X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=82021ac9ef6837eac663f6a8fb3a604ce3d9ae16;hb=5830c6b18969d8eb7801b9df28ea9fb2c4dd5152;hp=ab86707b3175932bafb3ddf34c7c97b2fb293adc;hpb=f36251d568f123f14631d4839362355a058dc673;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index ab86707..82021ac 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -20,21 +20,6 @@ */ package jalview.gui; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -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.util.Platform; -import jalview.viewmodel.ViewportListenerI; -import jalview.viewmodel.ViewportRanges; - import java.awt.AlphaComposite; import java.awt.Color; import java.awt.Dimension; @@ -59,13 +44,34 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import javax.swing.JColorChooser; 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.GraphLine; +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; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; + /** * AnnotationPanel displays visible portion of annotation rows below unwrapped * alignment @@ -77,6 +83,11 @@ 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"); @@ -109,7 +120,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public volatile BufferedImage fadedImage; - Graphics2D gg; + // private Graphics2D gg; public FontMetrics fm; @@ -120,11 +131,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // Used For mouse Dragging and resizing graphs int graphStretch = -1; - int graphStretchY = -1; + int mouseDragLastX = -1; + + int mouseDragLastY = -1; - int min; // used by mouseDragged to see if user + int firstDragX = -1; - int max; // used by mouseDragged to see if user + int firstDragY = -1; + + DragMode dragMode = DragMode.Undefined; boolean mouseDragging = false; @@ -137,6 +152,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, private MouseWheelListener[] _mwl; + private boolean notJustOne; + /** * Creates a new AnnotationPanel object. * @@ -310,7 +327,7 @@ 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) @@ -342,24 +359,31 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } else if (action.equals(COLOUR)) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_foreground_colour"), - Color.black); - - for (int index : av.getColumnSelection().getSelected()) + final Annotation[] fAnot = anot; + String title = MessageManager + .getString("label.select_foreground_colour"); + ColourChooserListener listener = new ColourChooserListener() { - if (!av.getAlignment().getHiddenColumns().isVisible(index)) - { - continue; - } - - if (anot[index] == null) + @Override + public void colourSelected(Color c) { - anot[index] = new Annotation("", "", ' ', 0); - } - - anot[index].colour = col; - } + HiddenColumns hiddenColumns = av.getAlignment() + .getHiddenColumns(); + for (int index : av.getColumnSelection().getSelected()) + { + if (hiddenColumns.isVisible(index)) + { + if (fAnot[index] == null) + { + fAnot[index] = new Annotation("", "", ' ', 0); + } + fAnot[index].colour = c; + } + } + }; + }; + JalviewColourChooser.showColourChooser(this, title, Color.black, + listener); } else // HELIX, SHEET or STEM @@ -500,10 +524,11 @@ 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) @@ -514,11 +539,19 @@ 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) @@ -532,13 +565,14 @@ 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; } } @@ -553,7 +587,85 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - ap.getScalePanel().mousePressed(evt); + if (graphStretch != -1) + { + + if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP) + { + // data in row has position on y as well as x axis + if (evt.isAltDown() || evt.isAltGraphDown()) + { + dragMode = DragMode.MatrixSelect; + firstDragX = mouseDragLastX; + firstDragY = mouseDragLastY; + } + else + { + GraphLine thr = aa[graphStretch].getThreshold(); + 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); + // select corresponding range in segment under mouse + { + for (int c = fr; c <= to; c++) + { + av.getColumnSelection().addElement(c); + } + av.getColumnSelection().addElement(currentX); + } + // PAE SPECIFIC + // and also select everything lower than the max range adjacent + // (kind of works) + if (PAEContactMatrix.PAEMATRIX.equals(aa[graphStretch].getCalcId())) + { + int c = fr - 1; + ContactRange cr = forCurrentX.getRangeFor(fr, to); + double cval; + while (c > 0) + { + cval = forCurrentX.getContactAt(c); + if (// cr.getMin() <= cval && + cval <= cr.getMax()) + { + av.getColumnSelection().addElement(c--); + } + else + { + break; + } + } + c = to; + while (c < forCurrentX.getContactHeight()) + { + cval = forCurrentX.getContactAt(c); + if (// cr.getMin() <= cval && + cval <= cr.getMax()) + { + av.getColumnSelection().addElement(c++); + } + else + { + break; + } + } + } + } + } + } + } + else + { + ap.getScalePanel().mousePressed(evt); + } } /** @@ -604,17 +716,30 @@ 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); /* @@ -637,14 +762,15 @@ 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) @@ -653,33 +779,227 @@ 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; + notJustOne = evt.isShiftDown(); + + /* + * but could also be a matrix drag + */ + if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)) + { + /* + * 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); + if (notJustOne) + { + for (AlignmentAnnotation similar : av.getAlignment() + .findAnnotations(null, graphAnnotation.getCalcId(), + graphAnnotation.label)) + { + similar.graphHeight = newHeight; + } + + } + else + { + 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 fromX = Math.min(firstDragX, evt.getX()); + int toX = Math.max(firstDragX, evt.getX()); + + int deltaY = toY - fromY; + int deltaX = toX - fromX; + + 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 lastX = getColumnForXPos(fromX); + int currentX = getColumnForXPos(toX); + int fromXc = Math.min(lastX, currentX); + int toXc = Math.max(lastX, currentX); + ContactListI forFromX = av.getContactList(cma, fromXc); + ContactListI forToX = av.getContactList(cma, toXc); + + if (forFromX != null && forToX != null) + { + ContactGeometry lastXcgeom = new ContactGeometry(forFromX, + cma.graphHeight); + ContactGeometry.contactInterval