X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=ccc086ccc5d589670203d7d571d35ef14e63f84c;hb=0d326d33340305d0eaa539cbf903f778001ebeb7;hp=bd7d5fb78bea6d976e136d7967df91deef49f685;hpb=f5d6c0018555b2c453c2c0354c84cd5d2d81e3b9;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index bd7d5fb..ccc086c 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.Annotation; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.SequenceI; -import jalview.gui.JalviewColourChooser.ColourChooserListener; -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; @@ -65,6 +50,26 @@ 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 @@ -78,7 +83,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { enum DragMode { - Select, Resize, Undefined + Select, Resize, Undefined, MatrixSelect }; String HELIX = MessageManager.getString("label.helix"); @@ -128,6 +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; @@ -149,9 +158,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public AnnotationPanel(AlignmentPanel ap) { -// setBackground(Color.white); // BH 2019 - - ToolTipManager.sharedInstance().registerComponent(this); + ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); this.ap = ap; @@ -356,7 +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)) @@ -367,10 +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 @@ -535,8 +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) @@ -550,12 +561,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { activeRow = i; } - else if (aa[i].graph > 0) + else if (aa[i].graph != 0) { /* * we have clicked on a resizable graph annotation */ graphStretch = i; + yOffset = height - y; } break; } @@ -571,7 +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); + } } /** @@ -631,10 +680,20 @@ 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) + { + ap.adjustAnnotationHeight(); + } dragMode = DragMode.Undefined; ap.getScalePanel().mouseReleased(evt); @@ -675,16 +734,25 @@ 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) { /* - * todo: if dragMode is Undefined: + * if dragMode is Undefined: * - set to Select if dx > dy * - set to Resize if dy > dx * - do nothing if dx == dy @@ -708,10 +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 @@ -738,6 +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 { /* @@ -753,6 +845,82 @@ 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 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); + } + } + + } + /** * Constructs the tooltip, and constructs and displays a status message, for * the current mouse position @@ -762,120 +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.setStatus(" "); + 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 @@ -884,7 +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) @@ -900,7 +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")) @@ -910,7 +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)); @@ -931,7 +1152,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } - ap.alignFrame.setStatus(text.toString()); + return text.toString(); } /** @@ -973,7 +1194,9 @@ 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! @@ -984,27 +1207,28 @@ 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; } @@ -1051,11 +1275,13 @@ 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(); @@ -1091,19 +1317,22 @@ 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 + if (imgWidth > Math.abs(horizontal * av.getCharWidth())) { - transX = (er - sr - horizontal) * av.getCharWidth(); - sr = er - horizontal; - } - else if (horizontal < 0) - { - 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); @@ -1111,7 +1340,7 @@ 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 @@ -1207,6 +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 @@ -1255,7 +1495,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ap = null; image = null; fadedImage = null; -// gg = null; + // gg = null; _mwl = null; /*