X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=dc2d3e9b2d453ee136e6dd3fabbb79c1c0e5bd71;hb=3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a;hp=0135e9d84096377b116e7a9125ec11c71def4006;hpb=793e6d46ae572461a030e2751c0d748f2521b71e;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 0135e9d..dc2d3e9 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,14 +20,34 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Point; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.MouseWheelEvent; +import java.awt.event.MouseWheelListener; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; + +import javax.swing.JPanel; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; + import jalview.api.AlignViewportI; import jalview.bin.Cache; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@ -48,23 +68,8 @@ import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; - -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Point; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; -import java.awt.event.MouseMotionListener; -import java.awt.event.MouseWheelEvent; -import java.awt.event.MouseWheelListener; -import java.util.Collections; -import java.util.List; - -import javax.swing.JPanel; -import javax.swing.SwingUtilities; -import javax.swing.ToolTipManager; +import jalview.viewmodel.ViewportRanges; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; /** * DOCUMENT ME! @@ -76,6 +81,82 @@ public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener, SequenceListener, SelectionListener { + /* + * a class that holds computed mouse position + * - column of the alignment (0...) + * - sequence offset (0...) + * - annotation row offset (0...) + * where annotation offset is -1 unless the alignment is shown + * in wrapped mode, annotations are shown, and the mouse is + * over an annnotation row + */ + static class MousePos + { + /* + * alignment column position of cursor (0...) + */ + final int column; + + /* + * index in alignment of sequence under cursor, + * or nearest above if cursor is not over a sequence + */ + final int seqIndex; + + /* + * index in annotations array of annotation under the cursor + * (only possible in wrapped mode with annotations shown), + * or -1 if cursor is not over an annotation row + */ + final int annotationIndex; + + MousePos(int col, int seq, int ann) + { + column = col; + seqIndex = seq; + annotationIndex = ann; + } + + boolean isOverAnnotation() + { + return annotationIndex != -1; + } + + @Override + public boolean equals(Object obj) + { + if (obj == null || !(obj instanceof MousePos)) + { + return false; + } + MousePos o = (MousePos) obj; + boolean b = (column == o.column && seqIndex == o.seqIndex + && annotationIndex == o.annotationIndex); + // System.out.println(obj + (b ? "= " : "!= ") + this); + return b; + } + + /** + * A simple hashCode that ensures that instances that satisfy equals() have + * the same hashCode + */ + @Override + public int hashCode() + { + return column + seqIndex + annotationIndex; + } + + /** + * toString method for debug output purposes only + */ + @Override + public String toString() + { + return String.format("c%d:s%d:a%d", column, seqIndex, + annotationIndex); + } + } + private static final int MAX_TOOLTIP_LENGTH = 300; public SeqCanvas seqCanvas; @@ -83,18 +164,13 @@ public class SeqPanel extends JPanel public AlignmentPanel ap; /* - * last column position for mouseMoved event + * last position for mouseMoved event */ - private int lastMouseColumn; + private MousePos lastMousePosition; - /* - * last sequence offset for mouseMoved event - */ - private int lastMouseSeq; + protected int editLastRes; - protected int lastres; - - protected int startseq; + protected int editStartSeq; protected AlignViewport av; @@ -131,8 +207,6 @@ public class SeqPanel extends JPanel StringBuffer keyboardNo2; - java.net.URL linkImageURL; - private final SequenceAnnotationReport seqARep; StringBuilder tooltipText = new StringBuilder(); @@ -153,8 +227,7 @@ public class SeqPanel extends JPanel */ public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { - linkImageURL = getClass().getResource("/images/link.gif"); - seqARep = new SequenceAnnotationReport(linkImageURL.toString()); + seqARep = new SequenceAnnotationReport(true); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -176,9 +249,6 @@ public class SeqPanel extends JPanel ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } - - lastMouseColumn = -1; - lastMouseSeq = -1; } int startWrapBlock = -1; @@ -186,6 +256,73 @@ public class SeqPanel extends JPanel int wrappedBlock = -1; /** + * Computes the column and sequence row (and possibly annotation row when in + * wrapped mode) for the given mouse position + * + * @param evt + * @return + */ + MousePos findMousePosition(MouseEvent evt) + { + int col = findColumn(evt); + int seqIndex = -1; + int annIndex = -1; + int y = evt.getY(); + + int charHeight = av.getCharHeight(); + int alignmentHeight = av.getAlignment().getHeight(); + if (av.getWrapAlignment()) + { + seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(), + seqCanvas.getHeight()); + + /* + * yPos modulo height of repeating width + */ + int yOffsetPx = y % seqCanvas.wrappedRepeatHeightPx; + + /* + * height of sequences plus space / scale above, + * plus gap between sequences and annotations + */ + int alignmentHeightPixels = seqCanvas.wrappedSpaceAboveAlignment + + alignmentHeight * charHeight + + SeqCanvas.SEQS_ANNOTATION_GAP; + if (yOffsetPx >= alignmentHeightPixels) + { + /* + * mouse is over annotations; find annotation index, also set + * last sequence above (for backwards compatible behaviour) + */ + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + int rowOffsetPx = yOffsetPx - alignmentHeightPixels; + annIndex = AnnotationPanel.getRowIndex(rowOffsetPx, anns); + seqIndex = alignmentHeight - 1; + } + else + { + /* + * mouse is over sequence (or the space above sequences) + */ + yOffsetPx -= seqCanvas.wrappedSpaceAboveAlignment; + if (yOffsetPx >= 0) + { + seqIndex = Math.min(yOffsetPx / charHeight, alignmentHeight - 1); + } + } + } + else + { + ViewportRanges ranges = av.getRanges(); + seqIndex = Math.min((y / charHeight) + ranges.getStartSeq(), + alignmentHeight - 1); + seqIndex = Math.min(seqIndex, ranges.getEndSeq()); + } + + return new MousePos(col, seqIndex, annIndex); + } + /** * Returns the aligned sequence position (base 0) at the mouse position, or * the closest visible one * @@ -197,10 +334,11 @@ public class SeqPanel extends JPanel int res = 0; int x = evt.getX(); - int startRes = av.getRanges().getStartRes(); + final int startRes = av.getRanges().getStartRes(); + final int charWidth = av.getCharWidth(); + if (av.getWrapAlignment()) { - int hgap = av.getCharHeight(); if (av.getScaleAboveWrapped()) { @@ -212,35 +350,40 @@ public class SeqPanel extends JPanel int y = evt.getY(); y = Math.max(0, y - hgap); - x = Math.max(0, x - seqCanvas.getLabelWidthWest()); + x -= seqCanvas.getLabelWidthWest(); + if (x < 0) + { + // mouse is over left scale + return -1; + } int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) { return 0; } + if (x >= cwidth * charWidth) + { + // mouse is over right scale + return -1; + } wrappedBlock = y / cHeight; wrappedBlock += startRes / cwidth; // allow for wrapped view scrolled right (possible from Overview) int startOffset = startRes % cwidth; res = wrappedBlock * cwidth + startOffset - + +Math.min(cwidth - 1, x / av.getCharWidth()); + + Math.min(cwidth - 1, x / charWidth); } else { - if (x > seqCanvas.getX() + seqCanvas.getWidth()) - { - // make sure we calculate relative to visible alignment, rather than - // right-hand gutter - x = seqCanvas.getX() + seqCanvas.getWidth(); - } - res = (x / av.getCharWidth()) + startRes; - if (res > av.getRanges().getEndRes()) - { - // moused off right - res = av.getRanges().getEndRes(); - } + /* + * make sure we calculate relative to visible alignment, + * rather than right-hand gutter + */ + x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth()); + res = (x / charWidth) + startRes; + res = Math.min(res, av.getRanges().getEndRes()); } if (av.hasHiddenColumns()) @@ -250,38 +393,6 @@ public class SeqPanel extends JPanel } return res; - - } - - int findSeq(MouseEvent evt) - { - int seq = 0; - int y = evt.getY(); - - if (av.getWrapAlignment()) - { - int hgap = av.getCharHeight(); - if (av.getScaleAboveWrapped()) - { - hgap += av.getCharHeight(); - } - - int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap + seqCanvas.getAnnotationHeight(); - - y -= hgap; - - seq = Math.min((y % cHeight) / av.getCharHeight(), - av.getAlignment().getHeight() - 1); - } - else - { - seq = Math.min( - (y / av.getCharHeight()) + av.getRanges().getStartSeq(), - av.getAlignment().getHeight() - 1); - } - - return seq; } /** @@ -303,8 +414,8 @@ public class SeqPanel extends JPanel /* * Tidy up come what may... */ - startseq = -1; - lastres = -1; + editStartSeq = -1; + editLastRes = -1; editingSeqs = false; groupEditing = false; keyboardNo1 = null; @@ -532,8 +643,8 @@ public class SeqPanel extends JPanel void insertGapAtCursor(boolean group) { groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX; editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -541,8 +652,8 @@ public class SeqPanel extends JPanel void deleteGapAtCursor(boolean group) { groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX + getKeyboardNo1(); + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX + getKeyboardNo1(); editSequence(false, false, seqCanvas.cursorX); endEditing(); } @@ -551,8 +662,8 @@ public class SeqPanel extends JPanel { // TODO not called - delete? groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX; editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -617,24 +728,31 @@ public class SeqPanel extends JPanel @Override public void mouseReleased(MouseEvent evt) { + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } + boolean didDrag = mouseDragging; // did we come here after a drag mouseDragging = false; mouseWheelPressed = false; if (evt.isPopupTrigger()) // Windows: mouseReleased { - showPopupMenu(evt); + showPopupMenu(evt, pos); evt.consume(); return; } - if (!editingSeqs) + if (editingSeqs) + { + endEditing(); + } + else { doMouseReleasedDefineMode(evt, didDrag); - return; } - - endEditing(); } /** @@ -647,6 +765,11 @@ public class SeqPanel extends JPanel public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } if (SwingUtilities.isMiddleMouseButton(evt)) { @@ -665,28 +788,23 @@ public class SeqPanel extends JPanel } else { - doMousePressedDefineMode(evt); + doMousePressedDefineMode(evt, pos); return; } - int seq = findSeq(evt); - int res = findColumn(evt); - - if (seq < 0 || res < 0) - { - return; - } + int seq = pos.seqIndex; + int res = pos.column; if ((seq < av.getAlignment().getHeight()) && (res < av.getAlignment().getSequenceAt(seq).getLength())) { - startseq = seq; - lastres = res; + editStartSeq = seq; + editLastRes = res; } else { - startseq = -1; - lastres = -1; + editStartSeq = -1; + editLastRes = -1; } return; @@ -714,11 +832,11 @@ public class SeqPanel extends JPanel * the start of the highlighted region. */ @Override - public void highlightSequence(SearchResultsI results) + public String highlightSequence(SearchResultsI results) { if (results == null || results.equals(lastSearchResults)) { - return; + return null; } lastSearchResults = results; @@ -731,7 +849,7 @@ public class SeqPanel extends