X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=e1193c92505d13694f6348c8478de23b5b0c9952;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=84f3e6c56925862ad035d072827b838b98c3a074;hpb=97b26ba418dec7a6e926378205d25470bf098633;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 84f3e6c..e1193c9 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -20,16 +20,6 @@ */ package jalview.gui; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.datamodel.ColumnSelection; -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 java.awt.AlphaComposite; import java.awt.Color; import java.awt.Dimension; @@ -49,17 +39,43 @@ 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.BitSet; 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.ContactMatrixI; +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.Format; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; +import jalview.ws.datamodel.MappableContactMatrixI; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; + /** * AnnotationPanel displays visible portion of annotation rows below unwrapped * alignment @@ -69,8 +85,13 @@ import javax.swing.ToolTipManager; */ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, MouseListener, MouseWheelListener, MouseMotionListener, - ActionListener, AdjustmentListener, Scrollable + ActionListener, AdjustmentListener, Scrollable, ViewportListenerI { + enum DragMode + { + Select, Resize, Undefined, MatrixSelect + }; + String HELIX = MessageManager.getString("label.helix"); String SHEET = MessageManager.getString("label.sheet"); @@ -103,7 +124,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public volatile BufferedImage fadedImage; - Graphics2D gg; + // private Graphics2D gg; public FontMetrics fm; @@ -114,11 +135,15 @@ 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; @@ -131,6 +156,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, private MouseWheelListener[] _mwl; + private boolean notJustOne; + /** * Creates a new AnnotationPanel object. * @@ -155,6 +182,8 @@ 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) @@ -169,13 +198,14 @@ 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 @@ -199,7 +229,8 @@ 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 @@ -279,7 +310,8 @@ 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; @@ -290,7 +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)) { anot[index] = null; } @@ -299,7 +331,7 @@ 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) @@ -314,7 +346,7 @@ 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; } @@ -331,24 +363,31 @@ 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.getColumnSelection().isVisible(index)) + @Override + public void colourSelected(Color c) { - continue; - } - - if (anot[index] == null) - { - 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 @@ -397,7 +436,7 @@ 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; } @@ -407,8 +446,8 @@ 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; } @@ -440,17 +479,18 @@ 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; } @@ -488,10 +528,11 @@ 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) @@ -502,11 +543,19 @@ 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) @@ -520,13 +569,14 @@ 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; } } @@ -541,7 +591,222 @@ 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 + { + // no row (or row that can be adjusted) was pressed. Simulate a ruler + // click + ap.getScalePanel().mousePressed(evt); + } + } + + /** + * checks whether the annotation row under the mouse click evt's handles the + * event + * + * @param evt + * @return false if evt was not handled + */ + boolean matrix_clicked(MouseEvent evt) + { + int[] rowIndex = getRowIndexAndOffset(evt.getY(), + av.getAlignment().getAlignmentAnnotation()); + if (rowIndex == null) + { + jalview.bin.Console + .error("IMPLEMENTATION ERROR: matrix click out of range."); + return false; + } + int yOffset = rowIndex[1]; + AlignmentAnnotation[] allAnnotation = av.getAlignment() + .getAlignmentAnnotation(); + if (allAnnotation == null || rowIndex[0] < 0 + || rowIndex[0] >= allAnnotation.length) + { + return false; + } + AlignmentAnnotation clicked = av.getAlignment() + .getAlignmentAnnotation()[rowIndex[0]]; + if (clicked.graph != AlignmentAnnotation.CONTACT_MAP) + { + return false; + } + + // TODO - use existing threshold to select related sections of matrix + GraphLine thr = clicked.getThreshold(); + + int currentX = getColumnForXPos(evt.getX()); + ContactListI forCurrentX = av.getContactList(clicked, currentX); + if (forCurrentX != null) + { + ContactGeometry cXcgeom = new ContactGeometry(forCurrentX, + clicked.graphHeight); + ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset); + if (cXci != null) + { + /** + * start and end range corresponding to the row range under the mouse at + * column currentX + */ + int fr, to; + fr = Math.min(cXci.cStart, cXci.cEnd); + to = Math.max(cXci.cStart, cXci.cEnd); + + // double click selects the whole group + if (evt.getClickCount() == 2) + { + ContactMatrixI matrix = av.getContactMatrix(clicked); + + if (matrix != null) + { + // simplest approach is to select all group containing column + if (matrix.hasGroups()) + { + SequenceI rseq = clicked.sequenceRef; + BitSet grp = new BitSet(); + grp.or(matrix.getGroupsFor(currentX)); + // TODO: cXci needs to be mapped to real groups + for (int c = fr; c <= to; c++) + { + BitSet additionalGrp = matrix.getGroupsFor(c); + grp.or(additionalGrp); + } + + HiddenColumns hc = av.getAlignment().getHiddenColumns(); + ColumnSelection cs = av.getColumnSelection(); + + for (int p = grp.nextSetBit(0); p >= 0; p = grp + .nextSetBit(p + 1)) + { + if (matrix instanceof MappableContactMatrixI) + { + // find the end of this run of set bits + int nextp = grp.nextClearBit(p) - 1; + int[] pos = ((MappableContactMatrixI) matrix) + .getMappedPositionsFor(rseq, p, nextp); + p = nextp; + + if (pos != null) + { + for (int pos_p = pos[0]; pos_p <= pos[1]; pos_p++) + { + int col = rseq.findIndex(pos_p) - 1; + if (col >= 0 && (!av.hasHiddenColumns() + || hc.isVisible(col))) + { + cs.addElement(col); + } + } + } + } + else + { + int offp = (rseq != null) + ? rseq.findIndex(rseq.getStart() - 1 + p) + : p; + + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + cs.addElement(offp); + } + } + } + } + // possible alternative for interactive selection - threshold + // gives 'ceiling' for forming a cluster + // when a row+column is selected, farthest common ancestor less + // than thr is used to compute cluster + + } + } + else + { + // select corresponding range in segment under mouse + { + int[] rng = forCurrentX.getMappedPositionsFor(fr, to); + if (rng != null) + { + av.getColumnSelection().addRangeOfElements(rng, true); + } + av.getColumnSelection().addElement(currentX); + } + // PAE SPECIFIC + // and also select everything lower than the max range adjacent + // (kind of works) + if (evt.isControlDown() + && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId())) + { + int c = fr; + ContactRange cr = forCurrentX.getRangeFor(fr, to); + double cval; + // TODO: could use GraphLine instead of arbitrary picking + // TODO: could report mean/median/variance for partitions + // (contiguous selected vs unselected regions and inter-contig + // regions) + // controls feathering - what other elements in row/column + // should we select + double thresh = cr.getMean() + + (cr.getMax() - cr.getMean()) * .15; + while (c >= 0) + { + cval = forCurrentX.getContactAt(c); + if (// cr.getMin() <= cval && + cval <= thresh) + { + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) + { + av.getColumnSelection().addRangeOfElements(cols, true); + } + else + { + break; + } + } + c--; + } + c = to; + while (c < forCurrentX.getContactHeight()) + { + cval = forCurrentX.getContactAt(c); + if (// cr.getMin() <= cval && + cval <= thresh) + { + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) + { + av.getColumnSelection().addRangeOfElements(cols, true); + } + } + else + { + break; + } + c++; + + } + } + + } + } + } + ap.paintAlignment(false, false); + PaintRefresher.Refresh(ap, av.getSequenceSetId()); + av.sendSelection(); + return true; } /** @@ -592,18 +857,34 @@ 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; - ap.getScalePanel().mouseReleased(evt); + if (dragMode == DragMode.Resize) + { + ap.adjustAnnotationHeight(); + } + dragMode = DragMode.Undefined; + if (!matrix_clicked(evt)) + { + ap.getScalePanel().mouseReleased(evt); + } /* * isPopupTrigger is set in mouseReleased on Windows @@ -625,14 +906,15 @@ 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) @@ -641,30 +923,220 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * DOCUMENT ME! + * Action on starting or continuing a mouse drag. There are two possible + * actions: + *
    + *
  • drag up or down on a graphed annotation increases or decreases the + * height of the graph
    • + *
  • dragging left or right selects the columns dragged across
    • + *
+ * 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) + { + int dx = Math.abs(x - mouseDragLastX); + int dy = Math.abs(y - mouseDragLastY); + if (graphStretch == -1 || dx > dy) + { + /* + * 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; + } + } + } + + if (dragMode == DragMode.Undefined) + + { + /* + * drag is diagonal - defer deciding whether to + * treat as up/down or left/right + */ + return; + } + + try { - av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - - evt.getY(); - if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0) + if (dragMode == DragMode.Resize) { - av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0; + /* + * 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); } - graphStretchY = evt.getY(); - adjustPanelHeight(); - ap.paintAlignment(true); + else + { + /* + * for mouse drag left or right, delegate to + * ScalePanel to adjust the column selection + */ + ap.getScalePanel().mouseDragged(evt); + } + } finally + { + mouseDragLastX = x; + mouseDragLastY = y; } - else + } + + 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) + { + jalview.bin.Console.trace("Drag out of range. needs to be clipped"); + + } + if (rowIndex[0] != toRowIndex[0]) + { + jalview.bin.Console + .trace("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) { - ap.getScalePanel().mouseDragged(evt); + // FIXME will need two ContactGeometry objects when handling contact + // matrices with differing numbers of rows at each + // column + ContactGeometry xcgeom = new ContactGeometry(forFromX, + cma.graphHeight); + ContactGeometry.contactInterval lastXci = xcgeom.mapFor(rowIndex[1]); + ContactGeometry.contactInterval cXci = xcgeom + .mapFor(rowIndex[1] + deltaY); + + // mark rectangular region formed by drag + jalview.bin.Console.trace("Matrix Selection from last(" + fromXc + + ",[" + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + + toXc + ",[" + cXci.cStart + "," + cXci.cEnd + "])"); + int fr, to; + fr = Math.min(lastXci.cStart, cXci.cStart); + to = Math.max(lastXci.cEnd, cXci.cEnd); + int[] mappedPos = forFromX.getMappedPositionsFor(fr, to); + if (mappedPos != null) + { + jalview.bin.Console.trace("Marking " + fr + " to " + to + + " mapping to sequence positions " + mappedPos[0] + " to " + + mappedPos[1]); + for (int pair = 0; pair < mappedPos.length; pair += 