X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=d31e52d5999c1392e7c5afd08d21ae35d1ce83d1;hb=e70614203293e8f04d7640729851725a763ae130;hp=908addfafa54bb1f3ca9870311e013c3f5a08d6a;hpb=2e8825511b435aa511396c5a2bdcbc600b91340b;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 908addf..d31e52d 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -50,15 +50,19 @@ 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; @@ -79,7 +83,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { enum DragMode { - Select, Resize, Undefined + Select, Resize, Undefined, MatrixSelect }; String HELIX = MessageManager.getString("label.helix"); @@ -129,6 +133,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int mouseDragLastY = -1; + int firstDragX = -1; + + int firstDragY = -1; + DragMode dragMode = DragMode.Undefined; boolean mouseDragging = false; @@ -355,7 +363,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override 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)) @@ -366,10 +375,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } fAnot[index].colour = c; } - }}; + } + }; }; - JalviewColourChooser.showColourChooser(this, - title, Color.black, listener); + JalviewColourChooser.showColourChooser(this, title, Color.black, + listener); } else // HELIX, SHEET or STEM @@ -534,8 +544,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ 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) @@ -555,6 +567,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * we have clicked on a resizable graph annotation */ graphStretch = i; + yOffset = height - y; } break; } @@ -570,7 +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); + } } /** @@ -630,9 +680,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseReleased(MouseEvent evt) { + if (dragMode == DragMode.MatrixSelect) + { + matrixSelectRange(evt); + } graphStretch = -1; mouseDragLastX = -1; mouseDragLastY = -1; + firstDragX = -1; + firstDragY = -1; mouseDragging = false; if (dragMode == DragMode.Resize) { @@ -720,10 +776,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * 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; + } } } if (dragMode == DragMode.Undefined) + { /* * drag is diagonal - defer deciding whether to @@ -750,6 +821,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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 { /* @@ -765,6 +845,104 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } + 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); + } + } + + } + /** * Constructs the tooltip, and constructs and displays a status message, for * the current mouse position @@ -776,8 +954,8 @@ 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) { @@ -785,24 +963,18 @@ 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) { - String toolTip = buildToolTip(ann, column, aa); + 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); + String msg = getStatusMessage(av.getAlignment(), column, ann, + rowAndOffset[1], av); ap.alignFrame.setStatus(msg); } else @@ -812,6 +984,19 @@ 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 @@ -828,23 +1013,37 @@ 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; } /** @@ -855,9 +1054,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @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) @@ -889,7 +1090,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { tooltip = ann.annotations[column].description; } - + // TODO abstract tooltip generator so different implementations can be built + if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER) + { + 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; } @@ -899,9 +1118,10 @@ 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 @@ -999,7 +1219,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } private volatile boolean imageFresh = false; - private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle(); + + private Rectangle visibleRect = new Rectangle(), + clipBounds = new Rectangle(); /** * DOCUMENT ME! @@ -1010,27 +1232,28 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void paintComponent(Graphics 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. + + // 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, visibleRect.width, visibleRect.height); if (image != null) { - // BH 2018 optimizing generation of new Rectangle(). - if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width) - || (visibleRect.height != clipBounds.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); + g.drawImage(image, 0, 0, this); fastPaint = false; return; } @@ -1077,11 +1300,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, image.getHeight()); imageFresh = true; - } else { - gg = (Graphics2D) image.getGraphics(); + } + else + { + gg = (Graphics2D) image.getGraphics(); } - + drawComponent(gg, av.getRanges().getStartRes(), av.getRanges().getEndRes() + 1); gg.dispose(); @@ -1117,19 +1342,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, Graphics2D gg = (Graphics2D) image.getGraphics(); - 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) + 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); @@ -1137,7 +1365,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.translate(-transX, 0); gg.dispose(); - + fastPaint = true; // Call repaint on alignment panel so that repaints from other alignment @@ -1233,6 +1461,17 @@ 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 @@ -1281,7 +1520,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ap = null; image = null; fadedImage = null; -// gg = null; + // gg = null; _mwl = null; /*