X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=87e655bc53aa330c0f6ab8079ef28d79b5e33744;hb=7aa1e482163172b1ea16622eb2195fc8f2039951;hp=06568ca55946caa8d594a1297151e2fd825f9c48;hpb=4c6cd08af580ff73cfce39bec34ae4658a4b4b34;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 06568ca..87e655b 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -59,7 +59,6 @@ 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; @@ -73,15 +72,14 @@ import javax.swing.ToolTipManager; * @author $author$ * @version $Revision: 1.130 $ */ -public class SeqPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener, SequenceListener, - SelectionListener - +public class SeqPanel extends JPanel + implements MouseListener, MouseMotionListener, MouseWheelListener, + SequenceListener, SelectionListener { - /** DOCUMENT ME!! */ + private static final int MAX_TOOLTIP_LENGTH = 300; + public SeqCanvas seqCanvas; - /** DOCUMENT ME!! */ public AlignmentPanel ap; /* @@ -94,9 +92,9 @@ public class SeqPanel extends JPanel implements MouseListener, */ private int lastMouseSeq; - protected int lastres; + protected int editLastRes; - protected int startseq; + protected int editStartSeq; protected AlignViewport av; @@ -148,35 +146,33 @@ public class SeqPanel extends JPanel implements MouseListener, SearchResultsI lastSearchResults; /** - * Creates a new SeqPanel object. + * Creates a new SeqPanel object * - * @param avp - * DOCUMENT ME! - * @param p - * DOCUMENT ME! + * @param viewport + * @param alignPanel */ - public SeqPanel(AlignViewport av, AlignmentPanel ap) + public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { linkImageURL = getClass().getResource("/images/link.gif"); seqARep = new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = av; + this.av = viewport; setBackground(Color.white); - seqCanvas = new SeqCanvas(ap); + seqCanvas = new SeqCanvas(alignPanel); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); - this.ap = ap; + this.ap = alignPanel; - if (!av.isDataset()) + if (!viewport.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = av.getStructureSelectionManager(); + ssm = viewport.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@ -201,6 +197,7 @@ public class SeqPanel extends JPanel implements MouseListener, int res = 0; int x = evt.getX(); + int startRes = av.getRanges().getStartRes(); if (av.getWrapAlignment()) { @@ -214,8 +211,8 @@ public class SeqPanel extends JPanel implements MouseListener, + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); - y -= hgap; - x -= seqCanvas.LABEL_WEST; + y = Math.max(0, y - hgap); + x = Math.max(0, x - seqCanvas.getLabelWidthWest()); int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) @@ -224,10 +221,11 @@ public class SeqPanel extends JPanel implements MouseListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.getRanges().getStartRes() / cwidth; - - res = wrappedBlock * cwidth + x / av.getCharWidth(); - + 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()); } else { @@ -237,7 +235,7 @@ public class SeqPanel extends JPanel implements MouseListener, // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } - res = (x / av.getCharWidth()) + av.getRanges().getStartRes(); + res = (x / av.getCharWidth()) + startRes; if (res > av.getRanges().getEndRes()) { // moused off right @@ -248,7 +246,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.hasHiddenColumns()) { res = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(res); + .visibleToAbsoluteColumn(res); } return res; @@ -273,15 +271,14 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() - .getHeight() - 1); + 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); + seq = Math.min( + (y / av.getCharHeight()) + av.getRanges().getStartSeq(), + av.getAlignment().getHeight() - 1); } return seq; @@ -298,16 +295,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (editCommand != null && editCommand.getSize() > 0) { ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, av.getAlignment() - .getSequences()); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); } } finally { /* * Tidy up come what may... */ - startseq = -1; - lastres = -1; + editStartSeq = -1; + editLastRes = -1; editingSeqs = false; groupEditing = false; keyboardNo1 = null; @@ -319,13 +316,13 @@ public class SeqPanel extends JPanel implements MouseListener, void setCursorRow() { seqCanvas.cursorY = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorColumn() { seqCanvas.cursorX = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorRowAndColumn() @@ -338,7 +335,7 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX = getKeyboardNo1() - 1; seqCanvas.cursorY = getKeyboardNo2() - 1; - scrollToVisible(); + scrollToVisible(true); } } @@ -347,7 +344,7 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; - scrollToVisible(); + scrollToVisible(true); } void moveCursor(int dx, int dy) @@ -357,16 +354,30 @@ public class SeqPanel extends JPanel implements MouseListener, HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - if (av.hasHiddenColumns() - && !hidden.isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!hidden.isVisible(seqCanvas.cursorX) - && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) + if (!hidden.isVisible(seqCanvas.cursorX)) { - seqCanvas.cursorX += dx; + int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx); + int[] region = hidden.getRegionWithEdgeAtRes(visx); + + if (region != null) // just in case + { + if (dx == 1) + { + // moving right + seqCanvas.cursorX = region[1] + 1; + } + else if (dx == -1) + { + // moving left + seqCanvas.cursorX = region[0] - 1; + } + } + seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX; } if (seqCanvas.cursorX >= maxWidth @@ -376,10 +387,16 @@ public class SeqPanel extends JPanel implements MouseListener, } } - scrollToVisible(); + scrollToVisible(false); } - void scrollToVisible() + /** + * Scroll to make the cursor visible in the viewport. + * + * @param jump + * just jump to the location rather than scrolling + */ + void scrollToVisible(boolean jump) { if (seqCanvas.cursorX < 0) { @@ -400,21 +417,44 @@ public class SeqPanel extends JPanel implements MouseListener, } endEditing(); - if (av.getWrapAlignment()) + + boolean repaintNeeded = true; + if (jump) { - av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); + // only need to repaint if the viewport did not move, as otherwise it will + // get a repaint + repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX, + seqCanvas.cursorY); } else { - av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY, - av); + if (av.getWrapAlignment()) + { + // scrollToWrappedVisible expects x-value to have hidden cols subtracted + int x = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(seqCanvas.cursorX); + av.getRanges().scrollToWrappedVisible(x); + } + else + { + av.getRanges().scrollToVisible(seqCanvas.cursorX, + seqCanvas.cursorY); + } } - setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), + + if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX)) + { + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); + } - seqCanvas.repaint(); + if (repaintNeeded) + { + seqCanvas.repaint(); + } } + void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); @@ -485,15 +525,15 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(sg); } - ap.paintAlignment(false); + ap.paintAlignment(false, false); av.sendSelection(); } 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(); } @@ -501,8 +541,8 @@ public class SeqPanel extends JPanel implements MouseListener, 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(); } @@ -511,8 +551,8 @@ public class SeqPanel extends JPanel implements MouseListener, { // 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(); } @@ -640,13 +680,13 @@ public class SeqPanel extends JPanel implements MouseListener, 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; @@ -682,6 +722,8 @@ public class SeqPanel extends JPanel implements MouseListener, } lastSearchResults = results; + boolean wasScrolled = false; + if (av.isFollowHighlight()) { // don't allow highlight of protein/cDNA to also scroll a complementary @@ -689,14 +731,19 @@ public class SeqPanel extends JPanel implements MouseListener, // 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, false)) + wasScrolled = ap.scrollToPosition(results, false); + if (wasScrolled) { seqCanvas.revalidate(); } ap.setToScrollComplementPanel(true); } - setStatusMessage(results); - seqCanvas.highlightSearchResults(results); + + boolean noFastPaint = wasScrolled && av.getWrapAlignment(); + if (seqCanvas.highlightSearchResults(results, noFastPaint)) + { + setStatusMessage(results); + } } @Override @@ -713,10 +760,12 @@ public class SeqPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Action on mouse movement is to update the status bar to show the current + * sequence position, and (if features are shown) to show any features at the + * position in a tooltip. Does nothing if the mouse move does not change + * residue position. * * @param evt - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) @@ -729,7 +778,8 @@ public class SeqPanel extends JPanel implements MouseListener, } final int column = findColumn(evt); - int seq = findSeq(evt); + final int seq = findSeq(evt); + if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { lastMouseSeq = -1; @@ -796,7 +846,7 @@ public class SeqPanel extends JPanel implements MouseListener, List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); seqARep.appendFeatures(tooltipText, pos, features, - this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); + this.ap.getSeqPanel().seqCanvas.fr); } if (tooltipText.length() == 6) // { @@ -805,6 +855,11 @@ public class SeqPanel extends JPanel implements MouseListener, } else { + if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant + { + tooltipText.setLength(MAX_TOOLTIP_LENGTH); + tooltipText.append("..."); + } String textString = tooltipText.toString(); if (lastTooltip == null || !lastTooltip.equals(textString)) { @@ -832,8 +887,9 @@ public class SeqPanel extends JPanel implements MouseListener, Point p = lastp; if (!event.isShiftDown() || p == null) { - p = (tooltipText != null && tooltipText.length() > 6) ? new Point( - event.getX() + wdth, event.getY() - 20) : null; + p = (tooltipText != null && tooltipText.length() > 6) + ? new Point(event.getX() + wdth, event.getY() - 20) + : null; } /* * TODO: try to modify position region is not obcured by tooltip @@ -845,11 +901,12 @@ public class SeqPanel extends JPanel implements MouseListener, /** * 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 + * shading in overviews and structures to be recalculated. this could be + * changed to a something more expressive that indicates what actually has + * changed, so selective redraws can be applied (ie. only structures, only + * overview, etc) */ - private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller + private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller /** * set if av.getSelectionGroup() refers to a group that is defined on the @@ -869,19 +926,48 @@ public class SeqPanel extends JPanel implements MouseListener, * aligned sequence object * @param column * alignment column - * @param seq + * @param seqIndex * index of sequence in alignment * @return sequence position of residue at column, or adjacent residue if at a * gap */ - int setStatusMessage(SequenceI sequence, final int column, int seq) + int setStatusMessage(SequenceI sequence, final int column, int seqIndex) + { + char sequenceChar = sequence.getCharAt(column); + int pos = sequence.findPosition(column); + setStatusMessage(sequence, seqIndex, sequenceChar, pos); + + return pos; + } + + /** + * Builds the status message for the current cursor location and writes it to + * the status bar, for example + * + * 
+   * Sequence 3 ID: FER1_SOLLC
+   * Sequence 5 ID: FER1_PEA Residue: THR (4)
+   * Sequence 5 ID: FER1_PEA Residue: B (3)
+   * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+   *
+ * + * @param sequence + * @param seqIndex + * sequence position in the alignment (1..) + * @param sequenceChar + * the character under the cursor + * @param residuePos + * the sequence residue position (if not over a gap) + */ + protected void setStatusMessage(SequenceI sequence, int seqIndex, + char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); /* * Sequence number (if known), and sequence name. */ - String seqno = seq == -1 ? "" : " " + (seq + 1); + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") .append(sequence.getName()); @@ -890,31 +976,28 @@ public class SeqPanel extends JPanel implements MouseListener, /* * Try to translate the display character to residue name (null for gap). */ - final String displayChar = String.valueOf(sequence.getCharAt(column)); - boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); - int pos = sequence.findPosition(column); + boolean isGapped = Comparison.isGap(sequenceChar); if (!isGapped) { boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); if (nucleotide) { residue = ResidueProperties.nucleotideName.get(displayChar); } else { - residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" - .equals(displayChar) ? "STOP" - : ResidueProperties.aa2Triplet.get(displayChar)); + residue = "X".equalsIgnoreCase(displayChar) ? "X" + : ("*".equals(displayChar) ? "STOP" + : ResidueProperties.aa2Triplet.get(displayChar)); } text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") .append(": ").append(residue == null ? displayChar : residue); - text.append(" (").append(Integer.toString(pos)).append(")"); + text.append(" (").append(Integer.toString(residuePos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); - - return pos; } /** @@ -942,12 +1025,9 @@ public class SeqPanel extends JPanel implements MouseListener, if (seq == ds) { - /* - * Convert position in sequence (base 1) to sequence character array - * index (base 0) - */ - int start = m.getStart() - m.getSequence().getStart(); - setStatusMessage(seq, start, sequenceIndex); + int start = m.getStart(); + setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), + start); return; } } @@ -967,8 +1047,8 @@ public class SeqPanel extends JPanel implements MouseListener, int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? - if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt - .getX() - lastMousePress.getX())) + if (Math.abs(evt.getY() - lastMousePress.getY()) > Math + .abs(evt.getX() - lastMousePress.getX())) { /* * on drag up or down, decrement or increment font size @@ -1027,7 +1107,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (newWidth > 0) { - ap.paintAlignment(false); + ap.paintAlignment(false, false); if (copyChanges) { /* @@ -1065,12 +1145,12 @@ public class SeqPanel extends JPanel implements MouseListener, 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); @@ -1081,22 +1161,46 @@ public class SeqPanel extends JPanel implements MouseListener, } mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } } - // 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()) @@ -1108,47 +1212,44 @@ public class SeqPanel extends JPanel implements MouseListener, } } - StringBuilder