X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=2177a269aba985e3e1965f73c8deddb3f6e3b7c9;hb=f3d6a13271e3f34dfb4e40d6a2a7df1d392f8014;hp=786696cb353fa4c0d8ed679ce17e1fd145c72cbc;hpb=6e670b92ab0119650fa78ec4c968f600c077babc;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 786696c..2177a26 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; @@ -69,6 +72,7 @@ import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; /** * AnnotationPanel displays visible portion of annotation rows below unwrapped @@ -588,43 +592,181 @@ 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 + } + } + 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) { - 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); - int fr, to; - fr = Math.min(cXci.cStart, cXci.cEnd); - to = Math.max(cXci.cStart, cXci.cEnd); + SequenceI rseq = clicked.sequenceRef; + BitSet grp = matrix.getGroupsFor(currentX); + // TODO: cXci needs to be mapped to real groups for (int c = fr; c <= to; c++) { - av.getColumnSelection().addElement(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)) + { + int offp = (rseq != null) + ? rseq.findIndex(rseq.getStart() - 1 + p) + : p; + + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + av.getColumnSelection().addElement(offp); + } } - av.getColumnSelection().addElement(currentX); } + // 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 - 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) + { + 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; } - /** * Construct and display a context menu at the right-click position * @@ -697,7 +839,10 @@ 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 @@ -784,7 +929,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * 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 @@ -881,12 +1026,12 @@ 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 @@ -913,44 +1058,62 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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) - { - int col = cma.sequenceRef.findIndex(c); - av.getColumnSelection().addElement(col); - } - else + for (int pair = 0; pair < mappedPos.length; pair += 2) { - 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); @@ -1107,7 +1270,7 @@ 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) { ContactListI clist = av.getContactList(ann, column); if (clist != null) @@ -1117,12 +1280,28 @@ 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;