JPanel // over residue to change abruptly, causing highlighted residue in panel 2 // to change, causing a scroll in panel 1 etc) ap.setToScrollComplementPanel(false); - wasScrolled = ap.scrollToPosition(results, false); + wasScrolled = ap.scrollToPosition(results); if (wasScrolled) { seqCanvas.revalidate(); @@ -744,6 +862,79 @@ public class SeqPanel extends JPanel { setStatusMessage(results); } + // JAL-3303 feature suppressed for now pending review + return null; // results.isEmpty() ? null : getHighlightInfo(results); + } + + /** + * temporary hack: answers a message suitable to show on structure hover + * label. This is normally null. It is a peptide variation description if + * + * in which case the answer is of the format (e.g.) "p.Glu388Asp" + * + * @param results + * @return + */ + private String getHighlightInfo(SearchResultsI results) + { + /* + * ideally, just find mapped CDS (as we don't care about render style here); + * for now, go via split frame complement's FeatureRenderer + */ + AlignViewportI complement = ap.getAlignViewport().getCodingComplement(); + if (complement == null) + { + return null; + } + AlignFrame af = Desktop.getAlignFrameFor(complement); + FeatureRendererModel fr2 = af.getFeatureRenderer(); + + List matches = results.getResults(); + int j = matches.size(); + List infos = new ArrayList<>(); + for (int i = 0; i < j; i++) + { + SearchResultMatchI match = matches.get(i); + int pos = match.getStart(); + if (pos == match.getEnd()) + { + SequenceI seq = match.getSequence(); + SequenceI ds = seq.getDatasetSequence() == null ? seq + : seq.getDatasetSequence(); + MappedFeatures mf = fr2 + .findComplementFeaturesAtResidue(ds, pos); + if (mf != null) + { + for (SequenceFeature sf : mf.features) + { + String pv = mf.findProteinVariants(sf); + if (pv.length() > 0 && !infos.contains(pv)) + { + infos.add(pv); + } + } + } + } + } + + if (infos.isEmpty()) + { + return null; + } + StringBuilder sb = new StringBuilder(); + for (String info : infos) + { + if (sb.length() > 0) + { + sb.append("|"); + } + sb.append(info); + } + return sb.toString(); } @Override @@ -777,23 +968,32 @@ public class SeqPanel extends JPanel mouseDragged(evt); } - final int column = findColumn(evt); - final int seq = findSeq(evt); + final MousePos mousePos = findMousePosition(evt); + if (mousePos.equals(lastMousePosition)) + { + /* + * just a pixel move without change of 'cell' + */ + return; + } + lastMousePosition = mousePos; - if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + if (mousePos.isOverAnnotation()) { - lastMouseSeq = -1; + mouseMovedOverAnnotation(mousePos); return; } - if (column == lastMouseColumn && seq == lastMouseSeq) + final int seq = mousePos.seqIndex; + + final int column = mousePos.column; + if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { - /* - * just a pixel move without change of residue - */ + lastMousePosition = null; + setToolTipText(null); + lastTooltip = null; + ap.alignFrame.setStatus(""); return; } - lastMouseColumn = column; - lastMouseSeq = seq; SequenceI sequence = av.getAlignment().getSequenceAt(seq); @@ -841,25 +1041,56 @@ public class SeqPanel extends JPanel * add features that straddle the gap (pos may be the residue before or * after the gap) */ + int unshownFeatures = 0; if (av.isShowSequenceFeatures()) { List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - seqARep.appendFeatures(tooltipText, pos, features, - this.ap.getSeqPanel().seqCanvas.fr); + unshownFeatures = seqARep.appendFeatures(tooltipText, pos, + features, this.ap.getSeqPanel().seqCanvas.fr, + MAX_TOOLTIP_LENGTH); + + /* + * add features in CDS/protein complement at the corresponding + * position if configured to do so + */ + if (av.isShowComplementFeatures()) + { + if (!Comparison.isGap(sequence.getCharAt(column))) + { + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + AlignFrame af = Desktop.getAlignFrameFor(complement); + FeatureRendererModel fr2 = af.getFeatureRenderer(); + MappedFeatures mf = fr2.findComplementFeaturesAtResidue(sequence, + pos); + if (mf != null) + { + unshownFeatures = seqARep.appendFeatures(tooltipText, + pos, mf, fr2, MAX_TOOLTIP_LENGTH); + } + } + } } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 6) // "" { setToolTipText(null); lastTooltip = null; } else { - if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant + if (tooltipText.length() > MAX_TOOLTIP_LENGTH) { tooltipText.setLength(MAX_TOOLTIP_LENGTH); tooltipText.append("..."); } + if (unshownFeatures > 0) + { + tooltipText.append("
").append("... ").append("") + .append(MessageManager.formatMessage( + "label.features_not_shown", unshownFeatures)) + .append(""); + } String textString = tooltipText.toString(); if (lastTooltip == null || !lastTooltip.equals(textString)) { @@ -871,6 +1102,35 @@ public class SeqPanel extends JPanel } } + /** + * When the view is in wrapped mode, and the mouse is over an annotation row, + * shows the corresponding tooltip and status message (if any) + * + * @param pos + * @param column + */ + protected void mouseMovedOverAnnotation(MousePos pos) + { + final int column = pos.column; + final int rowIndex = pos.annotationIndex; + + if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation() + || rowIndex < 0) + { + return; + } + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + + String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column, + anns); + setToolTipText(tooltip); + lastTooltip = tooltip; + + String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column, + anns[rowIndex]); + ap.alignFrame.setStatus(msg); + } + private Point lastp = null; /* @@ -881,20 +1141,26 @@ public class SeqPanel extends JPanel @Override public Point getToolTipLocation(MouseEvent