message = new StringBuilder(64); + /* + * make a name for the edit action, for + * status bar message and Undo/Redo menu + */ + String label = null; if (groupEditing) { - message.append("Edit group:"); - if (editCommand == null) - { - editCommand = new EditCommand( - MessageManager.getString("action.edit_group")); - } + label = MessageManager.getString("action.edit_group"); } else { - message.append("Edit sequence: " + seq.getName()); - String label = seq.getName(); + label = seq.getName(); if (label.length() > 10) { label = label.substring(0, 10); } - if (editCommand == null) - { - editCommand = new EditCommand(MessageManager.formatMessage( - "label.edit_params", new String[] { label })); - } + label = MessageManager.formatMessage("label.edit_params", + new String[] + { label }); } - if (insertGap) - { - message.append(" insert "); - } - else + /* + * initialise the edit command if there is not + * already one being extended + */ + if (editCommand == null) { - message.append(" delete "); + editCommand = new EditCommand(label); } - message.append(Math.abs(startres - lastres) + " gaps."); - ap.alignFrame.statusBar.setText(message.toString()); - - // Are we editing within a selection group? - if (groupEditing - || (sg != null && sg.getSequences(av.getHiddenRepSequences()) - .contains(seq))) + /* + * 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; @@ -1167,10 +1268,10 @@ public class SeqPanel extends JPanel implements MouseListener, 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; @@ -1192,12 +1293,12 @@ public class SeqPanel extends JPanel implements MouseListener, { fixedColumns = true; int y1 = av.getAlignment().getHiddenColumns() - .getHiddenBoundaryLeft(startres); + .getNextHiddenBoundary(true, startres); int y2 = av.getAlignment().getHiddenColumns() - .getHiddenBoundaryRight(startres); + .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; @@ -1218,6 +1319,54 @@ public class SeqPanel extends JPanel implements MouseListener, } } + 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.statusBar.setText(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) { List vseqs = sg.getSequences(av.getHiddenRepSequences()); @@ -1236,7 +1385,8 @@ public class SeqPanel extends JPanel implements MouseListener, 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(); } @@ -1244,15 +1394,16 @@ public class SeqPanel extends JPanel implements MouseListener, // Find the next gap before the end // of the visible region boundary boolean blank = false; - for (fixedRight = fixedRight; 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; @@ -1269,11 +1420,11 @@ public class SeqPanel extends JPanel implements MouseListener, { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av.getAlignment() - .getHiddenColumns().getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() + && startres < av.getAlignment().getHiddenColumns() + .getNextHiddenBoundary(false, startres))) { - endEditing(); - return; + return false; } int alWidth = av.getAlignment().getWidth(); @@ -1288,13 +1439,12 @@ public class SeqPanel extends JPanel implements MouseListener, } // 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; } } } @@ -1307,7 +1457,7 @@ public class SeqPanel extends JPanel implements MouseListener, 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) { @@ -1317,8 +1467,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (!Comparison.isGap(groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid - endEditing(); - return; + return false; } } } @@ -1329,15 +1478,15 @@ public class SeqPanel extends JPanel implements MouseListener, // 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); + appendEdit(Action.INSERT_GAP, groupSeqs, startres, + startres - editLastRes, false); } } else @@ -1345,36 +1494,44 @@ public class SeqPanel extends JPanel implements MouseListener, // 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); } } else { - appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres - - startres); + appendEdit(Action.DELETE_GAP, groupSeqs, startres, + editLastRes - startres, false); } - } } else - // ///Editing a single sequence/////////// { + /* + * 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 @@ -1384,21 +1541,20 @@ public class SeqPanel extends JPanel implements MouseListener, // 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))) { @@ -1406,11 +1562,9 @@ public class SeqPanel extends JPanel implements MouseListener, } max++; } - if (max > 0) { - appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, - startres, max); + appendEdit(Action.DELETE_GAP, seqs, startres, max, false); } } } @@ -1418,25 +1572,82 @@ public class SeqPanel extends JPanel implements MouseListener, {// 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. Answers null if inserts and deletes cancel out. + * + * @param editCommand + * a command containing the list of individual edits + * @return + */ + protected static String getEditStatusMessage(EditCommand editCommand) + { + if (editCommand == null) + { + return null; + } + + /* + * 