X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=8321741627876bf99dcb3d5746b139f758527314;hb=6081884ff7c5a50b2a9f6615f7a864bdc5699bf2;hp=b112383673a5967c4694441cad748d4e7af75124;hpb=a8349faec60666eff52c3060565116935b66e544;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index b112383..8321741 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -72,6 +72,7 @@ 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; /** @@ -601,128 +602,196 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, firstDragX = mouseDragLastX; firstDragY = mouseDragLastY; } - else + } + } + 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 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, + yOffset); + /** + * 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) { - GraphLine thr = aa[graphStretch].getThreshold(); - - int currentX = getColumnForXPos(evt.getX()); - ContactListI forCurrentX = av.getContactList(aa[graphStretch], - currentX); - if (forCurrentX != null) + // simplest approach is to select all group containing column + if (matrix.hasGroups()) { - ContactGeometry cXcgeom = new ContactGeometry(forCurrentX, - aa[graphStretch].graphHeight); - ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset, - yOffset); - /** - * 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); - - if (evt.isControlDown()) + 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)) { - ContactMatrixI matrix = av.getContactMatrix(aa[graphStretch]); - - if (matrix != null) + if (matrix instanceof MappableContactMatrixI) { - // simplest approach is to select all group containing column - if (matrix.hasGroups()) + // 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) { - SequenceI rseq = aa[graphStretch].sequenceRef; - BitSet grp = matrix.getGroupsFor(currentX); - for (int c=fr;c<=to; c++) - { - BitSet additionalGrp = matrix.getGroupsFor(c); - grp.or(additionalGrp); - } - HiddenColumns hc = av.getAlignment().getHiddenColumns(); - for (int p = grp.nextSetBit(0); p >= 0; p = grp - .nextSetBit(p + 1)) + for (int pos_p = pos[0];pos_p<=pos[1];pos_p++) { - int offp = (rseq != null) - ? rseq.findIndex(rseq.getStart() - 1 + p) - : p; - - if (!av.hasHiddenColumns() || hc.isVisible(offp)) + int col = rseq.findIndex(pos_p)-1; + if (col>=0 && (!av.hasHiddenColumns() || hc.isVisible(col))) { - av.getColumnSelection().addElement(offp); + cs.addElement(col); } } } - // 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 offp = (rseq != null) + ? rseq.findIndex(rseq.getStart() - 1 + p) + : p; + + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + cs.addElement(offp); + } } } - else + } + // 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) { - // select corresponding range in segment under mouse + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) { - for (int c = fr; c <= to; c++) - { - av.getColumnSelection().addElement(c); - } - av.getColumnSelection().addElement(currentX); + av.getColumnSelection().addRangeOfElements(cols, true); } - // PAE SPECIFIC - // and also select everything lower than the max range adjacent - // (kind of works) - if (PAEContactMatrix.PAEMATRIX - .equals(aa[graphStretch].getCalcId())) + else { - int c = fr - 1; - 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) - { - av.getColumnSelection().addElement(c--); - } - else - { - break; - } - } - c = to; - while (c < forCurrentX.getContactHeight()) - { - cval = forCurrentX.getContactAt(c); - if (// cr.getMin() <= cval && - cval <= thresh) - { - av.getColumnSelection().addElement(c++); - } - else - { - break; - } - } + 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; } /** @@ -797,7 +866,10 @@ 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 @@ -981,12 +1053,13 @@ 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 @@ -1005,52 +1078,71 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, ContactGeometry lastXcgeom = new ContactGeometry(forFromX, cma.graphHeight); ContactGeometry.contactInterval lastXci = lastXcgeom - .mapFor(rowIndex[1], rowIndex[1] - deltaY); + .mapFor(rowIndex[1], rowIndex[1] + deltaY); ContactGeometry cXcgeom = new ContactGeometry(forToX, cma.graphHeight); ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1], - rowIndex[1] - deltaY); + 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 + "])"); + 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++) + int[] mappedPos = forFromX.getMappedPositionsFor(fr, to); + if (mappedPos != null) { - if (cma.sequenceRef != null) - { - int col = cma.sequenceRef.findIndex(c); - av.getColumnSelection().addElement(col); - } - else + 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) { - av.getColumnSelection().addElement(c); + 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); + } } } + // and again for most recent corner of drag 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++) + mappedPos = forFromX.getMappedPositionsFor(fr, to); + if (mappedPos != null) { - if (cma.sequenceRef != null) + for (int pair = 0; pair < mappedPos.length; pair += 2) { - int col = cma.sequenceRef.findIndex(c); - av.getColumnSelection().addElement(col); - } - else - { - av.getColumnSelection().addElement(c); + jalview.bin.Console.trace("Marking " + fr + " to " + to + + " mapping to sequence positions " + mappedPos[pair] + + " to " + mappedPos[pair + 1]); + 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); + } + } } } 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); @@ -1155,7 +1247,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { row = i; res[0] = row; - res[1] = height - yPos; + res[1] = yPos-lheight; break; } } @@ -1209,6 +1301,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // TODO abstract tooltip generator so different implementations can be built if (ann.graph == AlignmentAnnotation.CONTACT_MAP) { + if (rowAndOffset>=ann.graphHeight) + { + return null; + } ContactListI clist = av.getContactList(ann, column); if (clist != null) { @@ -1217,12 +1313,28 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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); + 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, new int[][] - { new int[] { col, col }, - new int[] - { ci.cStart, ci.cEnd } }, null); + .highlightPositionsOn(ann.sequenceRef, highlightPos, null); } } return tooltip; @@ -1374,8 +1486,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } } - imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() - + 1) * av.getCharWidth(); + updateFadedImageWidth(); if (imgWidth < 1) { return; @@ -1443,6 +1554,13 @@ 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 */ @@ -1618,6 +1736,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public int getFadedImageWidth() { + updateFadedImageWidth(); return imgWidth; }