event) { - int x = event.getX(), w = getWidth(); - int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too - // close to edge + if (tooltipText == null || tooltipText.length() <= 6) + { + lastp = null; + return null; + } + + int x = event.getX(); + int w = getWidth(); + // switch sides when tooltip is too close to edge + int wdth = (w - x < 200) ? -(w / 2) : 5; Point p = lastp; if (!event.isShiftDown() || p == null) { - p = (tooltipText != null && tooltipText.length() > 6) - ? new Point(event.getX() + wdth, event.getY() - 20) - : null; + p = new Point(event.getX() + wdth, event.getY() - 20); + lastp = p; } /* - * TODO: try to modify position region is not obcured by tooltip + * TODO: try to set position so region is not obscured by tooltip */ - return lastp = p; + return p; } String lastTooltip; @@ -935,7 +1201,7 @@ public class SeqPanel extends JPanel { char sequenceChar = sequence.getCharAt(column); int pos = sequence.findPosition(column); - setStatusMessage(sequence, seqIndex, sequenceChar, pos); + setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos); return pos; } @@ -951,7 +1217,7 @@ public class SeqPanel extends JPanel * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2) * * - * @param sequence + * @param seqName * @param seqIndex * sequence position in the alignment (1..) * @param sequenceChar @@ -959,7 +1225,7 @@ public class SeqPanel extends JPanel * @param residuePos * the sequence residue position (if not over a gap) */ - protected void setStatusMessage(SequenceI sequence, int seqIndex, + protected void setStatusMessage(String seqName, int seqIndex, char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); @@ -969,7 +1235,7 @@ public class SeqPanel extends JPanel */ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") - .append(sequence.getName()); + .append(seqName); String residue = null; @@ -997,7 +1263,7 @@ public class SeqPanel extends JPanel text.append(" (").append(Integer.toString(residuePos)).append(")"); } - ap.alignFrame.statusBar.setText(text.toString()); + ap.alignFrame.setStatus(text.toString()); } /** @@ -1014,7 +1280,8 @@ public class SeqPanel extends JPanel { return; } - SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + SequenceI alignedSeq = al.getSequenceAt(sequenceIndex); + SequenceI ds = alignedSeq.getDatasetSequence(); for (SearchResultMatchI m : results.getResults()) { SequenceI seq = m.getSequence(); @@ -1026,8 +1293,8 @@ public class SeqPanel extends JPanel if (seq == ds) { int start = m.getStart(); - setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), - start); + setStatusMessage(alignedSeq.getName(), sequenceIndex, + seq.getCharAt(start - 1), start); return; } } @@ -1039,6 +1306,12 @@ public class SeqPanel extends JPanel @Override public void mouseDragged(MouseEvent evt) { + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.column == -1) + { + return; + } + if (mouseWheelPressed) { boolean inSplitFrame = ap.av.getCodingComplement() != null; @@ -1134,23 +1407,23 @@ public class SeqPanel extends JPanel if (!editingSeqs) { - doMouseDraggedDefineMode(evt); + dragStretchGroup(evt); return; } - int res = findColumn(evt); + int res = pos.column; if (res < 0) { res = 0; } - if ((lastres == -1) || (lastres == res)) + if ((editLastRes == -1) || (editLastRes == res)) { return; } - if ((res < av.getAlignment().getWidth()) && (res < lastres)) + if ((res < av.getAlignment().getWidth()) && (res < editLastRes)) { // dragLeft, delete gap editSequence(false, false, res); @@ -1161,22 +1434,46 @@ public class SeqPanel extends JPanel } mouseDragging = true; - if ((scrollThread != null) && (scrollThread.isRunning())) + if (scrollThread != null) { - scrollThread.setEvent(evt); + scrollThread.setMousePosition(evt.getPoint()); } } - // TODO: Make it more clever than many booleans + /** + * Edits the sequence to insert or delete one or more gaps, in response to a + * mouse drag or cursor mode command. The number of inserts/deletes may be + * specified with the cursor command, or else depends on the mouse event + * (normally one column, but potentially more for a fast mouse drag). + *

+ * Delete gaps is limited to the number of gaps left of the cursor position + * (mouse drag), or at or right of the cursor position (cursor mode). + *

+ * In group editing mode (Ctrl or Cmd down), the edit acts on all sequences in + * the current selection group. + *

+ * In locked editing mode (with a selection group present), inserts/deletions + * within the selection group are limited to its boundaries (and edits outside + * the group stop at its border). + * + * @param insertGap + * true to insert gaps, false to delete gaps + * @param editSeq + * (unused parameter) + * @param startres + * the column at which to perform the action; the number of columns + * affected depends on this.editLastRes (cursor column + * position) + */ synchronized void editSequence(boolean insertGap, boolean editSeq, - int startres) + final int startres) { int fixedLeft = -1; int fixedRight = -1; boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); - SequenceI seq = av.getAlignment().getSequenceAt(startseq); + final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq); // No group, but the sequence may represent a group if (!groupEditing && av.hasHiddenRows()) @@ -1188,34 +1485,60 @@ public class SeqPanel extends JPanel } } + StringBuilder message = new StringBuilder(64); // for status bar + + /* + * make a name for the edit action, for + * status bar message and Undo/Redo menu + */ + String label = null; + if (groupEditing) + { + message.append("Edit group:"); + label = MessageManager.getString("action.edit_group"); + } + else + { + message.append("Edit sequence: " + seq.getName()); + label = seq.getName(); + if (label.length() > 10) + { + label = label.substring(0, 10); + } + label = MessageManager.formatMessage("label.edit_params", + new String[] + { label }); + } + /* * initialise the edit command if there is not * already one being extended */ if (editCommand == null) { - if (groupEditing) - { - editCommand = new EditCommand( - MessageManager.getString("action.edit_group")); - } - else - { - String label = seq.getName(); - if (label.length() > 10) - { - label = label.substring(0, 10); - } - editCommand = new EditCommand(MessageManager - .formatMessage("label.edit_params", new String[] - { label })); - } + editCommand = new EditCommand(label); } + if (insertGap) + { + message.append(" insert "); + } + else + { + message.append(" delete "); + } - // Are we editing within a selection group? - if (groupEditing || (sg != null - && sg.getSequences(av.getHiddenRepSequences()).contains(seq))) + message.append(Math.abs(startres - editLastRes) + " gaps."); + ap.alignFrame.setStatus(message.toString()); + + /* + * is there a selection group containing the sequence being edited? + * if so the boundary of the group is the limit of the edit + * (but the edit may be inside or outside the selection group) + */ + boolean inSelectionGroup = sg != null + && sg.getSequences(av.getHiddenRepSequences()).contains(seq); + if (groupEditing || inSelectionGroup) { fixedColumns = true; @@ -1234,10 +1557,10 @@ public class SeqPanel extends JPanel fixedLeft = sg.getStartRes(); fixedRight = sg.getEndRes(); - if ((startres < fixedLeft && lastres >= fixedLeft) - || (startres >= fixedLeft && lastres < fixedLeft) - || (startres > fixedRight && lastres <= fixedRight) - || (startres <= fixedRight && lastres > fixedRight)) + if ((startres < fixedLeft && editLastRes >= fixedLeft) + || (startres >= fixedLeft && editLastRes < fixedLeft) + || (startres > fixedRight && editLastRes <= fixedRight) + || (startres <= fixedRight && editLastRes > fixedRight)) { endEditing(); return; @@ -1263,8 +1586,8 @@ public class SeqPanel extends JPanel int y2 = av.getAlignment().getHiddenColumns() .getNextHiddenBoundary(false, startres); - if ((insertGap && startres > y1 && lastres < y1) - || (!insertGap && startres < y2 && lastres > y2)) + if ((insertGap && startres > y1 && editLastRes < y1) + || (!insertGap && startres < y2 && editLastRes > y2)) { endEditing(); return; @@ -1285,9 +1608,56 @@ public class SeqPanel extends JPanel } } + boolean success = doEditSequence(insertGap, editSeq, startres, + fixedRight, fixedColumns, sg); + + /* + * report what actually happened (might be less than + * what was requested), by inspecting the edit commands added + */ + String msg = getEditStatusMessage(editCommand); + ap.alignFrame.setStatus(msg == null ? " " : msg); + if (!success) + { + endEditing(); + } + + editLastRes = startres; + seqCanvas.repaint(); + } + + /** + * A helper method that performs the requested editing to insert or delete + * gaps (if possible). Answers true if the edit was successful, false if could + * only be performed in part or not at all. Failure may occur in 'locked edit' + * mode, when an insertion requires a matching gapped position (or column) to + * delete, and deletion requires an adjacent gapped position (or column) to + * remove. + * + * @param insertGap + * true if inserting gap(s), false if deleting + * @param editSeq + * (unused parameter, currently always false) + * @param startres + * the column at which to perform the edit + * @param fixedRight + * fixed right boundary column of a locked edit (within or to the + * left of a selection group) + * @param fixedColumns + * true if this is a locked edit + * @param sg + * the sequence group (if group edit is being performed) + * @return + */ + protected boolean doEditSequence(final boolean insertGap, + final boolean editSeq, final int startres, int fixedRight, + final boolean fixedColumns, final SequenceGroup sg) + { + final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq); + SequenceI[] seqs = new SequenceI[] { seq }; + if (groupEditing) { - ap.alignFrame.statusBar.setText(" "); // defer this as difficult! List vseqs = sg.getSequences(av.getHiddenRepSequences()); int g, groupSize = vseqs.size(); SequenceI[] groupSeqs = new SequenceI[groupSize]; @@ -1304,7 +1674,8 @@ public class SeqPanel extends JPanel if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight && sg.getEndRes() == av.getAlignment().getWidth() - 1) { - sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); + sg.setEndRes( + av.getAlignment().getWidth() + startres - editLastRes); fixedRight = sg.getEndRes(); } @@ -1312,15 +1683,16 @@ public class SeqPanel extends JPanel // Find the next gap before the end // of the visible region boundary boolean blank = false; - for (; fixedRight > lastres; fixedRight--) + for (; fixedRight > editLastRes; fixedRight--) { blank = true; for (g = 0; g < groupSize; g++) { - for (int j = 0; j < startres - lastres; j++) + for (int j = 0; j < startres - editLastRes; j++) { - if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) + if (!Comparison + .isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -1337,12 +1709,11 @@ public class SeqPanel extends JPanel { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av.getAlignment() - .getHiddenColumns() - .getNextHiddenBoundary(false, startres))) + if ((av.hasHiddenColumns() + && startres < av.getAlignment().getHiddenColumns() + .getNextHiddenBoundary(false, startres))) { - endEditing(); - return; + return false; } int alWidth = av.getAlignment().getWidth(); @@ -1357,13 +1728,12 @@ public class SeqPanel extends JPanel } // We can still insert gaps if the selectionGroup // contains all the sequences - sg.setEndRes(sg.getEndRes() + startres - lastres); - fixedRight = alWidth + startres - lastres; + sg.setEndRes(sg.getEndRes() + startres - editLastRes); + fixedRight = alWidth + startres - editLastRes; } else { - endEditing(); - return; + return false; } } } @@ -1376,7 +1746,7 @@ public class SeqPanel extends JPanel for (g = 0; g < groupSize; g++) { - for (int j = startres; j < lastres; j++) + for (int j = startres; j < editLastRes; j++) { if (groupSeqs[g].getLength() <= j) { @@ -1386,8 +1756,7 @@ public class SeqPanel extends JPanel if (!Comparison.isGap(groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid - endEditing(); - return; + return false; } } } @@ -1398,15 +1767,15 @@ public class SeqPanel extends JPanel // dragging to the right if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, groupSeqs, fixedRight); + insertGap(j, groupSeqs, fixedRight); } } else { appendEdit(Action.INSERT_GAP, groupSeqs, startres, - startres - lastres); + startres - editLastRes, false); } } else @@ -1414,7 +1783,7 @@ public class SeqPanel extends JPanel // dragging to the left if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j > startres; j--) + for (int j = editLastRes; j > startres; j--) { deleteChar(startres, groupSeqs, fixedRight); } @@ -1422,37 +1791,36 @@ public class SeqPanel extends JPanel else { appendEdit(Action.DELETE_GAP, groupSeqs, startres, - lastres - startres); + editLastRes - startres, false); } - } } else - // ///Editing a single sequence/////////// { - if (fixedRight == -1) - { - String msg = getEditStatusMessage(insertGap, seq.getName()); - ap.alignFrame.statusBar.setText(msg); - } - else - { - ap.alignFrame.statusBar.setText(" "); - } + /* + * editing a single sequence + */ if (insertGap) { // dragging to the right if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, new SequenceI[] { seq }, fixedRight); + if (!insertGap(j, seqs, fixedRight)) + { + /* + * e.g. cursor mode command specified + * more inserts than are possible + */ + return false; + } } } else { - appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, - startres - lastres); + appendEdit(Action.INSERT_GAP, seqs, editLastRes, + startres - editLastRes, false); } } else @@ -1462,21 +1830,20 @@ public class SeqPanel extends JPanel // dragging to the left if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j > startres; j--) + for (int j = editLastRes; j > startres; j--) { if (!Comparison.isGap(seq.getCharAt(startres))) { - endEditing(); - break; + return false; } - deleteChar(startres, new SequenceI[] { seq }, fixedRight); + deleteChar(startres, seqs, fixedRight); } } else { // could be a keyboard edit trying to delete none gaps int max = 0; - for (int m = startres; m < lastres; m++) + for (int m = startres; m < editLastRes; m++) { if (!Comparison.isGap(seq.getCharAt(m))) { @@ -1484,11 +1851,9 @@ public class SeqPanel extends JPanel } max++; } - if (max > 0) { - appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, - startres, max); + appendEdit(Action.DELETE_GAP, seqs, startres, max, false); } } } @@ -1496,75 +1861,82 @@ public class SeqPanel extends JPanel {// insertGap==false AND editSeq==TRUE; if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, new SequenceI[] { seq }, fixedRight); + insertGap(j, seqs, fixedRight); } } else { - appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, - startres - lastres); + appendEdit(Action.INSERT_NUC, seqs, editLastRes, + startres - editLastRes, false); } } } } - lastres = startres; - seqCanvas.repaint(); + return true; } /** * Constructs an informative status bar message while dragging to insert or - * delete gaps + * delete gaps. Answers null if inserts and deletes cancel out. * - * @param insert - * @param seqName + * @param editCommand + * a command containing the list of individual edits * @return */ - protected String getEditStatusMessage(boolean insert, String seqName) + protected static String getEditStatusMessage(EditCommand editCommand) { + if (editCommand == null) + { + return null; + } + /* - * add any inserts, and subtract any deletes, so far + * add any inserts, and subtract any deletes, + * not counting those auto-inserted when doing a 'locked edit' + * (so only counting edits 'under the cursor') */ int count = 0; for (Edit cmd : editCommand.getEdits()) { - count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber() - : -cmd.getNumber(); + if (!cmd.isSystemGenerated()) + { + count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber() + : -cmd.getNumber(); + } } - /* - * add the current action - */ - count += insert ? 1 : -1; - if (count == 0) { /* * inserts and deletes cancel out */ - return " "; - } - StringBuilder message = new StringBuilder(64); - if (groupEditing) - { - message.append("Edit group:"); - } - else - { - message.append("Edit sequence: ").append(seqName); + return null; } - message.append(count > 0 ? " insert " : " delete "); + String msgKey = count > 1 ? "label.insert_gaps" + : (count == 1 ? "label.insert_gap" + : (count == -1 ? "label.delete_gap" + : "label.delete_gaps")); count = Math.abs(count); - message.append(String.valueOf(count)); - message.append(count > 1 ? " gaps" : " gap"); - String msg = message.toString(); - return msg; + + return MessageManager.formatMessage(msgKey, String.valueOf(count)); } - void insertChar(int j, SequenceI[] seq, int fixedColumn) + /** + * Inserts one gap at column j, deleting the right-most gapped column up to + * (and including) fixedColumn. Returns true if the edit is successful, false + * if no blank column is available to allow the insertion to be balanced by a + * deletion. + * + * @param j + * @param seq + * @param fixedColumn + * @return + */ + boolean insertGap(int j, SequenceI[] seq, int