X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=d46cc346eb4c74fe5137aa2d93f795a5c850d9bd;hb=cd126a7085c5ebcfc8c05378c71bd862abc4fd91;hp=8cfd2dcb89d7ad4fd833e17918413fb2933ecd32;hpb=4f094851cd2247ea2d982e7829a6f5b663042573;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 8cfd2dc..d46cc34 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -25,6 +25,7 @@ import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@ -41,6 +42,7 @@ import jalview.structure.VamsasSource; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Font; @@ -179,19 +181,22 @@ public class SeqPanel extends Panel implements MouseMotionListener, seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; if (av.hasHiddenColumns() - && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + && !av.getAlignment().getHiddenColumns() + .isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) + while (!av.getAlignment().getHiddenColumns() + .isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + || !av.getAlignment().getHiddenColumns() + .isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@ -226,16 +231,18 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - while (seqCanvas.cursorY < av.startSeq) + ViewportRanges ranges = av.getRanges(); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + while (seqCanvas.cursorY < ranges.getStartSeq()) { ap.scrollUp(true); } - while (seqCanvas.cursorY + 1 > av.endSeq) + while (seqCanvas.cursorY > ranges.getEndSeq()) { ap.scrollUp(false); } - while (seqCanvas.cursorX < av.getColumnSelection() - .adjustForHiddenColumns(av.startRes)) + while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges + .getStartRes())) { if (!ap.scrollRight(false)) @@ -243,8 +250,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, break; } } - while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(av.endRes)) + while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges + .getEndRes())) { if (!ap.scrollRight(true)) { @@ -624,19 +631,20 @@ public class SeqPanel extends Panel implements MouseMotionListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.getStartRes() / cwidth; + wrappedBlock += av.getRanges().getStartRes() / cwidth; res = wrappedBlock * cwidth + x / av.getCharWidth(); } else { - res = (x / av.getCharWidth()) + av.getStartRes(); + res = (x / av.getCharWidth()) + av.getRanges().getStartRes(); } if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + res = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(res); } return res; @@ -681,7 +689,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + seq = Math.min((y / av.getCharHeight()) + + av.getRanges().getStartSeq(), + av .getAlignment().getHeight() - 1); if (seq < 0) { @@ -955,7 +965,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, fontSize = 1; } - av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); + av.setFont( + new Font(av.font.getName(), av.font.getStyle(), fontSize), + true); av.setCharWidth(oldWidth); } else @@ -1127,8 +1139,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (av.hasHiddenColumns()) { fixedColumns = true; - int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); - int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + int y1 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryLeft(startres); + int y2 = av.getAlignment().getHiddenColumns() + .getHiddenBoundaryRight(startres); if ((insertGap && startres > y1 && lastres < y1) || (!insertGap && startres < y2 && lastres > y2)) @@ -1199,8 +1213,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av - .getColumnSelection().getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() && startres < av.getAlignment() + .getHiddenColumns().getHiddenBoundaryRight(startres))) { endEditing(); return; @@ -1423,34 +1437,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, stretchGroup = av.getSelectionGroup(); - if (stretchGroup == null) + if (stretchGroup == null || !stretchGroup.contains(sequence, res)) { stretchGroup = av.getAlignment().findGroup(sequence, res); - av.setSelectionGroup(stretchGroup); - } - - if (stretchGroup == null - || !stretchGroup.getSequences(null).contains(sequence) - || stretchGroup.getStartRes() > res - || stretchGroup.getEndRes() < res) - { - stretchGroup = null; - - SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); - - if (allGroups != null) + if (stretchGroup != null) { - for (int i = 0; i < allGroups.length; i++) - { - if (allGroups[i].getStartRes() <= res - && allGroups[i].getEndRes() >= res) - { - stretchGroup = allGroups[i]; - break; - } - } + // only update the current selection if the popup menu has a group to + // focus on + av.setSelectionGroup(stretchGroup); } - av.setSelectionGroup(stretchGroup); } // DETECT RIGHT MOUSE BUTTON IN AWT @@ -1662,8 +1657,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, oldSeq = -1; } - if (res > av.endRes || res < av.startRes || y < av.startSeq - || y > av.endSeq) + if (res > av.getRanges().getEndRes() + || res < av.getRanges().getStartRes() + || y < av.getRanges().getStartSeq() + || y > av.getRanges().getEndSeq()) { mouseExited(evt); } @@ -1761,13 +1758,15 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (evt != null) { - if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0) + if (mouseDragging && evt.getY() < 0 + && av.getRanges().getStartSeq() > 0) { running = ap.scrollUp(true); } if (mouseDragging && evt.getY() >= getSize().height - && av.getAlignment().getHeight() > av.getEndSeq()) + && av.getAlignment().getHeight() > av.getRanges() + .getEndSeq()) { running = ap.scrollUp(false); } @@ -1798,7 +1797,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, */ @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, - SelectionSource source) + HiddenColumns hidden, SelectionSource source) { // TODO: fix this hack - source of messages is align viewport, but SeqPanel // handles selection messages... @@ -1815,7 +1814,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, * Check for selection in a view of which this one is a dna/protein * complement. */ - if (selectionFromTranslation(seqsel, colsel, source)) + if (selectionFromTranslation(seqsel, colsel, hidden, source)) { return; } @@ -1881,15 +1880,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - av.getColumnSelection().setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel, + av.getAlignment().getHiddenColumns()); } } repaint |= av.isColSelChanged(true); } if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection() - .getHiddenColumns() == null)) + && (av.getColumnSelection() == null || av.getAlignment() + .getHiddenColumns().getHiddenRegions() == null)) { System.err.println("Bad things"); } @@ -1909,8 +1909,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, public void scrollTo(int row, int column) { - row = row < 0 ? ap.av.startSeq : row; - column = column < 0 ? ap.av.startRes : column; + row = row < 0 ? ap.av.getRanges().getStartSeq() : row; + column = column < 0 ? ap.av.getRanges().getStartRes() : column; ap.scrollTo(column, column, row, true, true); } @@ -1922,8 +1922,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, public void scrollToRow(int row) { - row = row < 0 ? ap.av.startSeq : row; - ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true); + row = row < 0 ? ap.av.getRanges().getStartSeq() : row; + ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges() + .getStartRes(), row, true, true); } /** @@ -1934,8 +1935,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, public void scrollToColumn(int column) { - column = column < 0 ? ap.av.startRes : column; - ap.scrollTo(column, column, ap.av.startSeq, true, true); + column = column < 0 ? ap.av.getRanges().getStartRes() : column; + ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true); } /** @@ -1948,7 +1949,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, * @param source */ protected boolean selectionFromTranslation(SequenceGroup seqsel, - ColumnSelection colsel, SelectionSource source) + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { if (!(source instanceof AlignViewportI)) { @@ -1971,9 +1973,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, /* * Map column selection */ - ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, - av); + // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, + // av); + ColumnSelection cs = new ColumnSelection(); + HiddenColumns hs = new HiddenColumns(); + MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs); av.setColumnSelection(cs); + av.getAlignment().setHiddenColumns(hs); ap.scalePanelHolder.repaint(); ap.repaint();