X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=f01d7be2b06f0d698c99e376d7b98db1b178fa79;hb=f047ab25cc45bfc9d130f67d2c56a940751d9c91;hp=ee4c32770effd007ab2730c483a797f13c2399bc;hpb=985903ad810d9ef6ba0d09ff2b29d24e22c0708d;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index ee4c327..f01d7be 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -648,144 +648,152 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { 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) + ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset); + if (cXci != null) { - ContactMatrixI matrix = av.getContactMatrix(clicked); + /** + * 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 (matrix != null) + // double click selects the whole group + if (evt.getClickCount() == 2) { - // simplest approach is to select all group containing column - if (matrix.hasGroups()) + ContactMatrixI matrix = av.getContactMatrix(clicked); + + if (matrix != null) { - 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++) + // simplest approach is to select all group containing column + if (matrix.hasGroups()) { - BitSet additionalGrp = matrix.getGroupsFor(c); - grp.or(additionalGrp); - } + 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) + HiddenColumns hc = av.getAlignment().getHiddenColumns(); + ColumnSelection cs = av.getColumnSelection(); + + for (int p = grp.nextSetBit(0); p >= 0; p = grp + .nextSetBit(p + 1)) { - // 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) + if (matrix instanceof MappableContactMatrixI) { - for (int pos_p = pos[0];pos_p<=pos[1];pos_p++) + // 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) { - int col = rseq.findIndex(pos_p)-1; - if (col>=0 && (!av.hasHiddenColumns() || hc.isVisible(col))) + for (int pos_p = pos[0]; pos_p <= pos[1]; pos_p++) { - cs.addElement(col); + 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)) + else { - cs.addElement(offp); + 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 + // 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())) + else { - 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) + // select corresponding range in segment under mouse { - cval = forCurrentX.getContactAt(c); - if (// cr.getMin() <= cval && - cval <= thresh) + int[] rng = forCurrentX.getMappedPositionsFor(fr, to); + if (rng != null) { - int[] cols = forCurrentX.getMappedPositionsFor(c, c); - if (cols != null) - { - av.getColumnSelection().addRangeOfElements(cols, true); - } - else - { - break; - } + av.getColumnSelection().addRangeOfElements(rng, true); } - c--; + av.getColumnSelection().addElement(currentX); } - c = to; - while (c < forCurrentX.getContactHeight()) + // PAE SPECIFIC + // and also select everything lower than the max range adjacent + // (kind of works) + if (evt.isControlDown() + && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId())) { - cval = forCurrentX.getContactAt(c); - if (// cr.getMin() <= cval && - cval <= thresh) + 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) { - int[] cols = forCurrentX.getMappedPositionsFor(c, c); - if (cols != null) + cval = forCurrentX.getContactAt(c); + if (// cr.getMin() <= cval && + cval <= thresh) { - av.getColumnSelection().addRangeOfElements(cols, true); + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) + { + av.getColumnSelection().addRangeOfElements(cols, true); + } + else + { + break; + } } + c--; } - else + c = to; + while (c < forCurrentX.getContactHeight()) { - break; - } - c++; + 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++; + } } + } } } @@ -1076,23 +1084,21 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (forFromX != null && forToX != null) { - ContactGeometry lastXcgeom = new ContactGeometry(forFromX, - cma.graphHeight); - ContactGeometry.contactInterval lastXci = lastXcgeom - .mapFor(rowIndex[1], rowIndex[1] + deltaY); - - ContactGeometry cXcgeom = new ContactGeometry(forToX, + // 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 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); + fr = Math.min(lastXci.cStart, cXci.cStart); + to = Math.max(lastXci.cEnd, cXci.cEnd); int[] mappedPos = forFromX.getMappedPositionsFor(fr, to); if (mappedPos != null) { @@ -1110,33 +1116,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // } // 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); - mappedPos = forFromX.getMappedPositionsFor(fr, to); - if (mappedPos != null) - { - for (int pair = 0; pair < mappedPos.length; pair += 2) - { - 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); - } + av.getColumnSelection().addElement(c-1); } } }