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()) + { + if (!cmd.isSystemGenerated()) + { + count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber() + : -cmd.getNumber(); + } + } + + if (count == 0) + { + /* + * inserts and deletes cancel out + */ + return null; + } + + String msgKey = count > 1 ? "label.insert_gaps" + : (count == 1 ? "label.insert_gap" + : (count == -1 ? "label.delete_gap" + : "label.delete_gaps")); + count = Math.abs(count); + + 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++) @@ -1457,40 +1668,53 @@ public class SeqPanel extends JPanel implements MouseListener, { 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); } /** @@ -1507,9 +1731,9 @@ public class SeqPanel extends JPanel implements MouseListener, oldSeq = 0; } - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } } @@ -1528,7 +1752,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - if (mouseDragging) + if (mouseDragging && scrollThread == null) { scrollThread = new ScrollThread(); } @@ -1570,7 +1794,7 @@ public class SeqPanel extends JPanel implements MouseListener, SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); - seqCanvas.highlightSearchResults(highlight); + seqCanvas.highlightSearchResults(highlight, false); /* * open the Amend Features dialog; clear highlighting afterwards, @@ -1579,7 +1803,8 @@ public class SeqPanel extends JPanel implements MouseListener, List seqs = Collections.singletonList(sequence); seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, ap); - seqCanvas.highlightSearchResults(null); + av.setSearchResults(null); // clear highlighting + seqCanvas.repaint(); // draw new/amended features } } } @@ -1588,7 +1813,8 @@ public class SeqPanel extends JPanel implements MouseListener, public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); - if (e.getWheelRotation() > 0) + double wheelRotation = e.getPreciseWheelRotation(); + if (wheelRotation > 0) { if (e.isShiftDown()) { @@ -1600,7 +1826,7 @@ public class SeqPanel extends JPanel implements MouseListener, av.getRanges().scrollUp(false); } } - else + else if (wheelRotation < 0) { if (e.isShiftDown()) { @@ -1611,7 +1837,13 @@ public class SeqPanel extends JPanel implements MouseListener, av.getRanges().scrollUp(true); } } - // TODO Update tooltip for new position. + + /* + * update status bar and tooltip for new position + * (need to synthesize a mouse movement to refresh tooltip) + */ + mouseMoved(e); + ToolTipManager.sharedInstance().mouseMoved(e); } /** @@ -1625,14 +1857,15 @@ public class SeqPanel extends JPanel implements MouseListener, final int res = findColumn(evt); final int seq = findSeq(evt); oldSeq = seq; - needOverviewUpdate = false; + updateOverviewAndStructs = false; startWrapBlock = wrappedBlock; if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("label.cannot_edit_annotations_in_wrapped_view"), + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString( + "label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), JvOptionPane.WARNING_MESSAGE); return; @@ -1689,43 +1922,53 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup == null) { - // Only if left mouse button do we want to change group sizes + createStretchGroup(res, sequence); + } - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; + if (stretchGroup != null) + { + stretchGroup.addPropertyChangeListener(seqCanvas); + } - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, av.getResidueShading(), - ap.getViewName()); - } + seqCanvas.repaint(); + } - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), - ap.getViewName()); - } - // TODO: stretchGroup will always be not null. Is this a merge error ? - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { - // Edit end res position of selected group - changeEndRes = true; - } - else if ((stretchGroup != null) - && (stretchGroup.getStartRes() == res)) - { - // Edit end res position of selected group - changeStartRes = true; - } - stretchGroup.getWidth(); + private void createStretchGroup(int res, SequenceI sequence) + { + // Only if left mouse button do we want to change group sizes + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } - seqCanvas.repaint(); + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); + } + // TODO: stretchGroup will always be not null. Is this a merge error ? + // or is there a threading issue here? + if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); + } /** @@ -1740,21 +1983,10 @@ public class SeqPanel extends JPanel implements MouseListener, final int column = findColumn(evt); final int seq = findSeq(evt); SequenceI sequence = av.getAlignment().getSequenceAt(seq); - List allFeatures = ap.getFeatureRenderer() + List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - List links = new ArrayList<>(); - for (SequenceFeature sf : allFeatures) - { - if (sf.links != null) - { - for (String link : sf.links) - { - links.add(link); - } - } - } - PopupMenu pop = new PopupMenu(ap, null, links); + PopupMenu pop = new PopupMenu(ap, null, features); pop.show(this, evt.getX(), evt.getY()); } @@ -1773,17 +2005,21 @@ public class SeqPanel extends JPanel implements MouseListener, { return; } + + stretchGroup.removePropertyChangeListener(seqCanvas); + // always do this - annotation has own state // but defer colourscheme update until hidden sequences are passed in boolean vischange = stretchGroup.recalcConservation(true); - needOverviewUpdate |= vischange && av.isSelectionDefinedGroup() + updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup() && afterDrag; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, av.getHiddenRepSequences()); - ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme(); + ResidueShaderI groupColourScheme = stretchGroup + .getGroupColourScheme(); String name = stretchGroup.getName(); if (stretchGroup.cs.conservationApplied()) { @@ -1795,8 +2031,10 @@ public class SeqPanel extends JPanel implements MouseListener, } } PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(needOverviewUpdate); - needOverviewUpdate = false; + // TODO: structure colours only need updating if stretchGroup used to or now + // does contain sequences with structure views + ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs); + updateOverviewAndStructs = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1850,7 +2088,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1858,7 +2096,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1892,7 +2130,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } else { @@ -1902,7 +2140,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1913,21 +2151,45 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } - seqCanvas.repaint(); + /* + * construct a status message showing the range of the selection + */ + StringBuilder status = new StringBuilder(64); + List seqs = stretchGroup.getSequences(); + String name = seqs.get(0).getName(); + if (name.length() > 20) + { + name = name.substring(0, 20); + } + status.append(name).append(" - "); + name = seqs.get(seqs.size() - 1).getName(); + if (name.length() > 20) + { + name = name.substring(0, 20); + } + status.append(name).append(" "); + int startRes = stretchGroup.getStartRes(); + status.append(" cols ").append(String.valueOf(startRes + 1)) + .append("-"); + int endRes = stretchGroup.getEndRes(); + status.append(String.valueOf(endRes + 1)); + status.append(" (").append(String.valueOf(seqs.size())).append(" x ") + .append(String.valueOf(endRes - startRes + 1)).append(")"); + ap.alignFrame.setStatus(status.toString()); } void scrollCanvas(MouseEvent evt) { if (evt == null) { - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } mouseDragging = false; @@ -1950,7 +2212,7 @@ public class SeqPanel extends JPanel implements MouseListener, { MouseEvent evt; - boolean running = false; + private volatile boolean threadRunning = true; public ScrollThread() { @@ -1964,38 +2226,40 @@ public class SeqPanel extends JPanel implements MouseListener, public void stopScrolling() { - running = false; + threadRunning = false; + } + + public boolean isRunning() + { + return threadRunning; } @Override public void run() { - running = true; - - while (running) + while (threadRunning) { if (evt != null) { if (mouseDragging && (evt.getY() < 0) && (av.getRanges().getStartSeq() > 0)) { - running = av.getRanges().scrollUp(true); + av.getRanges().scrollUp(true); } - if (mouseDragging && (evt.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getRanges() - .getEndSeq())) + if (mouseDragging && (evt.getY() >= getHeight()) && (av + .getAlignment().getHeight() > av.getRanges().getEndSeq())) { - running = av.getRanges().scrollUp(false); + av.getRanges().scrollUp(false); } if (mouseDragging && (evt.getX() < 0)) { - running = av.getRanges().scrollRight(false); + av.getRanges().scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = av.getRanges().scrollRight(true); + av.getRanges().scrollRight(true); } } @@ -2020,8 +2284,10 @@ public class SeqPanel extends JPanel implements MouseListener, // handles selection messages... // TODO: extend config options to allow user to control if selections may be // shared between viewports. - boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) - .getSequenceSetId().equals(av.getSequenceSetId()))); + boolean iSentTheSelection = (av == source + || (source instanceof AlignViewport + && ((AlignmentViewport) source).getSequenceSetId() + .equals(av.getSequenceSetId()))); if (iSentTheSelection) { @@ -2123,10 +2389,8 @@ public class SeqPanel extends JPanel implements MouseListener, repaint = true; } - if (copycolsel - && av.hasHiddenColumns() - && (av.getAlignment().getHiddenColumns() == null || av - .getAlignment().getHiddenColumns().getHiddenRegions() == null)) + if (copycolsel && av.hasHiddenColumns() + && (av.getAlignment().getHiddenColumns() == null)) { System.err.println("Bad things"); } @@ -2197,4 +2461,13 @@ public class SeqPanel extends JPanel implements MouseListener, return true; } + + /** + * + * @return null or last search results handled by this panel + */ + public SearchResultsI getLastSearchResults() + { + return lastSearchResults; + } }