fixedColumn) { int blankColumn = fixedColumn; for (int s = 0; s < seq.length; s++) @@ -1585,47 +1957,60 @@ public class SeqPanel extends JPanel { blankColumn = fixedColumn; endEditing(); - return; + return false; } } - appendEdit(Action.DELETE_GAP, seq, blankColumn, 1); + appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, true); - appendEdit(Action.INSERT_GAP, seq, j, 1); + appendEdit(Action.INSERT_GAP, seq, j, 1, false); + return true; } /** - * Helper method to add and perform one edit action. + * Helper method to add and perform one edit action * * @param action * @param seq * @param pos * @param count + * @param systemGenerated + * true if the edit is a 'balancing' delete (or insert) to match a + * user's insert (or delete) in a locked editing region */ protected void appendEdit(Action action, SequenceI[] seq, int pos, - int count) + int count, boolean systemGenerated) { final Edit edit = new EditCommand().new Edit(action, seq, pos, count, av.getAlignment().getGapCharacter()); + edit.setSystemGenerated(systemGenerated); editCommand.appendEdit(edit, av.getAlignment(), true, null); } - void deleteChar(int j, SequenceI[] seq, int fixedColumn) + /** + * Deletes the character at column j, and inserts a gap at fixedColumn, in + * each of the given sequences. The caller should ensure that all sequences + * are gapped in column j. + * + * @param j + * @param seqs + * @param fixedColumn + */ + void deleteChar(int j, SequenceI[] seqs, int fixedColumn) { + appendEdit(Action.DELETE_GAP, seqs, j, 1, false); - appendEdit(Action.DELETE_GAP, seq, j, 1); - - appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1); + appendEdit(Action.INSERT_GAP, seqs, fixedColumn, 1, true); } /** - * DOCUMENT ME! + * On reentering the panel, stops any scrolling that was started on dragging + * out of the panel * * @param e - * DOCUMENT ME! */ @Override public void mouseEntered(MouseEvent e) @@ -1634,23 +2019,20 @@ public class SeqPanel extends JPanel { oldSeq = 0; } - - if ((scrollThread != null) && (scrollThread.isRunning())) - { - scrollThread.stopScrolling(); - scrollThread = null; - } + stopScrolling(); } /** - * DOCUMENT ME! + * On leaving the panel, if the mouse is being dragged, starts a thread to + * scroll it until the mouse is released (in unwrapped mode only) * * @param e - * DOCUMENT ME! */ @Override public void mouseExited(MouseEvent e) { + lastMousePosition = null; + ap.alignFrame.setStatus(" "); if (av.getWrapAlignment()) { return; @@ -1671,8 +2053,13 @@ public class SeqPanel extends JPanel public void mouseClicked(MouseEvent evt) { SequenceGroup sg = null; - SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); - if (evt.getClickCount() > 1) + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } + + if (evt.getClickCount() > 1 && av.isShowSequenceFeatures()) { sg = av.getSelectionGroup(); if (sg != null && sg.getSize() == 1 @@ -1681,12 +2068,13 @@ public class SeqPanel extends JPanel av.setSelectionGroup(null); } - int column = findColumn(evt); + int column = pos.column; /* * find features at the position (if not gapped), or straddling * the position (if at a gap) */ + SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex); List features = seqCanvas.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); @@ -1753,32 +2141,22 @@ public class SeqPanel extends JPanel /** * DOCUMENT ME! * - * @param evt + * @param pos * DOCUMENT ME! */ - public void doMousePressedDefineMode(MouseEvent evt) + protected void doMousePressedDefineMode(MouseEvent evt, MousePos pos) { - final int res = findColumn(evt); - final int seq = findSeq(evt); - oldSeq = seq; - updateOverviewAndStructs = false; - - startWrapBlock = wrappedBlock; - - if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString( - "label.cannot_edit_annotations_in_wrapped_view"), - MessageManager.getString("label.wrapped_view_no_edit"), - JvOptionPane.WARNING_MESSAGE); return; } - if (seq < 0 || res < 0) - { - return; - } + final int res = pos.column; + final int seq = pos.seqIndex; + oldSeq = seq; + updateOverviewAndStructs = false; + + startWrapBlock = wrappedBlock; SequenceI sequence = av.getAlignment().getSequenceAt(seq); @@ -1802,7 +2180,7 @@ public class SeqPanel extends JPanel if (evt.isPopupTrigger()) // Mac: mousePressed { - showPopupMenu(evt); + showPopupMenu(evt, pos); return; } @@ -1818,8 +2196,8 @@ public class SeqPanel extends JPanel if (av.cursorMode) { - seqCanvas.cursorX = findColumn(evt); - seqCanvas.cursorY = findSeq(evt); + seqCanvas.cursorX = res; + seqCanvas.cursorY = seq; seqCanvas.repaint(); return; } @@ -1877,21 +2255,20 @@ public class SeqPanel extends JPanel /** * Build and show a pop-up menu at the right-click mouse position - * + * * @param evt - * @param res - * @param sequences + * @param pos */ - void showPopupMenu(MouseEvent evt) + void showPopupMenu(MouseEvent evt, MousePos pos) { - final int column = findColumn(evt); - final int seq = findSeq(evt); + final int column = pos.column; + final int seq = pos.seqIndex; SequenceI sequence = av.getAlignment().getSequenceAt(seq); - List features = ap.getFeatureRenderer() - .findFeaturesAtColumn(sequence, column + 1); - - PopupMenu pop = new PopupMenu(ap, null, features); - pop.show(this, evt.getX(), evt.getY()); + if (sequence != null) + { + PopupMenu pop = new PopupMenu(ap, sequence, column); + pop.show(this, evt.getX(), evt.getY()); + } } /** @@ -1903,7 +2280,8 @@ public class SeqPanel extends JPanel * true if this event is happening after a mouse drag (rather than a * mouse down) */ - public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag) + protected void doMouseReleasedDefineMode(MouseEvent evt, + boolean afterDrag) { if (stretchGroup == null) { @@ -1919,8 +2297,11 @@ public