X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=f0ec51ce57ab19bee297368ce6ec3152f12360ec;hb=fe654aee9b43fb9c9307830c277f1e63576826ae;hp=97830a322be86a536b22001b87ed4e2a0149546b;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 97830a3..f0ec51c 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -25,8 +25,10 @@ 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.SearchResults.Match; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -37,9 +39,11 @@ import jalview.structure.SelectionSource; import jalview.structure.SequenceListener; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; +import jalview.util.Comparison; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Font; @@ -50,6 +54,10 @@ import java.awt.event.InputEvent; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.ListIterator; import java.util.Vector; public class SeqPanel extends Panel implements MouseMotionListener, @@ -178,19 +186,22 @@ 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; } @@ -221,31 +232,33 @@ public class SeqPanel extends Panel implements MouseMotionListener, endEditing(); if (av.getWrapAlignment()) { - ap.scrollToWrappedVisible(seqCanvas.cursorX); + av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); } else { - while (seqCanvas.cursorY < av.startSeq) + ViewportRanges ranges = av.getRanges(); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + while (seqCanvas.cursorY < ranges.getStartSeq()) { - ap.scrollUp(true); + ranges.scrollUp(true); } - while (seqCanvas.cursorY + 1 > av.endSeq) + while (seqCanvas.cursorY > ranges.getEndSeq()) { - ap.scrollUp(false); + ranges.scrollUp(false); } - while (seqCanvas.cursorX < av.getColumnSelection() - .adjustForHiddenColumns(av.startRes)) + while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges + .getStartRes())) { - if (!ap.scrollRight(false)) + if (!ranges.scrollRight(false)) { break; } } - while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(av.endRes)) + while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges + .getEndRes())) { - if (!ap.scrollRight(true)) + if (!ranges.scrollRight(true)) { break; } @@ -404,13 +417,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, * * @param sequence * aligned sequence object - * @param res + * @param column * alignment column * @param seq * index of sequence in alignment - * @return position of res in sequence + * @return position of column in sequence or -1 if at gap */ - void setStatusMessage(SequenceI sequence, int res, int seq) + void setStatusMessage(SequenceI sequence, int column, int seq) { // TODO remove duplication of identical gui method StringBuilder text = new StringBuilder(32); @@ -421,7 +434,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, /* * Try to translate the display character to residue name (null for gap). */ - final String displayChar = String.valueOf(sequence.getCharAt(res)); + final String displayChar = String.valueOf(sequence.getCharAt(column)); if (av.getAlignment().isNucleotide()) { residue = ResidueProperties.nucleotideName.get(displayChar); @@ -444,7 +457,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, int pos = -1; if (residue != null) { - pos = sequence.findPosition(res); + pos = sequence.findPosition(column); text.append(" (").append(Integer.toString(pos)).append(")"); } @@ -458,7 +471,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, * @param results * @return true if results were matched, false if not */ - private boolean setStatusMessage(SearchResults results) + private boolean setStatusMessage(SearchResultsI results) { AlignmentI al = this.av.getAlignment(); int sequenceIndex = al.findIndex(results); @@ -467,7 +480,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, return false; } SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); - for (Match m : results.getResults()) + for (SearchResultMatchI m : results.getResults()) { SequenceI seq = m.getSequence(); if (seq.getDatasetSequence() != null) @@ -489,6 +502,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, return false; } + @Override public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); @@ -539,6 +553,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, return; } + @Override public void mouseClicked(MouseEvent evt) { SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); @@ -552,35 +567,39 @@ public class SeqPanel extends Panel implements MouseMotionListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes(sequence, - sequence.findPosition(findRes(evt))); - - if (features != null && features.length > 0) + int column = findRes(evt); + boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); + List features = findFeaturesAtRes(sequence, + sequence.findPosition(column)); + if (isGapped) { - SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); - seqCanvas.highlightSearchResults(highlight); + removeAdjacentFeatures(features, column + 1, sequence); } - if (features != null && features.length > 0) + + if (!features.isEmpty()) { + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); + seqCanvas.highlightSearchResults(highlight); seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, features, false, ap); + Collections.singletonList(sequence), features, false, ap); seqCanvas.highlightSearchResults(null); } } } + @Override public void mouseReleased(MouseEvent evt) { + boolean didDrag = mouseDragging; // did we come here after a drag mouseDragging = false; mouseWheelPressed = false; - ap.paintAlignment(true); if (!editingSeqs) { - doMouseReleasedDefineMode(evt); + doMouseReleasedDefineMode(evt, didDrag); return; } @@ -620,19 +639,20 @@ 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; @@ -677,7 +697,9 @@ 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) { @@ -715,6 +737,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, String lastMessage; + @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { String tmp = sequence.hashCode() + index + ""; @@ -726,14 +749,21 @@ public class SeqPanel extends Panel implements MouseMotionListener, lastMessage = tmp; } - public void highlightSequence(SearchResults results) + @Override + public void highlightSequence(SearchResultsI results) { if (av.isFollowHighlight()) { + // don't allow highlight of protein/cDNA to also scroll a complementary + // panel,as this sets up a feedback loop (scrolling panel 1 causes moused + // over residue to change abruptly, causing highlighted residue in panel 2 + // to change, causing a scroll in panel 1 etc) + ap.setToScrollComplementPanel(false); if (ap.scrollToPosition(results, true)) { ap.alignFrame.repaint(); } + ap.setToScrollComplementPanel(true); } setStatusMessage(results); seqCanvas.highlightSearchResults(results); @@ -746,18 +776,20 @@ public class SeqPanel extends Panel implements MouseMotionListener, return this.ap == null ? null : this.ap.av; } + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); // repaint(); } + @Override public void mouseMoved(MouseEvent evt) { - int res = findRes(evt); + final int column = findRes(evt); int seq = findSeq(evt); - if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0) + if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0) { if (tooltip != null) { @@ -767,7 +799,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if (res > sequence.getLength()) + if (column > sequence.getLength()) { if (tooltip != null) { @@ -776,38 +808,34 @@ public class SeqPanel extends Panel implements MouseMotionListener, return; } - int respos = sequence.findPosition(res); - if (ssm != null) + final char ch = sequence.getCharAt(column); + boolean isGapped = Comparison.isGap(ch); + // find residue at column (or nearest if at a gap) + int respos = sequence.findPosition(column); + + if (ssm != null && !isGapped) { - mouseOverSequence(sequence, res, respos); + mouseOverSequence(sequence, column, respos); } StringBuilder text = new StringBuilder(); text.append("Sequence ").append(Integer.toString(seq + 1)) .append(" ID: ").append(sequence.getName()); - String obj = null; - final String ch = String.valueOf(sequence.getCharAt(res)); - if (av.getAlignment().isNucleotide()) + if (!isGapped) { - obj = ResidueProperties.nucleotideName.get(ch); - if (obj != null) + if (av.getAlignment().isNucleotide()) { - text.append(" Nucleotide: ").append(obj); + String base = ResidueProperties.nucleotideName.get(ch); + text.append(" Nucleotide: ").append(base == null ? ch : base); } - } - else - { - obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet - .get(ch); - if (obj != null) + else { - text.append(" Residue: ").append(obj); + String residue = (ch == 'x' || ch == 'X') ? "X" + : ResidueProperties.aa2Triplet + .get(String.valueOf(ch)); + text.append(" Residue: ").append(residue == null ? ch : residue); } - } - - if (obj != null) - { text.append(" (").append(Integer.toString(respos)).append(")"); } @@ -819,7 +847,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { for (int g = 0; g < groups.length; g++) { - if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res) + if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column) { if (!groups[g].getName().startsWith("JTreeGroup") && !groups[g].getName().startsWith("JGroup")) @@ -835,33 +863,37 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } - // use aa to see if the mouse pointer is on a - SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, - sequence.findPosition(res)); - - int index = 0; - while (index < allFeatures.length) + /* + * add feature details to tooltip, including