X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=e1193c92505d13694f6348c8478de23b5b0c9952;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=ccc086ccc5d589670203d7d571d35ef14e63f84c;hpb=0d326d33340305d0eaa539cbf903f778001ebeb7;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index ccc086c..e1193c9 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -41,6 +41,7 @@ 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; @@ -56,7 +57,9 @@ 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; @@ -65,10 +68,13 @@ 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 @@ -150,6 +156,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, private MouseWheelListener[] _mwl; + private boolean notJustOne; + /** * Creates a new AnnotationPanel object. * @@ -586,41 +594,219 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (graphStretch != -1) { - if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER) + 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 { - int currentX = getColumnForXPos(evt.getX()); - ContactListI forCurrentX = av.getContactList(aa[graphStretch], - currentX); - if (forCurrentX != null) + // select corresponding range in segment under mouse { - 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++) + int[] rng = forCurrentX.getMappedPositionsFor(fr, to); + if (rng != null) { - av.getColumnSelection().addElement(c); + 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++; + + } + } + } } } - else - { - ap.getScalePanel().mousePressed(evt); - } + ap.paintAlignment(false, false); + PaintRefresher.Refresh(ap, av.getSequenceSetId()); + av.sendSelection(); + return true; } /** @@ -695,7 +881,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ap.adjustAnnotationHeight(); } dragMode = DragMode.Undefined; - ap.getScalePanel().mouseReleased(evt); + if (!matrix_clicked(evt)) + { + ap.getScalePanel().mouseReleased(evt); + } /* * isPopupTrigger is set in mouseReleased on Windows @@ -776,12 +965,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * 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.CUSTOMRENDERER)) + .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)) { /* * dragging in a matrix @@ -816,7 +1006,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, AlignmentAnnotation graphAnnotation = av.getAlignment() .getAlignmentAnnotation()[graphStretch]; int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY); - graphAnnotation.graphHeight = newHeight; + 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); } @@ -852,7 +1055,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ 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()); @@ -861,58 +1068,69 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (rowIndex == null || toRowIndex == null) { - System.out.println("Drag out of range. needs to be clipped"); + jalview.bin.Console.trace("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"); + 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 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) + 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(forLastX, - cma.graphHeight); - ContactGeometry.contactInterval lastXci = lastXcgeom.mapFor( - rowIndex[1], - rowIndex[1] + ((fromY == firstDragY) ? -deltaY : deltaY)); - ContactGeometry cXcgeom = new ContactGeometry(forCurrentX, + // 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 cXci = cXcgeom.mapFor(rowIndex[1], - rowIndex[1] + deltaY); + ContactGeometry.contactInterval lastXci = xcgeom.mapFor(rowIndex[1]); + ContactGeometry.contactInterval cXci = xcgeom + .mapFor(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 + ")"); + 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, 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++) + fr = Math.min(lastXci.cStart, cXci.cStart); + to = Math.max(lastXci.cEnd, cXci.cEnd); + int[] mappedPos = forFromX.getMappedPositionsFor(fr, to); + if (mappedPos != null) { - av.getColumnSelection().addElement(c); + 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); - System.err.println("Marking " + fr + " to " + to); + jalview.bin.Console.trace("Marking " + fr + " to " + to); for (int c = fr; c <= to; c++) { av.getColumnSelection().addElement(c); @@ -997,15 +1215,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa) { int[] res = new int[2]; + res[0] = -1; + res[1] = 0; if (aa == null) { - 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) @@ -1018,7 +1235,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { row = i; res[0] = row; - res[1] = height - yPos; + res[1] = yPos - lheight; break; } } @@ -1070,18 +1287,45 @@ 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) + if (ann.graph == AlignmentAnnotation.CONTACT_MAP) { + 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, - rowAndOffset); - tooltip += "Contact from " + ci.cStart + " to " + ci.cEnd; - - // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef, - // new int[] {column, ci.cStart,ci.cEnd}, -1, null) + 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; @@ -1233,8 +1477,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } } - imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() - + 1) * av.getCharWidth(); + updateFadedImageWidth(); if (imgWidth < 1) { return; @@ -1243,24 +1486,37 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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(); @@ -1289,6 +1545,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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 */ @@ -1378,7 +1641,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, && (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); @@ -1464,6 +1728,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public int getFadedImageWidth() { + updateFadedImageWidth(); return imgWidth; }