class SeqPanel extends JPanel && afterDrag; if (stretchGroup.cs != null) { - stretchGroup.cs.alignmentChanged(stretchGroup, - av.getHiddenRepSequences()); + if (afterDrag) + { + stretchGroup.cs.alignmentChanged(stretchGroup, + av.getHiddenRepSequences()); + } ResidueShaderI groupColourScheme = stretchGroup .getGroupColourScheme(); @@ -1946,31 +2327,34 @@ public class SeqPanel extends JPanel } /** - * DOCUMENT ME! + * Resizes the borders of a selection group depending on the direction of + * mouse drag * * @param evt - * DOCUMENT ME! */ - public void doMouseDraggedDefineMode(MouseEvent evt) + protected void dragStretchGroup(MouseEvent evt) { - int res = findColumn(evt); - int y = findSeq(evt); - - if (wrappedBlock != startWrapBlock) + if (stretchGroup == null) { return; } - if (stretchGroup == null) + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.column == -1 || pos.seqIndex == -1) { return; } - if (res >= av.getAlignment().getWidth()) + int res = pos.column; + int y = pos.seqIndex; + + if (wrappedBlock != startWrapBlock) { - res = av.getAlignment().getWidth() - 1; + return; } + res = Math.min(res, av.getAlignment().getWidth()-1); + if (stretchGroup.getEndRes() == res) { // Edit end res position of selected group @@ -2055,9 +2439,9 @@ public class SeqPanel extends JPanel mouseDragging = true; - if ((scrollThread != null) && (scrollThread.isRunning())) + if (scrollThread != null) { - scrollThread.setEvent(evt); + scrollThread.setMousePosition(evt.getPoint()); } /* @@ -2087,83 +2471,120 @@ public class SeqPanel extends JPanel ap.alignFrame.setStatus(status.toString()); } - void scrollCanvas(MouseEvent evt) + /** + * Stops the scroll thread if it is running + */ + void stopScrolling() { - if (evt == null) + if (scrollThread != null) { - if ((scrollThread != null) && (scrollThread.isRunning())) - { - scrollThread.stopScrolling(); - scrollThread = null; - } - mouseDragging = false; + scrollThread.stopScrolling(); + scrollThread = null; } - else - { - if (scrollThread == null) - { - scrollThread = new ScrollThread(); - } + mouseDragging = false; + } - mouseDragging = true; - scrollThread.setEvent(evt); + /** + * Starts a thread to scroll the alignment, towards a given mouse position + * outside the panel bounds + * + * @param mousePos + */ + void startScrolling(Point mousePos) + { + if (scrollThread == null) + { + scrollThread = new ScrollThread(); } + mouseDragging = true; + scrollThread.setMousePosition(mousePos); } - // this class allows scrolling off the bottom of the visible alignment + /** + * Performs scrolling of the visible alignment left, right, up or down + */ class ScrollThread extends Thread { - MouseEvent evt; + private Point mousePos; private volatile boolean threadRunning = true; + /** + * Constructor + */ public ScrollThread() { + setName("SeqPanel$ScrollThread"); start(); } - public void setEvent(MouseEvent e) + /** + * Sets the position of the mouse that determines the direction of the + * scroll to perform + * + * @param p + */ + public void setMousePosition(Point p) { - evt = e; + mousePos = p; } + /** + * Sets a flag that will cause the thread to exit + */ public void stopScrolling() { threadRunning = false; } - public boolean isRunning() - { - return threadRunning; - } - + /** + * Scrolls the alignment left or right, and/or up or down, depending on the + * last notified mouse position, until the limit of the alignment is + * reached, or a flag is set to stop the scroll + */ @Override public void run() { - while (threadRunning) + while (threadRunning && mouseDragging) { - if (evt != null) + if (mousePos != null) { - if (mouseDragging && (evt.getY() < 0) - && (av.getRanges().getStartSeq() > 0)) + boolean scrolled = false; + ViewportRanges ranges = SeqPanel.this.av.getRanges(); + + /* + * scroll up or down + */ + if (mousePos.y < 0) { - av.getRanges().scrollUp(true); + // mouse is above this panel - try scroll up + scrolled = ranges.scrollUp(true); } - - if (mouseDragging && (evt.getY() >= getHeight()) && (av - .getAlignment().getHeight() > av.getRanges().getEndSeq())) + else if (mousePos.y >= getHeight()) { - av.getRanges().scrollUp(false); + // mouse is below this panel - try scroll down + scrolled = ranges.scrollUp(false); } - if (mouseDragging && (evt.getX() < 0)) + /* + * scroll left or right + */ + if (mousePos.x < 0) + { + scrolled |= ranges.scrollRight(false); + } + else if (mousePos.x >= getWidth()) { - av.getRanges().scrollRight(false); + scrolled |= ranges.scrollRight(true); } - else if (mouseDragging && (evt.getX() >= getWidth())) + if (!scrolled) { - av.getRanges().scrollRight(true); + /* + * we have reached the limit of the visible alignment - quit + */ + threadRunning = false; + SeqPanel.this.ap.repaint(); } } @@ -2341,7 +2762,7 @@ public class SeqPanel extends JPanel * Map sequence selection */ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av); - av.setSelectionGroup(sg); + av.setSelectionGroup(sg != null && sg.getSize() > 0 ? sg : null); av.isSelectionGroupChanged(true); /* @@ -2353,7 +2774,7 @@ public class SeqPanel extends JPanel HiddenColumns hs = new HiddenColumns(); MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs); av.setColumnSelection(cs); - av.getAlignment().setHiddenColumns(hs); + boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs); // lastly, update any dependent dialogs if (ap.getCalculationDialog() != null) @@ -2361,7 +2782,11 @@ public class SeqPanel extends JPanel ap.getCalculationDialog().validateCalcTypes(); } - PaintRefresher.Refresh(this, av.getSequenceSetId()); + /* + * repaint alignment, and also Overview or Structure + * if hidden column selection has changed + */ + ap.paintAlignment(hiddenChanged, hiddenChanged); return true; }