lastXci = lastXcgeom + .mapFor(rowIndex[1], rowIndex[1] - deltaY); + + ContactGeometry cXcgeom = new ContactGeometry(forToX, + 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(" + fromXc + ",[" + + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + toXc + + ",[" + 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++) + { + if (cma.sequenceRef != null) + { + int col = cma.sequenceRef.findIndex(c); + av.getColumnSelection().addElement(col); + } + else + { + 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++) + { + if (cma.sequenceRef != null) + { + int col = cma.sequenceRef.findIndex(c); + av.getColumnSelection().addElement(col); + } + else + { + 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); + } + } + } /** @@ -693,8 +1013,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { int yPos = evt.getY(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - - int row = getRowIndex(yPos, aa); + int rowAndOffset[] = getRowIndexAndOffset(yPos, aa); + int row = rowAndOffset[0]; if (row == -1) { @@ -702,22 +1022,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - int column = (evt.getX() / av.getCharWidth()) - + av.getRanges().getStartRes(); - column = Math.min(column, av.getRanges().getEndRes()); - - if (av.hasHiddenColumns()) - { - column = av.getAlignment().getHiddenColumns() - .visibleToAbsoluteColumn(column); - } + int column = getColumnForXPos(evt.getX()); AlignmentAnnotation ann = aa[row]; if (row > -1 && ann.annotations != null && column < ann.annotations.length) { - setToolTipText(buildToolTip(ann, column, aa)); - String msg = getStatusMessage(av.getAlignment(), column, ann); + 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); } else @@ -727,6 +1043,19 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } + 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; + } + /** * 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 @@ -743,77 +1072,101 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { return -1; } - int row = -1; - int height = 0; + return getRowIndexAndOffset(yPos, aa)[0]; + } + static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa) + { + int[] res = new int[2]; + res[0] = -1; + res[1] = 0; + if (aa == null) + { + 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 row; + return res; } /** - * Answers 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 */ static String buildToolTip(AlignmentAnnotation ann, int column, - AlignmentAnnotation[] anns) + 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); - tooltip = tip.toString() + ""; - } + tooltip = first ? null : tip.toString(); } else if (column < ann.annotations.length && ann.annotations[column] != null) { - String description = ann.annotations[column].description; - if (description != null && description.length() > 0) - { - tooltip = JvSwingUtils.wrapTooltip(true, description); - } - else - { - tooltip = 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.CONTACT_MAP) { - // clear the tooltip. - tooltip = null; + ContactListI clist = av.getContactList(ann, column); + if (clist != null) + { + ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight); + ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset); + ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd); + tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart + + " - " + ci.cEnd + "]" + "
Mean:" + cr.getMean(); + int col = ann.sequenceRef.findPosition(column); + ap.getStructureSelectionManager() + .highlightPositionsOn(ann.sequenceRef, new int[][] + { new int[] { col, col }, + new int[] + { ci.cStart, ci.cEnd } }, null); + } } return tooltip; } @@ -824,9 +1177,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @param al * @param column * @param ann + * @param rowAndOffset */ static String getStatusMessage(AlignmentI al, int column, - AlignmentAnnotation ann) + AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av) { /* * show alignment column and annotation description if any @@ -925,6 +1279,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, private volatile boolean imageFresh = false; + private Rectangle visibleRect = new Rectangle(), + clipBounds = new Rectangle(); + /** * DOCUMENT ME! * @@ -934,16 +1291,27 @@ 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; @@ -955,27 +1323,41 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { return; } + Graphics2D gg; if (image == null || imgWidth != image.getWidth(this) || image.getHeight(this) != getHeight()) { - try - { - image = new BufferedImage(imgWidth, - ap.getAnnotationPanel().getHeight(), - BufferedImage.TYPE_INT_RGB); - } catch (OutOfMemoryError oom) + boolean tried = false; + image = null; + while (image == null && !tried) { try { - System.gc(); - } catch (Exception x) + image = new BufferedImage(imgWidth, + ap.getAnnotationPanel().getHeight(), + BufferedImage.TYPE_INT_RGB); + tried = true; + } catch (IllegalArgumentException exc) { + System.err.println( + "Serious issue with viewport geometry imgWidth requested was " + + imgWidth); + return; + } catch (OutOfMemoryError oom) + { + try + { + System.gc(); + } catch (Exception x) + { + } + ; + new OOMWarning( + "Couldn't allocate memory to redraw screen. Please restart Jalview", + oom); + return; } - ; - new OOMWarning( - "Couldn't allocate memory to redraw screen. Please restart Jalview", - oom); - return; + } gg = (Graphics2D) image.getGraphics(); @@ -991,9 +1373,15 @@ 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); } @@ -1011,7 +1399,7 @@ 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()) @@ -1024,25 +1412,32 @@ 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 @@ -1138,6 +1533,17 @@ 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 @@ -1186,7 +1592,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ap = null; image = null; fadedImage = null; - gg = null; + // gg = null; _mwl = null; /* @@ -1240,7 +1646,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * hscroll, status bar, insets. */ int stuff = (ap.getViewName() != null ? 30 : 0) - + (Platform.isAMac() ? 120 : 140); + + (Platform.isAMacAndNotJS() ? 120 : 140); int availableHeight = ap.alignFrame.getHeight() - stuff; int rowHeight = av.getCharHeight();