any that straddle + * a gapped position + */ + if (av.isShowSequenceFeatures()) { - SequenceFeature sf = allFeatures[index]; - - tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); - - if (sf.getDescription() != null) + List allFeatures = findFeaturesAtRes(sequence, + sequence.findPosition(column)); + if (isGapped) { - tooltipText.append(" " + sf.getDescription()); + removeAdjacentFeatures(allFeatures, column + 1, sequence); } - - if (sf.getValue("status") != null) + for (SequenceFeature sf : allFeatures) { - String status = sf.getValue("status").toString(); - if (status.length() > 0) + tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); + + if (sf.getDescription() != null) { - tooltipText.append(" (" + sf.getValue("status") + ")"); + tooltipText.append(" " + sf.getDescription()); } - } - tooltipText.append("\n"); - index++; + if (sf.getValue("status") != null) + { + String status = sf.getValue("status").toString(); + if (status.length() > 0) + { + tooltipText.append(" (" + sf.getValue("status") + ")"); + } + } + tooltipText.append("\n"); + } } if (tooltip == null) @@ -874,9 +906,35 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } - SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) + /** + * Removes from the list of features any that start after, or end before, the + * given column position. This allows us to retain only those features + * adjacent to a gapped position that straddle the position. + * + * @param features + * @param column + * alignment column (1..) + * @param sequence + */ + protected void removeAdjacentFeatures(List features, + int column, SequenceI sequence) { - Vector tmp = new Vector(); + // TODO should this be an AlignViewController method (shared by gui)? + ListIterator it = features.listIterator(); + while (it.hasNext()) + { + SequenceFeature sf = it.next(); + if (sequence.findIndex(sf.getBegin()) > column + || sequence.findIndex(sf.getEnd()) < column) + { + it.remove(); + } + } + } + + List findFeaturesAtRes(SequenceI sequence, int res) + { + List result = new ArrayList(); SequenceFeature[] features = sequence.getSequenceFeatures(); if (features != null) { @@ -899,19 +957,25 @@ public class SeqPanel extends Panel implements MouseMotionListener, if ((features[i].getBegin() <= res) && (features[i].getEnd() >= res)) { - tmp.addElement(features[i]); + result.add(features[i]); } } } - features = new SequenceFeature[tmp.size()]; - tmp.copyInto(features); - - return features; + return result; } Tooltip tooltip; + /** + * set when the current UI interaction has resulted in a change that requires + * overview shading to be recalculated. this could be changed to something + * more expressive that indicates what actually has changed, so selective + * redraws can be applied + */ + private boolean needOverviewUpdate; // TODO: refactor to avcontroller + + @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) @@ -938,7 +1002,9 @@ 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 @@ -1110,8 +1176,10 @@ 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)) @@ -1182,8 +1250,8 @@ 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; @@ -1406,64 +1474,35 @@ 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); - if (stretchGroup != null && res > stretchGroup.getStartRes() - && res < stretchGroup.getEndRes()) + stretchGroup = av.getAlignment().findGroup(sequence, res); + if (stretchGroup != null) { + // only update the current selection if the popup menu has a group to + // focus on av.setSelectionGroup(stretchGroup); } - else - { - stretchGroup = null; - } - } - - else if (!stretchGroup.getSequences(null).contains(sequence) - || stretchGroup.getStartRes() > res - || stretchGroup.getEndRes() < res) - { - stretchGroup = null; - - SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); - - if (allGroups != null) - { - for (int i = 0; i < allGroups.length; i++) - { - if (allGroups[i].getStartRes() <= res - && allGroups[i].getEndRes() >= res) - { - stretchGroup = allGroups[i]; - break; - } - } - } - av.setSelectionGroup(stretchGroup); } // DETECT RIGHT MOUSE BUTTON IN AWT if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, + List allFeatures = findFeaturesAtRes(sequence, sequence.findPosition(res)); Vector links = null; - if (allFeatures != null) + for (SequenceFeature sf : allFeatures) { - for (int i = 0; i < allFeatures.length; i++) + if (sf.links != null) { - if (allFeatures[i].links != null) + if (links == null) { - if (links == null) - { - links = new Vector(); - } - for (int j = 0; j < allFeatures[i].links.size(); j++) - { - links.addElement(allFeatures[i].links.elementAt(j)); - } + links = new Vector(); + } + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); } } } @@ -1495,27 +1534,30 