRect.height != clipBounds.height)) { + g.drawImage(image, 0, 0, this); fastPaint = false; return; @@ -936,6 +1239,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { return; } + Graphics2D gg; if (image == null || imgWidth != image.getWidth(this) || image.getHeight(this) != getHeight()) { @@ -972,9 +1276,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.fillRect(0, 0, imgWidth, image.getHeight()); imageFresh = true; } - + else + { + gg = (Graphics2D) image.getGraphics(); + + } + drawComponent(gg, av.getRanges().getStartRes(), av.getRanges().getEndRes() + 1); + gg.dispose(); imageFresh = false; g.drawImage(image, 0, 0, this); } @@ -992,7 +1302,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public void fastPaint(int horizontal) { - if ((horizontal == 0) || gg == null + if ((horizontal == 0) || image == null || av.getAlignment().getAlignmentAnnotation() == null || av.getAlignment().getAlignmentAnnotation().length < 1 || av.isCalcInProgress()) @@ -1005,25 +1315,32 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int er = av.getRanges().getEndRes() + 1; int transX = 0; - gg.copyArea(0, 0, imgWidth, getHeight(), - -horizontal * av.getCharWidth(), 0); + Graphics2D gg = (Graphics2D) image.getGraphics(); - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.getCharWidth(); - sr = er - horizontal; - } - else if (horizontal < 0) + if (imgWidth > Math.abs(horizontal * av.getCharWidth())) { - er = sr - horizontal; - } + // scroll is less than imgWidth away so can re-use buffered graphics + gg.copyArea(0, 0, imgWidth, getHeight(), + -horizontal * av.getCharWidth(), 0); + if (horizontal > 0) // scrollbar pulled right, image to the left + { + transX = (er - sr - horizontal) * av.getCharWidth(); + sr = er - horizontal; + } + else if (horizontal < 0) + { + er = sr - horizontal; + } + } gg.translate(transX, 0); drawComponent(gg, sr, er); gg.translate(-transX, 0); + gg.dispose(); + fastPaint = true; // Call repaint on alignment panel so that repaints from other alignment @@ -1119,6 +1436,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { fadedImage = oldFaded; } + if (dragMode == DragMode.MatrixSelect) + { + g.setColor(Color.yellow); + g.drawRect(Math.min(firstDragX, mouseDragLastX), + Math.min(firstDragY, mouseDragLastY), + Math.max(firstDragX, mouseDragLastX) + - Math.min(firstDragX, mouseDragLastX), + Math.max(firstDragY, mouseDragLastY) + - Math.min(firstDragY, mouseDragLastY)); + + } } @Override @@ -1167,7 +1495,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ap = null; image = null; fadedImage = null; - gg = null; + // gg = null; _mwl = null; /* @@ -1202,4 +1530,49 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, repaint(); } } + + /** + * computes the visible height of the annotation panel + * + * @param adjustPanelHeight + * - when false, just adjust existing height according to other + * windows + * @param annotationHeight + * @return height to use for the ScrollerPreferredVisibleSize + */ + public int adjustForAlignFrame(boolean adjustPanelHeight, + int annotationHeight) + { + /* + * 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 = (ap.getViewName() != null ? 30 : 0) + + (Platform.isAMacAndNotJS() ? 120 : 140); + int availableHeight = ap.alignFrame.getHeight() - stuff; + int rowHeight = av.getCharHeight(); + + if (adjustPanelHeight) + { + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + + /* + * 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 = Math.min(ap.annotationScroller.getSize().height, + availableHeight - 2 * rowHeight); + } + return annotationHeight; + } }