2) + { + for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++) + // { + // if (cma.sequenceRef != null) + // { + // int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c); + // av.getColumnSelection().addElement(col); + // } + // else + { + av.getColumnSelection().addElement(c - 1); + } + } + } + fr = Math.min(lastX, currentX); + to = Math.max(lastX, currentX); + + jalview.bin.Console.trace("Marking " + fr + " to " + to); + for (int c = fr; c <= to; c++) + { + av.getColumnSelection().addElement(c); + } } + } /** @@ -676,115 +1148,199 @@ 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.getColumnSelection().adjustForHiddenColumns(column); + 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]; + res[0] = -1; + res[1] = 0; + if (aa == null) { - this.setToolTipText(null); - ap.alignFrame.statusBar.setText(" "); + 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] = yPos - lheight; + 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)); - } + 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. - this.setToolTipText(null); + if (rowAndOffset >= ann.graphHeight) + { + return 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); + StringBuilder tooltipb = new StringBuilder(); + tooltipb.append("Contact from ").append(clist.getPosition()) + .append(", [").append(ci.cStart).append(" - ") + .append(ci.cEnd).append("]").append("
Mean:"); + Format.appendPercentage(tooltipb, (float) cr.getMean(), 2); + tooltip = tooltipb.toString(); + int col = ann.sequenceRef.findPosition(column); + int[][] highlightPos; + int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd); + if (mappedPos != null) + { + highlightPos = new int[1 + mappedPos.length][2]; + highlightPos[0] = new int[] { col, col }; + for (int p = 0, h = 0; p < mappedPos.length; h++, p += 2) + { + highlightPos[h][0] = ann.sequenceRef + .findPosition(mappedPos[p] - 1); + highlightPos[h][1] = ann.sequenceRef + .findPosition(mappedPos[p + 1] - 1); + } + } + else + { + highlightPos = new int[][] { new int[] { col, col } }; + } + ap.getStructureSelectionManager() + .highlightPositionsOn(ann.sequenceRef, highlightPos, 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 @@ -793,7 +1349,7 @@ 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) @@ -809,29 +1365,29 @@ 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")) + text.append(", ").append(MessageManager.getString("label.sequence")) .append(" ").append(seqIndex + 1); char residue = seqref.getCharAt(column); if (!Comparison.isGap(residue)) { text.append(" "); String name; - if (av.getAlignment().isNucleotide()) + if (al.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); @@ -840,7 +1396,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } - ap.alignFrame.statusBar.setText(text.toString()); + return text.toString(); } /** @@ -883,6 +1439,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, private volatile boolean imageFresh = false; + private Rectangle visibleRect = new Rectangle(), + clipBounds = new Rectangle(); + /** * DOCUMENT ME! * @@ -892,45 +1451,72 @@ 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. + + 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; } } - imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1) - * av.getCharWidth(); + updateFadedImageWidth(); if (imgWidth < 1) { 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) + { + jalview.bin.Console.errPrintln( + "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(); @@ -946,13 +1532,26 @@ 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); + drawComponent(gg, av.getRanges().getStartRes(), + av.getRanges().getEndRes() + 1); + gg.dispose(); imageFresh = false; g.drawImage(image, 0, 0, this); } + public void updateFadedImageWidth() + { + imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + + 1) * av.getCharWidth(); + + } + /** * set true to enable redraw timing debug output on stderr */ @@ -966,7 +1565,7 @@ 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()) @@ -974,40 +1573,43 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, repaint(); return; } - long stime = System.currentTimeMillis(); - gg.copyArea(0, 0, imgWidth, getHeight(), - -horizontal * av.getCharWidth(), 0); - long mtime = System.currentTimeMillis(); + int sr = av.getRanges().getStartRes(); int er = av.getRanges().getEndRes() + 1; int transX = 0; - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.getCharWidth(); - sr = er - horizontal; - } - else if (horizontal < 0) + Graphics2D gg = (Graphics2D) image.getGraphics(); + + 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); - long dtime = System.currentTimeMillis(); + + gg.dispose(); + 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; @@ -1036,10 +1638,11 @@ 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 ? + // jalview.bin.Console.errPrintln("redraw faded image + // ("+(fadedImage==null ? // "null image" : "") + " lastGood="+lastImageGood+")"); fadedImage = new BufferedImage(imgWidth, image.getHeight(), BufferedImage.TYPE_INT_RGB); @@ -1049,8 +1652,8 @@ 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); } @@ -1091,12 +1694,23 @@ 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; } + 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 @@ -1114,6 +1728,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public int getFadedImageWidth() { + updateFadedImageWidth(); return imgWidth; } @@ -1145,7 +1760,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ap = null; image = null; fadedImage = null; - gg = null; + // gg = null; _mwl = null; /* @@ -1156,4 +1771,73 @@ 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(); + } + } + + /** + * 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; + } }