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (av.getConservationSelected()) { - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } if (av.getAbovePIDThreshold()) { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); } } } - public void doMouseReleasedDefineMode(MouseEvent evt) + public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag) { if (stretchGroup == null) { return; } - - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + // always do this - annotation has own state + // but defer colourscheme update until hidden sequences are passed in + boolean vischange = stretchGroup.recalcConservation(true); + // here we rely on stretchGroup == av.getSelection() + needOverviewUpdate |= vischange && av.isSelectionDefinedGroup() + && afterDrag; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1526,17 +1568,18 @@ public class SeqPanel extends Panel implements MouseMotionListener, SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); } - else + if (stretchGroup.cs.getThreshold() > 0) { SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName()); } } + PaintRefresher.Refresh(ap, av.getSequenceSetId()); + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; - PaintRefresher.Refresh(ap, av.getSequenceSetId()); - ap.paintAlignment(true); av.sendSelection(); } @@ -1588,6 +1631,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1595,6 +1639,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1628,6 +1673,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } else { @@ -1637,6 +1683,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1645,8 +1692,10 @@ 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); } @@ -1659,6 +1708,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, seqCanvas.repaint(); } + @Override public void mouseEntered(MouseEvent e) { if (oldSeq < 0) @@ -1673,6 +1723,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -1732,6 +1783,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, running = false; } + @Override public void run() { running = true; @@ -1741,25 +1793,27 @@ 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); + running = av.getRanges().scrollUp(true); } if (mouseDragging && evt.getY() >= getSize().height - && av.getAlignment().getHeight() > av.getEndSeq()) + && av.getAlignment().getHeight() > av.getRanges() + .getEndSeq()) { - running = ap.scrollUp(false); + running = av.getRanges().scrollUp(false); } if (mouseDragging && evt.getX() < 0) { - running = ap.scrollRight(false); + running = av.getRanges().scrollRight(false); } else if (mouseDragging && evt.getX() >= getSize().width) { - running = ap.scrollRight(true); + running = av.getRanges().scrollRight(true); } } @@ -1776,8 +1830,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, /** * modify current selection according to a received message. */ + @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... @@ -1794,16 +1849,19 @@ 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; } // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) - // rules are: colsel is copied if there is a real intersection between - // sequence selection - boolean repaint = false, copycolsel = true; + /* + * only copy colsel if there is a real intersection between + * sequence selection and this panel's alignment + */ + boolean repaint = false; + boolean copycolsel = false; if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true)) { SequenceGroup sgroup = null; @@ -1820,11 +1878,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, } sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); - if ((sgroup == null || sgroup.getSize() == 0) - && (colsel == null || colsel.size() == 0)) + if ((sgroup != null && sgroup.getSize() > 0)) { - // don't copy columns if the region didn't intersect. - copycolsel = false; + copycolsel = true; } } if (sgroup != null && sgroup.getSize() > 0) @@ -1843,7 +1899,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { // the current selection is unset or from a previous message // so import the new colsel. - if (colsel == null || colsel.size() == 0) + if (colsel == null || colsel.isEmpty()) { if (av.getColumnSelection() != null) { @@ -1859,15 +1915,16 @@ 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"); } @@ -1887,8 +1944,8 @@ 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); } @@ -1900,8 +1957,9 @@ 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); } /** @@ -1912,8 +1970,8 @@ 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); } /** @@ -1926,7 +1984,8 @@ 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)) { @@ -1949,10 +2008,13 @@ 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.isColSelChanged(true); + av.getAlignment().setHiddenColumns(hs); ap.scalePanelHolder.repaint(); ap.repaint();