X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=8a957bc66cff010f5d4199afe340d8d5980cb75a;hb=1d4324b37f248818b6bf5ba18e144f57299dc308;hp=c7751e3cdceb43415f07cf93ab42b825238e4db8;hpb=947f3eec987c61ea044731137930ef7d0c89128f;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index c7751e3..8a957bc 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; /** @@ -605,7 +606,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } else { - // no row (or row that can be adjusted) was pressed. Simulate a ruler click + // no row (or row that can be adjusted) was pressed. Simulate a ruler + // click ap.getScalePanel().mousePressed(evt); } } @@ -621,12 +623,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { int[] rowIndex = getRowIndexAndOffset(evt.getY(), av.getAlignment().getAlignmentAnnotation()); - int yOffset = rowIndex[1]; - if (rowIndex == null) { - System.err.println("IMPLEMENTATION ERROR: matrix click out of range."); + 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) @@ -653,7 +657,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, fr = Math.min(cXci.cStart, cXci.cEnd); to = Math.max(cXci.cStart, cXci.cEnd); - if (evt.isControlDown()) + // double click selects the whole group + if (evt.getClickCount() == 2) { ContactMatrixI matrix = av.getContactMatrix(clicked); @@ -663,23 +668,48 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (matrix.hasGroups()) { SequenceI rseq = clicked.sequenceRef; - BitSet grp = matrix.getGroupsFor(currentX); + 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(); - for (int p = grp.nextSetBit(0); p >= 0; p = grp + ColumnSelection cs = av.getColumnSelection(); + + 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)) + if (matrix instanceof MappableContactMatrixI) { - av.getColumnSelection().addElement(offp); + // 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); + } } } } @@ -694,18 +724,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { // select corresponding range in segment under mouse { - 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 (PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId())) + if (evt.isControlDown() + && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId())) { - int c = fr - 1; + int c = fr; ContactRange cr = forCurrentX.getRangeFor(fr, to); double cval; // TODO: could use GraphLine instead of arbitrary picking @@ -715,18 +747,23 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // controls feathering - what other elements in row/column // should we select double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15; - while (c > 0) + while (c >= 0) { cval = forCurrentX.getContactAt(c); if (// cr.getMin() <= cval && cval <= thresh) { - av.getColumnSelection().addElement(c--); - } - else - { - break; + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) + { + av.getColumnSelection().addRangeOfElements(cols, true); + } + else + { + break; + } } + c--; } c = to; while (c < forCurrentX.getContactHeight()) @@ -735,20 +772,28 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (// cr.getMin() <= cval && cval <= thresh) { - av.getColumnSelection().addElement(c++); + int[] cols = forCurrentX.getMappedPositionsFor(c, c); + if (cols != null) + { + av.getColumnSelection().addRangeOfElements(cols, true); + } } else { break; } + c++; + } } } } ap.paintAlignment(false, false); - + PaintRefresher.Refresh(ap, av.getSequenceSetId()); + av.sendSelection(); return true; } + /** * Construct and display a context menu at the right-click position * @@ -1008,12 +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 @@ -1032,52 +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); @@ -1182,7 +1247,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { row = i; res[0] = row; - res[1] = height - yPos; + res[1] = yPos-lheight; break; } } @@ -1236,6 +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) { @@ -1244,12 +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; @@ -1401,8 +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; @@ -1423,7 +1507,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, tried = true; } catch (IllegalArgumentException exc) { - System.err.println( + jalview.bin.Console.errPrintln( "Serious issue with viewport geometry imgWidth requested was " + imgWidth); return; @@ -1470,6 +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 */ @@ -1559,7 +1650,7 @@ 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); @@ -1645,6 +1736,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public int getFadedImageWidth() { + updateFadedImageWidth(); return imgWidth; }